id int32 0 165k | repo stringlengths 7 58 | path stringlengths 12 218 | func_name stringlengths 3 140 | original_string stringlengths 73 34.1k | language stringclasses 1 value | code stringlengths 73 34.1k | code_tokens list | docstring stringlengths 3 16k | docstring_tokens list | sha stringlengths 40 40 | url stringlengths 105 339 |
|---|---|---|---|---|---|---|---|---|---|---|---|
31,800 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodInstallation.java | EcodInstallation.domainsAvailable | private boolean domainsAvailable() {
domainsFileLock.readLock().lock();
logger.trace("LOCK readlock");
try {
File f = getDomainFile();
if (!f.exists() || f.length() <= 0 )
return false;
// Re-download old copies of "latest"
if(updateFrequency != null && requestedVersion == DEFAULT_VERSION ) {
long mod = f.lastModified();
// Time of last update
Date lastUpdate = new Date();
Calendar cal = Calendar.getInstance();
cal.setTime(lastUpdate);
cal.add(Calendar.DAY_OF_WEEK, -updateFrequency);
long updateTime = cal.getTimeInMillis();
// Check if file predates last update
if( mod < updateTime ) {
logger.info("{} is out of date.",f);
return false;
}
}
return true;
} finally {
logger.trace("UNLOCK readlock");
domainsFileLock.readLock().unlock();
}
} | java | private boolean domainsAvailable() {
domainsFileLock.readLock().lock();
logger.trace("LOCK readlock");
try {
File f = getDomainFile();
if (!f.exists() || f.length() <= 0 )
return false;
// Re-download old copies of "latest"
if(updateFrequency != null && requestedVersion == DEFAULT_VERSION ) {
long mod = f.lastModified();
// Time of last update
Date lastUpdate = new Date();
Calendar cal = Calendar.getInstance();
cal.setTime(lastUpdate);
cal.add(Calendar.DAY_OF_WEEK, -updateFrequency);
long updateTime = cal.getTimeInMillis();
// Check if file predates last update
if( mod < updateTime ) {
logger.info("{} is out of date.",f);
return false;
}
}
return true;
} finally {
logger.trace("UNLOCK readlock");
domainsFileLock.readLock().unlock();
}
} | [
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... | Checks that the domains file has been downloaded
@return | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodInstallation.java#L361-L390 |
31,801 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodInstallation.java | EcodInstallation.downloadDomains | private void downloadDomains() throws IOException {
domainsFileLock.writeLock().lock();
logger.trace("LOCK writelock");
try {
URL domainsURL = new URL( url + DOMAINS_PATH + getDomainFilename());
File localFile = getDomainFile();
logger.info("Downloading {} to: {}",domainsURL, localFile);
FileDownloadUtils.downloadFile(domainsURL, localFile);
} catch (MalformedURLException e) {
logger.error("Malformed url: "+ url + DOMAINS_PATH + getDomainFilename(),e);
} finally {
logger.trace("UNLOCK writelock");
domainsFileLock.writeLock().unlock();
}
} | java | private void downloadDomains() throws IOException {
domainsFileLock.writeLock().lock();
logger.trace("LOCK writelock");
try {
URL domainsURL = new URL( url + DOMAINS_PATH + getDomainFilename());
File localFile = getDomainFile();
logger.info("Downloading {} to: {}",domainsURL, localFile);
FileDownloadUtils.downloadFile(domainsURL, localFile);
} catch (MalformedURLException e) {
logger.error("Malformed url: "+ url + DOMAINS_PATH + getDomainFilename(),e);
} finally {
logger.trace("UNLOCK writelock");
domainsFileLock.writeLock().unlock();
}
} | [
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@throws IOException | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodInstallation.java#L396-L411 |
31,802 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodInstallation.java | EcodInstallation.parseDomains | private void parseDomains() throws IOException {
domainsFileLock.writeLock().lock();
logger.trace("LOCK writelock");
try {
EcodParser parser = new EcodParser(getDomainFile());
allDomains = parser.getDomains();
parsedVersion = parser.getVersion();
} finally {
logger.trace("UNLOCK writelock");
domainsFileLock.writeLock().unlock();
}
} | java | private void parseDomains() throws IOException {
domainsFileLock.writeLock().lock();
logger.trace("LOCK writelock");
try {
EcodParser parser = new EcodParser(getDomainFile());
allDomains = parser.getDomains();
parsedVersion = parser.getVersion();
} finally {
logger.trace("UNLOCK writelock");
domainsFileLock.writeLock().unlock();
}
} | [
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31,803 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodInstallation.java | EcodInstallation.indexDomains | private void indexDomains() throws IOException {
domainsFileLock.writeLock().lock();
logger.trace("LOCK writelock");
try {
if( allDomains == null) {
ensureDomainsFileInstalled();
}
// Leave enough space for all PDBs as of 2015
domainMap = new HashMap<String, List<EcodDomain>>((int) (150000/.85),.85f);
// Index with domainMap
for(EcodDomain d : allDomains) {
// Get the PDB ID, either directly or from the domain ID
String pdbId = d.getPdbId();
if( pdbId == null ) {
String ecodId = d.getDomainId();
if( ecodId != null && !ecodId.isEmpty() ) {
Matcher match = ECOD_RE.matcher(ecodId);
pdbId = match.group(1);
}
}
// Add current domain to the map
List<EcodDomain> currDomains;
if( domainMap.containsKey(pdbId) ) {
currDomains = domainMap.get(pdbId);
} else {
currDomains = new LinkedList<EcodDomain>();
domainMap.put(pdbId,currDomains);
}
currDomains.add(d);
}
} finally {
logger.trace("UNLOCK writelock");
domainsFileLock.writeLock().unlock();
}
} | java | private void indexDomains() throws IOException {
domainsFileLock.writeLock().lock();
logger.trace("LOCK writelock");
try {
if( allDomains == null) {
ensureDomainsFileInstalled();
}
// Leave enough space for all PDBs as of 2015
domainMap = new HashMap<String, List<EcodDomain>>((int) (150000/.85),.85f);
// Index with domainMap
for(EcodDomain d : allDomains) {
// Get the PDB ID, either directly or from the domain ID
String pdbId = d.getPdbId();
if( pdbId == null ) {
String ecodId = d.getDomainId();
if( ecodId != null && !ecodId.isEmpty() ) {
Matcher match = ECOD_RE.matcher(ecodId);
pdbId = match.group(1);
}
}
// Add current domain to the map
List<EcodDomain> currDomains;
if( domainMap.containsKey(pdbId) ) {
currDomains = domainMap.get(pdbId);
} else {
currDomains = new LinkedList<EcodDomain>();
domainMap.put(pdbId,currDomains);
}
currDomains.add(d);
}
} finally {
logger.trace("UNLOCK writelock");
domainsFileLock.writeLock().unlock();
}
} | [
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... | Populates domainMap from allDomains
@throws IOException | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodInstallation.java#L471-L509 |
31,804 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/AbstractUserArgumentProcessor.java | AbstractUserArgumentProcessor.runDbSearch | private void runDbSearch(AtomCache cache, String searchFile,
String outputFile,int useNrCPUs, StartupParameters params) throws ConfigurationException {
System.out.println("will use " + useNrCPUs + " CPUs.");
PDBFileReader reader = new PDBFileReader();
Structure structure1 = null ;
try {
structure1 = reader.getStructure(searchFile);
} catch (IOException e) {
throw new ConfigurationException("could not parse as PDB file: " + searchFile);
}
File searchF = new File(searchFile);
String name1 = "CUSTOM";
StructureAlignment algorithm = getAlgorithm();
MultiThreadedDBSearch dbSearch = new MultiThreadedDBSearch(name1,
structure1,
outputFile,
algorithm,
useNrCPUs,
params.isDomainSplit());
dbSearch.setCustomFile1(searchF.getAbsolutePath());
dbSearch.run();
} | java | private void runDbSearch(AtomCache cache, String searchFile,
String outputFile,int useNrCPUs, StartupParameters params) throws ConfigurationException {
System.out.println("will use " + useNrCPUs + " CPUs.");
PDBFileReader reader = new PDBFileReader();
Structure structure1 = null ;
try {
structure1 = reader.getStructure(searchFile);
} catch (IOException e) {
throw new ConfigurationException("could not parse as PDB file: " + searchFile);
}
File searchF = new File(searchFile);
String name1 = "CUSTOM";
StructureAlignment algorithm = getAlgorithm();
MultiThreadedDBSearch dbSearch = new MultiThreadedDBSearch(name1,
structure1,
outputFile,
algorithm,
useNrCPUs,
params.isDomainSplit());
dbSearch.setCustomFile1(searchF.getAbsolutePath());
dbSearch.run();
} | [
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@param cache
@param searchFile
@param outputFile
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31,805 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/AbstractUserArgumentProcessor.java | AbstractUserArgumentProcessor.checkWriteFile | private void checkWriteFile( AFPChain afpChain, Atom[] ca1, Atom[] ca2, boolean dbsearch) throws IOException, ClassNotFoundException, NoSuchMethodException, InvocationTargetException, IllegalAccessException, StructureException
{
String output = null;
if ( params.isOutputPDB()){
if (! GuiWrapper.isGuiModuleInstalled()) {
System.err.println("The biojava-structure-gui module is not installed. Please install!");
output = AFPChainXMLConverter.toXML(afpChain,ca1,ca2);
} else {
Structure tmp = AFPAlignmentDisplay.createArtificalStructure(afpChain, ca1, ca2);
output = "TITLE " + afpChain.getAlgorithmName() + " " + afpChain.getVersion() + " ";
output += afpChain.getName1() + " vs. " + afpChain.getName2();
output += newline;
output += tmp.toPDB();
}
} else if ( params.getOutFile() != null) {
// output by default is XML
// write the XML to a file...
output = AFPChainXMLConverter.toXML(afpChain,ca1,ca2);
} else if ( params.getSaveOutputDir() != null){
output = AFPChainXMLConverter.toXML(afpChain,ca1,ca2);
}
// no output requested.
if ( output == null)
return;
String fileName = null;
if ( dbsearch ){
if ( params.getSaveOutputDir() != null) {
// we currently don't have a naming convention for how to store results for custom files
// they will be re-created on the fly
if ( afpChain.getName1().startsWith("file:") || afpChain.getName2().startsWith("file:"))
return;
fileName = params.getSaveOutputDir();
fileName += getAutoFileName(afpChain);
} else {
return;
}
//
//else {
// fileName = getAutoFileName(afpChain);
//}
} else
if ( params.getOutFile() != null) {
fileName = params.getOutFile();
}
if (fileName == null) {
System.err.println("Can't write outputfile. Either provide a filename using -outFile or set -autoOutputFile to true .");
System.exit(1); return;
}
//System.out.println("writing results to " + fileName + " " + params.getSaveOutputDir());
FileOutputStream out; // declare a file output object
PrintStream p; // declare a print stream object
// Create a new file output stream
out = new FileOutputStream(fileName);
// Connect print stream to the output stream
p = new PrintStream( out );
p.println (output);
p.close();
} | java | private void checkWriteFile( AFPChain afpChain, Atom[] ca1, Atom[] ca2, boolean dbsearch) throws IOException, ClassNotFoundException, NoSuchMethodException, InvocationTargetException, IllegalAccessException, StructureException
{
String output = null;
if ( params.isOutputPDB()){
if (! GuiWrapper.isGuiModuleInstalled()) {
System.err.println("The biojava-structure-gui module is not installed. Please install!");
output = AFPChainXMLConverter.toXML(afpChain,ca1,ca2);
} else {
Structure tmp = AFPAlignmentDisplay.createArtificalStructure(afpChain, ca1, ca2);
output = "TITLE " + afpChain.getAlgorithmName() + " " + afpChain.getVersion() + " ";
output += afpChain.getName1() + " vs. " + afpChain.getName2();
output += newline;
output += tmp.toPDB();
}
} else if ( params.getOutFile() != null) {
// output by default is XML
// write the XML to a file...
output = AFPChainXMLConverter.toXML(afpChain,ca1,ca2);
} else if ( params.getSaveOutputDir() != null){
output = AFPChainXMLConverter.toXML(afpChain,ca1,ca2);
}
// no output requested.
if ( output == null)
return;
String fileName = null;
if ( dbsearch ){
if ( params.getSaveOutputDir() != null) {
// we currently don't have a naming convention for how to store results for custom files
// they will be re-created on the fly
if ( afpChain.getName1().startsWith("file:") || afpChain.getName2().startsWith("file:"))
return;
fileName = params.getSaveOutputDir();
fileName += getAutoFileName(afpChain);
} else {
return;
}
//
//else {
// fileName = getAutoFileName(afpChain);
//}
} else
if ( params.getOutFile() != null) {
fileName = params.getOutFile();
}
if (fileName == null) {
System.err.println("Can't write outputfile. Either provide a filename using -outFile or set -autoOutputFile to true .");
System.exit(1); return;
}
//System.out.println("writing results to " + fileName + " " + params.getSaveOutputDir());
FileOutputStream out; // declare a file output object
PrintStream p; // declare a print stream object
// Create a new file output stream
out = new FileOutputStream(fileName);
// Connect print stream to the output stream
p = new PrintStream( out );
p.println (output);
p.close();
} | [
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@param params2
@param afpChain
@param ca1
@param ca2
@throws IOException If an error occurs when writing the afpChain to XML
@throws ClassNotFoundException If an error occurs when invoking jmol
@throws NoSuchMethodException If an error occurs when invoking jmol
@throws InvocationTargetException If an error occurs when invoking jmol
@throws IllegalAccessException If an error occurs when invoking jmol
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31,806 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/AbstractUserArgumentProcessor.java | AbstractUserArgumentProcessor.fixStructureName | private Structure fixStructureName(Structure s, String file) {
if ( s.getName() != null && (! s.getName().equals("")))
return s;
s.setName(s.getPDBCode());
if ( s.getName() == null || s.getName().equals("")){
File f = new File(file);
s.setName(f.getName());
}
return s;
} | java | private Structure fixStructureName(Structure s, String file) {
if ( s.getName() != null && (! s.getName().equals("")))
return s;
s.setName(s.getPDBCode());
if ( s.getName() == null || s.getName().equals("")){
File f = new File(file);
s.setName(f.getName());
}
return s;
} | [
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... | apply a number of rules to fix the name of the structure if it did not get set during loading.
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31,807 | biojava/biojava | biojava-structure/src/main/java/demo/DemoMmtfReader.java | DemoMmtfReader.main | public static void main(String[] args) throws IOException, StructureException {
Structure structure = MmtfActions.readFromWeb("4cup");
System.out.println(structure.getChains().size());
} | java | public static void main(String[] args) throws IOException, StructureException {
Structure structure = MmtfActions.readFromWeb("4cup");
System.out.println(structure.getChains().size());
} | [
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@param args no args to specify
@throws IOException
@throws StructureException | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/demo/DemoMmtfReader.java#L42-L45 |
31,808 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/StructureAlignmentOptimizer.java | StructureAlignmentOptimizer.runOptimization | public void runOptimization(int maxi) throws StructureException{
superimposeBySet();
if ( debug)
System.err.println(" initial rmsd " + rmsd);
// if (showAlig)
// showCurrentAlignment(equLen, equSet, "after initial superimposeBySet Len:" +equLen + " rmsd:" +rmsd);
maxKeepStep = 4;
keepStep = 0;
optimize(maxi);
} | java | public void runOptimization(int maxi) throws StructureException{
superimposeBySet();
if ( debug)
System.err.println(" initial rmsd " + rmsd);
// if (showAlig)
// showCurrentAlignment(equLen, equSet, "after initial superimposeBySet Len:" +equLen + " rmsd:" +rmsd);
maxKeepStep = 4;
keepStep = 0;
optimize(maxi);
} | [
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@param maxi maximum nr. of iterations
@throws StructureException | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/StructureAlignmentOptimizer.java#L199-L211 |
31,809 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/StructureAlignmentOptimizer.java | StructureAlignmentOptimizer.superimposeBySet | private void superimposeBySet ()
throws StructureException
{
//extract the coordinations of equivalent residues
Atom[] tmp1 = new Atom[equLen];
Atom[] tmp2 = new Atom[equLen];
int i, r1, r2;
for(i = 0; i < equLen; i ++) {
r1 = equSet[0][i];
r2 = equSet[1][i];
tmp1[i] = cod1[ r1 ];
tmp2[i] = (Atom)cod2[ r2 ].clone(); // have to be cloned!
//tmp2[i] = cod2[ r2 ];
/*try {
System.out.println("before superimpos: " + equSet[0][i]+"-"+ equSet[1][i]+ " dist:" + Calc.getDistance(tmp1[i], cod2[equSet[1][i]]));
} catch (Exception e){
e.printStackTrace();
}*/
}
//superimpose the equivalent residues
Matrix4d trans = SuperPositions.superpose(Calc.atomsToPoints(tmp1),
Calc.atomsToPoints(tmp2));
Calc.transform(tmp2, trans);
// weird, why does it take the RMSD before the rotation?
// the rmsd is only for the subset contained in the tmp arrays.
rmsd = Calc.rmsd(tmp1,tmp2);
//System.err.println("rmsd after superimpose by set: " + rmsd);
//transform structure 2 according to the superimposition of the equivalent residues
Calc.transform(cod2, trans);
// for(i = 0; i < equLen; i ++) {
// try {
// System.err.println("after superimpos: " + equSet[0][i]+"-"+ equSet[1][i]+ " dist:" + Calc.getDistance(tmp1[i], cod2[equSet[1][i]]));
// } catch (Exception e){
// e.printStackTrace();
// }
// }
} | java | private void superimposeBySet ()
throws StructureException
{
//extract the coordinations of equivalent residues
Atom[] tmp1 = new Atom[equLen];
Atom[] tmp2 = new Atom[equLen];
int i, r1, r2;
for(i = 0; i < equLen; i ++) {
r1 = equSet[0][i];
r2 = equSet[1][i];
tmp1[i] = cod1[ r1 ];
tmp2[i] = (Atom)cod2[ r2 ].clone(); // have to be cloned!
//tmp2[i] = cod2[ r2 ];
/*try {
System.out.println("before superimpos: " + equSet[0][i]+"-"+ equSet[1][i]+ " dist:" + Calc.getDistance(tmp1[i], cod2[equSet[1][i]]));
} catch (Exception e){
e.printStackTrace();
}*/
}
//superimpose the equivalent residues
Matrix4d trans = SuperPositions.superpose(Calc.atomsToPoints(tmp1),
Calc.atomsToPoints(tmp2));
Calc.transform(tmp2, trans);
// weird, why does it take the RMSD before the rotation?
// the rmsd is only for the subset contained in the tmp arrays.
rmsd = Calc.rmsd(tmp1,tmp2);
//System.err.println("rmsd after superimpose by set: " + rmsd);
//transform structure 2 according to the superimposition of the equivalent residues
Calc.transform(cod2, trans);
// for(i = 0; i < equLen; i ++) {
// try {
// System.err.println("after superimpos: " + equSet[0][i]+"-"+ equSet[1][i]+ " dist:" + Calc.getDistance(tmp1[i], cod2[equSet[1][i]]));
// } catch (Exception e){
// e.printStackTrace();
// }
// }
} | [
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31,810 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBBioAssemblyParser.java | PDBBioAssemblyParser.saveMatrix | private void saveMatrix() {
for (String chainId : currentChainIDs) {
BiologicalAssemblyTransformation transformation = new BiologicalAssemblyTransformation();
transformation.setRotationMatrix(currentMatrix.getArray());
transformation.setTranslation(shift);
transformation.setId(String.valueOf(modelNumber));
transformation.setChainId(chainId);
transformations.add(transformation);
}
if (!transformationMap.containsKey(currentBioMolecule)) {
BioAssemblyInfo bioAssembly = new BioAssemblyInfo();
bioAssembly.setId(currentBioMolecule);
bioAssembly.setTransforms(transformations);
transformationMap.put(currentBioMolecule,bioAssembly);
}
} | java | private void saveMatrix() {
for (String chainId : currentChainIDs) {
BiologicalAssemblyTransformation transformation = new BiologicalAssemblyTransformation();
transformation.setRotationMatrix(currentMatrix.getArray());
transformation.setTranslation(shift);
transformation.setId(String.valueOf(modelNumber));
transformation.setChainId(chainId);
transformations.add(transformation);
}
if (!transformationMap.containsKey(currentBioMolecule)) {
BioAssemblyInfo bioAssembly = new BioAssemblyInfo();
bioAssembly.setId(currentBioMolecule);
bioAssembly.setTransforms(transformations);
transformationMap.put(currentBioMolecule,bioAssembly);
}
} | [
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31,811 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBBioAssemblyParser.java | PDBBioAssemblyParser.setMacromolecularSizes | public void setMacromolecularSizes() {
for (BioAssemblyInfo bioAssembly : transformationMap.values()) {
bioAssembly.setMacromolecularSize(bioAssembly.getTransforms().size());
}
} | java | public void setMacromolecularSizes() {
for (BioAssemblyInfo bioAssembly : transformationMap.values()) {
bioAssembly.setMacromolecularSize(bioAssembly.getTransforms().size());
}
} | [
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This can only be called after the full PDB file has been read so that
all the info for all bioassemblies has been gathered.
