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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
31,900 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/domain/PDBDomainProvider.java | PDBDomainProvider.getDomainNames | @Override
public SortedSet<String> getDomainNames(String name) {
if ( name.length() < 4)
throw new IllegalArgumentException("Can't interpret IDs that are shorter than 4 residues!");
String url = String.format("%srepresentativeDomains?cluster=%s&structureId=%s",
base, cutoff, name);
return requestRepresentativeDomains(url);
} | java | @Override
public SortedSet<String> getDomainNames(String name) {
if ( name.length() < 4)
throw new IllegalArgumentException("Can't interpret IDs that are shorter than 4 residues!");
String url = String.format("%srepresentativeDomains?cluster=%s&structureId=%s",
base, cutoff, name);
return requestRepresentativeDomains(url);
} | [
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31,901 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/domain/PDBDomainProvider.java | PDBDomainProvider.getRepresentativeDomains | @Override
public SortedSet<String> getRepresentativeDomains() {
String url = base + "representativeDomains?cluster="+ cutoff;
return requestRepresentativeDomains(url);
} | java | @Override
public SortedSet<String> getRepresentativeDomains() {
String url = base + "representativeDomains?cluster="+ cutoff;
return requestRepresentativeDomains(url);
} | [
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31,902 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/domain/PDBDomainProvider.java | PDBDomainProvider.requestRepresentativeDomains | private SortedSet<String> requestRepresentativeDomains(String url) {
try {
//System.out.println(url);
final SortedSet<String> results = new TreeSet<String>();
DefaultHandler handler = new DefaultHandler() {
@Override
public void startElement(String uri, String localName,String qName,
Attributes attributes) throws SAXException {
//System.out.println("Start Element :" + qName);
if (qName.equalsIgnoreCase("representative")) {
String name = attributes.getValue("name");
results.add(name);
}
}
};
handleRestRequest(url,handler);
return results;
} catch (MalformedURLException e) {
e.printStackTrace();
} catch (IOException e) {
e.printStackTrace();
} catch (SAXException e) {
e.printStackTrace();
} catch (ParserConfigurationException e) {
e.printStackTrace();
}
return null;
} | java | private SortedSet<String> requestRepresentativeDomains(String url) {
try {
//System.out.println(url);
final SortedSet<String> results = new TreeSet<String>();
DefaultHandler handler = new DefaultHandler() {
@Override
public void startElement(String uri, String localName,String qName,
Attributes attributes) throws SAXException {
//System.out.println("Start Element :" + qName);
if (qName.equalsIgnoreCase("representative")) {
String name = attributes.getValue("name");
results.add(name);
}
}
};
handleRestRequest(url,handler);
return results;
} catch (MalformedURLException e) {
e.printStackTrace();
} catch (IOException e) {
e.printStackTrace();
} catch (SAXException e) {
e.printStackTrace();
} catch (ParserConfigurationException e) {
e.printStackTrace();
}
return null;
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@param url Eg "http://www.rcsb.org/pdb/rest/representativeDomains"
@return The names of all domain representatives | [
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31,903 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/domain/PDBDomainProvider.java | PDBDomainProvider.handleRestRequest | private static void handleRestRequest(String url, DefaultHandler handler) throws SAXException, IOException, ParserConfigurationException {
// Fetch XML stream
URL u = new URL(url);
InputStream response = URLConnectionTools.getInputStream(u);
InputSource xml = new InputSource(response);
// Parse XML
SAXParserFactory factory = SAXParserFactory.newInstance();
SAXParser saxParser = factory.newSAXParser();
saxParser.parse(xml, handler);
} | java | private static void handleRestRequest(String url, DefaultHandler handler) throws SAXException, IOException, ParserConfigurationException {
// Fetch XML stream
URL u = new URL(url);
InputStream response = URLConnectionTools.getInputStream(u);
InputSource xml = new InputSource(response);
// Parse XML
SAXParserFactory factory = SAXParserFactory.newInstance();
SAXParser saxParser = factory.newSAXParser();
saxParser.parse(xml, handler);
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@param url REST request
@param handler SAX XML parser
@throws SAXException
@throws IOException
@throws ParserConfigurationException | [
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31,904 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/FragmentJoiner.java | FragmentJoiner.getDensity | private double getDensity(Atom[] ca1subset, Atom[] ca2subset ) throws StructureException{
Atom centroid1 = Calc.getCentroid(ca1subset);
Atom centroid2 = Calc.getCentroid(ca2subset);
// get Average distance to centroid ...
