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 ) {
... | 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 ) {
... | [
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@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);
FileDownload... | 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);
FileDownload... | [
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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");
doma... | 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");
doma... | [
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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),.... | 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),.... | [
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@throws IOException | [
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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 = re... | 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 = re... | [
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@param cache
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@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.isGuiModuleIns... | 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.isGuiModuleIns... | [
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@throws IOException If an error occurs when writing the afpChain to XML
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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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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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@throws IOException
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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 = ... | 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 = ... | [
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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 ];... | 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 ];... | [
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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)... | java | private void saveMatrix() {
for (String chainId : currentChainIDs) {
BiologicalAssemblyTransformation transformation = new BiologicalAssemblyTransformation();
transformation.setRotationMatrix(currentMatrix.getArray());
transformation.setTranslation(shift);
transformation.setId(String.valueOf(modelNumber)... | [
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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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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 (Except... | 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 (Except... | [
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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.selectSingleEleme... | 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.selectSingleEleme... | [
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@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, ... | 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, ... | [
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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, "en... | 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, "en... | [
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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-Age... | 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-Age... | [
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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 (geneElem... | 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 (geneElem... | [
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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");
... | 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");
... | [
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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... | java | @Override
public LinkedHashMap<String, ArrayList<DBReferenceInfo>> getDatabaseReferences() {
LinkedHashMap<String, ArrayList<DBReferenceInfo>> databaseReferencesHashMap = new LinkedHashMap<String, ArrayList<DBReferenceInfo>>();
if (uniprotDoc == null) {
return databaseReferencesHashMap;
}
try {
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@return | [
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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 ... | 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 ... | [
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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 = ... | 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 = ... | [
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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]);
... | 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]);
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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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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("le... | 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("le... | [
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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) {
logge... | 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) {
logge... | [
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@param <E> each task calculates a value of type E
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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 IllegalArgumentEx... | 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())) {
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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, PairwiseSequenceA... | 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, PairwiseSequenceA... | [
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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:
... | 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) {
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case GLOBAL:
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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.le... | 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.le... | [
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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://stack... | 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://stack... | [
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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.end... | 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.end... | [
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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... | 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... | [
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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... | 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... | [
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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> chromosome... | java | static public LinkedHashMap<String, ChromosomeSequence> loadFastaAddGeneFeaturesFromGeneIDGFF2(File fastaSequenceFile, File gffFile) throws Exception {
LinkedHashMap<String, DNASequence> dnaSequenceList = FastaReaderHelper.readFastaDNASequence(fastaSequenceFile);
LinkedHashMap<String, ChromosomeSequence> chromosome... | [
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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);
LinkedHash... | java | static public LinkedHashMap<String, ChromosomeSequence> loadFastaAddGeneFeaturesFromGmodGFF3(File fastaSequenceFile, File gffFile,boolean lazyloadsequences) throws Exception {
LinkedHashMap<String, DNASequence> dnaSequenceList = FastaReaderHelper.readFastaDNASequence(fastaSequenceFile,lazyloadsequences);
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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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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;
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String pdb2 = null;
try {
pdb1 = this.getPdbId();
} catch (StructureException e) {}
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} catch (StructureException e) {}
int comp = 0;
// Sort those with PDBIDs ... | java | @Override
public int compareTo(StructureName o) {
if ( this.equals(o))
return 0;
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try {
pdb1 = this.getPdbId();
} catch (StructureException e) {}
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} catch (StructureException e) {}
int comp = 0;
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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()) { //7890123456789012345678901234567890123456789012345678901234... | 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()) { //7890123456789012345678901234567890123456789012345678901234... | [
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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);
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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 fie... | 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 fie... | [
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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 ... | 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 ... | [
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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.
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@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")... | 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));
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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);
fo... | 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);
fo... | [
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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 ... | 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);
}
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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. Fo... | 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. Fo... | [
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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) )
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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);... | 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);... | [
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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> alignedRe... | 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
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@throws StructureException | [
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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 aminoAcidMatrice... | java | private static SubstitutionMatrix<AminoAcidCompound> getAminoAcidMatrix(String file) {
if (!aminoAcidMatrices.containsKey(file)) {
aminoAcidMatrices.put(file, new SimpleSubstitutionMatrix<AminoAcidCompound>(
AminoAcidCompoundSet.getAminoAcidCompoundSet(), getReader(file), file));
}
return aminoAcidMatrice... | [
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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 nucleotideMatr... | java | private static SubstitutionMatrix<NucleotideCompound> getNucleotideMatrix(String file) {
if (!nucleotideMatrices.containsKey(file)) {
nucleotideMatrices.put(file, new SimpleSubstitutionMatrix<NucleotideCompound>(
AmbiguityDNACompoundSet.getDNACompoundSet(), getReader(file), file));
}
return nucleotideMatr... | [
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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... | 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... | [
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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()... | 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
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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);
logge... | 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);
logge... | [
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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 uniquel... | [
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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){
bioAssemblyPar... | 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){
bioAssemblyPar... | [
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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.s... | 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;
}
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String seqNum1 = line.substring(17,21).trim();
String icode1 = line.s... | [
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COLUMNS DATA TYPE FIELD DEFINITION
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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 l... | 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 l... | [
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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(ch... | 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(ch... | [
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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)) {
no... | 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)) {
no... | [
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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.... | 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.... | [
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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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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 = get... | 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 = get... | [
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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... | 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... | [
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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... | 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... | [
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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 b... | 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(
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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 + line... | 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 + line... | [
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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_... | 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_... | [
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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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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 P... | 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 P... | [
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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(... | 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(... | [
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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 ne... | 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 ne... | [
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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 g... | 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());
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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> twi... | 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> twi... | [
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@param afpChain the container of the alignment
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@param ca2 atoms for protein 2
@return a protein structure with 2 models.
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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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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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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, "comp... | 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, "comp... | [
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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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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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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 ) { ... | 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 ) { ... | [
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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 ... | 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 ... | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/CrystalTransform.java#L431-L455 |
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 transformat... | 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 transformat... | [
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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#L164-L182 |
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 ... | 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 ... | [
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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#L410-L478 |
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 = getReferenceAxisDihedralWithSubunit... | java | private void refineReferenceVector() {
referenceVector = new Vector3d(Y_AXIS);
if (rotationGroup.getPointGroup().startsWith("C")) {
referenceVector = getReferenceAxisCylicWithSubunitAlignment();
} else if (rotationGroup.getPointGroup().startsWith("D")) {
referenceVector = getReferenceAxisDihedralWithSubunit... | [
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@return minor rotation axis | [
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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> wide... | 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> wide... | [
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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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] | 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-urle... | 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-urle... | [
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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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