Note that an explicit method to set the field is necessary here because
in PDB files the transformations contain only the author chain ids, corresponding
to polymeric chains, whilst in mmCIF files the transformations
contain all asym ids of both polymers and non-polymers. | [
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31,812 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java | UniprotProxySequenceReader.parseUniprotXMLString | public static <C extends Compound> UniprotProxySequenceReader<C> parseUniprotXMLString(String xml, CompoundSet<C> compoundSet) {
try {
Document document = XMLHelper.inputStreamToDocument(new ByteArrayInputStream(xml.getBytes()));
return new UniprotProxySequenceReader<C>(document, compoundSet);
} catch (Exception e) {
logger.error("Exception on xml parse of: {}", xml);
}
return null;
} | java | public static <C extends Compound> UniprotProxySequenceReader<C> parseUniprotXMLString(String xml, CompoundSet<C> compoundSet) {
try {
Document document = XMLHelper.inputStreamToDocument(new ByteArrayInputStream(xml.getBytes()));
return new UniprotProxySequenceReader<C>(document, compoundSet);
} catch (Exception e) {
logger.error("Exception on xml parse of: {}", xml);
}
return null;
} | [
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If an error occurs throw an exception. We could have a bad uniprot id
@param xml
@param compoundSet
@return UniprotProxySequenceReader
@throws Exception | [
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31,813 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java | UniprotProxySequenceReader.getAccessions | public ArrayList<AccessionID> getAccessions() throws XPathExpressionException {
ArrayList<AccessionID> accessionList = new ArrayList<AccessionID>();
if (uniprotDoc == null) {
return accessionList;
}
Element uniprotElement = uniprotDoc.getDocumentElement();
Element entryElement = XMLHelper.selectSingleElement(uniprotElement, "entry");
ArrayList<Element> keyWordElementList = XMLHelper.selectElements(entryElement, "accession");
for (Element element : keyWordElementList) {
AccessionID accessionID = new AccessionID(element.getTextContent(), DataSource.UNIPROT);
accessionList.add(accessionID);
}
return accessionList;
} | java | public ArrayList<AccessionID> getAccessions() throws XPathExpressionException {
ArrayList<AccessionID> accessionList = new ArrayList<AccessionID>();
if (uniprotDoc == null) {
return accessionList;
}
Element uniprotElement = uniprotDoc.getDocumentElement();
Element entryElement = XMLHelper.selectSingleElement(uniprotElement, "entry");
ArrayList<Element> keyWordElementList = XMLHelper.selectElements(entryElement, "accession");
for (Element element : keyWordElementList) {
AccessionID accessionID = new AccessionID(element.getTextContent(), DataSource.UNIPROT);
accessionList.add(accessionID);
}
return accessionList;
} | [
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"uniprotDoc",... | Pull uniprot accessions associated with this sequence
@return
@throws XPathExpressionException | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java#L346-L360 |
31,814 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java | UniprotProxySequenceReader.getProteinAliases | public ArrayList<String> getProteinAliases() throws XPathExpressionException {
ArrayList<String> aliasList = new ArrayList<String>();
if (uniprotDoc == null) {
return aliasList;
}
Element uniprotElement = uniprotDoc.getDocumentElement();
Element entryElement = XMLHelper.selectSingleElement(uniprotElement, "entry");
Element proteinElement = XMLHelper.selectSingleElement(entryElement, "protein");
// An alternativeName can contain multiple fullNames and multiple shortNames, so we are careful to catch them all
ArrayList<Element> keyWordElementList = XMLHelper.selectElements(proteinElement, "alternativeName");
for (Element element : keyWordElementList) {
Element fullNameElement = XMLHelper.selectSingleElement(element, "fullName");
aliasList.add(fullNameElement.getTextContent());
ArrayList<Element> shortNameElements = XMLHelper.selectElements(element, "shortName");
for(Element shortNameElement : shortNameElements) {
if(null != shortNameElement) {
String shortName = shortNameElement.getTextContent();
if(null != shortName && !shortName.trim().isEmpty()) {
aliasList.add(shortName);
}
}
}
}
// recommendedName seems to allow only one fullName, to be on the safe side, we double check for multiple shortNames for the recommendedName
keyWordElementList = XMLHelper.selectElements(proteinElement, "recommendedName");
for (Element element : keyWordElementList) {
Element fullNameElement = XMLHelper.selectSingleElement(element, "fullName");
aliasList.add(fullNameElement.getTextContent());
ArrayList<Element> shortNameElements = XMLHelper.selectElements(element, "shortName");
for(Element shortNameElement : shortNameElements) {
if(null != shortNameElement) {
String shortName = shortNameElement.getTextContent();
if(null != shortName && !shortName.trim().isEmpty()) {
aliasList.add(shortName);
}
}
}
}
Element cdAntigen = XMLHelper.selectSingleElement(proteinElement, "cdAntigenName");
if(null != cdAntigen) {
String cdAntigenName = cdAntigen.getTextContent();
if(null != cdAntigenName && !cdAntigenName.trim().isEmpty()) {
aliasList.add(cdAntigenName);
}
}
return aliasList;
} | java | public ArrayList<String> getProteinAliases() throws XPathExpressionException {
ArrayList<String> aliasList = new ArrayList<String>();
if (uniprotDoc == null) {
return aliasList;
}
Element uniprotElement = uniprotDoc.getDocumentElement();
Element entryElement = XMLHelper.selectSingleElement(uniprotElement, "entry");
Element proteinElement = XMLHelper.selectSingleElement(entryElement, "protein");
// An alternativeName can contain multiple fullNames and multiple shortNames, so we are careful to catch them all
ArrayList<Element> keyWordElementList = XMLHelper.selectElements(proteinElement, "alternativeName");
for (Element element : keyWordElementList) {
Element fullNameElement = XMLHelper.selectSingleElement(element, "fullName");
aliasList.add(fullNameElement.getTextContent());
ArrayList<Element> shortNameElements = XMLHelper.selectElements(element, "shortName");
for(Element shortNameElement : shortNameElements) {
if(null != shortNameElement) {
String shortName = shortNameElement.getTextContent();
if(null != shortName && !shortName.trim().isEmpty()) {
aliasList.add(shortName);
}
}
}
}
// recommendedName seems to allow only one fullName, to be on the safe side, we double check for multiple shortNames for the recommendedName
keyWordElementList = XMLHelper.selectElements(proteinElement, "recommendedName");
for (Element element : keyWordElementList) {
Element fullNameElement = XMLHelper.selectSingleElement(element, "fullName");
aliasList.add(fullNameElement.getTextContent());
ArrayList<Element> shortNameElements = XMLHelper.selectElements(element, "shortName");
for(Element shortNameElement : shortNameElements) {
if(null != shortNameElement) {
String shortName = shortNameElement.getTextContent();
if(null != shortName && !shortName.trim().isEmpty()) {
aliasList.add(shortName);
}
}
}
}
Element cdAntigen = XMLHelper.selectSingleElement(proteinElement, "cdAntigenName");
if(null != cdAntigen) {
String cdAntigenName = cdAntigen.getTextContent();
if(null != cdAntigenName && !cdAntigenName.trim().isEmpty()) {
aliasList.add(cdAntigenName);
}
}
return aliasList;
} | [
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@return
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31,815 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java | UniprotProxySequenceReader.getGeneAliases | public ArrayList<String> getGeneAliases() throws XPathExpressionException {
ArrayList<String> aliasList = new ArrayList<String>();
if (uniprotDoc == null) {
return aliasList;
}
Element uniprotElement = uniprotDoc.getDocumentElement();
Element entryElement = XMLHelper.selectSingleElement(uniprotElement, "entry");
ArrayList<Element> proteinElements = XMLHelper.selectElements(entryElement, "gene");
for(Element proteinElement : proteinElements) {
ArrayList<Element> keyWordElementList = XMLHelper.selectElements(proteinElement, "name");
for (Element element : keyWordElementList) {
aliasList.add(element.getTextContent());
}
}
return aliasList;
} | java | public ArrayList<String> getGeneAliases() throws XPathExpressionException {
ArrayList<String> aliasList = new ArrayList<String>();
if (uniprotDoc == null) {
return aliasList;
}
Element uniprotElement = uniprotDoc.getDocumentElement();
Element entryElement = XMLHelper.selectSingleElement(uniprotElement, "entry");
ArrayList<Element> proteinElements = XMLHelper.selectElements(entryElement, "gene");
for(Element proteinElement : proteinElements) {
ArrayList<Element> keyWordElementList = XMLHelper.selectElements(proteinElement, "name");
for (Element element : keyWordElementList) {
aliasList.add(element.getTextContent());
}
}
return aliasList;
} | [
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@return
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31,816 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java | UniprotProxySequenceReader.openURLConnection | private static HttpURLConnection openURLConnection(URL url) throws IOException {
// This method should be moved to a utility class in BioJava 5.0
final int timeout = 5000;
final String useragent = "BioJava";
HttpURLConnection conn = (HttpURLConnection) url.openConnection();
conn.setRequestProperty("User-Agent", useragent);
conn.setInstanceFollowRedirects(true);
conn.setConnectTimeout(timeout);
conn.setReadTimeout(timeout);
int status = conn.getResponseCode();
while (status == HttpURLConnection.HTTP_MOVED_TEMP
|| status == HttpURLConnection.HTTP_MOVED_PERM
|| status == HttpURLConnection.HTTP_SEE_OTHER) {
// Redirect!
String newUrl = conn.getHeaderField("Location");
if(newUrl.equals(url.toString())) {
throw new IOException("Cyclic redirect detected at "+newUrl);
}
// Preserve cookies
String cookies = conn.getHeaderField("Set-Cookie");
// open the new connection again
url = new URL(newUrl);
conn.disconnect();
conn = (HttpURLConnection) url.openConnection();
if(cookies != null) {
conn.setRequestProperty("Cookie", cookies);
}
conn.addRequestProperty("User-Agent", useragent);
conn.setInstanceFollowRedirects(true);
conn.setConnectTimeout(timeout);
conn.setReadTimeout(timeout);
conn.connect();
status = conn.getResponseCode();
logger.info("Redirecting from {} to {}", url, newUrl);
}
conn.connect();
return conn;
} | java | private static HttpURLConnection openURLConnection(URL url) throws IOException {
// This method should be moved to a utility class in BioJava 5.0
final int timeout = 5000;
final String useragent = "BioJava";
HttpURLConnection conn = (HttpURLConnection) url.openConnection();
conn.setRequestProperty("User-Agent", useragent);
conn.setInstanceFollowRedirects(true);
conn.setConnectTimeout(timeout);
conn.setReadTimeout(timeout);
int status = conn.getResponseCode();
while (status == HttpURLConnection.HTTP_MOVED_TEMP
|| status == HttpURLConnection.HTTP_MOVED_PERM
|| status == HttpURLConnection.HTTP_SEE_OTHER) {
// Redirect!
String newUrl = conn.getHeaderField("Location");
if(newUrl.equals(url.toString())) {
throw new IOException("Cyclic redirect detected at "+newUrl);
}
// Preserve cookies
String cookies = conn.getHeaderField("Set-Cookie");
// open the new connection again
url = new URL(newUrl);
conn.disconnect();
conn = (HttpURLConnection) url.openConnection();
if(cookies != null) {
conn.setRequestProperty("Cookie", cookies);
}
conn.addRequestProperty("User-Agent", useragent);
conn.setInstanceFollowRedirects(true);
conn.setConnectTimeout(timeout);
conn.setReadTimeout(timeout);
conn.connect();
status = conn.getResponseCode();
logger.info("Redirecting from {} to {}", url, newUrl);
}
conn.connect();
return conn;
} | [
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Follows redirects.
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31,817 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java | UniprotProxySequenceReader.getGeneName | public String getGeneName() {
if (uniprotDoc == null) {
return "";
}
try {
Element uniprotElement = uniprotDoc.getDocumentElement();
Element entryElement = XMLHelper.selectSingleElement(uniprotElement, "entry");
Element geneElement = XMLHelper.selectSingleElement(entryElement, "gene");
if (geneElement == null) {
return "";
}
Element nameElement = XMLHelper.selectSingleElement(geneElement, "name");
if (nameElement == null) {
return "";
}
return nameElement.getTextContent();
} catch (XPathExpressionException e) {
logger.error("Problems while parsing gene name in UniProt XML: {}. Gene name will be blank.",e.getMessage());
return "";
}
} | java | public String getGeneName() {
if (uniprotDoc == null) {
return "";
}
try {
Element uniprotElement = uniprotDoc.getDocumentElement();
Element entryElement = XMLHelper.selectSingleElement(uniprotElement, "entry");
Element geneElement = XMLHelper.selectSingleElement(entryElement, "gene");
if (geneElement == null) {
return "";
}
Element nameElement = XMLHelper.selectSingleElement(geneElement, "name");
if (nameElement == null) {
return "";
}
return nameElement.getTextContent();
} catch (XPathExpressionException e) {
logger.error("Problems while parsing gene name in UniProt XML: {}. Gene name will be blank.",e.getMessage());
return "";
}
} | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java#L690-L710 |
31,818 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java | UniprotProxySequenceReader.getKeyWords | @Override
public ArrayList<String> getKeyWords() {
ArrayList<String> keyWordsList = new ArrayList<String>();
if (uniprotDoc == null) {
return keyWordsList;
}
try {
Element uniprotElement = uniprotDoc.getDocumentElement();
Element entryElement = XMLHelper.selectSingleElement(uniprotElement, "entry");
ArrayList<Element> keyWordElementList = XMLHelper.selectElements(entryElement, "keyword");
for (Element element : keyWordElementList) {
keyWordsList.add(element.getTextContent());
}
} catch (XPathExpressionException e) {
logger.error("Problems while parsing keywords in UniProt XML: {}. No keywords will be available.",e.getMessage());
return new ArrayList<String>();
}
return keyWordsList;
} | java | @Override
public ArrayList<String> getKeyWords() {
ArrayList<String> keyWordsList = new ArrayList<String>();
if (uniprotDoc == null) {
return keyWordsList;
}
try {
Element uniprotElement = uniprotDoc.getDocumentElement();
Element entryElement = XMLHelper.selectSingleElement(uniprotElement, "entry");
ArrayList<Element> keyWordElementList = XMLHelper.selectElements(entryElement, "keyword");
for (Element element : keyWordElementList) {
keyWordsList.add(element.getTextContent());
}
} catch (XPathExpressionException e) {
logger.error("Problems while parsing keywords in UniProt XML: {}. No keywords will be available.",e.getMessage());
return new ArrayList<String>();
}
return keyWordsList;
} | [
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31,819 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java | UniprotProxySequenceReader.getDatabaseReferences | @Override
public LinkedHashMap<String, ArrayList<DBReferenceInfo>> getDatabaseReferences() {
LinkedHashMap<String, ArrayList<DBReferenceInfo>> databaseReferencesHashMap = new LinkedHashMap<String, ArrayList<DBReferenceInfo>>();
if (uniprotDoc == null) {
return databaseReferencesHashMap;
}
try {
Element uniprotElement = uniprotDoc.getDocumentElement();
Element entryElement = XMLHelper.selectSingleElement(uniprotElement, "entry");
ArrayList<Element> dbreferenceElementList = XMLHelper.selectElements(entryElement, "dbReference");
for (Element element : dbreferenceElementList) {
String type = element.getAttribute("type");
String id = element.getAttribute("id");
ArrayList<DBReferenceInfo> idlist = databaseReferencesHashMap.get(type);
if (idlist == null) {
idlist = new ArrayList<DBReferenceInfo>();
databaseReferencesHashMap.put(type, idlist);
}
DBReferenceInfo dbreferenceInfo = new DBReferenceInfo(type, id);
ArrayList<Element> propertyElementList = XMLHelper.selectElements(element, "property");
for (Element propertyElement : propertyElementList) {
String propertyType = propertyElement.getAttribute("type");
String propertyValue = propertyElement.getAttribute("value");
dbreferenceInfo.addProperty(propertyType, propertyValue);
}
idlist.add(dbreferenceInfo);
}
} catch (XPathExpressionException e) {
logger.error("Problems while parsing db references in UniProt XML: {}. No db references will be available.",e.getMessage());
return new LinkedHashMap<String, ArrayList<DBReferenceInfo>>();
}
return databaseReferencesHashMap;
} | java | @Override
public LinkedHashMap<String, ArrayList<DBReferenceInfo>> getDatabaseReferences() {
LinkedHashMap<String, ArrayList<DBReferenceInfo>> databaseReferencesHashMap = new LinkedHashMap<String, ArrayList<DBReferenceInfo>>();
if (uniprotDoc == null) {
return databaseReferencesHashMap;
}
try {
Element uniprotElement = uniprotDoc.getDocumentElement();
Element entryElement = XMLHelper.selectSingleElement(uniprotElement, "entry");
ArrayList<Element> dbreferenceElementList = XMLHelper.selectElements(entryElement, "dbReference");
for (Element element : dbreferenceElementList) {
String type = element.getAttribute("type");
String id = element.getAttribute("id");
ArrayList<DBReferenceInfo> idlist = databaseReferencesHashMap.get(type);
if (idlist == null) {
idlist = new ArrayList<DBReferenceInfo>();
databaseReferencesHashMap.put(type, idlist);
}
DBReferenceInfo dbreferenceInfo = new DBReferenceInfo(type, id);
ArrayList<Element> propertyElementList = XMLHelper.selectElements(element, "property");
for (Element propertyElement : propertyElementList) {
String propertyType = propertyElement.getAttribute("type");
String propertyValue = propertyElement.getAttribute("value");
dbreferenceInfo.addProperty(propertyType, propertyValue);
}
idlist.add(dbreferenceInfo);
}
} catch (XPathExpressionException e) {
logger.error("Problems while parsing db references in UniProt XML: {}. No db references will be available.",e.getMessage());
return new LinkedHashMap<String, ArrayList<DBReferenceInfo>>();
}
return databaseReferencesHashMap;
} | [
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31,820 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/FastaAFPChainConverter.java | FastaAFPChainConverter.fastaToAfpChain | public static AFPChain fastaToAfpChain(Map<String, ProteinSequence> sequences, Structure structure1,
Structure structure2) throws StructureException {
if (sequences.size() != 2) {
throw new IllegalArgumentException("There must be exactly 2 sequences, but there were " + sequences.size());
}
if (structure1 == null || structure2 == null) {
throw new IllegalArgumentException("A structure is null");
}
List<ProteinSequence> seqs = new ArrayList<ProteinSequence>();
List<String> names = new ArrayList<String>(2);
for (Map.Entry<String, ProteinSequence> entry : sequences.entrySet()) {
seqs.add(entry.getValue());
names.add(entry.getKey());
}
return fastaToAfpChain(seqs.get(0), seqs.get(1), structure1, structure2);
} | java | public static AFPChain fastaToAfpChain(Map<String, ProteinSequence> sequences, Structure structure1,
Structure structure2) throws StructureException {
if (sequences.size() != 2) {
throw new IllegalArgumentException("There must be exactly 2 sequences, but there were " + sequences.size());
}
if (structure1 == null || structure2 == null) {
throw new IllegalArgumentException("A structure is null");
}
List<ProteinSequence> seqs = new ArrayList<ProteinSequence>();
List<String> names = new ArrayList<String>(2);
for (Map.Entry<String, ProteinSequence> entry : sequences.entrySet()) {
seqs.add(entry.getValue());
names.add(entry.getKey());
}
return fastaToAfpChain(seqs.get(0), seqs.get(1), structure1, structure2);
} | [
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@param sequences
A Map containing exactly two entries from sequence names as Strings to gapped ProteinSequences; the name is ignored
@see #fastaToAfpChain(ProteinSequence, ProteinSequence, Structure, Structure)
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31,821 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/FastaAFPChainConverter.java | FastaAFPChainConverter.fastaToAfpChain | public static AFPChain fastaToAfpChain(SequencePair<Sequence<AminoAcidCompound>, AminoAcidCompound> alignment,
Structure structure1, Structure structure2) throws StructureException {
List<AlignedSequence<Sequence<AminoAcidCompound>, AminoAcidCompound>> seqs = alignment.getAlignedSequences();
StringBuilder sb1 = new StringBuilder();
for (AminoAcidCompound a : seqs.get(0)) {
sb1.append(a.getBase());
}
try {
ProteinSequence seq1 = new ProteinSequence(sb1.toString());
StringBuilder sb2 = new StringBuilder();
for (AminoAcidCompound a : seqs.get(1)) {
sb1.append(a.getBase());
}
ProteinSequence seq2 = new ProteinSequence(sb2.toString());
LinkedHashMap<String, ProteinSequence> map = new LinkedHashMap<String, ProteinSequence>();
map.put(structure1.getName(), seq1);
map.put(structure2.getName(), seq2);
return fastaToAfpChain(map, structure1, structure2);
} catch (CompoundNotFoundException e) {
logger.error("Unexpected error while creating protein sequences: {}. This is most likely a bug.",e.getMessage());
return null;
}
} | java | public static AFPChain fastaToAfpChain(SequencePair<Sequence<AminoAcidCompound>, AminoAcidCompound> alignment,
Structure structure1, Structure structure2) throws StructureException {
List<AlignedSequence<Sequence<AminoAcidCompound>, AminoAcidCompound>> seqs = alignment.getAlignedSequences();
StringBuilder sb1 = new StringBuilder();
for (AminoAcidCompound a : seqs.get(0)) {
sb1.append(a.getBase());
}
try {
ProteinSequence seq1 = new ProteinSequence(sb1.toString());
StringBuilder sb2 = new StringBuilder();
for (AminoAcidCompound a : seqs.get(1)) {
sb1.append(a.getBase());
}
ProteinSequence seq2 = new ProteinSequence(sb2.toString());
LinkedHashMap<String, ProteinSequence> map = new LinkedHashMap<String, ProteinSequence>();
map.put(structure1.getName(), seq1);
map.put(structure2.getName(), seq2);
return fastaToAfpChain(map, structure1, structure2);
} catch (CompoundNotFoundException e) {
logger.error("Unexpected error while creating protein sequences: {}. This is most likely a bug.",e.getMessage());
return null;
}
} | [
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@see #fastaToAfpChain(ProteinSequence, ProteinSequence, Structure, Structure)
@throws StructureException | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FastaAFPChainConverter.java#L310-L332 |
31,822 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/FastaAFPChainConverter.java | FastaAFPChainConverter.main | public static void main(String[] args) throws StructureException, IOException {
if (args.length != 3) {
System.err.println("Usage: FastaAFPChainConverter fasta-file structure-1-name structure-2-name");
return;
}
File fasta = new File(args[0]);
Structure structure1 = StructureTools.getStructure(args[1]);
Structure structure2 = StructureTools.getStructure(args[2]);
if (structure1 == null) throw new IllegalArgumentException("No structure for " + args[1] + " was found");
if (structure2 == null) throw new IllegalArgumentException("No structure for " + args[2] + " was found");
AFPChain afpChain = fastaFileToAfpChain(fasta, structure1, structure2);
String xml = AFPChainXMLConverter.toXML(afpChain);
System.out.println(xml);
} | java | public static void main(String[] args) throws StructureException, IOException {
if (args.length != 3) {
System.err.println("Usage: FastaAFPChainConverter fasta-file structure-1-name structure-2-name");
return;
}
File fasta = new File(args[0]);
Structure structure1 = StructureTools.getStructure(args[1]);
Structure structure2 = StructureTools.getStructure(args[2]);
if (structure1 == null) throw new IllegalArgumentException("No structure for " + args[1] + " was found");
if (structure2 == null) throw new IllegalArgumentException("No structure for " + args[2] + " was found");
AFPChain afpChain = fastaFileToAfpChain(fasta, structure1, structure2);
String xml = AFPChainXMLConverter.toXML(afpChain);
System.out.println(xml);
} | [
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31,823 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/math/SymbolTable.java | SymbolTable.put | public void put(Key key, Value val) {
if (val == null) st.remove(key);
else st.put(key, val);
} | java | public void put(Key key, Value val) {
if (val == null) st.remove(key);
else st.put(key, val);
} | [
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] | Put key-value pair into the symbol table. Remove key from table if
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31,824 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/math/SymbolTable.java | SymbolTable.ceil | public Key ceil(Key k) {
SortedMap<Key, Value> tail = st.tailMap(k);
if (tail.isEmpty()) return null;
else return tail.firstKey();
} | java | public Key ceil(Key k) {
SortedMap<Key, Value> tail = st.tailMap(k);
if (tail.isEmpty()) return null;
else return tail.firstKey();
} | [
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31,825 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/math/SymbolTable.java | SymbolTable.floor | public Key floor(Key k) {
if (st.containsKey(k)) return k;
// does not include key if present (!)