double d1 = 0;
double d2 = 0;
for ( int i = 0 ; i < ca1subset.length;i++){
double dd1 = Calc.getDistance(centroid1, ca1subset[i]);
double dd2 = Calc.getDistance(centroid2, ca2subset[i]);
d1 += dd1;
d2 += dd2;
}
double avd1 = d1 / ca1subset.length;
double avd2 = d2 / ca2subset.length;
return Math.min(avd1,avd2);
} | java | private double getDensity(Atom[] ca1subset, Atom[] ca2subset ) throws StructureException{
Atom centroid1 = Calc.getCentroid(ca1subset);
Atom centroid2 = Calc.getCentroid(ca2subset);
// get Average distance to centroid ...
double d1 = 0;
double d2 = 0;
for ( int i = 0 ; i < ca1subset.length;i++){
double dd1 = Calc.getDistance(centroid1, ca1subset[i]);
double dd2 = Calc.getDistance(centroid2, ca2subset[i]);
d1 += dd1;
d2 += dd2;
}
double avd1 = d1 / ca1subset.length;
double avd2 = d2 / ca2subset.length;
return Math.min(avd1,avd2);
} | [
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@param ca1subset
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@return a double
@throws StructureException | [
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31,905 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/FragmentJoiner.java | FragmentJoiner.getRMS | public static double getRMS(Atom[] ca1, Atom[]ca2,JointFragments frag) throws StructureException {
// now svd ftmp and check if the rms is < X ...
AlternativeAlignment ali = new AlternativeAlignment();
ali.apairs_from_idxlst(frag);
double rms = 999;
int[] idx1 = ali.getIdx1();
int[] idx2 = ali.getIdx2();
Atom[] ca1subset = AlignUtils.getFragmentFromIdxList(ca1, idx1);
Atom[] ca2subset = AlignUtils.getFragmentFromIdxList(ca2,idx2);
ali.calculateSuperpositionByIdx(ca1,ca2);
Matrix rot = ali.getRotationMatrix();
Atom atom = ali.getShift();
for (Atom a : ca2subset) {
Calc.rotate(a, rot);
Calc.shift(a, atom);
}
rms = Calc.rmsd(ca1subset,ca2subset);
return rms;
} | java | public static double getRMS(Atom[] ca1, Atom[]ca2,JointFragments frag) throws StructureException {
// now svd ftmp and check if the rms is < X ...
AlternativeAlignment ali = new AlternativeAlignment();
ali.apairs_from_idxlst(frag);
double rms = 999;
int[] idx1 = ali.getIdx1();
int[] idx2 = ali.getIdx2();
Atom[] ca1subset = AlignUtils.getFragmentFromIdxList(ca1, idx1);
Atom[] ca2subset = AlignUtils.getFragmentFromIdxList(ca2,idx2);
ali.calculateSuperpositionByIdx(ca1,ca2);
Matrix rot = ali.getRotationMatrix();
Atom atom = ali.getShift();
for (Atom a : ca2subset) {
Calc.rotate(a, rot);
Calc.shift(a, atom);
}
rms = Calc.rmsd(ca1subset,ca2subset);
return rms;
} | [
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@param ca1 the array of all atoms of structure1
@param ca2 the array of all atoms of structure1
@param frag the JointFragments object that contains the list of identical positions
@return the rms | [
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31,906 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Stoichiometry.java | Stoichiometry.getComponent | public Stoichiometry getComponent(int i) {
return new Stoichiometry(Collections.singletonList(orderedClusters.get(i)),this.strategy,false);
} | java | public Stoichiometry getComponent(int i) {
return new Stoichiometry(Collections.singletonList(orderedClusters.get(i)),this.strategy,false);
} | [
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@param i component index
@return new {@link Stoichiometry} object. | [
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31,907 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Stoichiometry.java | Stoichiometry.setStrategy | public void setStrategy(StringOverflowStrategy strategy) {
if(strategy==StringOverflowStrategy.CUSTOM) {
throw new IllegalArgumentException("Set this strategy by providing a function of the type Function<List<SubunitCluster>,String>.");
}
if(this.strategy != strategy) {
this.strategy = strategy;
if(orderedClusters.size()>alphabet.length())
doResetAlphas();
}
} | java | public void setStrategy(StringOverflowStrategy strategy) {
if(strategy==StringOverflowStrategy.CUSTOM) {
throw new IllegalArgumentException("Set this strategy by providing a function of the type Function<List<SubunitCluster>,String>.");
}
if(this.strategy != strategy) {
this.strategy = strategy;
if(orderedClusters.size()>alphabet.length())
doResetAlphas();
}
} | [
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This action may invalidate alphas already assigned to the clusters.