SortedMap<Key, Value> head = st.headMap(k);
if (head.isEmpty()) return null;
else return head.lastKey();
} | java | public Key floor(Key k) {
if (st.containsKey(k)) return k;
// does not include key if present (!)
SortedMap<Key, Value> head = st.headMap(k);
if (head.isEmpty()) return null;
else return head.lastKey();
} | [
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31,826 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericFastaHeaderParser.java | GenericFastaHeaderParser.getHeaderValues | private String[] getHeaderValues(String header) {
String[] data = new String[0];
ArrayList<String> values = new ArrayList<String>();
StringBuffer sb = new StringBuffer();
//commented out 1/11/2012 to resolve an issue where headers do contain a length= at the end that are not recognized
//if(header.indexOf("length=") != -1){
// data = new String[1];
// int index = header.indexOf("length=");
// data[0] = header.substring(0, index).trim();
// logger.debug("accession=" + data[0]);
// return data;
//} else
if (!header.startsWith("PDB:")) {
for (int i = 0; i < header.length(); i++) {
if (header.charAt(i) == '|') {
values.add(sb.toString());
sb.setLength(0);//faster than = new StringBuffer();
} else if (i == header.length() - 1) {
sb.append(header.charAt(i));
values.add(sb.toString());
} else {
sb.append(header.charAt(i));
}
data = new String[values.size()];
values.toArray(data);
}
} else {
data = header.split(" ");
}
return data;
} | java | private String[] getHeaderValues(String header) {
String[] data = new String[0];
ArrayList<String> values = new ArrayList<String>();
StringBuffer sb = new StringBuffer();
//commented out 1/11/2012 to resolve an issue where headers do contain a length= at the end that are not recognized
//if(header.indexOf("length=") != -1){
// data = new String[1];
// int index = header.indexOf("length=");
// data[0] = header.substring(0, index).trim();
// logger.debug("accession=" + data[0]);
// return data;
//} else
if (!header.startsWith("PDB:")) {
for (int i = 0; i < header.length(); i++) {
if (header.charAt(i) == '|') {
values.add(sb.toString());
sb.setLength(0);//faster than = new StringBuffer();
} else if (i == header.length() - 1) {
sb.append(header.charAt(i));
values.add(sb.toString());
} else {
sb.append(header.charAt(i));
}
data = new String[values.size()];
values.toArray(data);
}
} else {
data = header.split(" ");
}
return data;
} | [
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31,827 | biojava/biojava | biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java | Alignments.getListFromFutures | static <E> List<E> getListFromFutures(List<Future<E>> futures) {
List<E> list = new ArrayList<E>();
for (Future<E> f : futures) {
// TODO when added to ConcurrencyTools, log completions and exceptions instead of printing stack traces
try {
list.add(f.get());
} catch (InterruptedException e) {
logger.error("Interrupted Exception: ", e);
} catch (ExecutionException e) {
logger.error("Execution Exception: ", e);
}
}
return list;
} | java | static <E> List<E> getListFromFutures(List<Future<E>> futures) {
List<E> list = new ArrayList<E>();
for (Future<E> f : futures) {
// TODO when added to ConcurrencyTools, log completions and exceptions instead of printing stack traces
try {
list.add(f.get());
} catch (InterruptedException e) {
logger.error("Interrupted Exception: ", e);
} catch (ExecutionException e) {
logger.error("Execution Exception: ", e);
}
}
return list;
} | [
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31,828 | biojava/biojava | biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java | Alignments.getPairwiseAligner | public static <S extends Sequence<C>, C extends Compound> PairwiseSequenceAligner<S, C> getPairwiseAligner(
S query, S target, PairwiseSequenceAlignerType type, GapPenalty gapPenalty,
SubstitutionMatrix<C> subMatrix) {
if (!query.getCompoundSet().equals(target.getCompoundSet())) {
throw new IllegalArgumentException("Sequence compound sets must be the same");
}
switch (type) {
default:
case GLOBAL:
return new NeedlemanWunsch<S, C>(query, target, gapPenalty, subMatrix);
case LOCAL:
return new SmithWaterman<S, C>(query, target, gapPenalty, subMatrix);
case GLOBAL_LINEAR_SPACE:
case LOCAL_LINEAR_SPACE:
// TODO other alignment options (Myers-Miller, Thompson)
throw new UnsupportedOperationException(Alignments.class.getSimpleName() + " does not yet support " +
type + " alignment");
}
} | java | public static <S extends Sequence<C>, C extends Compound> PairwiseSequenceAligner<S, C> getPairwiseAligner(
S query, S target, PairwiseSequenceAlignerType type, GapPenalty gapPenalty,
SubstitutionMatrix<C> subMatrix) {
if (!query.getCompoundSet().equals(target.getCompoundSet())) {
throw new IllegalArgumentException("Sequence compound sets must be the same");
}
switch (type) {
default:
case GLOBAL:
return new NeedlemanWunsch<S, C>(query, target, gapPenalty, subMatrix);
case LOCAL:
return new SmithWaterman<S, C>(query, target, gapPenalty, subMatrix);
case GLOBAL_LINEAR_SPACE:
case LOCAL_LINEAR_SPACE:
// TODO other alignment options (Myers-Miller, Thompson)
throw new UnsupportedOperationException(Alignments.class.getSimpleName() + " does not yet support " +
type + " alignment");
}
} | [
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@param query the first {@link Sequence} to align
@param target the second {@link Sequence} to align
@param type chosen type from list of pairwise sequence alignment routines
@param gapPenalty the gap penalties used during alignment
@param subMatrix the set of substitution scores used during alignment
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31,829 | biojava/biojava | biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java | Alignments.getPairwiseScorer | static <S extends Sequence<C>, C extends Compound> PairwiseSequenceScorer<S, C> getPairwiseScorer(
S query, S target, PairwiseSequenceScorerType type, GapPenalty gapPenalty,
SubstitutionMatrix<C> subMatrix) {
switch (type) {
default:
case GLOBAL:
return getPairwiseAligner(query, target, PairwiseSequenceAlignerType.GLOBAL, gapPenalty, subMatrix);
case GLOBAL_IDENTITIES:
return new FractionalIdentityScorer<S, C>(getPairwiseAligner(query, target,
PairwiseSequenceAlignerType.GLOBAL, gapPenalty, subMatrix));
case GLOBAL_SIMILARITIES:
return new FractionalSimilarityScorer<S, C>(getPairwiseAligner(query, target,
PairwiseSequenceAlignerType.GLOBAL, gapPenalty, subMatrix));
case LOCAL:
return getPairwiseAligner(query, target, PairwiseSequenceAlignerType.LOCAL, gapPenalty, subMatrix);
case LOCAL_IDENTITIES:
return new FractionalIdentityScorer<S, C>(getPairwiseAligner(query, target,
PairwiseSequenceAlignerType.LOCAL, gapPenalty, subMatrix));
case LOCAL_SIMILARITIES:
return new FractionalSimilarityScorer<S, C>(getPairwiseAligner(query, target,
PairwiseSequenceAlignerType.LOCAL, gapPenalty, subMatrix));
case KMERS:
case WU_MANBER:
// TODO other scoring options
throw new UnsupportedOperationException(Alignments.class.getSimpleName() + " does not yet support " +
type + " scoring");
}
} | java | static <S extends Sequence<C>, C extends Compound> PairwiseSequenceScorer<S, C> getPairwiseScorer(
S query, S target, PairwiseSequenceScorerType type, GapPenalty gapPenalty,
SubstitutionMatrix<C> subMatrix) {
switch (type) {
default:
case GLOBAL:
return getPairwiseAligner(query, target, PairwiseSequenceAlignerType.GLOBAL, gapPenalty, subMatrix);
case GLOBAL_IDENTITIES:
return new FractionalIdentityScorer<S, C>(getPairwiseAligner(query, target,
PairwiseSequenceAlignerType.GLOBAL, gapPenalty, subMatrix));
case GLOBAL_SIMILARITIES:
return new FractionalSimilarityScorer<S, C>(getPairwiseAligner(query, target,
PairwiseSequenceAlignerType.GLOBAL, gapPenalty, subMatrix));
case LOCAL:
return getPairwiseAligner(query, target, PairwiseSequenceAlignerType.LOCAL, gapPenalty, subMatrix);
case LOCAL_IDENTITIES:
return new FractionalIdentityScorer<S, C>(getPairwiseAligner(query, target,
PairwiseSequenceAlignerType.LOCAL, gapPenalty, subMatrix));
case LOCAL_SIMILARITIES:
return new FractionalSimilarityScorer<S, C>(getPairwiseAligner(query, target,
PairwiseSequenceAlignerType.LOCAL, gapPenalty, subMatrix));
case KMERS:
case WU_MANBER:
// TODO other scoring options
throw new UnsupportedOperationException(Alignments.class.getSimpleName() + " does not yet support " +
type + " scoring");
}
} | [
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@param target the second {@link Sequence} to score
@param type chosen type from list of pairwise sequence scoring routines
@param gapPenalty the gap penalties used during alignment
@param subMatrix the set of substitution scores used during alignment
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31,830 | biojava/biojava | biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java | Alignments.getProfileProfileAligner | static <S extends Sequence<C>, C extends Compound> ProfileProfileAligner<S, C> getProfileProfileAligner(
Future<ProfilePair<S, C>> profile1, Future<ProfilePair<S, C>> profile2, ProfileProfileAlignerType type,
GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix) {
switch (type) {
default:
case GLOBAL:
return new SimpleProfileProfileAligner<S, C>(profile1, profile2, gapPenalty, subMatrix);
case GLOBAL_LINEAR_SPACE:
case GLOBAL_CONSENSUS:
case LOCAL:
case LOCAL_LINEAR_SPACE:
case LOCAL_CONSENSUS:
// TODO other alignment options (Myers-Miller, consensus, local)
throw new UnsupportedOperationException(Alignments.class.getSimpleName() + " does not yet support " +
type + " alignment");
}
} | java | static <S extends Sequence<C>, C extends Compound> ProfileProfileAligner<S, C> getProfileProfileAligner(
Future<ProfilePair<S, C>> profile1, Future<ProfilePair<S, C>> profile2, ProfileProfileAlignerType type,
GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix) {
switch (type) {
default:
case GLOBAL:
return new SimpleProfileProfileAligner<S, C>(profile1, profile2, gapPenalty, subMatrix);
case GLOBAL_LINEAR_SPACE:
case GLOBAL_CONSENSUS:
case LOCAL:
case LOCAL_LINEAR_SPACE:
case LOCAL_CONSENSUS:
// TODO other alignment options (Myers-Miller, consensus, local)
throw new UnsupportedOperationException(Alignments.class.getSimpleName() + " does not yet support " +
type + " alignment");
}
} | [
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@param profile2 the second {@link Profile} to align
@param type chosen type from list of profile-profile alignment routines
@param gapPenalty the gap penalties used during alignment
@param subMatrix the set of substitution scores used during alignment
@return profile-profile aligner | [
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31,831 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/FastaStructureParser.java | FastaStructureParser.process | public void process() throws IOException, StructureException {
if(sequences == null) { // only process once, then return cached values
LinkedHashMap<String, ProteinSequence> sequenceMap = reader.process();
sequences = sequenceMap.values().toArray(new ProteinSequence[0]);
accessions = new String[sequences.length];
structures = new Structure[sequences.length];
residues = new ResidueNumber[sequences.length][];
// Match each sequence to a series of PDB Residue numbers
for(int i=0;i<sequences.length;i++) {
accessions[i] = sequences[i].getAccession().getID();
//System.out.println("Fetching "+accession);
structures[i] = cache.getStructure(accessions[i]);
residues[i] = StructureSequenceMatcher.matchSequenceToStructure(sequences[i], structures[i]);
assert( residues[i].length == sequences[i].getLength());
}
}
} | java | public void process() throws IOException, StructureException {
if(sequences == null) { // only process once, then return cached values
LinkedHashMap<String, ProteinSequence> sequenceMap = reader.process();
sequences = sequenceMap.values().toArray(new ProteinSequence[0]);
accessions = new String[sequences.length];
structures = new Structure[sequences.length];
residues = new ResidueNumber[sequences.length][];
// Match each sequence to a series of PDB Residue numbers
for(int i=0;i<sequences.length;i++) {
accessions[i] = sequences[i].getAccession().getID();
//System.out.println("Fetching "+accession);
structures[i] = cache.getStructure(accessions[i]);
residues[i] = StructureSequenceMatcher.matchSequenceToStructure(sequences[i], structures[i]);
assert( residues[i].length == sequences[i].getLength());
}
}
} | [
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@throws StructureException | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FastaStructureParser.java#L110-L131 |
31,832 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java | FileDownloadUtils.downloadFile | public static void downloadFile(URL url, File destination) throws IOException {
int count = 0;
int maxTries = 10;
int timeout = 60000; //60 sec
File tempFile = File.createTempFile(getFilePrefix(destination), "." + getFileExtension(destination));
// Took following recipe from stackoverflow:
// http://stackoverflow.com/questions/921262/how-to-download-and-save-a-file-from-internet-using-java
// It seems to be the most efficient way to transfer a file
// See: http://docs.oracle.com/javase/7/docs/api/java/nio/channels/FileChannel.html
ReadableByteChannel rbc = null;
FileOutputStream fos = null;
while (true) {
try {
URLConnection connection = prepareURLConnection(url.toString(), timeout);
connection.connect();
InputStream inputStream = connection.getInputStream();
rbc = Channels.newChannel(inputStream);
fos = new FileOutputStream(tempFile);
fos.getChannel().transferFrom(rbc, 0, Long.MAX_VALUE);
break;
} catch (SocketTimeoutException e) {
if (++count == maxTries) throw e;
} finally {
if (rbc != null) {
rbc.close();
}
if (fos != null) {
fos.close();
}
}
}
logger.debug("Copying temp file {} to final location {}", tempFile, destination);
copy(tempFile, destination);
// delete the tmp file
tempFile.delete();
} | java | public static void downloadFile(URL url, File destination) throws IOException {
int count = 0;
int maxTries = 10;
int timeout = 60000; //60 sec
File tempFile = File.createTempFile(getFilePrefix(destination), "." + getFileExtension(destination));
// Took following recipe from stackoverflow:
// http://stackoverflow.com/questions/921262/how-to-download-and-save-a-file-from-internet-using-java
// It seems to be the most efficient way to transfer a file
// See: http://docs.oracle.com/javase/7/docs/api/java/nio/channels/FileChannel.html
ReadableByteChannel rbc = null;
FileOutputStream fos = null;
while (true) {
try {
URLConnection connection = prepareURLConnection(url.toString(), timeout);
connection.connect();
InputStream inputStream = connection.getInputStream();
rbc = Channels.newChannel(inputStream);
fos = new FileOutputStream(tempFile);
fos.getChannel().transferFrom(rbc, 0, Long.MAX_VALUE);
break;
} catch (SocketTimeoutException e) {
if (++count == maxTries) throw e;
} finally {
if (rbc != null) {
rbc.close();
}
if (fos != null) {
fos.close();
}
}
}
logger.debug("Copying temp file {} to final location {}", tempFile, destination);
copy(tempFile, destination);
// delete the tmp file
tempFile.delete();
} | [
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@param url
@param destination
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31,833 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java | FileDownloadUtils.toUnixPath | public static String toUnixPath(String path) {
String uPath = path;
if (uPath.contains("\\")) {
uPath = uPath.replaceAll("\\\\", "/");
}
// this should be removed, it's need since "\" is added AtomCache code
if (uPath.endsWith("//")) {
uPath = uPath.substring(0, uPath.length() - 1);
}
if (!uPath.endsWith("/")) {
uPath = uPath + "/";
}
return uPath;
} | java | public static String toUnixPath(String path) {
String uPath = path;
if (uPath.contains("\\")) {
uPath = uPath.replaceAll("\\\\", "/");
}
// this should be removed, it's need since "\" is added AtomCache code
if (uPath.endsWith("//")) {
uPath = uPath.substring(0, uPath.length() - 1);
}
if (!uPath.endsWith("/")) {
uPath = uPath + "/";
}
return uPath;
} | [
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31,834 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java | FileDownloadUtils.expandUserHome | public static String expandUserHome(String file) {
if (file.startsWith("~" + File.separator)) {
file = System.getProperty("user.home") + file.substring(1);
}
return file;
} | java | public static String expandUserHome(String file) {
if (file.startsWith("~" + File.separator)) {
file = System.getProperty("user.home") + file.substring(1);
}
return file;
} | [
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31,835 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java | FileDownloadUtils.deleteDirectory | public static void deleteDirectory(Path dir) throws IOException {
if(dir == null || !Files.exists(dir))
return;
Files.walkFileTree(dir, new SimpleFileVisitor<Path>() {
@Override
public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) throws IOException {
Files.delete(file);
return FileVisitResult.CONTINUE;
}
@Override
public FileVisitResult postVisitDirectory(Path dir, IOException e) throws IOException {
if (e != null) {
throw e;
}
Files.delete(dir);
return FileVisitResult.CONTINUE;
}
});
} | java | public static void deleteDirectory(Path dir) throws IOException {
if(dir == null || !Files.exists(dir))
return;
Files.walkFileTree(dir, new SimpleFileVisitor<Path>() {
@Override
public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) throws IOException {
Files.delete(file);
return FileVisitResult.CONTINUE;
}
@Override
public FileVisitResult postVisitDirectory(Path dir, IOException e) throws IOException {
if (e != null) {
throw e;
}
Files.delete(dir);
return FileVisitResult.CONTINUE;
}
});
} | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-core/src/main/java/org/biojava/nbio/core/util/FileDownloadUtils.java#L255-L274 |
31,836 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ChemicalComponentDictionary.java | ChemicalComponentDictionary.getParent | public ChemComp getParent(ChemComp c){
if (c.hasParent()){
return dictionary.get(c.getMon_nstd_parent_comp_id());
}
return null;
} | java | public ChemComp getParent(ChemComp c){
if (c.hasParent()){
return dictionary.get(c.getMon_nstd_parent_comp_id());
}
return null;
} | [
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31,837 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/ChemicalComponentDictionary.java | ChemicalComponentDictionary.addChemComp | public void addChemComp(ChemComp comp){
dictionary.put(comp.getId(),comp);
String rep = comp.getPdbx_replaces();
if ( (rep != null) && ( ! rep.equals("?"))){
replaces.put(comp.getId(),rep);
}
String isrep = comp.getPdbx_replaced_by();
if ( (isrep != null) && ( ! isrep.equals("?"))){
isreplacedby.put(comp.getId(),isrep);
}
} | java | public void addChemComp(ChemComp comp){
dictionary.put(comp.getId(),comp);
String rep = comp.getPdbx_replaces();
if ( (rep != null) && ( ! rep.equals("?"))){
replaces.put(comp.getId(),rep);
}
String isrep = comp.getPdbx_replaced_by();
if ( (isrep != null) && ( ! isrep.equals("?"))){
isreplacedby.put(comp.getId(),isrep);
}
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31,838 | biojava/biojava | biojava-genome/src/main/java/org/biojava/nbio/genome/GeneFeatureHelper.java | GeneFeatureHelper.loadFastaAddGeneFeaturesFromGeneIDGFF2 | static public LinkedHashMap<String, ChromosomeSequence> loadFastaAddGeneFeaturesFromGeneIDGFF2(File fastaSequenceFile, File gffFile) throws Exception {
LinkedHashMap<String, DNASequence> dnaSequenceList = FastaReaderHelper.readFastaDNASequence(fastaSequenceFile);
LinkedHashMap<String, ChromosomeSequence> chromosomeSequenceList = GeneFeatureHelper.getChromosomeSequenceFromDNASequence(dnaSequenceList);
FeatureList listGenes = GeneIDGFF2Reader.read(gffFile.getAbsolutePath());
addGeneIDGFF2GeneFeatures(chromosomeSequenceList, listGenes);
return chromosomeSequenceList;
} | java | static public LinkedHashMap<String, ChromosomeSequence> loadFastaAddGeneFeaturesFromGeneIDGFF2(File fastaSequenceFile, File gffFile) throws Exception {
LinkedHashMap<String, DNASequence> dnaSequenceList = FastaReaderHelper.readFastaDNASequence(fastaSequenceFile);
LinkedHashMap<String, ChromosomeSequence> chromosomeSequenceList = GeneFeatureHelper.getChromosomeSequenceFromDNASequence(dnaSequenceList);
FeatureList listGenes = GeneIDGFF2Reader.read(gffFile.getAbsolutePath());
addGeneIDGFF2GeneFeatures(chromosomeSequenceList, listGenes);
return chromosomeSequenceList;
} | [
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31,839 | biojava/biojava | biojava-genome/src/main/java/org/biojava/nbio/genome/GeneFeatureHelper.java | GeneFeatureHelper.loadFastaAddGeneFeaturesFromGmodGFF3 | static public LinkedHashMap<String, ChromosomeSequence> loadFastaAddGeneFeaturesFromGmodGFF3(File fastaSequenceFile, File gffFile,boolean lazyloadsequences) throws Exception {
LinkedHashMap<String, DNASequence> dnaSequenceList = FastaReaderHelper.readFastaDNASequence(fastaSequenceFile,lazyloadsequences);
LinkedHashMap<String, ChromosomeSequence> chromosomeSequenceList = GeneFeatureHelper.getChromosomeSequenceFromDNASequence(dnaSequenceList);
FeatureList listGenes = GFF3Reader.read(gffFile.getAbsolutePath());
addGmodGFF3GeneFeatures(chromosomeSequenceList, listGenes);
return chromosomeSequenceList;
} | java | static public LinkedHashMap<String, ChromosomeSequence> loadFastaAddGeneFeaturesFromGmodGFF3(File fastaSequenceFile, File gffFile,boolean lazyloadsequences) throws Exception {
LinkedHashMap<String, DNASequence> dnaSequenceList = FastaReaderHelper.readFastaDNASequence(fastaSequenceFile,lazyloadsequences);
LinkedHashMap<String, ChromosomeSequence> chromosomeSequenceList = GeneFeatureHelper.getChromosomeSequenceFromDNASequence(dnaSequenceList);
FeatureList listGenes = GFF3Reader.read(gffFile.getAbsolutePath());
addGmodGFF3GeneFeatures(chromosomeSequenceList, listGenes);
return chromosomeSequenceList;
} | [
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included but can be extracted from other data elements.