@param strategy
{@link StringOverflowStrategy} used in this stoichiometry
to construct human-readable representation in case number
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31,908 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/Stoichiometry.java | Stoichiometry.setCustomStringGenerator | public void setCustomStringGenerator(Function<List<SubunitCluster>,String> customStringGenerator) {
this.strategy = StringOverflowStrategy.CUSTOM;
this.customStringGenerator = customStringGenerator;
} | java | public void setCustomStringGenerator(Function<List<SubunitCluster>,String> customStringGenerator) {
this.strategy = StringOverflowStrategy.CUSTOM;
this.customStringGenerator = customStringGenerator;
} | [
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@param customStringGenerator
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31,909 | biojava/biojava | biojava-structure-gui/src/main/java/demo/DemoStructureFromFasta.java | DemoStructureFromFasta.displayStructure | private static void displayStructure(Structure structure,
ResidueNumber[] residues) {
//Display each structure
BiojavaJmol jmol = new BiojavaJmol();
jmol.setStructure(structure);
//Highlight non-null atoms
jmol.evalString("select *; spacefill off; wireframe off; color chain; backbone 0.4; ");
String selectionCmd = buildJmolSelection(residues);
jmol.evalString(selectionCmd);
jmol.evalString("backbone 1.0; select none;");
} | java | private static void displayStructure(Structure structure,
ResidueNumber[] residues) {
//Display each structure
BiojavaJmol jmol = new BiojavaJmol();
jmol.setStructure(structure);
//Highlight non-null atoms
jmol.evalString("select *; spacefill off; wireframe off; color chain; backbone 0.4; ");
String selectionCmd = buildJmolSelection(residues);
jmol.evalString(selectionCmd);
jmol.evalString("backbone 1.0; select none;");
} | [
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@param residues A list of residues to highlight | [
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31,910 | biojava/biojava | biojava-structure-gui/src/main/java/demo/DemoStructureFromFasta.java | DemoStructureFromFasta.buildJmolSelection | private static String buildJmolSelection(ResidueNumber[] residues) {
StringBuilder cmd = new StringBuilder("select ");
for(ResidueNumber res : residues) {
if(res != null) {
cmd.append(String.format("%d^%s:%s.CA or ", res.getSeqNum(),
res.getInsCode()==null?" ":res.getInsCode(),
res.getChainName()));
}
}
cmd.append("none;");//easier than removing the railing 'or'
return cmd.toString();
} | java | private static String buildJmolSelection(ResidueNumber[] residues) {
StringBuilder cmd = new StringBuilder("select ");
for(ResidueNumber res : residues) {
if(res != null) {
cmd.append(String.format("%d^%s:%s.CA or ", res.getSeqNum(),
res.getInsCode()==null?" ":res.getInsCode(),
res.getChainName()));
}
}
cmd.append("none;");//easier than removing the railing 'or'
return cmd.toString();
} | [
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<p>For example, "select 11^ :A.CA or 12^ :A.CA;" would select the
CA atoms of residues 11-12 on chain A.
@param residues Residues to include in the selection. Nulls are ignored.
@return | [
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31,911 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/AFPChainXMLConverter.java | AFPChainXMLConverter.toXML | public synchronized static String toXML(AFPChain afpChain, Atom[] ca1, Atom[]ca2) throws IOException{
StringWriter result = new StringWriter();
toXML(afpChain,result,ca1,ca2);
return result.toString();
} | java | public synchronized static String toXML(AFPChain afpChain, Atom[] ca1, Atom[]ca2) throws IOException{
StringWriter result = new StringWriter();
toXML(afpChain,result,ca1,ca2);
return result.toString();
} | [
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@param afpChain
@return XML representation of the AFPCHain | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/AFPChainXMLConverter.java#L44-L48 |
31,912 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/AFPChainXMLConverter.java | AFPChainXMLConverter.toXML | public synchronized static void toXML(AFPChain afpChain, StringWriter swriter,Atom[] ca1, Atom[]ca2) throws IOException{
PrintWriter writer = new PrintWriter(swriter);
PrettyXMLWriter xml = new PrettyXMLWriter(writer);
xml.openTag("AFPChain");
printXMLHeader(xml,afpChain);
// that is the initial alignment...
// we don't serialize that at the present.
//int[] blockResSize = afpChain.getBlockResSize();
//int[][][] blockResList = afpChain.getBlockResList();
// get the alignment blocks
int blockNum = afpChain.getBlockNum();
//int[] optLen = afpChain.getOptLen();
//int[] blockSize = afpChain.getBlockSize();
for(int bk = 0; bk < blockNum; bk ++) {
xml.openTag("block");
printXMLBlockHeader(xml,afpChain, bk);
if ( ca1 == null || ca2 == null) {
try {
printXMLEQRKnownPositions(xml,afpChain,bk);
} catch (StructureException ex ){
throw new IOException(ex.getMessage());
}
}
else
printXMLEQRInferPositions(xml, afpChain,bk,ca1,ca2);
printXMLMatrixShift(xml, afpChain, bk);
xml.closeTag("block");
}
xml.closeTag("AFPChain");
writer.close();
} | java | public synchronized static void toXML(AFPChain afpChain, StringWriter swriter,Atom[] ca1, Atom[]ca2) throws IOException{
PrintWriter writer = new PrintWriter(swriter);
PrettyXMLWriter xml = new PrettyXMLWriter(writer);
xml.openTag("AFPChain");
printXMLHeader(xml,afpChain);
// that is the initial alignment...
// we don't serialize that at the present.
//int[] blockResSize = afpChain.getBlockResSize();
//int[][][] blockResList = afpChain.getBlockResList();
// get the alignment blocks
int blockNum = afpChain.getBlockNum();
//int[] optLen = afpChain.getOptLen();
//int[] blockSize = afpChain.getBlockSize();
for(int bk = 0; bk < blockNum; bk ++) {
xml.openTag("block");
printXMLBlockHeader(xml,afpChain, bk);
if ( ca1 == null || ca2 == null) {
try {
printXMLEQRKnownPositions(xml,afpChain,bk);
} catch (StructureException ex ){
throw new IOException(ex.getMessage());
}
}
else
printXMLEQRInferPositions(xml, afpChain,bk,ca1,ca2);
printXMLMatrixShift(xml, afpChain, bk);
xml.closeTag("block");
}
xml.closeTag("AFPChain");
writer.close();
} | [
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@param afpChain
@param swriter
@throws IOException | [
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"StringWriter"
] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/align/xml/AFPChainXMLConverter.java#L56-L102 |
31,913 | biojava/biojava | biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java | NCBIQBlastAlignmentProperties.getAlignmentOptions | @Override
public Set<String> getAlignmentOptions() {
Set<String> result = new HashSet<String>();
for (BlastAlignmentParameterEnum parameter : param.keySet()) {
result.add(parameter.name());
}
return result;
} | java | @Override
public Set<String> getAlignmentOptions() {
Set<String> result = new HashSet<String>();
for (BlastAlignmentParameterEnum parameter : param.keySet()) {
result.add(parameter.name());
}
return result;
} | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java#L70-L77 |
31,914 | biojava/biojava | biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java | NCBIQBlastAlignmentProperties.setBlastProgram | public void setBlastProgram(BlastProgramEnum program) {
if (BlastProgramEnum.megablast != program) {
setAlignmentOption(PROGRAM, program.name());
removeAlignmentOption(MEGABLAST);
} else {
setAlignmentOption(PROGRAM, BlastProgramEnum.blastn.name());
setAlignmentOption(MEGABLAST, "on");
}
} | java | public void setBlastProgram(BlastProgramEnum program) {
if (BlastProgramEnum.megablast != program) {
setAlignmentOption(PROGRAM, program.name());
removeAlignmentOption(MEGABLAST);
} else {
setAlignmentOption(PROGRAM, BlastProgramEnum.blastn.name());
setAlignmentOption(MEGABLAST, "on");
}
} | [
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@param program : one of blastall programs | [
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"to",
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"used",
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"blastall"
] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java#L114-L122 |
31,915 | biojava/biojava | biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java | NCBIQBlastAlignmentProperties.getBlastWordSize | public int getBlastWordSize() {
if (param.containsKey(WORD_SIZE)) {
return Integer.parseInt(getAlignmentOption(WORD_SIZE));
}
// return default word size value
try {
BlastProgramEnum programType = getBlastProgram();
switch (programType) {
case blastn:
return 11;
case megablast:
return 28;
case blastp:
case blastx:
case tblastn:
case tblastx:
return 3;
default:
throw new UnsupportedOperationException("Blast program " + programType.name() + " is not supported.");
}
} catch (IllegalArgumentException e) {