@param fastaSequenceFile
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@param lazyloadsequences If set to true then the fasta file will be parsed for accession id but sequences will be read from disk when needed to save memory
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31,840 | biojava/biojava | biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/twobit/TwoBitFacade.java | TwoBitFacade.setChromosome | public void setChromosome(String chr) throws Exception {
if ( twoBitParser == null){
}
twoBitParser.close();
String[] names = twoBitParser.getSequenceNames();
for(int i=0;i<names.length;i++) {
if ( names[i].equalsIgnoreCase(chr) ) {
twoBitParser.setCurrentSequence(names[i]);
break;
}
}
} | java | public void setChromosome(String chr) throws Exception {
if ( twoBitParser == null){
}
twoBitParser.close();
String[] names = twoBitParser.getSequenceNames();
for(int i=0;i<names.length;i++) {
if ( names[i].equalsIgnoreCase(chr) ) {
twoBitParser.setCurrentSequence(names[i]);
break;
}
}
} | [
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31,841 | biojava/biojava | biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/twobit/TwoBitFacade.java | TwoBitFacade.getSequence | public String getSequence(String chromosomeName, int start, int end) throws Exception {
twoBitParser.close();
twoBitParser.setCurrentSequence(chromosomeName);
return twoBitParser.loadFragment(start,end-start);
} | java | public String getSequence(String chromosomeName, int start, int end) throws Exception {
twoBitParser.close();
twoBitParser.setCurrentSequence(chromosomeName);
return twoBitParser.loadFragment(start,end-start);
} | [
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@return the DNASequence from the requested coordinates.
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31,842 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/StructureName.java | StructureName.compareTo | @Override
public int compareTo(StructureName o) {
if ( this.equals(o))
return 0;
String pdb1 = null;
String pdb2 = null;
try {
pdb1 = this.getPdbId();
} catch (StructureException e) {}
try {
pdb2 = this.getPdbId();
} catch (StructureException e) {}
int comp = 0;
// Sort those with PDBIDs before those without
if( pdb1 == null ) {
if( pdb2 != null) {
return 1; // this > o
}
// both null
} else if( pdb2 == null){
return -1; // this < o
} else {
// neither null
comp = pdb1.compareTo(pdb2);
}
if( comp != 0 ) {
return comp;
}
// break tie with full identifiers
pdb1 = this.getIdentifier();
pdb2 = o.getIdentifier();
// Throws NPE for nulls
return pdb1.compareTo(pdb2);
} | java | @Override
public int compareTo(StructureName o) {
if ( this.equals(o))
return 0;
String pdb1 = null;
String pdb2 = null;
try {
pdb1 = this.getPdbId();
} catch (StructureException e) {}
try {
pdb2 = this.getPdbId();
} catch (StructureException e) {}
int comp = 0;
// Sort those with PDBIDs before those without
if( pdb1 == null ) {
if( pdb2 != null) {
return 1; // this > o
}
// both null
} else if( pdb2 == null){
return -1; // this < o
} else {
// neither null
comp = pdb1.compareTo(pdb2);
}
if( comp != 0 ) {
return comp;
}
// break tie with full identifiers
pdb1 = this.getIdentifier();
pdb2 = o.getIdentifier();
// Throws NPE for nulls
return pdb1.compareTo(pdb2);
} | [
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31,843 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/FileConvert.java | FileConvert.printPDBConnections | private String printPDBConnections(){
StringBuilder str = new StringBuilder();
for (Chain c:structure.getChains()) {
for (Group g:c.getAtomGroups()) {
for (Atom a:g.getAtoms()) {
if (a.getBonds()!=null) {
for (Bond b:a.getBonds()) { //7890123456789012345678901234567890123456789012345678901234567890
str.append(String.format("CONECT%5d%5d "+newline, b.getAtomA().getPDBserial(), b.getAtomB().getPDBserial()));
}
}
}
}
}
return str.toString();
} | java | private String printPDBConnections(){
StringBuilder str = new StringBuilder();
for (Chain c:structure.getChains()) {
for (Group g:c.getAtomGroups()) {
for (Atom a:g.getAtoms()) {
if (a.getBonds()!=null) {
for (Bond b:a.getBonds()) { //7890123456789012345678901234567890123456789012345678901234567890
str.append(String.format("CONECT%5d%5d "+newline, b.getAtomA().getPDBserial(), b.getAtomB().getPDBserial()));
}
}
}
}
}
return str.toString();
} | [
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Rewritten since 5.0 to use {@link Bond}s
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31,844 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/FileConvert.java | FileConvert.toPDB | public static String toPDB(Atom a){
StringBuffer w = new StringBuffer();
toPDB(a,w);
return w.toString();
} | java | public static String toPDB(Atom a){
StringBuffer w = new StringBuffer();
toPDB(a,w);
return w.toString();
} | [
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31,845 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/FileConvert.java | FileConvert.toPDB | public static String toPDB(Chain chain){
StringBuffer w = new StringBuffer();
int nrGroups = chain.getAtomLength();
for ( int h=0; h<nrGroups;h++){
Group g= chain.getAtomGroup(h);
toPDB(g,w);
}
return w.toString();
} | java | public static String toPDB(Chain chain){
StringBuffer w = new StringBuffer();
int nrGroups = chain.getAtomLength();
for ( int h=0; h<nrGroups;h++){
Group g= chain.getAtomGroup(h);
toPDB(g,w);
}
return w.toString();
} | [
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31,846 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/FileConvert.java | FileConvert.toPDB | public static String toPDB(Group g){
StringBuffer w = new StringBuffer();
toPDB(g,w);
return w.toString();
} | java | public static String toPDB(Group g){
StringBuffer w = new StringBuffer();
toPDB(g,w);
return w.toString();
} | [
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31,847 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/FileConvert.java | FileConvert.hasInsertionCode | private static boolean hasInsertionCode(String pdbserial) {
try {
Integer.parseInt(pdbserial) ;
} catch (NumberFormatException e) {
return true ;
}
return false ;
} | java | private static boolean hasInsertionCode(String pdbserial) {
try {
Integer.parseInt(pdbserial) ;
} catch (NumberFormatException e) {
return true ;
}
return false ;
} | [
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31,848 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MMCIFFileTools.java | MMCIFFileTools.toSingleLoopLineMmCifString | private static String toSingleLoopLineMmCifString(Object record, Field[] fields, int[] sizes) {
StringBuilder str = new StringBuilder();
Class<?> c = record.getClass();
if(fields == null)
fields = getFields(c);
if (sizes.length!=fields.length)
throw new IllegalArgumentException("The given sizes of fields differ from the number of declared fields");
int i = -1;
for (Field f : fields) {
i++;
f.setAccessible(true);
try {
Object obj = f.get(record);
String val;
if (obj==null) {
logger.debug("Field {} is null, will write it out as {}",f.getName(),MMCIF_MISSING_VALUE);
val = MMCIF_MISSING_VALUE;
} else {
val = (String) obj;
}
str.append(String.format("%-"+sizes[i]+"s ", addMmCifQuoting(val)));
} catch (IllegalAccessException e) {
logger.warn("Field {} is inaccessible", f.getName());
continue;
} catch (ClassCastException e) {
logger.warn("Could not cast value to String for field {}",f.getName());
continue;
}
}
str.append(newline);
return str.toString();
} | java | private static String toSingleLoopLineMmCifString(Object record, Field[] fields, int[] sizes) {
StringBuilder str = new StringBuilder();
Class<?> c = record.getClass();
if(fields == null)
fields = getFields(c);
if (sizes.length!=fields.length)
throw new IllegalArgumentException("The given sizes of fields differ from the number of declared fields");
int i = -1;
for (Field f : fields) {
i++;
f.setAccessible(true);
try {
Object obj = f.get(record);
String val;
if (obj==null) {
logger.debug("Field {} is null, will write it out as {}",f.getName(),MMCIF_MISSING_VALUE);
val = MMCIF_MISSING_VALUE;
} else {
val = (String) obj;
}
str.append(String.format("%-"+sizes[i]+"s ", addMmCifQuoting(val)));
} catch (IllegalAccessException e) {
logger.warn("Field {} is inaccessible", f.getName());
continue;
} catch (ClassCastException e) {
logger.warn("Could not cast value to String for field {}",f.getName());
continue;
}
}
str.append(newline);
return str.toString();
} | [
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@param sizes the size of each of the fields
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31,849 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MMCIFFileTools.java | MMCIFFileTools.getFieldSizes | private static <T> int[] getFieldSizes(List<T> list, Field[] fields) {
if (list.isEmpty()) throw new IllegalArgumentException("List of beans is empty!");
if(fields == null)
fields = getFields(list.get(0).getClass());
int[] sizes = new int [fields.length];
for (T a:list) {
int i = -1;
for (Field f : fields) {
i++;
f.setAccessible(true);
try {
Object obj = f.get(a);
int length;
if (obj==null) {
length = MMCIF_MISSING_VALUE.length();
} else {
String val = (String) obj;
length = addMmCifQuoting(val).length();
}
if (length>sizes[i]) sizes[i] = length;
} catch (IllegalAccessException e) {
logger.warn("Field {} is inaccessible", f.getName());
continue;
} catch (ClassCastException e) {
logger.warn("Could not cast value to String for field {}",f.getName());
continue;
}
}
}
return sizes;
} | java | private static <T> int[] getFieldSizes(List<T> list, Field[] fields) {
if (list.isEmpty()) throw new IllegalArgumentException("List of beans is empty!");
if(fields == null)
fields = getFields(list.get(0).getClass());
int[] sizes = new int [fields.length];
for (T a:list) {
int i = -1;
for (Field f : fields) {
i++;
f.setAccessible(true);
try {
Object obj = f.get(a);
int length;
if (obj==null) {
length = MMCIF_MISSING_VALUE.length();
} else {
String val = (String) obj;
length = addMmCifQuoting(val).length();
}
if (length>sizes[i]) sizes[i] = length;
} catch (IllegalAccessException e) {
logger.warn("Field {} is inaccessible", f.getName());
continue;
} catch (ClassCastException e) {
logger.warn("Could not cast value to String for field {}",f.getName());
continue;
}
}
}
return sizes;
} | [
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@param fields Set of fields for the record. If null, will be calculated from the class of the first record
@return
@see #toMMCIF(List, Class) | [
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31,850 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/MMCIFFileTools.java | MMCIFFileTools.getMaxStringLength | private static int getMaxStringLength(String[] names) {
int size = 0;
for(String s : names) {
if(s.length()>size) {
size = s.length();
}
}
return size;
} | java | private static int getMaxStringLength(String[] names) {
int size = 0;
for(String s : names) {
if(s.length()>size) {
size = s.length();
}
}
return size;
} | [
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Useful for producing mmCIF single-record data that is aligned for all values.
@param names
@return
@see #toMMCIF(String, Object) | [
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31,851 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/HasResultXMLConverter.java | HasResultXMLConverter.toXML | public String toXML(boolean hasResult) throws IOException{
StringWriter swriter = new StringWriter();
PrintWriter writer = new PrintWriter(swriter);
PrettyXMLWriter xml = new PrettyXMLWriter(writer);
xml.openTag("alignment");
xml.attribute("hasResult", String.valueOf(hasResult));
xml.closeTag("alignment");
xml.close();
return swriter.toString();
} | java | public String toXML(boolean hasResult) throws IOException{
StringWriter swriter = new StringWriter();
PrintWriter writer = new PrintWriter(swriter);
PrettyXMLWriter xml = new PrettyXMLWriter(writer);
xml.openTag("alignment");
xml.attribute("hasResult", String.valueOf(hasResult));
xml.closeTag("alignment");
xml.close();
return swriter.toString();
} | [
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... | return flag if the server has a result
@param hasResult
@return flag if there is a result | [
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31,852 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmResult.java | CeSymmResult.getRepeatsID | public List<StructureIdentifier> getRepeatsID() throws StructureException {
if (!isRefined())
return null;
List<StructureIdentifier> repeats = new ArrayList<StructureIdentifier>(
numRepeats);
String pdbId = structureId.toCanonical().getPdbId();
Block align = multipleAlignment.getBlocks().get(0);
for (int su = 0; su < numRepeats; su++) {
// Get the start and end residues of the repeat
ResidueNumber res1 = atoms[align.getStartResidue(su)].getGroup()
.getResidueNumber();
ResidueNumber res2 = atoms[align.getFinalResidue(su)].getGroup()
.getResidueNumber();
ResidueRange range = new ResidueRange(res1.getChainName(), res1, res2);
StructureIdentifier id = new SubstructureIdentifier(pdbId,
Arrays.asList(range));
repeats.add(id);
}
return repeats;
} | java | public List<StructureIdentifier> getRepeatsID() throws StructureException {
if (!isRefined())
return null;
List<StructureIdentifier> repeats = new ArrayList<StructureIdentifier>(
numRepeats);
String pdbId = structureId.toCanonical().getPdbId();
Block align = multipleAlignment.getBlocks().get(0);
for (int su = 0; su < numRepeats; su++) {
// Get the start and end residues of the repeat
ResidueNumber res1 = atoms[align.getStartResidue(su)].getGroup()
.getResidueNumber();
ResidueNumber res2 = atoms[align.getFinalResidue(su)].getGroup()
.getResidueNumber();
ResidueRange range = new ResidueRange(res1.getChainName(), res1, res2);
StructureIdentifier id = new SubstructureIdentifier(pdbId,
Arrays.asList(range));
repeats.add(id);
}
return repeats;
} | [
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... | Return the symmetric repeats as structure identifiers, if the result is
symmetric and it was refined, return null otherwise.
@return List of StructureIdentifiers or null if not defined
@throws StructureException | [
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31,853 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymmResult.java | CeSymmResult.getReason | public String getReason() {
// Cases:
// 1. Asymmetric because insignificant self-alignment (1itb.A_1-100)
double tm = selfAlignment.getTMScore();
if (tm < params.getUnrefinedScoreThreshold()) {
return String.format("Insignificant self-alignment (TM=%.2f)", tm);
}
// 2. Asymmetric because order detector returned 1
if (numRepeats == 1) {
return String.format(
"Order detector found asymmetric alignment (TM=%.2f)", tm);
}
// Check that the user requested refinement
if (params.getRefineMethod() != RefineMethod.NOT_REFINED) {
// 3. Asymmetric because refinement failed
if (!refined) {
return "Refinement failed";
}
tm = multipleAlignment
.getScore(MultipleAlignmentScorer.AVGTM_SCORE);
// 4. Asymmetric because refinement & optimization were not
// significant
if (!isSignificant()) {
return String.format(
"Refinement was not significant (TM=%.2f)", tm);
}
} else {
// 4. Not refined, but result was not significant
if (!isSignificant()) {
return String
.format("Result was not significant (TM=%.2f)", tm);
}
}
String hierarchical = "";
if (axes.getNumLevels() > 1) {
hierarchical = String.format("; Contains %d levels of symmetry",
axes.getNumLevels());
}
// 5. Symmetric.
// a. Open. Give # repeats (1n0r.A)
if (axes.getElementaryAxis(0).getSymmType() == SymmetryType.OPEN) {
return String.format("Contains %d open repeats (TM=%.2f)%s",
getNumRepeats(), tm, hierarchical);
}
// b. Closed, non-hierarchical (1itb.A)
// c. Closed, heirarchical (4gcr)
return String.format("Significant (TM=%.2f)%s", tm, hierarchical);
} | java | public String getReason() {
// Cases:
// 1. Asymmetric because insignificant self-alignment (1itb.A_1-100)
double tm = selfAlignment.getTMScore();
if (tm < params.getUnrefinedScoreThreshold()) {
return String.format("Insignificant self-alignment (TM=%.2f)", tm);
}
// 2. Asymmetric because order detector returned 1
if (numRepeats == 1) {
return String.format(
"Order detector found asymmetric alignment (TM=%.2f)", tm);
}
// Check that the user requested refinement
if (params.getRefineMethod() != RefineMethod.NOT_REFINED) {
// 3. Asymmetric because refinement failed
if (!refined) {
return "Refinement failed";
}
tm = multipleAlignment
.getScore(MultipleAlignmentScorer.AVGTM_SCORE);
// 4. Asymmetric because refinement & optimization were not
// significant
if (!isSignificant()) {
return String.format(
"Refinement was not significant (TM=%.2f)", tm);
}
} else {
// 4. Not refined, but result was not significant
if (!isSignificant()) {
return String
.format("Result was not significant (TM=%.2f)", tm);
}
}
String hierarchical = "";
if (axes.getNumLevels() > 1) {
hierarchical = String.format("; Contains %d levels of symmetry",
axes.getNumLevels());
}
// 5. Symmetric.
// a. Open. Give # repeats (1n0r.A)
if (axes.getElementaryAxis(0).getSymmType() == SymmetryType.OPEN) {
return String.format("Contains %d open repeats (TM=%.2f)%s",
getNumRepeats(), tm, hierarchical);
}
// b. Closed, non-hierarchical (1itb.A)
// c. Closed, heirarchical (4gcr)
return String.format("Significant (TM=%.2f)%s", tm, hierarchical);
} | [
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this particular result.
@return String decision reason | [
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31,854 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SequenceFunctionRefiner.java | SequenceFunctionRefiner.initializeEligible | private static List<Integer> initializeEligible(Map<Integer, Integer> alignment,
Map<Integer, Double> scores, List<Integer> eligible, int k, NavigableSet<Integer> forwardLoops, NavigableSet<Integer> backwardLoops) {
// Eligible if:
// 1. score(x)>0
// 2. f^K-1(x) is defined
// 3. score(f^K-1(x))>0
// 4. For all y, score(y)==0 implies sign(f^K-1(x)-y) == sign(x-f(y) )
// 5. Not in a loop of length less than k
// Assume all residues are eligible to start
if(eligible == null) {
eligible = new LinkedList<Integer>(alignment.keySet());
}
// Precalculate f^K-1(x)
// Map<Integer, Integer> alignK1 = AlignmentTools.applyAlignment(alignment, k-1);
Map<Integer, Integer> alignK1 = applyAlignmentAndCheckCycles(alignment, k - 1, eligible);
// Remove ineligible residues
Iterator<Integer> eligibleIt = eligible.iterator();
while(eligibleIt.hasNext()) {
Integer res = eligibleIt.next();
// 2. f^K-1(x) is defined
if(!alignK1.containsKey(res)) {
eligibleIt.remove();
continue;
}
Integer k1 = alignK1.get(res);
if(k1 == null) {
eligibleIt.remove();
continue;
}
// 1. score(x)>0
Double score = scores.get(res);
if(score == null || score <= 0.0) {
eligibleIt.remove();
// res is in a loop. Add it to the proper set
if(res <= alignment.get(res)) {
//forward
forwardLoops.add(res);
} else {
//backward
backwardLoops.add(res);
}
continue;
}
// 3. score(f^K-1(x))>0
Double scoreK1 = scores.get(k1);
if(scoreK1 == null || scoreK1 <= 0.0) {
eligibleIt.remove();
continue;
}
}
// Now that loops are up-to-date, check for loop crossings
eligibleIt = eligible.iterator();
while(eligibleIt.hasNext()) {
Integer res = eligibleIt.next();
//4. For all y, score(y)==0 implies sign(f^K-1(x)-y) == sign(x-f(y) )
//Test equivalent: All loop edges should be properly ordered wrt edge f^k-1(x) -> x
Integer src = alignK1.get(res);
if( src < res ) {
//forward
// get interval [a,b) containing res
Integer a = forwardLoops.floor(src);
Integer b = forwardLoops.higher(src);
// Ineligible unless f(a) < res < f(b)
if(a != null && alignment.get(a) > res ) {
eligibleIt.remove();
continue;
}
if(b != null && alignment.get(b) < res ) {
eligibleIt.remove();
continue;
}
}
}
return eligible;
} | java | private static List<Integer> initializeEligible(Map<Integer, Integer> alignment,
Map<Integer, Double> scores, List<Integer> eligible, int k, NavigableSet<Integer> forwardLoops, NavigableSet<Integer> backwardLoops) {
// Eligible if:
// 1. score(x)>0
// 2. f^K-1(x) is defined
// 3. score(f^K-1(x))>0
// 4. For all y, score(y)==0 implies sign(f^K-1(x)-y) == sign(x-f(y) )
// 5. Not in a loop of length less than k
// Assume all residues are eligible to start
if(eligible == null) {
eligible = new LinkedList<Integer>(alignment.keySet());
}
// Precalculate f^K-1(x)
// Map<Integer, Integer> alignK1 = AlignmentTools.applyAlignment(alignment, k-1);
Map<Integer, Integer> alignK1 = applyAlignmentAndCheckCycles(alignment, k - 1, eligible);
// Remove ineligible residues
Iterator<Integer> eligibleIt = eligible.iterator();
while(eligibleIt.hasNext()) {
Integer res = eligibleIt.next();
// 2. f^K-1(x) is defined
if(!alignK1.containsKey(res)) {
eligibleIt.remove();
continue;
}
Integer k1 = alignK1.get(res);
if(k1 == null) {
eligibleIt.remove();
continue;
}
// 1. score(x)>0
Double score = scores.get(res);
if(score == null || score <= 0.0) {
eligibleIt.remove();
// res is in a loop. Add it to the proper set
if(res <= alignment.get(res)) {
//forward
forwardLoops.add(res);
} else {
//backward
backwardLoops.add(res);
}
continue;
}
// 3. score(f^K-1(x))>0
Double scoreK1 = scores.get(k1);
if(scoreK1 == null || scoreK1 <= 0.0) {
eligibleIt.remove();
continue;
}
}
// Now that loops are up-to-date, check for loop crossings
eligibleIt = eligible.iterator();
while(eligibleIt.hasNext()) {
Integer res = eligibleIt.next();
//4. For all y, score(y)==0 implies sign(f^K-1(x)-y) == sign(x-f(y) )
//Test equivalent: All loop edges should be properly ordered wrt edge f^k-1(x) -> x
Integer src = alignK1.get(res);
if( src < res ) {
//forward
// get interval [a,b) containing res
Integer a = forwardLoops.floor(src);
Integer b = forwardLoops.higher(src);
// Ineligible unless f(a) < res < f(b)
if(a != null && alignment.get(a) > res ) {
eligibleIt.remove();
continue;
}
if(b != null && alignment.get(b) < res ) {
eligibleIt.remove();
continue;
}
}
}
return eligible;
} | [
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Eligible if:
1. score(x)>0
2. f^K-1(x) is defined
3. score(f^K-1(x))>0
4. For all y, score(y)==0 implies sign(f^K-1(x)-y) == sign(x-f(y) )
@param alignment The alignment with respect to which to calculate eligibility
@param scores An up-to-date map from residues to their scores
@param eligible Starting list of eligible residues. If null will be generated.
@param k
@param backwardLoops
@param forwardLoops
@return eligible after modification | [
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31,855 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SequenceFunctionRefiner.java | SequenceFunctionRefiner.initializeScores | private static Map<Integer, Double> initializeScores(Map<Integer, Integer> alignment,
Map<Integer, Double> scores, int k) {
if(scores == null) {
scores = new HashMap<Integer, Double>(alignment.size());
} else {
scores.clear();
}
Map<Integer,Integer> alignK = AlignmentTools.applyAlignment(alignment, k);
// calculate input range
int maxPre = Integer.MIN_VALUE;
int minPre = Integer.MAX_VALUE;
for(Integer pre : alignment.keySet()) {
if(pre>maxPre) maxPre = pre;
if(pre<minPre) minPre = pre;
}
for(Integer pre : alignment.keySet()) {
Integer image = alignK.get(pre);
// Use the absolute error score, |x - f^k(x)|
double score = scoreAbsError(pre,image,minPre,maxPre);
scores.put(pre, score);
}
return scores;
} | java | private static Map<Integer, Double> initializeScores(Map<Integer, Integer> alignment,
Map<Integer, Double> scores, int k) {
if(scores == null) {
scores = new HashMap<Integer, Double>(alignment.size());
} else {
scores.clear();
}
Map<Integer,Integer> alignK = AlignmentTools.applyAlignment(alignment, k);
// calculate input range
int maxPre = Integer.MIN_VALUE;
int minPre = Integer.MAX_VALUE;
for(Integer pre : alignment.keySet()) {
if(pre>maxPre) maxPre = pre;
if(pre<minPre) minPre = pre;
}
for(Integer pre : alignment.keySet()) {
Integer image = alignK.get(pre);
// Use the absolute error score, |x - f^k(x)|
double score = scoreAbsError(pre,image,minPre,maxPre);
scores.put(pre, score);
}
return scores;
} | [
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@param alignment
@param scores A mapping from residues to scores, which will be updated or
created if null
@return scores | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SequenceFunctionRefiner.java#L372-L397 |
31,856 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SequenceFunctionRefiner.java | SequenceFunctionRefiner.partitionAFPchain | private static AFPChain partitionAFPchain(AFPChain afpChain,
Atom[] ca1, Atom[] ca2, int order) throws StructureException{
int[][][] newAlgn = new int[order][][];
int repeatLen = afpChain.getOptLength()/order;
//Extract all the residues considered in the first chain of the alignment
List<Integer> alignedRes = new ArrayList<Integer>();
for (int su=0; su<afpChain.getBlockNum(); su++){
for (int i=0; i<afpChain.getOptLen()[su]; i++){
alignedRes.add(afpChain.getOptAln()[su][0][i]);
}
}
//Build the new alignment
for (int su=0; su<order; su++){
newAlgn[su] = new int[2][];
newAlgn[su][0] = new int[repeatLen];
newAlgn[su][1] = new int[repeatLen];
for (int i=0; i<repeatLen; i++){
newAlgn[su][0][i] = alignedRes.get(repeatLen*su+i);
newAlgn[su][1][i] = alignedRes.get(
(repeatLen*(su+1)+i)%alignedRes.size());
}
}
return AlignmentTools.replaceOptAln(newAlgn, afpChain, ca1, ca2);
} | java | private static AFPChain partitionAFPchain(AFPChain afpChain,
Atom[] ca1, Atom[] ca2, int order) throws StructureException{
int[][][] newAlgn = new int[order][][];
int repeatLen = afpChain.getOptLength()/order;
//Extract all the residues considered in the first chain of the alignment
List<Integer> alignedRes = new ArrayList<Integer>();
for (int su=0; su<afpChain.getBlockNum(); su++){
for (int i=0; i<afpChain.getOptLen()[su]; i++){
alignedRes.add(afpChain.getOptAln()[su][0][i]);
}
}
//Build the new alignment
for (int su=0; su<order; su++){
newAlgn[su] = new int[2][];
newAlgn[su][0] = new int[repeatLen];
newAlgn[su][1] = new int[repeatLen];
for (int i=0; i<repeatLen; i++){
newAlgn[su][0][i] = alignedRes.get(repeatLen*su+i);
newAlgn[su][1][i] = alignedRes.get(
(repeatLen*(su+1)+i)%alignedRes.size());
}
}
return AlignmentTools.replaceOptAln(newAlgn, afpChain, ca1, ca2);
} | [
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... | Partitions an afpChain alignment into order blocks of aligned residues.
@param afpChain
@param ca1
@param ca2
@param order
@return
@throws StructureException | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SequenceFunctionRefiner.java#L440-L467 |
31,857 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java | SubstitutionMatrixHelper.getAminoAcidMatrix | private static SubstitutionMatrix<AminoAcidCompound> getAminoAcidMatrix(String file) {
if (!aminoAcidMatrices.containsKey(file)) {
aminoAcidMatrices.put(file, new SimpleSubstitutionMatrix<AminoAcidCompound>(
AminoAcidCompoundSet.getAminoAcidCompoundSet(), getReader(file), file));
}
return aminoAcidMatrices.get(file);
} | java | private static SubstitutionMatrix<AminoAcidCompound> getAminoAcidMatrix(String file) {
if (!aminoAcidMatrices.containsKey(file)) {
aminoAcidMatrices.put(file, new SimpleSubstitutionMatrix<AminoAcidCompound>(
AminoAcidCompoundSet.getAminoAcidCompoundSet(), getReader(file), file));
}
return aminoAcidMatrices.get(file);
} | [
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... | reads in an amino acid substitution matrix, if necessary | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java#L252-L258 |
31,858 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java | SubstitutionMatrixHelper.getNucleotideMatrix | private static SubstitutionMatrix<NucleotideCompound> getNucleotideMatrix(String file) {
if (!nucleotideMatrices.containsKey(file)) {
nucleotideMatrices.put(file, new SimpleSubstitutionMatrix<NucleotideCompound>(
AmbiguityDNACompoundSet.getDNACompoundSet(), getReader(file), file));
}
return nucleotideMatrices.get(file);
} | java | private static SubstitutionMatrix<NucleotideCompound> getNucleotideMatrix(String file) {
if (!nucleotideMatrices.containsKey(file)) {
nucleotideMatrices.put(file, new SimpleSubstitutionMatrix<NucleotideCompound>(
AmbiguityDNACompoundSet.getDNACompoundSet(), getReader(file), file));
}
return nucleotideMatrices.get(file);
} | [
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31,859 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java | SubstitutionMatrixHelper.getReader | private static InputStreamReader getReader(String file) {
String resourcePathPrefix = "matrices/";
return new InputStreamReader(SubstitutionMatrixHelper.class.getResourceAsStream(String.format("/%s.txt",
resourcePathPrefix+file)));
} | java | private static InputStreamReader getReader(String file) {
String resourcePathPrefix = "matrices/";
return new InputStreamReader(SubstitutionMatrixHelper.class.getResourceAsStream(String.format("/%s.txt",
resourcePathPrefix+file)));
} | [
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31,860 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java | PDBFileParser.getNewGroup | private Group getNewGroup(String recordName,Character aminoCode1, String aminoCode3) {
Group g = ChemCompGroupFactory.getGroupFromChemCompDictionary(aminoCode3);
if ( g != null && !g.getChemComp().isEmpty())
return g;
Group group;
if (aminoCode1 == null || StructureTools.UNKNOWN_GROUP_LABEL == aminoCode1 ){
group = new HetatomImpl();
} else if(StructureTools.isNucleotide(aminoCode3)) {
// it is a nucleotide
NucleotideImpl nu = new NucleotideImpl();
group = nu;
} else {
AminoAcidImpl aa = new AminoAcidImpl() ;
aa.setAminoType(aminoCode1);
group = aa ;
}
// System.out.println("new resNum type: "+ resNum.getType() );
return group ;
} | java | private Group getNewGroup(String recordName,Character aminoCode1, String aminoCode3) {
Group g = ChemCompGroupFactory.getGroupFromChemCompDictionary(aminoCode3);
if ( g != null && !g.getChemComp().isEmpty())
return g;
Group group;
if (aminoCode1 == null || StructureTools.UNKNOWN_GROUP_LABEL == aminoCode1 ){
group = new HetatomImpl();
} else if(StructureTools.isNucleotide(aminoCode3)) {
// it is a nucleotide
NucleotideImpl nu = new NucleotideImpl();
group = nu;
} else {
AminoAcidImpl aa = new AminoAcidImpl() ;
aa.setAminoType(aminoCode1);
group = aa ;
}
// System.out.println("new resNum type: "+ resNum.getType() );
return group ;
} | [
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31,861 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java | PDBFileParser.pdb_JRNL_Handler | private void pdb_JRNL_Handler(String line) {
//add the strings to the journalLines
//the actual JournalArticle is then built when the whole entry is being
//finalized with triggerEndFileChecks()
//JRNL TITL NMR SOLUTION STRUCTURE OF RECOMBINANT TICK 1TAP 10
if (line.substring(line.length() - 8, line.length() - 4).equals(pdbId)) {
//trim off the trailing PDB id from legacy files.
//are we really trying to still cater for these museum pieces?
logger.debug("trimming legacy PDB id from end of JRNL section line");
line = line.substring(0, line.length() - 8);
journalLines.add(line);
} else {
journalLines.add(line);
}
} | java | private void pdb_JRNL_Handler(String line) {
//add the strings to the journalLines
//the actual JournalArticle is then built when the whole entry is being
//finalized with triggerEndFileChecks()
//JRNL TITL NMR SOLUTION STRUCTURE OF RECOMBINANT TICK 1TAP 10
if (line.substring(line.length() - 8, line.length() - 4).equals(pdbId)) {
//trim off the trailing PDB id from legacy files.
//are we really trying to still cater for these museum pieces?
logger.debug("trimming legacy PDB id from end of JRNL section line");
line = line.substring(0, line.length() - 8);
journalLines.add(line);
} else {
journalLines.add(line);
}
} | [
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"//JRNL TITL NMR SOLUTION STRUCTURE OF RECOMBINANT TIC... | JRNL handler.
The JRNL record contains the primary literature citation that describes the experiment which resulted
in the deposited coordinate set. There is at most one JRNL reference per entry. If there is no primary
reference, then there is no JRNL reference. Other references are given in REMARK 1.
Record Format
<pre>
COLUMNS DATA TYPE FIELD DEFINITION
-----------------------------------------------------------------------
1 - 6 Record name "JRNL "
13 - 70 LString text See Details below.
</pre> | [
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31,862 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java | PDBFileParser.pdb_SOURCE_Handler | private void pdb_SOURCE_Handler(String line) {
// works in the same way as the pdb_COMPND_Handler.
String continuationNr = line.substring(9, 10).trim();
logger.debug("current continuationNo is "
+ continuationNr);
logger.debug("previousContinuationField is "
+ previousContinuationField);
logger.debug("current continuationField is "
+ continuationField);
logger.debug("current continuationString is "
+ continuationString);
logger.debug("current compound is "
+ current_compound);
// following the docs, the last valid character should be 79, chop off the rest
if (line.length() > 79) {
line = line.substring(0, 79);
}
line = line.substring(10, line.length());
logger.debug("LINE: >" + line + "<");
String[] fieldList = line.split("\\s+");
if (!fieldList[0].equals("")
&& sourceFieldValues.contains(fieldList[0])) {
// System.out.println("[PDBFileParser.pdb_COMPND_Handler] Setting continuationField to '" + fieldList[0] + "'");
continuationField = fieldList[0];
if (previousContinuationField.equals("")) {
previousContinuationField = continuationField;
}
} else if ((fieldList.length > 1) && ( sourceFieldValues.contains(fieldList[1]))) {
// System.out.println("[PDBFileParser.pdb_COMPND_Handler] Setting continuationField to '" + fieldList[1] + "'");
continuationField = fieldList[1];
if (previousContinuationField.equals("")) {
previousContinuationField = continuationField;
}
} else {
if (continuationNr.equals("")) {
logger.debug("looks like an old PDB file");
continuationField = "MOLECULE:";
if (previousContinuationField.equals("")) {
previousContinuationField = continuationField;
}
}
}
line = line.replace(continuationField, "").trim();
StringTokenizer compndTokens = new StringTokenizer(line);
// System.out.println("PDBFileParser.pdb_COMPND_Handler: Tokenizing '" + line + "'");
while (compndTokens.hasMoreTokens()) {
String token = compndTokens.nextToken();
if (previousContinuationField.equals("")) {
// System.out.println("previousContinuationField is empty. Setting to : " + continuationField);
previousContinuationField = continuationField;
}
if (previousContinuationField.equals(continuationField)
&& sourceFieldValues.contains(continuationField)) {
logger.debug("Still in field " + continuationField);
continuationString = continuationString.concat(token + " ");
logger.debug("continuationString = "
+ continuationString);
}
if (!continuationField.equals(previousContinuationField)) {
if (continuationString.equals("")) {
continuationString = token;
} else {
sourceValueSetter(previousContinuationField,
continuationString);
previousContinuationField = continuationField;
continuationString = token + " ";
}
} else if (ignoreCompndFieldValues.contains(token)) {
// this field shall be ignored
//continuationField = token;
}
}
if (isLastSourceLine) {
// final line in the section - finish off the compound
// System.out.println("[pdb_SOURCE_Handler] Final SOURCE line - Finishing off final MolID header.");
sourceValueSetter(continuationField, continuationString);
continuationString = "";
//compounds.add(current_compound);
}
} | java | private void pdb_SOURCE_Handler(String line) {
// works in the same way as the pdb_COMPND_Handler.
String continuationNr = line.substring(9, 10).trim();
logger.debug("current continuationNo is "
+ continuationNr);
logger.debug("previousContinuationField is "
+ previousContinuationField);
logger.debug("current continuationField is "
+ continuationField);
logger.debug("current continuationString is "
+ continuationString);
logger.debug("current compound is "
+ current_compound);
// following the docs, the last valid character should be 79, chop off the rest
if (line.length() > 79) {
line = line.substring(0, 79);
}
line = line.substring(10, line.length());
logger.debug("LINE: >" + line + "<");
String[] fieldList = line.split("\\s+");
if (!fieldList[0].equals("")
&& sourceFieldValues.contains(fieldList[0])) {
// System.out.println("[PDBFileParser.pdb_COMPND_Handler] Setting continuationField to '" + fieldList[0] + "'");
continuationField = fieldList[0];
if (previousContinuationField.equals("")) {
previousContinuationField = continuationField;
}
} else if ((fieldList.length > 1) && ( sourceFieldValues.contains(fieldList[1]))) {
// System.out.println("[PDBFileParser.pdb_COMPND_Handler] Setting continuationField to '" + fieldList[1] + "'");
continuationField = fieldList[1];
if (previousContinuationField.equals("")) {
previousContinuationField = continuationField;
}
} else {
if (continuationNr.equals("")) {
logger.debug("looks like an old PDB file");
continuationField = "MOLECULE:";
if (previousContinuationField.equals("")) {
previousContinuationField = continuationField;
}
}
}
line = line.replace(continuationField, "").trim();
StringTokenizer compndTokens = new StringTokenizer(line);
// System.out.println("PDBFileParser.pdb_COMPND_Handler: Tokenizing '" + line + "'");
while (compndTokens.hasMoreTokens()) {
String token = compndTokens.nextToken();
if (previousContinuationField.equals("")) {
// System.out.println("previousContinuationField is empty. Setting to : " + continuationField);
previousContinuationField = continuationField;
}
if (previousContinuationField.equals(continuationField)
&& sourceFieldValues.contains(continuationField)) {
logger.debug("Still in field " + continuationField);
continuationString = continuationString.concat(token + " ");
logger.debug("continuationString = "
+ continuationString);
}
if (!continuationField.equals(previousContinuationField)) {
if (continuationString.equals("")) {
continuationString = token;
} else {
sourceValueSetter(previousContinuationField,
continuationString);
previousContinuationField = continuationField;
continuationString = token + " ";
}
} else if (ignoreCompndFieldValues.contains(token)) {
// this field shall be ignored
//continuationField = token;
}
}
if (isLastSourceLine) {
// final line in the section - finish off the compound
// System.out.println("[pdb_SOURCE_Handler] Final SOURCE line - Finishing off final MolID header.");
sourceValueSetter(continuationField, continuationString);
continuationString = "";
//compounds.add(current_compound);
}
} | [
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SOURCE Record format
The SOURCE record specifies the biological and/or chemical source of each biological molecule in the entry. Sources are described by both the common name and the scientific name, e.g., genus and species. Strain and/or cell-line for immortalized cells are given when they help to uniquely identify the biological entity studied.