throw new IllegalArgumentException("Blast program " + getBlastProgram() + " is not supported.", e);
}
} | java | public int getBlastWordSize() {
if (param.containsKey(WORD_SIZE)) {
return Integer.parseInt(getAlignmentOption(WORD_SIZE));
}
// return default word size value
try {
BlastProgramEnum programType = getBlastProgram();
switch (programType) {
case blastn:
return 11;
case megablast:
return 28;
case blastp:
case blastx:
case tblastn:
case tblastx:
return 3;
default:
throw new UnsupportedOperationException("Blast program " + programType.name() + " is not supported.");
}
} catch (IllegalArgumentException e) {
throw new IllegalArgumentException("Blast program " + getBlastProgram() + " is not supported.", e);
}
} | [
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@return int value of WORD_SIZE used by this search
@throws IllegalArgumentException when program type is not set and program type is not supported | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java#L179-L203 |
31,916 | biojava/biojava | biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java | NCBIQBlastAlignmentProperties.setBlastGapCosts | public void setBlastGapCosts(int gapCreation, int gapExtension) {
String gc = Integer.toString(gapCreation);
String ge = Integer.toString(gapExtension);
setAlignmentOption(GAPCOSTS, gc + "+" + ge);
} | java | public void setBlastGapCosts(int gapCreation, int gapExtension) {
String gc = Integer.toString(gapCreation);
String ge = Integer.toString(gapExtension);
setAlignmentOption(GAPCOSTS, gc + "+" + ge);
} | [
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... | Sets the GAPCOSTS parameter
@param gapCreation integer to use as gap creation value
@param gapExtension integer to use as gap extension value | [
"Sets",
"the",
"GAPCOSTS",
"parameter"
] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-ws/src/main/java/org/biojava/nbio/ws/alignment/qblast/NCBIQBlastAlignmentProperties.java#L266-L270 |
31,917 | biojava/biojava | biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxInfo.java | CoxInfo.fmtpl | public String fmtpl(String d, int pad) {
int length = d.length();
int extra = pad - length;
if (extra < 0) {
extra = 0;
}
String v = d;
for (int i = 0; i < extra; i++) {
v = " " + v;
}
return v;
} | java | public String fmtpl(String d, int pad) {
int length = d.length();
int extra = pad - length;
if (extra < 0) {
extra = 0;
}
String v = d;
for (int i = 0; i < extra; i++) {
v = " " + v;
}
return v;
} | [
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";",
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"(",
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")",
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... | Pad left a string with spaces
@param d
@param pad
@return | [
"Pad",
"left",
"a",
"string",
"with",
"spaces"
] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxInfo.java#L464-L475 |
31,918 | biojava/biojava | biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SequenceMouseListener.java | SequenceMouseListener.getSeqPos | private int getSeqPos(MouseEvent e) {
int x = e.getX();
//int y = e.getY();
//float scale = seqScale.getScale();
//int DEFAULT_X_START = SequenceScalePanel.DEFAULT_X_START;
float scale = parent.getScale();
coordManager.setScale(scale);
int seqpos = coordManager.getSeqPos(x-2);
return seqpos ;
} | java | private int getSeqPos(MouseEvent e) {
int x = e.getX();
//int y = e.getY();
//float scale = seqScale.getScale();
//int DEFAULT_X_START = SequenceScalePanel.DEFAULT_X_START;
float scale = parent.getScale();
coordManager.setScale(scale);
int seqpos = coordManager.getSeqPos(x-2);
return seqpos ;
} | [
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"getSeqPos",
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"//float scale = seqScale.getScale();",
"//int DEFAULT_X_START = SequenceScalePanel.DEFAULT_X_START;",
"float",
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"paren... | get the sequence position of the current mouse event | [
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"the",
"sequence",
"position",
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"current",
"mouse",
"event"
] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SequenceMouseListener.java#L124-L138 |
31,919 | biojava/biojava | biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java | WorkSheet.clear | public void clear() {
columnLookup.clear();
rowLookup.clear();
data = null;
dataGrid.clear();
doubleValues.clear();
System.gc();
} | java | public void clear() {
columnLookup.clear();
rowLookup.clear();
data = null;
dataGrid.clear();
doubleValues.clear();
System.gc();
} | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java#L117-L124 |
31,920 | biojava/biojava | biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java | WorkSheet.getCopyWorkSheetSelectedRows | static public WorkSheet getCopyWorkSheetSelectedRows(WorkSheet copyWorkSheet, ArrayList<String> rows) throws Exception {
ArrayList<String> columns = copyWorkSheet.getColumns();
WorkSheet workSheet = new WorkSheet(rows, columns);
for (String row : rows) {
for (String col : columns) {
workSheet.addCell(row, col, copyWorkSheet.getCell(row, col));
}
}
workSheet.setMetaDataColumns(copyWorkSheet.getMetaDataColumns());
workSheet.setMetaDataRows(copyWorkSheet.getMetaDataRows());
return workSheet;
} | java | static public WorkSheet getCopyWorkSheetSelectedRows(WorkSheet copyWorkSheet, ArrayList<String> rows) throws Exception {
ArrayList<String> columns = copyWorkSheet.getColumns();
WorkSheet workSheet = new WorkSheet(rows, columns);
for (String row : rows) {
for (String col : columns) {
workSheet.addCell(row, col, copyWorkSheet.getCell(row, col));
}
}
workSheet.setMetaDataColumns(copyWorkSheet.getMetaDataColumns());
workSheet.setMetaDataRows(copyWorkSheet.getMetaDataRows());
return workSheet;
} | [
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... | Create a copy of a worksheet. If shuffling of columns or row for testing
a way to duplicate original worksheet
@param copyWorkSheet
@param rows
@return
@throws Exception | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java#L171-L186 |
31,921 | biojava/biojava | biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java | WorkSheet.shuffleColumnsAndThenRows | public void shuffleColumnsAndThenRows(ArrayList<String> columns, ArrayList<String> rows) throws Exception {
doubleValues.clear();
for (String column : columns) { //shuffle all values in the column
ArrayList<Integer> rowIndex = new ArrayList<Integer>();
for (int i = 0; i < rows.size(); i++) {
rowIndex.add(i);
}
Collections.shuffle(rowIndex);
for (int i = 0; i < rows.size(); i++) {
String row = rows.get(i);
int randomIndex = rowIndex.get(i);
String destinationRow = rows.get(randomIndex);
String temp = this.getCell(destinationRow, column);
String value = this.getCell(row, column);
this.addCell(destinationRow, column, value);
this.addCell(row, column, temp);
}
}
for (String row : rows) {
ArrayList<Integer> columnIndex = new ArrayList<Integer>();
for (int i = 0; i < columns.size(); i++) {
columnIndex.add(i);
}
Collections.shuffle(columnIndex);
for (int i = 0; i < columns.size(); i++) {
String column = columns.get(i);
int randomIndex = columnIndex.get(i);
String destinationCol = columns.get(randomIndex);
String temp = this.getCell(row, destinationCol);
String value = this.getCell(row, column);
this.addCell(row, destinationCol, value);
this.addCell(row, column, temp);
}
}
} | java | public void shuffleColumnsAndThenRows(ArrayList<String> columns, ArrayList<String> rows) throws Exception {
doubleValues.clear();
for (String column : columns) { //shuffle all values in the column
ArrayList<Integer> rowIndex = new ArrayList<Integer>();
for (int i = 0; i < rows.size(); i++) {
rowIndex.add(i);
}
Collections.shuffle(rowIndex);
for (int i = 0; i < rows.size(); i++) {
String row = rows.get(i);
int randomIndex = rowIndex.get(i);
String destinationRow = rows.get(randomIndex);
String temp = this.getCell(destinationRow, column);
String value = this.getCell(row, column);
this.addCell(destinationRow, column, value);
this.addCell(row, column, temp);
}
}
for (String row : rows) {
ArrayList<Integer> columnIndex = new ArrayList<Integer>();
for (int i = 0; i < columns.size(); i++) {
columnIndex.add(i);
}
Collections.shuffle(columnIndex);
for (int i = 0; i < columns.size(); i++) {
String column = columns.get(i);
int randomIndex = columnIndex.get(i);
String destinationCol = columns.get(randomIndex);
String temp = this.getCell(row, destinationCol);
String value = this.getCell(row, column);
this.addCell(row, destinationCol, value);
this.addCell(row, column, temp);
}
}
} | [
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data type if not probably doesn't make any sense.