Record Format
<pre>
COLUMNS DATA TYPE FIELD DEFINITION
-------------------------------------------------------------------------------
1 - 6 Record name "SOURCE"
9 - 10 Continuation continuation Allows concatenation of multiple records.
11 - 70 Specification srcName Identifies the source of the macromolecule in
list a token: value format.
</pre>
@param line the line to be parsed | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java#L1133-L1239 |
31,863 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java | PDBFileParser.pdb_REMARK_Handler | private void pdb_REMARK_Handler(String line) {
if ( line == null || line.length() < 11)
return;
if (line.startsWith("REMARK 800")) {
pdb_REMARK_800_Handler(line);
} else if ( line.startsWith("REMARK 350")){
if ( params.isParseBioAssembly()) {
if (bioAssemblyParser == null){
bioAssemblyParser = new PDBBioAssemblyParser();
}
bioAssemblyParser.pdb_REMARK_350_Handler(line);
}
// REMARK 3 (for R free)
// note: if more than 1 value present (occurring in hybrid experimental technique entries, e.g. 3ins, 4n9m)
// then last one encountered will be taken
} else if (line.startsWith("REMARK 3 FREE R VALUE")) {
// Rfree annotation is not very consistent in PDB format, it varies depending on the software
// Here we follow this strategy:
// a) take the '(NO CUTOFF)' value if the only one available (shelx software, e.g. 1x7q)
// b) don't take it if also a line without '(NO CUTOFF)' is present (CNX software, e.g. 3lak)
Pattern pR = Pattern.compile("^REMARK 3 FREE R VALUE\\s+(?:\\(NO CUTOFF\\))?\\s+:\\s+(\\d?\\.\\d+).*");
Matcher mR = pR.matcher(line);
if (mR.matches()) {
try {
rfreeNoCutoffLine = Float.parseFloat(mR.group(1));
} catch (NumberFormatException e) {
logger.info("Rfree value "+mR.group(1)+" does not look like a number, will ignore it");
}
}
pR = Pattern.compile("^REMARK 3 FREE R VALUE\\s+:\\s+(\\d?\\.\\d+).*");
mR = pR.matcher(line);
if (mR.matches()) {
try {
rfreeStandardLine = Float.parseFloat(mR.group(1));
} catch (NumberFormatException e) {
logger.info("Rfree value '{}' does not look like a number, will ignore it", mR.group(1));
}
}
// REMARK 3 RESOLUTION (contains more info than REMARK 2, for instance multiple resolutions in hybrid experimental technique entries)
// note: if more than 1 value present (occurring in hybrid experimental technique entries, e.g. 3ins, 4n9m)
// then last one encountered will be taken
} else if (line.startsWith("REMARK 3 RESOLUTION RANGE HIGH")){
Pattern pR = Pattern.compile("^REMARK 3 RESOLUTION RANGE HIGH \\(ANGSTROMS\\) :\\s+(\\d+\\.\\d+).*");
Matcher mR = pR.matcher(line);
if (mR.matches()) {
try {
float res = Float.parseFloat(mR.group(1));
if (pdbHeader.getResolution()!=PDBHeader.DEFAULT_RESOLUTION) {
logger.warn("More than 1 resolution value present, will use last one {} and discard previous {} "
,mR.group(1), String.format("%4.2f",pdbHeader.getResolution()));
}
pdbHeader.setResolution(res);
} catch (NumberFormatException e) {
logger.info("Could not parse resolution '{}', ignoring it",mR.group(1));
}
}
}
} | java | private void pdb_REMARK_Handler(String line) {
if ( line == null || line.length() < 11)
return;
if (line.startsWith("REMARK 800")) {
pdb_REMARK_800_Handler(line);
} else if ( line.startsWith("REMARK 350")){
if ( params.isParseBioAssembly()) {
if (bioAssemblyParser == null){
bioAssemblyParser = new PDBBioAssemblyParser();
}
bioAssemblyParser.pdb_REMARK_350_Handler(line);
}
// REMARK 3 (for R free)
// note: if more than 1 value present (occurring in hybrid experimental technique entries, e.g. 3ins, 4n9m)
// then last one encountered will be taken
} else if (line.startsWith("REMARK 3 FREE R VALUE")) {
// Rfree annotation is not very consistent in PDB format, it varies depending on the software
// Here we follow this strategy:
// a) take the '(NO CUTOFF)' value if the only one available (shelx software, e.g. 1x7q)
// b) don't take it if also a line without '(NO CUTOFF)' is present (CNX software, e.g. 3lak)
Pattern pR = Pattern.compile("^REMARK 3 FREE R VALUE\\s+(?:\\(NO CUTOFF\\))?\\s+:\\s+(\\d?\\.\\d+).*");
Matcher mR = pR.matcher(line);
if (mR.matches()) {
try {
rfreeNoCutoffLine = Float.parseFloat(mR.group(1));
} catch (NumberFormatException e) {
logger.info("Rfree value "+mR.group(1)+" does not look like a number, will ignore it");
}
}
pR = Pattern.compile("^REMARK 3 FREE R VALUE\\s+:\\s+(\\d?\\.\\d+).*");
mR = pR.matcher(line);
if (mR.matches()) {
try {
rfreeStandardLine = Float.parseFloat(mR.group(1));
} catch (NumberFormatException e) {
logger.info("Rfree value '{}' does not look like a number, will ignore it", mR.group(1));
}
}
// REMARK 3 RESOLUTION (contains more info than REMARK 2, for instance multiple resolutions in hybrid experimental technique entries)
// note: if more than 1 value present (occurring in hybrid experimental technique entries, e.g. 3ins, 4n9m)
// then last one encountered will be taken
} else if (line.startsWith("REMARK 3 RESOLUTION RANGE HIGH")){
Pattern pR = Pattern.compile("^REMARK 3 RESOLUTION RANGE HIGH \\(ANGSTROMS\\) :\\s+(\\d+\\.\\d+).*");
Matcher mR = pR.matcher(line);
if (mR.matches()) {
try {
float res = Float.parseFloat(mR.group(1));
if (pdbHeader.getResolution()!=PDBHeader.DEFAULT_RESOLUTION) {
logger.warn("More than 1 resolution value present, will use last one {} and discard previous {} "
,mR.group(1), String.format("%4.2f",pdbHeader.getResolution()));
}
pdbHeader.setResolution(res);
} catch (NumberFormatException e) {
logger.info("Could not parse resolution '{}', ignoring it",mR.group(1));
}
}
}
} | [
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31,864 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java | PDBFileParser.conect_helper | private Integer conect_helper (String line,int start,int end) {
if (line.length() < end) return null;
String sbond = line.substring(start,end).trim();
int bond = -1 ;
Integer b = null ;
if ( ! sbond.equals("")) {
bond = Integer.parseInt(sbond);
b = new Integer(bond);
}
return b ;
} | java | private Integer conect_helper (String line,int start,int end) {
if (line.length() < end) return null;
String sbond = line.substring(start,end).trim();
int bond = -1 ;
Integer b = null ;
if ( ! sbond.equals("")) {
bond = Integer.parseInt(sbond);
b = new Integer(bond);
}
return b ;
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31,865 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java | PDBFileParser.pdb_SSBOND_Handler | private void pdb_SSBOND_Handler(String line){
if (params.isHeaderOnly()) return;
if (line.length()<36) {
logger.info("SSBOND line has length under 36. Ignoring it.");
return;
}
String chain1 = line.substring(15,16);
String seqNum1 = line.substring(17,21).trim();
String icode1 = line.substring(21,22);
String chain2 = line.substring(29,30);
String seqNum2 = line.substring(31,35).trim();
String icode2 = line.substring(35,36);
if (line.length()>=72) {
String symop1 = line.substring(59, 65).trim();
String symop2 = line.substring(66, 72).trim();
// until we implement proper treatment of symmetry in biojava #220, we can't deal with sym-related parteners properly, skipping them
if (!symop1.equals("") && !symop2.equals("") && // in case the field is missing
(!symop1.equals("1555") || !symop2.equals("1555")) ) {
logger.info("Skipping ss bond between groups {} and {} belonging to different symmetry partners, because it is not supported yet", seqNum1+icode1, seqNum2+icode2);
return;
}
}
if (icode1.equals(" "))
icode1 = "";
if (icode2.equals(" "))
icode2 = "";
SSBondImpl ssbond = new SSBondImpl();
ssbond.setChainID1(chain1);
ssbond.setResnum1(seqNum1);
ssbond.setChainID2(chain2);
ssbond.setResnum2(seqNum2);
ssbond.setInsCode1(icode1);
ssbond.setInsCode2(icode2);
ssbonds.add(ssbond);
} | java | private void pdb_SSBOND_Handler(String line){
if (params.isHeaderOnly()) return;
if (line.length()<36) {
logger.info("SSBOND line has length under 36. Ignoring it.");
return;
}
String chain1 = line.substring(15,16);
String seqNum1 = line.substring(17,21).trim();
String icode1 = line.substring(21,22);
String chain2 = line.substring(29,30);
String seqNum2 = line.substring(31,35).trim();
String icode2 = line.substring(35,36);
if (line.length()>=72) {
String symop1 = line.substring(59, 65).trim();
String symop2 = line.substring(66, 72).trim();
// until we implement proper treatment of symmetry in biojava #220, we can't deal with sym-related parteners properly, skipping them
if (!symop1.equals("") && !symop2.equals("") && // in case the field is missing
(!symop1.equals("1555") || !symop2.equals("1555")) ) {
logger.info("Skipping ss bond between groups {} and {} belonging to different symmetry partners, because it is not supported yet", seqNum1+icode1, seqNum2+icode2);
return;
}
}
if (icode1.equals(" "))
icode1 = "";
if (icode2.equals(" "))
icode2 = "";
SSBondImpl ssbond = new SSBondImpl();
ssbond.setChainID1(chain1);
ssbond.setResnum1(seqNum1);
ssbond.setChainID2(chain2);
ssbond.setResnum2(seqNum2);
ssbond.setInsCode1(icode1);
ssbond.setInsCode2(icode2);
ssbonds.add(ssbond);
} | [
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<pre>
COLUMNS DATA TYPE FIELD DEFINITION
-------------------------------------------------------------------
1 - 6 Record name "SSBOND"
8 - 10 Integer serNum Serial number.
12 - 14 LString(3) "CYS" Residue name.
16 Character chainID1 Chain identifier.
18 - 21 Integer seqNum1 Residue sequence number.
22 AChar icode1 Insertion code.
26 - 28 LString(3) "CYS" Residue name.
30 Character chainID2 Chain identifier.
32 - 35 Integer seqNum2 Residue sequence number.
36 AChar icode2 Insertion code.
60 - 65 SymOP sym1 Symmetry oper for 1st resid
67 - 72 SymOP sym2 Symmetry oper for 2nd resid
</pre> | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java#L2214-L2256 |
31,866 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java | PDBFileParser.isKnownChain | private static Chain isKnownChain(String chainID, List<Chain> chains){
for (int i = 0; i< chains.size();i++){
Chain testchain = chains.get(i);
if (chainID.equals(testchain.getName())) {
return testchain;
}
}
return null;
} | java | private static Chain isKnownChain(String chainID, List<Chain> chains){
for (int i = 0; i< chains.size();i++){
Chain testchain = chains.get(i);
if (chainID.equals(testchain.getName())) {
return testchain;
}
}
return null;
} | [
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31,867 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java | PDBFileParser.makeCompounds | private void makeCompounds(List<String> compoundList,
List<String> sourceList) {
// System.out.println("[makeCompounds] making compounds from compoundLines");
for (String line : compoundList) {
if (compoundList.indexOf(line) + 1 == compoundList.size()) {
// System.out.println("[makeCompounds] Final line in compoundLines.");
isLastCompndLine = true;
}
pdb_COMPND_Handler(line);
}
// System.out.println("[makeCompounds] adding sources to compounds from sourceLines");
// since we're starting again from the first compound, reset it here
if ( entities.size() == 0){
current_compound = new EntityInfo();
} else {
current_compound = entities.get(0);
}
for (String line : sourceList) {
if (sourceList.indexOf(line) + 1 == sourceList.size()) {
// System.out.println("[makeCompounds] Final line in sourceLines.");
isLastSourceLine = true;
}
pdb_SOURCE_Handler(line);
}
} | java | private void makeCompounds(List<String> compoundList,
List<String> sourceList) {
// System.out.println("[makeCompounds] making compounds from compoundLines");
for (String line : compoundList) {
if (compoundList.indexOf(line) + 1 == compoundList.size()) {
// System.out.println("[makeCompounds] Final line in compoundLines.");
isLastCompndLine = true;
}
pdb_COMPND_Handler(line);
}
// System.out.println("[makeCompounds] adding sources to compounds from sourceLines");
// since we're starting again from the first compound, reset it here
if ( entities.size() == 0){
current_compound = new EntityInfo();
} else {
current_compound = entities.get(0);
}
for (String line : sourceList) {
if (sourceList.indexOf(line) + 1 == sourceList.size()) {
// System.out.println("[makeCompounds] Final line in sourceLines.");
isLastSourceLine = true;
}
pdb_SOURCE_Handler(line);
}
} | [
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@author Jules Jacobsen
@param compoundList
@param sourceList | [
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31,868 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java | PDBFileParser.findChains | private static List<List<Chain>> findChains(String chainName, List<List<Chain>> polyModels) {
List<List<Chain>> models = new ArrayList<>();
for (List<Chain> chains:polyModels) {
List<Chain> matchingChains = new ArrayList<>();
models.add(matchingChains);
for (Chain c:chains) {
if (c.getName().equals(chainName)) {
matchingChains.add(c);
}
}
}
return models;
} | java | private static List<List<Chain>> findChains(String chainName, List<List<Chain>> polyModels) {
List<List<Chain>> models = new ArrayList<>();
for (List<Chain> chains:polyModels) {
List<Chain> matchingChains = new ArrayList<>();
models.add(matchingChains);
for (Chain c:chains) {
if (c.getName().equals(chainName)) {
matchingChains.add(c);
}
}
}
return models;
} | [
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@param chainName
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31,869 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java | PDBFileParser.assignAsymIds | private void assignAsymIds(List<List<Chain>> polys, List<List<Chain>> nonPolys, List<List<Chain>> waters) {
for (int i=0; i<polys.size(); i++) {
String asymId = "A";
for (Chain poly:polys.get(i)) {
poly.setId(asymId);
asymId = getNextAsymId(asymId);
}
for (Chain nonPoly:nonPolys.get(i)) {
nonPoly.setId(asymId);
asymId = getNextAsymId(asymId);
}
for (Chain water:waters.get(i)) {
water.setId(asymId);
asymId = getNextAsymId(asymId);
}
}
} | java | private void assignAsymIds(List<List<Chain>> polys, List<List<Chain>> nonPolys, List<List<Chain>> waters) {
for (int i=0; i<polys.size(); i++) {
String asymId = "A";
for (Chain poly:polys.get(i)) {
poly.setId(asymId);
asymId = getNextAsymId(asymId);
}
for (Chain nonPoly:nonPolys.get(i)) {
nonPoly.setId(asymId);
asymId = getNextAsymId(asymId);
}
for (Chain water:waters.get(i)) {
water.setId(asymId);
asymId = getNextAsymId(asymId);
}
}
} | [
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... | Assign asym ids following the rules used by the PDB to assign asym ids in mmCIF files
@param polys
@param nonPolys
@param waters | [
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31,870 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java | PDBFileParser.linkSitesToGroups | private void linkSitesToGroups() {
//System.out.println("LINK SITES TO GROUPS:" + siteToResidueMap.keySet().size());
//link the map of siteIds : <ResidueNumber> with the sites by using ResidueNumber to get the correct group back.
//the return list
if ( siteMap == null || siteToResidueMap == null){
logger.info("Sites can not be linked to residues!");
return;
}
List<Site> sites = null;
//check that there are chains with which to associate the groups
if (structure.getChains().isEmpty()) {
sites = new ArrayList<Site>(siteMap.values());
logger.info("No chains to link Site Groups with - Sites will not be present in the Structure");
return;
}
//check that the keys in the siteMap and SiteToResidueMap are equal
if (! siteMap.keySet().equals(siteToResidueMap.keySet())) {
logger.info("Not all sites have been properly described in the PDB " + pdbId + " header - some Sites will not be present in the Structure");
logger.debug(siteMap.keySet() + " | " + siteToResidueMap.keySet());
//return;
}
//so we have chains - associate the siteResidues-related groups with the ones
//already in in the chains
for (String key : siteMap.keySet()) {
Site currentSite = siteMap.get(key);
List<ResidueNumber> linkedGroups = siteToResidueMap.get(key);
if ( linkedGroups == null)
continue;
for (ResidueNumber residueNumber : linkedGroups) {
String pdbCode = residueNumber.toString();
String chain = residueNumber.getChainName();
// System.out.println("chain: '" + chain + "'");
// String resNum = resNum.getSeqNum().toString();
// System.out.println("resNum: '" + resNum + "'");
Group linkedGroup = null;
try {
//TODO: implement findGroup(ResidueNumber resNum)
linkedGroup = structure.findGroup(chain, pdbCode);
} catch (StructureException ex) {
logger.info("Can't find group " + pdbCode + " in chain " + chain + " in order to link up SITE records (PDB ID " + pdbId +")");
continue;
}
// System.out.println("Adding group: " + linkedGroup.getSeqNum() + " to site " + site.getSiteID());
currentSite.getGroups().add(linkedGroup);
}
}
//System.out.println("SITEMAP: " + siteMap);
sites = new ArrayList<Site>(siteMap.values());
structure.setSites(sites);
//System.out.println("STRUCTURE SITES: " + structure.getSites().size());
// for (Site site : structure.getSites()) {
// System.out.println(site);
// }
// System.out.println("Linked Site Groups with Chains");
} | java | private void linkSitesToGroups() {
//System.out.println("LINK SITES TO GROUPS:" + siteToResidueMap.keySet().size());
//link the map of siteIds : <ResidueNumber> with the sites by using ResidueNumber to get the correct group back.
//the return list
if ( siteMap == null || siteToResidueMap == null){
logger.info("Sites can not be linked to residues!");
return;
}
List<Site> sites = null;
//check that there are chains with which to associate the groups
if (structure.getChains().isEmpty()) {
sites = new ArrayList<Site>(siteMap.values());
logger.info("No chains to link Site Groups with - Sites will not be present in the Structure");
return;
}
//check that the keys in the siteMap and SiteToResidueMap are equal
if (! siteMap.keySet().equals(siteToResidueMap.keySet())) {
logger.info("Not all sites have been properly described in the PDB " + pdbId + " header - some Sites will not be present in the Structure");
logger.debug(siteMap.keySet() + " | " + siteToResidueMap.keySet());
//return;
}
//so we have chains - associate the siteResidues-related groups with the ones
//already in in the chains
for (String key : siteMap.keySet()) {
Site currentSite = siteMap.get(key);
List<ResidueNumber> linkedGroups = siteToResidueMap.get(key);
if ( linkedGroups == null)
continue;
for (ResidueNumber residueNumber : linkedGroups) {
String pdbCode = residueNumber.toString();
String chain = residueNumber.getChainName();
// System.out.println("chain: '" + chain + "'");
// String resNum = resNum.getSeqNum().toString();
// System.out.println("resNum: '" + resNum + "'");
Group linkedGroup = null;
try {
//TODO: implement findGroup(ResidueNumber resNum)
linkedGroup = structure.findGroup(chain, pdbCode);
} catch (StructureException ex) {
logger.info("Can't find group " + pdbCode + " in chain " + chain + " in order to link up SITE records (PDB ID " + pdbId +")");
continue;
}
// System.out.println("Adding group: " + linkedGroup.getSeqNum() + " to site " + site.getSiteID());
currentSite.getGroups().add(linkedGroup);
}
}
//System.out.println("SITEMAP: " + siteMap);
sites = new ArrayList<Site>(siteMap.values());
structure.setSites(sites);
//System.out.println("STRUCTURE SITES: " + structure.getSites().size());
// for (Site site : structure.getSites()) {
// System.out.println(site);
// }
// System.out.println("Linked Site Groups with Chains");
} | [
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siteToResidueMap ResidueNumber.