@param columns
@param rows
@throws Exception | [
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31,922 | biojava/biojava | biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java | WorkSheet.shuffleColumnValues | public void shuffleColumnValues(ArrayList<String> columns) throws Exception {
doubleValues.clear();
ArrayList<String> rows = this.getDataRows();
for (String column : columns) { //shuffle all values in the column
ArrayList<Integer> rowIndex = new ArrayList<Integer>();
for (int i = 0; i < rows.size(); i++) {
rowIndex.add(i);
}
Collections.shuffle(rowIndex);
for (int i = 0; i < rows.size(); i++) {
String row = rows.get(i);
int randomIndex = rowIndex.get(i);
String destinationRow = rows.get(randomIndex);
String temp = this.getCell(destinationRow, column);
String value = this.getCell(row, column);
this.addCell(destinationRow, column, value);
this.addCell(row, column, temp);
}
}
} | java | public void shuffleColumnValues(ArrayList<String> columns) throws Exception {
doubleValues.clear();
ArrayList<String> rows = this.getDataRows();
for (String column : columns) { //shuffle all values in the column
ArrayList<Integer> rowIndex = new ArrayList<Integer>();
for (int i = 0; i < rows.size(); i++) {
rowIndex.add(i);
}
Collections.shuffle(rowIndex);
for (int i = 0; i < rows.size(); i++) {
String row = rows.get(i);
int randomIndex = rowIndex.get(i);
String destinationRow = rows.get(randomIndex);
String temp = this.getCell(destinationRow, column);
String value = this.getCell(row, column);
this.addCell(destinationRow, column, value);
this.addCell(row, column, temp);
}
}
} | [
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columns in the list will be shuffled together
@param columns
@throws Exception | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java#L343-L365 |
31,923 | biojava/biojava | biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java | WorkSheet.shuffleRowValues | public void shuffleRowValues(ArrayList<String> rows) throws Exception {
doubleValues.clear();
ArrayList<String> columns = this.getColumns();
for (String row : rows) {
ArrayList<Integer> columnIndex = new ArrayList<Integer>();
for (int i = 0; i < columns.size(); i++) {
columnIndex.add(i);
}
Collections.shuffle(columnIndex);
for (int i = 0; i < columns.size(); i++) {
String column = columns.get(i);
int randomIndex = columnIndex.get(i);
String destinationCol = columns.get(randomIndex);
String temp = this.getCell(row, destinationCol);
String value = this.getCell(row, column);
this.addCell(row, destinationCol, value);
this.addCell(row, column, temp);
}
}
} | java | public void shuffleRowValues(ArrayList<String> rows) throws Exception {
doubleValues.clear();
ArrayList<String> columns = this.getColumns();
for (String row : rows) {
ArrayList<Integer> columnIndex = new ArrayList<Integer>();
for (int i = 0; i < columns.size(); i++) {
columnIndex.add(i);
}
Collections.shuffle(columnIndex);
for (int i = 0; i < columns.size(); i++) {
String column = columns.get(i);
int randomIndex = columnIndex.get(i);
String destinationCol = columns.get(randomIndex);
String temp = this.getCell(row, destinationCol);
String value = this.getCell(row, column);
this.addCell(row, destinationCol, value);
this.addCell(row, column, temp);
}
}
} | [
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31,924 | biojava/biojava | biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java | WorkSheet.markMetaDataColumns | public void markMetaDataColumns(ArrayList<String> metaDataColumns) {
for (String column : metaDataColumns) {
metaDataColumnsHashMap.put(column, column);
}
} | java | public void markMetaDataColumns(ArrayList<String> metaDataColumns) {
for (String column : metaDataColumns) {
metaDataColumnsHashMap.put(column, column);
}
} | [
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@param metaDataColumns | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java#L485-L489 |
31,925 | biojava/biojava | biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java | WorkSheet.replaceColumnValues | public void replaceColumnValues(String column, HashMap<String, String> values) throws Exception {
for (String row : rowLookup.keySet()) {
String oldValue = this.getCell(row, column);
String newValue = values.get(oldValue);
this.addCell(row, column, newValue);
}
} | java | public void replaceColumnValues(String column, HashMap<String, String> values) throws Exception {
for (String row : rowLookup.keySet()) {
String oldValue = this.getCell(row, column);
String newValue = values.get(oldValue);
this.addCell(row, column, newValue);
}
} | [
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@param column
@param values
@throws Exception | [
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31,926 | biojava/biojava | biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java | WorkSheet.applyColumnFilter | public void applyColumnFilter(String column, ChangeValue changeValue) throws Exception {
for (String row : rowLookup.keySet()) {
String oldValue = this.getCell(row, column);
String newValue = changeValue.change(oldValue);