@author Jules Jacobsen
@return | [
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31,871 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/TranscriptionEngine.java | TranscriptionEngine.translate | public Sequence<AminoAcidCompound> translate(
Sequence<NucleotideCompound> dna) {
Map<Frame, Sequence<AminoAcidCompound>> trans = multipleFrameTranslation(
dna, Frame.ONE);
return trans.get(Frame.ONE);
} | java | public Sequence<AminoAcidCompound> translate(
Sequence<NucleotideCompound> dna) {
Map<Frame, Sequence<AminoAcidCompound>> trans = multipleFrameTranslation(
dna, Frame.ONE);
return trans.get(Frame.ONE);
} | [
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@param dna
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@return The Protein Sequence | [
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31,872 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/TranscriptionEngine.java | TranscriptionEngine.multipleFrameTranslation | public Map<Frame, Sequence<AminoAcidCompound>> multipleFrameTranslation(
Sequence<NucleotideCompound> dna, Frame... frames) {
Map<Frame, Sequence<AminoAcidCompound>> results = new EnumMap<Frame, Sequence<AminoAcidCompound>>(
Frame.class);
for (Frame frame : frames) {
Sequence<NucleotideCompound> rna = getDnaRnaTranslator()
.createSequence(dna, frame);
Sequence<AminoAcidCompound> peptide = getRnaAminoAcidTranslator()
.createSequence(rna);
results.put(frame, peptide);
}
return results;
} | java | public Map<Frame, Sequence<AminoAcidCompound>> multipleFrameTranslation(
Sequence<NucleotideCompound> dna, Frame... frames) {
Map<Frame, Sequence<AminoAcidCompound>> results = new EnumMap<Frame, Sequence<AminoAcidCompound>>(
Frame.class);
for (Frame frame : frames) {
Sequence<NucleotideCompound> rna = getDnaRnaTranslator()
.createSequence(dna, frame);
Sequence<AminoAcidCompound> peptide = getRnaAminoAcidTranslator()
.createSequence(rna);
results.put(frame, peptide);
}
return results;
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31,873 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitCluster.java | SubunitCluster.isIdenticalTo | public boolean isIdenticalTo(SubunitCluster other) {
String thisSequence = this.subunits.get(this.representative)
.getProteinSequenceString();
String otherSequence = other.subunits.get(other.representative)
.getProteinSequenceString();
return thisSequence.equals(otherSequence);
} | java | public boolean isIdenticalTo(SubunitCluster other) {
String thisSequence = this.subunits.get(this.representative)
.getProteinSequenceString();
String otherSequence = other.subunits.get(other.representative)
.getProteinSequenceString();
return thisSequence.equals(otherSequence);
} | [
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31,874 | biojava/biojava | biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/GUIAlignmentProgressListener.java | GUIAlignmentProgressListener.actionPerformed | @Override
public void actionPerformed(ActionEvent evt) {
//System.out.println("stopping!");
logStatus("terminating");
logStatus(" Total alignments processed: " + alignmentsProcessed);
stopButton.setEnabled(false);
setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR));
progressBar.setIndeterminate(true);
progressBar.setStringPainted(false);
System.out.println("terminating jobs");
farmJob.terminate();
setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
progressBar.setIndeterminate(false);
} | java | @Override
public void actionPerformed(ActionEvent evt) {
//System.out.println("stopping!");
logStatus("terminating");
logStatus(" Total alignments processed: " + alignmentsProcessed);
stopButton.setEnabled(false);
setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR));
progressBar.setIndeterminate(true);
progressBar.setStringPainted(false);
System.out.println("terminating jobs");
farmJob.terminate();
setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
progressBar.setIndeterminate(false);
} | [
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31,875 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/OptimalCECPMain.java | OptimalCECPMain.permuteArray | private static <T> void permuteArray(T[] arr, int cp) {
// Allow negative cp points for convenience.
if(cp == 0) {
return;
}
if(cp < 0) {
cp = arr.length+cp;
}
if(cp < 0 || cp >= arr.length) {
throw new ArrayIndexOutOfBoundsException(
"Permutation point ("+cp+") must be between -ca2.length and ca2.length-1" );
}
List<T> temp = new ArrayList<T>(cp);
// shift residues left
for(int i=0;i<cp;i++) {
temp.add(arr[i]);
}
for(int j=cp;j<arr.length;j++) {
arr[j-cp]=arr[j];
}
for(int i=0;i<cp;i++) {
arr[arr.length-cp+i] = temp.get(i);
}
} | java | private static <T> void permuteArray(T[] arr, int cp) {
// Allow negative cp points for convenience.
if(cp == 0) {
return;
}
if(cp < 0) {
cp = arr.length+cp;
}
if(cp < 0 || cp >= arr.length) {
throw new ArrayIndexOutOfBoundsException(
"Permutation point ("+cp+") must be between -ca2.length and ca2.length-1" );
}
List<T> temp = new ArrayList<T>(cp);
// shift residues left
for(int i=0;i<cp;i++) {
temp.add(arr[i]);
}
for(int j=cp;j<arr.length;j++) {
arr[j-cp]=arr[j];
}
for(int i=0;i<cp;i++) {
arr[arr.length-cp+i] = temp.get(i);
}
} | [
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@param <T>
@param arr The array to be permuted
@param cp The number of residues to shift leftward, or equivalently, the index of
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31,876 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/OptimalCECPMain.java | OptimalCECPMain.permuteAFPChain | private static void permuteAFPChain(AFPChain afpChain, int cp) {
int ca2len = afpChain.getCa2Length();
//fix up cp to be positive
if(cp == 0) {
return;
}
if(cp < 0) {
cp = ca2len+cp;
}
if(cp < 0 || cp >= ca2len) {
throw new ArrayIndexOutOfBoundsException(
"Permutation point ("+cp+") must be between -ca2.length and ca2.length-1" );
}
// Fix up optAln
permuteOptAln(afpChain,cp);
if(afpChain.getBlockNum() > 1)
afpChain.setSequentialAlignment(false);
// fix up matrices
// ca1 corresponds to row indices, while ca2 corresponds to column indices.
afpChain.setDistanceMatrix(permuteMatrix(afpChain.getDistanceMatrix(),0,-cp));
// this is square, so permute both
afpChain.setDisTable2(permuteMatrix(afpChain.getDisTable2(),-cp,-cp));
//TODO fix up other AFP parameters?
} | java | private static void permuteAFPChain(AFPChain afpChain, int cp) {
int ca2len = afpChain.getCa2Length();
//fix up cp to be positive
if(cp == 0) {
return;
}
if(cp < 0) {
cp = ca2len+cp;
}
if(cp < 0 || cp >= ca2len) {
throw new ArrayIndexOutOfBoundsException(
"Permutation point ("+cp+") must be between -ca2.length and ca2.length-1" );
}
// Fix up optAln
permuteOptAln(afpChain,cp);
if(afpChain.getBlockNum() > 1)
afpChain.setSequentialAlignment(false);
// fix up matrices
// ca1 corresponds to row indices, while ca2 corresponds to column indices.
afpChain.setDistanceMatrix(permuteMatrix(afpChain.getDistanceMatrix(),0,-cp));
// this is square, so permute both
afpChain.setDisTable2(permuteMatrix(afpChain.getDisTable2(),-cp,-cp));
//TODO fix up other AFP parameters?
} | [
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@param cp Amount leftwards (or rightward, if negative) to shift the
@return A new alignment equivalent to afpChain after the permutations | [
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31,877 | biojava/biojava | biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAlignmentCoordManager.java | MultipleAlignmentCoordManager.getSeqPos | public int getSeqPos(int aligSeq, Point p) {
int x = p.x - DEFAULT_X_SPACE - DEFAULT_LEGEND_SIZE;
int y = p.y - DEFAULT_Y_SPACE ;
y -= (DEFAULT_LINE_SEPARATION * aligSeq) - DEFAULT_CHAR_SIZE;
int lineNr = y / DEFAULT_Y_STEP;
int linePos = x / DEFAULT_CHAR_SIZE;
return lineNr * DEFAULT_LINE_LENGTH + linePos ;
} | java | public int getSeqPos(int aligSeq, Point p) {
int x = p.x - DEFAULT_X_SPACE - DEFAULT_LEGEND_SIZE;
int y = p.y - DEFAULT_Y_SPACE ;
y -= (DEFAULT_LINE_SEPARATION * aligSeq) - DEFAULT_CHAR_SIZE;
int lineNr = y / DEFAULT_Y_STEP;
int linePos = x / DEFAULT_CHAR_SIZE;
return lineNr * DEFAULT_LINE_LENGTH + linePos ;
} | [
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@param aligSeq sequence number
@param p point on panel
@return the sequence position for a point on the Panel | [
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31,878 | biojava/biojava | biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAlignmentCoordManager.java | MultipleAlignmentCoordManager.getPanelPos | public Point getPanelPos(int structure, int pos) {
Point p = new Point();
int lineNr = pos / DEFAULT_LINE_LENGTH;
int linePos = pos % DEFAULT_LINE_LENGTH;
int x = linePos * DEFAULT_CHAR_SIZE + DEFAULT_X_SPACE +
DEFAULT_LEGEND_SIZE;
int y = lineNr * DEFAULT_Y_STEP + DEFAULT_Y_SPACE;
y += DEFAULT_LINE_SEPARATION * structure;
p.setLocation(x, y);
return p;
} | java | public Point getPanelPos(int structure, int pos) {
Point p = new Point();
int lineNr = pos / DEFAULT_LINE_LENGTH;
int linePos = pos % DEFAULT_LINE_LENGTH;
int x = linePos * DEFAULT_CHAR_SIZE + DEFAULT_X_SPACE +
DEFAULT_LEGEND_SIZE;
int y = lineNr * DEFAULT_Y_STEP + DEFAULT_Y_SPACE;
y += DEFAULT_LINE_SEPARATION * structure;
p.setLocation(x, y);
return p;
} | [
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31,879 | biojava/biojava | biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAlignmentCoordManager.java | MultipleAlignmentCoordManager.getAligSeq | public int getAligSeq(Point point) {
for (int pos=0; pos<alignmentSize; pos++){
int i = getSeqPos(pos, point);
Point t = getPanelPos(pos,i);
if ( Math.abs(t.x - point.x) <= DEFAULT_CHAR_SIZE &&
Math.abs(t.y-point.y) < DEFAULT_CHAR_SIZE ) return pos;
}
return -1;
} | java | public int getAligSeq(Point point) {
for (int pos=0; pos<alignmentSize; pos++){
int i = getSeqPos(pos, point);
Point t = getPanelPos(pos,i);
if ( Math.abs(t.x - point.x) <= DEFAULT_CHAR_SIZE &&
Math.abs(t.y-point.y) < DEFAULT_CHAR_SIZE ) return pos;
}
return -1;
} | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/aligpanel/MultipleAlignmentCoordManager.java#L167-L177 |
31,880 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/DBRef.java | DBRef.toPDB | @Override
public String toPDB(){
StringBuffer buf = new StringBuffer();
toPDB(buf);
return buf.toString();
} | java | @Override
public String toPDB(){
StringBuffer buf = new StringBuffer();
toPDB(buf);
return buf.toString();
} | [
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] | Convert the DBRef object to a DBREF record as it is used in PDB files
@return a PDB - DBREF formatted line | [
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31,881 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/DBRef.java | DBRef.toPDB | @Override
public void toPDB(StringBuffer buf){
Formatter formatter = new Formatter(new StringBuilder(),Locale.UK);
// DBREF 3ETA A 990 1295 UNP P06213 INSR_HUMAN 1017 1322
// DBREF 3EH2 A 2 767 UNP P53992 SC24C_HUMAN 329 1094
// DBREF 3EH2 A 2 767 UNP P53992 SC24C_HUMAN 329 1094
// DBREF 3ETA A 990 1295 UNP P06213 INSR_HUMAN 1017 1322
formatter.format("DBREF %4s %1s %4d%1s %4d%1s %-6s %-8s %-12s%6d%1c%6d%1c ",
idCode, chainName,seqbegin,insertBegin,seqEnd,insertEnd,
database,dbAccession,dbIdCode,
dbSeqBegin,idbnsBegin,dbSeqEnd,idbnsEnd
);
buf.append(formatter.toString());
formatter.close();
} | java | @Override
public void toPDB(StringBuffer buf){
Formatter formatter = new Formatter(new StringBuilder(),Locale.UK);
// DBREF 3ETA A 990 1295 UNP P06213 INSR_HUMAN 1017 1322
// DBREF 3EH2 A 2 767 UNP P53992 SC24C_HUMAN 329 1094
// DBREF 3EH2 A 2 767 UNP P53992 SC24C_HUMAN 329 1094
// DBREF 3ETA A 990 1295 UNP P06213 INSR_HUMAN 1017 1322
formatter.format("DBREF %4s %1s %4d%1s %4d%1s %-6s %-8s %-12s%6d%1c%6d%1c ",
idCode, chainName,seqbegin,insertBegin,seqEnd,insertEnd,
database,dbAccession,dbIdCode,
dbSeqBegin,idbnsBegin,dbSeqEnd,idbnsEnd
);
buf.append(formatter.toString());
formatter.close();
} | [
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31,882 | biojava/biojava | biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DisplayAFP.java | DisplayAFP.getPDBresnum | public static final List<String> getPDBresnum(int aligPos, AFPChain afpChain, Atom[] ca){
List<String> lst = new ArrayList<String>();
if ( aligPos > 1) {
System.err.println("multiple alignments not supported yet!");
return lst;
}
int blockNum = afpChain.getBlockNum();
int[] optLen = afpChain.getOptLen();
int[][][] optAln = afpChain.getOptAln();
if ( optLen == null)
return lst;
for(int bk = 0; bk < blockNum; bk ++) {
for ( int i=0;i< optLen[bk];i++){
int pos = optAln[bk][aligPos][i];
if ( pos < ca.length) {
String pdbInfo = JmolTools.getPdbInfo(ca[pos]);
//lst.add(ca1[pos].getParent().getPDBCode());
lst.add(pdbInfo);
}
}
}
return lst;
} | java | public static final List<String> getPDBresnum(int aligPos, AFPChain afpChain, Atom[] ca){
List<String> lst = new ArrayList<String>();
if ( aligPos > 1) {
System.err.println("multiple alignments not supported yet!");
return lst;
}
int blockNum = afpChain.getBlockNum();
int[] optLen = afpChain.getOptLen();
int[][][] optAln = afpChain.getOptAln();
if ( optLen == null)
return lst;
for(int bk = 0; bk < blockNum; bk ++) {
for ( int i=0;i< optLen[bk];i++){
int pos = optAln[bk][aligPos][i];
if ( pos < ca.length) {
String pdbInfo = JmolTools.getPdbInfo(ca[pos]);
//lst.add(ca1[pos].getParent().getPDBCode());
lst.add(pdbInfo);
}
}
}
return lst;
} | [
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Only supports a pairwise alignment with the AFPChain DS.
@param aligPos
@param afpChain
@param ca | [
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31,883 | biojava/biojava | biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DisplayAFP.java | DisplayAFP.getAtomForAligPos | public static final Atom getAtomForAligPos(AFPChain afpChain,int chainNr, int aligPos, Atom[] ca , boolean getPrevious ) throws StructureException{
int[] optLen = afpChain.getOptLen();
// int[][][] optAln = afpChain.getOptAln();
if ( optLen == null)
return null;
if (chainNr < 0 || chainNr > 1){
throw new StructureException("So far only pairwise alignments are supported, but you requested results for alinged chain nr " + chainNr);
}
//if ( afpChain.getAlgorithmName().startsWith("jFatCat")){
/// for FatCat algorithms...
int capos = getUngappedFatCatPos(afpChain, chainNr, aligPos);
if ( capos < 0) {
capos = getNextFatCatPos(afpChain, chainNr, aligPos,getPrevious);
//System.out.println(" got next" + capos + " for " + chainNr + " alignedPos: " + aligPos);
} else {
//System.out.println("got aligned fatcat position: " + capos + " " + chainNr + " for alig pos: " + aligPos);
}
if ( capos < 0) {
System.err.println("could not match position " + aligPos + " in chain " + chainNr +". Returing null...");
return null;
}
if ( capos > ca.length){
System.err.println("Atom array "+ chainNr + " does not have " + capos +" atoms. Returning null.");
return null;
}
return ca[capos];
//}
//
//
// int ungappedPos = getUngappedPos(afpChain, aligPos);
// System.out.println("getAtomForAligPOs " + aligPos + " " + ungappedPos );
// return ca[ungappedPos];
//
// if ( ungappedPos >= optAln[bk][chainNr].length)
// return null;
// int pos = optAln[bk][chainNr][ungappedPos];
// if ( pos > ca.length)
// return null;
// return ca[pos];
} | java | public static final Atom getAtomForAligPos(AFPChain afpChain,int chainNr, int aligPos, Atom[] ca , boolean getPrevious ) throws StructureException{
int[] optLen = afpChain.getOptLen();
// int[][][] optAln = afpChain.getOptAln();
if ( optLen == null)
return null;
if (chainNr < 0 || chainNr > 1){
throw new StructureException("So far only pairwise alignments are supported, but you requested results for alinged chain nr " + chainNr);
}
//if ( afpChain.getAlgorithmName().startsWith("jFatCat")){
/// for FatCat algorithms...
int capos = getUngappedFatCatPos(afpChain, chainNr, aligPos);
if ( capos < 0) {
capos = getNextFatCatPos(afpChain, chainNr, aligPos,getPrevious);
//System.out.println(" got next" + capos + " for " + chainNr + " alignedPos: " + aligPos);
} else {
//System.out.println("got aligned fatcat position: " + capos + " " + chainNr + " for alig pos: " + aligPos);
}
if ( capos < 0) {
System.err.println("could not match position " + aligPos + " in chain " + chainNr +". Returing null...");
return null;
}
if ( capos > ca.length){
System.err.println("Atom array "+ chainNr + " does not have " + capos +" atoms. Returning null.");
return null;
}
return ca[capos];
//}
//
//
// int ungappedPos = getUngappedPos(afpChain, aligPos);
// System.out.println("getAtomForAligPOs " + aligPos + " " + ungappedPos );
// return ca[ungappedPos];
//
// if ( ungappedPos >= optAln[bk][chainNr].length)
// return null;
// int pos = optAln[bk][chainNr][ungappedPos];
// if ( pos > ca.length)
// return null;
// return ca[pos];
} | [
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@param chainNr the number of the aligned pair. 0... first chain, 1... second chain.
@param afpChain an afpChain object
@param aligPos position on the alignment
@param getPrevious gives the previous position if false, gives the next posible atom
@return a CA atom that is at a particular position of the alignment | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DisplayAFP.java#L148-L195 |
31,884 | biojava/biojava | biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DisplayAFP.java | DisplayAFP.getAtomArray | public static final Atom[] getAtomArray(Atom[] ca,List<Group> hetatms ) throws StructureException{
List<Atom> atoms = new ArrayList<Atom>();
Collections.addAll(atoms, ca);
logger.debug("got {} hetatoms", hetatms.size());
// we only add atom nr 1, since the getAlignedStructure method actually adds the parent group, and not the atoms...
for (Group g : hetatms){
if (g.size() < 1)
continue;
//if (debug)
// System.out.println("adding group " + g);
Atom a = g.getAtom(0);
//if (debug)
// System.out.println(a);
a.setGroup(g);
atoms.add(a);
}
Atom[] arr = atoms.toArray(new Atom[atoms.size()]);
return arr;
} | java | public static final Atom[] getAtomArray(Atom[] ca,List<Group> hetatms ) throws StructureException{
List<Atom> atoms = new ArrayList<Atom>();
Collections.addAll(atoms, ca);
logger.debug("got {} hetatoms", hetatms.size());
// we only add atom nr 1, since the getAlignedStructure method actually adds the parent group, and not the atoms...
for (Group g : hetatms){
if (g.size() < 1)
continue;
//if (debug)
// System.out.println("adding group " + g);
Atom a = g.getAtom(0);
//if (debug)
// System.out.println(a);
a.setGroup(g);
atoms.add(a);
}
Atom[] arr = atoms.toArray(new Atom[atoms.size()]);
return arr;
} | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DisplayAFP.java#L409-L431 |
31,885 | biojava/biojava | biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DisplayAFP.java | DisplayAFP.createArtificalStructure | public static Structure createArtificalStructure(AFPChain afpChain, Atom[] ca1,
Atom[] ca2) throws StructureException{
if ( afpChain.getNrEQR() < 1){
return AlignmentTools.getAlignedStructure(ca1, ca2);
}
Group[] twistedGroups = AlignmentTools.prepareGroupsForDisplay(afpChain,ca1, ca2);
List<Atom> twistedAs = new ArrayList<Atom>();
for ( Group g: twistedGroups){
if ( g == null )
continue;
if ( g.size() < 1)
continue;
Atom a = g.getAtom(0);
twistedAs.add(a);
}
Atom[] twistedAtoms = twistedAs.toArray(new Atom[twistedAs.size()]);
List<Group> hetatms = StructureTools.getUnalignedGroups(ca1);
List<Group> hetatms2 = StructureTools.getUnalignedGroups(ca2);
Atom[] arr1 = DisplayAFP.getAtomArray(ca1, hetatms);
Atom[] arr2 = DisplayAFP.getAtomArray(twistedAtoms, hetatms2);
Structure artificial = AlignmentTools.getAlignedStructure(arr1,arr2);
return artificial;
} | java | public static Structure createArtificalStructure(AFPChain afpChain, Atom[] ca1,
Atom[] ca2) throws StructureException{
if ( afpChain.getNrEQR() < 1){
return AlignmentTools.getAlignedStructure(ca1, ca2);
}
Group[] twistedGroups = AlignmentTools.prepareGroupsForDisplay(afpChain,ca1, ca2);
List<Atom> twistedAs = new ArrayList<Atom>();
for ( Group g: twistedGroups){
if ( g == null )
continue;
if ( g.size() < 1)
continue;
Atom a = g.getAtom(0);
twistedAs.add(a);
}
Atom[] twistedAtoms = twistedAs.toArray(new Atom[twistedAs.size()]);
List<Group> hetatms = StructureTools.getUnalignedGroups(ca1);
List<Group> hetatms2 = StructureTools.getUnalignedGroups(ca2);
Atom[] arr1 = DisplayAFP.getAtomArray(ca1, hetatms);
Atom[] arr2 = DisplayAFP.getAtomArray(twistedAtoms, hetatms2);
Structure artificial = AlignmentTools.getAlignedStructure(arr1,arr2);
return artificial;
} | [
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@param afpChain the container of the alignment
@param ca1 atoms for protein 1
@param ca2 atoms for protein 2
@return a protein structure with 2 models.
@throws StructureException | [
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31,886 | biojava/biojava | biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/HmmerResult.java | HmmerResult.getOverlapLength | public int getOverlapLength(HmmerResult other){
int overlap = 0;
for ( HmmerDomain d1 : getDomains()){
for (HmmerDomain d2 : other.getDomains()){
overlap += getOverlap(d1, d2);
}
}
return overlap;
} | java | public int getOverlapLength(HmmerResult other){
int overlap = 0;
for ( HmmerDomain d1 : getDomains()){
for (HmmerDomain d2 : other.getDomains()){
overlap += getOverlap(d1, d2);
}
}
return overlap;
} | [
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@param other
@return 0 if no overlap, otherwise the length of the overlap | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/HmmerResult.java#L154-L164 |
31,887 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/DownloadChemCompProvider.java | DownloadChemCompProvider.getPath | public static File getPath(){
if (path==null) {
UserConfiguration config = new UserConfiguration();
path = new File(config.getCacheFilePath());
}
return path;
} | java | public static File getPath(){
if (path==null) {
UserConfiguration config = new UserConfiguration();
path = new File(config.getCacheFilePath());
}
return path;
} | [
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... | Get this provider's cache path
@return | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/DownloadChemCompProvider.java#L122-L128 |
31,888 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/DownloadChemCompProvider.java | DownloadChemCompProvider.checkDoFirstInstall | public void checkDoFirstInstall(){
if ( ! downloadAll ) {
return;
}
// this makes sure there is a file separator between every component,
// if path has a trailing file separator or not, it will work for both cases
File dir = new File(getPath(), CHEM_COMP_CACHE_DIRECTORY);
File f = new File(dir, "components.cif.gz");
if ( ! f.exists()) {
downloadAllDefinitions();
} else {
// file exists.. did it get extracted?
FilenameFilter filter =new FilenameFilter() {
@Override
public boolean accept(File dir, String file) {
return file.endsWith(".cif.gz");
}
};
String[] files = dir.list(filter);
if ( files.length < 500) {
// not all did get unpacked
try {
split();
} catch (IOException e) {
logger.error("Could not split file {} into individual chemical component files. Error: {}",
f.toString(), e.getMessage());
}
}
}
} | java | public void checkDoFirstInstall(){
if ( ! downloadAll ) {
return;
}
// this makes sure there is a file separator between every component,
// if path has a trailing file separator or not, it will work for both cases
File dir = new File(getPath(), CHEM_COMP_CACHE_DIRECTORY);
File f = new File(dir, "components.cif.gz");
if ( ! f.exists()) {
downloadAllDefinitions();
} else {
// file exists.. did it get extracted?
FilenameFilter filter =new FilenameFilter() {
@Override
public boolean accept(File dir, String file) {
return file.endsWith(".cif.gz");
}
};
String[] files = dir.list(filter);
if ( files.length < 500) {
// not all did get unpacked
try {
split();
} catch (IOException e) {
logger.error("Could not split file {} into individual chemical component files. Error: {}",
f.toString(), e.getMessage());
}
}
}
} | [
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If not, will download the chemical components definitions file and split it up into small
subfiles. | [
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31,889 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/DownloadChemCompProvider.java | DownloadChemCompProvider.writeID | private void writeID(String contents, String currentID) throws IOException{
String localName = getLocalFileName(currentID);
try ( PrintWriter pw = new PrintWriter(new GZIPOutputStream(new FileOutputStream(localName))) ) {
pw.print(contents);
pw.flush();
}
} | java | private void writeID(String contents, String currentID) throws IOException{
String localName = getLocalFileName(currentID);
try ( PrintWriter pw = new PrintWriter(new GZIPOutputStream(new FileOutputStream(localName))) ) {
pw.print(contents);
pw.flush();
}
} | [
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@param contents File contents
@param currentID Chemical ID, used to determine the filename
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31,890 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/CrystalTransform.java | CrystalTransform.isEquivalent | public boolean isEquivalent(CrystalTransform other) {
Matrix4d mul = new Matrix4d();
mul.mul(this.matTransform,other.matTransform);
if (mul.epsilonEquals(IDENTITY, 0.0001)) {
return true;
}
return false;
} | java | public boolean isEquivalent(CrystalTransform other) {
Matrix4d mul = new Matrix4d();
mul.mul(this.matTransform,other.matTransform);
if (mul.epsilonEquals(IDENTITY, 0.0001)) {
return true;
}
return false;
} | [
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Two crystal transforms are equivalent if one is the inverse of the other, i.e.
their transformation matrices multiplication is equal to the identity.
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31,891 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/CrystalTransform.java | CrystalTransform.toXYZString | public String toXYZString() {
StringBuilder str = new StringBuilder();
for(int i=0;i<3;i++) { //for each row
boolean emptyRow = true;
double coef; // TODO work with rational numbers
// X
coef = matTransform.getElement(i, 0);
// Three cases for coef: zero, one, non-one
if(abs(coef) > 1e-6 ) { // Non-zero
if( abs( abs(coef)-1 ) < 1e-6 ) { // +/- 1
if( coef < 0 ) {
str.append("-");
}
} else {
str.append(formatCoef(coef));
str.append("*");
}
str.append("x");
emptyRow = false;
}
// Y
coef = matTransform.getElement(i, 1);
if(abs(coef) > 1e-6 ) { // Non-zero
if( abs( abs(coef)-1 ) < 1e-6 ) { // +/- 1
if( coef < 0 ) {
str.append("-");
} else if( !emptyRow ) {
str.append("+");
}
} else {
if( !emptyRow && coef > 0) {
str.append("+");
}
str.append(formatCoef(coef));
str.append("*");
}
str.append("y");
emptyRow = false;
}
// Z
coef = matTransform.getElement(i, 2);
if(abs(coef) > 1e-6 ) { // Non-zero
if( abs( abs(coef)-1 ) < 1e-6 ) { // +/- 1
if( coef < 0 ) {
str.append("-");
} else if( !emptyRow ) {
str.append("+");
}
} else {
if( !emptyRow && coef > 0) {
str.append("+");
}
str.append(formatCoef(coef));
str.append("*");
}
str.append("z");
emptyRow = false;
}
// Intercept
coef = matTransform.getElement(i, 3);
if(abs(coef) > 1e-6 ) { // Non-zero
if( !emptyRow && coef > 0) {
str.append("+");
}
str.append(formatCoef(coef));
}
if(i<2) {
str.append(",");
}
}
return str.toString();
} | java | public String toXYZString() {
StringBuilder str = new StringBuilder();
for(int i=0;i<3;i++) { //for each row
boolean emptyRow = true;
double coef; // TODO work with rational numbers
// X
coef = matTransform.getElement(i, 0);
// Three cases for coef: zero, one, non-one
if(abs(coef) > 1e-6 ) { // Non-zero
if( abs( abs(coef)-1 ) < 1e-6 ) { // +/- 1
if( coef < 0 ) {
str.append("-");
}
} else {
str.append(formatCoef(coef));
str.append("*");
}
str.append("x");
emptyRow = false;
}
// Y
coef = matTransform.getElement(i, 1);
if(abs(coef) > 1e-6 ) { // Non-zero
if( abs( abs(coef)-1 ) < 1e-6 ) { // +/- 1
if( coef < 0 ) {
str.append("-");
} else if( !emptyRow ) {
str.append("+");
}
} else {
if( !emptyRow && coef > 0) {
str.append("+");
}
str.append(formatCoef(coef));
str.append("*");
}
str.append("y");
emptyRow = false;
}
// Z
coef = matTransform.getElement(i, 2);
if(abs(coef) > 1e-6 ) { // Non-zero
if( abs( abs(coef)-1 ) < 1e-6 ) { // +/- 1
if( coef < 0 ) {
str.append("-");
} else if( !emptyRow ) {
str.append("+");
}
} else {
if( !emptyRow && coef > 0) {
str.append("+");
}
str.append(formatCoef(coef));
str.append("*");
}
str.append("z");
emptyRow = false;
}
// Intercept
coef = matTransform.getElement(i, 3);
if(abs(coef) > 1e-6 ) { // Non-zero
if( !emptyRow && coef > 0) {
str.append("+");
}
str.append(formatCoef(coef));
}
if(i<2) {
str.append(",");
}
}
return str.toString();
} | [
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31,892 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/CrystalTransform.java | CrystalTransform.formatCoef | private String formatCoef(double coef) {
double tol = 1e-6; // rounding tolerance
// zero case
if( Math.abs(coef) < tol) {
return "0";
}
// integer case
long num = Math.round(coef);
if( Math.abs(num - coef) < tol) {
return Long.toString(num);
}
// Other small cases
for(int denom = 2; denom < 12; denom++ ) {
num = Math.round(coef*denom);
if( num - coef*denom < tol ) {
return String.format("%d/%d",num, denom);
}
}
// Give up and use floating point;
return String.format("%.3f", coef);
} | java | private String formatCoef(double coef) {
double tol = 1e-6; // rounding tolerance
// zero case
if( Math.abs(coef) < tol) {
return "0";
}
// integer case
long num = Math.round(coef);
if( Math.abs(num - coef) < tol) {
return Long.toString(num);
}
// Other small cases
for(int denom = 2; denom < 12; denom++ ) {
num = Math.round(coef*denom);
if( num - coef*denom < tol ) {
return String.format("%d/%d",num, denom);
}
}
// Give up and use floating point;
return String.format("%.3f", coef);
} | [
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31,893 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/RotationAxisAligner.java | RotationAxisAligner.getGeometicCenterTransformation | @Override
public Matrix4d getGeometicCenterTransformation() {
run();
Matrix4d geometricCentered = new Matrix4d(reverseTransformationMatrix);
geometricCentered.setTranslation(new Vector3d(getGeometricCenter()));
return geometricCentered;
} | java | @Override
public Matrix4d getGeometicCenterTransformation() {
run();
Matrix4d geometricCentered = new Matrix4d(reverseTransformationMatrix);
geometricCentered.setTranslation(new Vector3d(getGeometricCenter()));
return geometricCentered;
} | [
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31,894 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/RotationAxisAligner.java | RotationAxisAligner.getGeometricCenter | @Override
public Point3d getGeometricCenter() {
run();
Point3d geometricCenter = new Point3d();
Vector3d translation = new Vector3d();
reverseTransformationMatrix.get(translation);
// calculate adjustment around z-axis and transform adjustment to
// original coordinate frame with the reverse transformation
if (rotationGroup.getPointGroup().startsWith("C")) {
Vector3d corr = new Vector3d(0,0, minBoundary.z+getDimension().z);
reverseTransformationMatrix.transform(corr);
geometricCenter.set(corr);
}
geometricCenter.add(translation);
return geometricCenter;
} | java | @Override
public Point3d getGeometricCenter() {
run();
Point3d geometricCenter = new Point3d();
Vector3d translation = new Vector3d();
reverseTransformationMatrix.get(translation);
// calculate adjustment around z-axis and transform adjustment to
// original coordinate frame with the reverse transformation
if (rotationGroup.getPointGroup().startsWith("C")) {
Vector3d corr = new Vector3d(0,0, minBoundary.z+getDimension().z);
reverseTransformationMatrix.transform(corr);
geometricCenter.set(corr);
}
geometricCenter.add(translation);
return geometricCenter;
} | [
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31,895 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/RotationAxisAligner.java | RotationAxisAligner.alignAxes | private Matrix4d alignAxes(Vector3d[] axisVectors, Vector3d[] referenceVectors) {
Matrix4d m1 = new Matrix4d();
AxisAngle4d a = new AxisAngle4d();
Vector3d axis = new Vector3d();
// calculate rotation matrix to rotate refPoints[0] into coordPoints[0]
Vector3d v1 = new Vector3d(axisVectors[0]);
Vector3d v2 = new Vector3d(referenceVectors[0]);
double dot = v1.dot(v2);
if (Math.abs(dot) < 0.999) {
axis.cross(v1,v2);
axis.normalize();
a.set(axis, v1.angle(v2));
m1.set(a);
// make sure matrix element m33 is 1.0. It's 0 on Linux.
m1.setElement(3, 3, 1.0);
} else if (dot > 0) {
// parallel axis, nothing to do -> identity matrix
m1.setIdentity();
} else if (dot < 0) {
// anti-parallel axis, flip around x-axis
m1.set(flipX());
}
// apply transformation matrix to all refPoints
m1.transform(axisVectors[0]);
m1.transform(axisVectors[1]);
// calculate rotation matrix to rotate refPoints[1] into coordPoints[1]
v1 = new Vector3d(axisVectors[1]);
v2 = new Vector3d(referenceVectors[1]);
Matrix4d m2 = new Matrix4d();
dot = v1.dot(v2);
if (Math.abs(dot) < 0.999) {
axis.cross(v1,v2);
axis.normalize();
a.set(axis, v1.angle(v2));
m2.set(a);
// make sure matrix element m33 is 1.0. It's 0 on Linux.
m2.setElement(3, 3, 1.0);
} else if (dot > 0) {
// parallel axis, nothing to do -> identity matrix
m2.setIdentity();
} else if (dot < 0) {
// anti-parallel axis, flip around z-axis
m2.set(flipZ());
}
// apply transformation matrix to all refPoints
m2.transform(axisVectors[0]);
m2.transform(axisVectors[1]);
// combine the two rotation matrices
m2.mul(m1);
// the RMSD should be close to zero
Point3d[] axes = new Point3d[2];
axes[0] = new Point3d(axisVectors[0]);
axes[1] = new Point3d(axisVectors[1]);
Point3d[] ref = new Point3d[2];
ref[0] = new Point3d(referenceVectors[0]);
ref[1] = new Point3d(referenceVectors[1]);
if (CalcPoint.rmsd(axes, ref) > 0.1) {
logger.warn("AxisTransformation: axes alignment is off. RMSD: "
+ CalcPoint.rmsd(axes, ref));
}
return m2;
} | java | private Matrix4d alignAxes(Vector3d[] axisVectors, Vector3d[] referenceVectors) {
Matrix4d m1 = new Matrix4d();
AxisAngle4d a = new AxisAngle4d();
Vector3d axis = new Vector3d();
// calculate rotation matrix to rotate refPoints[0] into coordPoints[0]
Vector3d v1 = new Vector3d(axisVectors[0]);
Vector3d v2 = new Vector3d(referenceVectors[0]);
double dot = v1.dot(v2);
if (Math.abs(dot) < 0.999) {
axis.cross(v1,v2);
axis.normalize();
a.set(axis, v1.angle(v2));
m1.set(a);
// make sure matrix element m33 is 1.0. It's 0 on Linux.
m1.setElement(3, 3, 1.0);
} else if (dot > 0) {
// parallel axis, nothing to do -> identity matrix
m1.setIdentity();
} else if (dot < 0) {
// anti-parallel axis, flip around x-axis
m1.set(flipX());
}
// apply transformation matrix to all refPoints
m1.transform(axisVectors[0]);
m1.transform(axisVectors[1]);
// calculate rotation matrix to rotate refPoints[1] into coordPoints[1]
v1 = new Vector3d(axisVectors[1]);
v2 = new Vector3d(referenceVectors[1]);
Matrix4d m2 = new Matrix4d();
dot = v1.dot(v2);
if (Math.abs(dot) < 0.999) {
axis.cross(v1,v2);
axis.normalize();
a.set(axis, v1.angle(v2));
m2.set(a);
// make sure matrix element m33 is 1.0. It's 0 on Linux.
m2.setElement(3, 3, 1.0);
} else if (dot > 0) {
// parallel axis, nothing to do -> identity matrix
m2.setIdentity();
} else if (dot < 0) {
// anti-parallel axis, flip around z-axis
m2.set(flipZ());
}
// apply transformation matrix to all refPoints
m2.transform(axisVectors[0]);
m2.transform(axisVectors[1]);
// combine the two rotation matrices
m2.mul(m1);
// the RMSD should be close to zero
Point3d[] axes = new Point3d[2];
axes[0] = new Point3d(axisVectors[0]);
axes[1] = new Point3d(axisVectors[1]);
Point3d[] ref = new Point3d[2];
ref[0] = new Point3d(referenceVectors[0]);
ref[1] = new Point3d(referenceVectors[1]);
if (CalcPoint.rmsd(axes, ref) > 0.1) {
logger.warn("AxisTransformation: axes alignment is off. RMSD: "
+ CalcPoint.rmsd(axes, ref));
}
return m2;
} | [
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31,896 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/RotationAxisAligner.java | RotationAxisAligner.refineReferenceVector | private void refineReferenceVector() {
referenceVector = new Vector3d(Y_AXIS);
if (rotationGroup.getPointGroup().startsWith("C")) {
referenceVector = getReferenceAxisCylicWithSubunitAlignment();
} else if (rotationGroup.getPointGroup().startsWith("D")) {
referenceVector = getReferenceAxisDihedralWithSubunitAlignment();
}
referenceVector = orthogonalize(principalRotationVector, referenceVector);
} | java | private void refineReferenceVector() {
referenceVector = new Vector3d(Y_AXIS);
if (rotationGroup.getPointGroup().startsWith("C")) {
referenceVector = getReferenceAxisCylicWithSubunitAlignment();
} else if (rotationGroup.getPointGroup().startsWith("D")) {
referenceVector = getReferenceAxisDihedralWithSubunitAlignment();
}
referenceVector = orthogonalize(principalRotationVector, referenceVector);
} | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/RotationAxisAligner.java#L702-L711 |
31,897 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/RotationAxisAligner.java | RotationAxisAligner.getReferenceAxisCylicWithSubunitAlignment | private Vector3d getReferenceAxisCylicWithSubunitAlignment() {
if (rotationGroup.getPointGroup().equals("C2")) {
return referenceVector;
}
// find subunit that extends the most in the xy-plane
List<List<Integer>> orbits = getOrbitsByXYWidth();
// get the last orbit which is the widest
List<Integer> widestOrbit = orbits.get(orbits.size()-1);
List<Point3d> centers = subunits.getCenters();
int subunit = widestOrbit.get(0);
// calculate reference vector
Vector3d refAxis = new Vector3d();
refAxis.sub(centers.get(subunit), subunits.getCentroid());
refAxis.normalize();
return refAxis;
} | java | private Vector3d getReferenceAxisCylicWithSubunitAlignment() {
if (rotationGroup.getPointGroup().equals("C2")) {
return referenceVector;
}
// find subunit that extends the most in the xy-plane
List<List<Integer>> orbits = getOrbitsByXYWidth();
// get the last orbit which is the widest
List<Integer> widestOrbit = orbits.get(orbits.size()-1);
List<Point3d> centers = subunits.getCenters();
int subunit = widestOrbit.get(0);
// calculate reference vector
Vector3d refAxis = new Vector3d();
refAxis.sub(centers.get(subunit), subunits.getCentroid());
refAxis.normalize();
return refAxis;
} | [
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@return reference vector | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/axis/RotationAxisAligner.java#L767-L784 |
31,898 | biojava/biojava | biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastService.java | NCBIQBlastService.init | private void init(String svcUrl) {
try {
serviceUrl = new URL(svcUrl);
} catch (MalformedURLException e) {
throw new RuntimeException("It looks like the URL for remote NCBI BLAST service ("
+ svcUrl + ") is wrong. Cause: " + e.getMessage(), e);
}
} | java | private void init(String svcUrl) {
try {
serviceUrl = new URL(svcUrl);
} catch (MalformedURLException e) {
throw new RuntimeException("It looks like the URL for remote NCBI BLAST service ("
+ svcUrl + ") is wrong. Cause: " + e.getMessage(), e);
}
} | [
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@throws MalformedURLException on invalid URL | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastService.java#L99-L106 |
31,899 | biojava/biojava | biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastService.java | NCBIQBlastService.setQBlastServiceProperties | private URLConnection setQBlastServiceProperties(URLConnection conn) {
conn.setDoOutput(true);
conn.setUseCaches(false);
conn.setRequestProperty("User-Agent", "Biojava/NCBIQBlastService");
conn.setRequestProperty("Connection", "Keep-Alive");
conn.setRequestProperty("Content-type", "application/x-www-form-urlencoded");
conn.setRequestProperty("Content-length", "200");
return conn;
} | java | private URLConnection setQBlastServiceProperties(URLConnection conn) {
conn.setDoOutput(true);
conn.setUseCaches(false);
conn.setRequestProperty("User-Agent", "Biojava/NCBIQBlastService");
conn.setRequestProperty("Connection", "Keep-Alive");
conn.setRequestProperty("Content-type", "application/x-www-form-urlencoded");
conn.setRequestProperty("Content-length", "200");
return conn;
} | [
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@param conn URLConnection to set properties for
@return given object after setting properties | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastService.java#L377-L385 |
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