this.addCell(row, column, newValue);
}
} | java | public void applyColumnFilter(String column, ChangeValue changeValue) throws Exception {
for (String row : rowLookup.keySet()) {
String oldValue = this.getCell(row, column);
String newValue = changeValue.change(oldValue);
this.addCell(row, column, newValue);
}
} | [
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based on some range
@param column
@param changeValue
@throws Exception | [
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31,927 | biojava/biojava | biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java | WorkSheet.addColumns | public void addColumns(ArrayList<String> columns, String defaultValue) {
CompactCharSequence dv = new CompactCharSequence(defaultValue);
for (int i = 0; i < data.length; i++) {
CompactCharSequence[] row = data[i];
int oldrowlength = data[i].length;
data[i] = (CompactCharSequence[]) resizeArray(row, oldrowlength + columns.size());
for (int c = 0; c < columns.size(); c++) {
data[i][oldrowlength + c] = dv;
}
if (i == 0) {
for (int c = 0; c < columns.size(); c++) {
String column = columns.get(c);
data[0][oldrowlength + c] = new CompactCharSequence(column);
columnLookup.put(column, new HeaderInfo(oldrowlength + c));
}
}
}
// columnLookup.get("ZNF30");
// int startIndex = columnLookup.size() + 1;
// for (String column : columns) {
// if(column.equals("ttr")){
// int dummy = 1;
// }
// columnLookup.put(column, new HeaderInfo(startIndex));
// startIndex++;
// }
} | java | public void addColumns(ArrayList<String> columns, String defaultValue) {
CompactCharSequence dv = new CompactCharSequence(defaultValue);
for (int i = 0; i < data.length; i++) {
CompactCharSequence[] row = data[i];
int oldrowlength = data[i].length;
data[i] = (CompactCharSequence[]) resizeArray(row, oldrowlength + columns.size());
for (int c = 0; c < columns.size(); c++) {
data[i][oldrowlength + c] = dv;
}
if (i == 0) {
for (int c = 0; c < columns.size(); c++) {
String column = columns.get(c);
data[0][oldrowlength + c] = new CompactCharSequence(column);
columnLookup.put(column, new HeaderInfo(oldrowlength + c));
}
}
}
// columnLookup.get("ZNF30");
// int startIndex = columnLookup.size() + 1;
// for (String column : columns) {
// if(column.equals("ttr")){
// int dummy = 1;
// }
// columnLookup.put(column, new HeaderInfo(startIndex));
// startIndex++;
// }
} | [
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... | Add columns to worksheet and set default value
@param columns
@param defaultValue | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java#L660-L689 |
31,928 | biojava/biojava | biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java | WorkSheet.addRows | public void addRows(ArrayList<String> rows, String defaultValue) {
CompactCharSequence dv = new CompactCharSequence(defaultValue);
int oldlength = data.length;
int numColumns = 0;
if (data.length > 0 && data[0] != null) {
numColumns = data[0].length;
}
data = (CompactCharSequence[][]) resizeArray(data, data.length + rows.size());
for (int r = 0; r < rows.size(); r++) {
data[oldlength + r] = new CompactCharSequence[numColumns];
for (int c = 0; c < numColumns; c++) {
data[oldlength + r][c] = dv;
}
data[oldlength + r][0] = new CompactCharSequence(rows.get(r));
rowLookup.put(rows.get(r), new HeaderInfo(r + oldlength));
}
} | java | public void addRows(ArrayList<String> rows, String defaultValue) {
CompactCharSequence dv = new CompactCharSequence(defaultValue);
int oldlength = data.length;
int numColumns = 0;
if (data.length > 0 && data[0] != null) {
numColumns = data[0].length;
}
data = (CompactCharSequence[][]) resizeArray(data, data.length + rows.size());
for (int r = 0; r < rows.size(); r++) {
data[oldlength + r] = new CompactCharSequence[numColumns];
for (int c = 0; c < numColumns; c++) {
data[oldlength + r][c] = dv;
}
data[oldlength + r][0] = new CompactCharSequence(rows.get(r));
rowLookup.put(rows.get(r), new HeaderInfo(r + oldlength));
}
} | [
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@param rows
@param defaultValue | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java#L708-L724 |
31,929 | biojava/biojava | biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java | WorkSheet.resizeArray | private static Object resizeArray(Object oldArray, int newSize) {
int oldSize = java.lang.reflect.Array.getLength(oldArray);
Class<?> elementType = oldArray.getClass().getComponentType();
Object newArray = java.lang.reflect.Array.newInstance(
elementType, newSize);
int preserveLength = Math.min(oldSize, newSize);
if (preserveLength > 0) {
System.arraycopy(oldArray, 0, newArray, 0, preserveLength);
}
return newArray;
} | java | private static Object resizeArray(Object oldArray, int newSize) {
int oldSize = java.lang.reflect.Array.getLength(oldArray);
Class<?> elementType = oldArray.getClass().getComponentType();
Object newArray = java.lang.reflect.Array.newInstance(
elementType, newSize);
int preserveLength = Math.min(oldSize, newSize);
if (preserveLength > 0) {
System.arraycopy(oldArray, 0, newArray, 0, preserveLength);
}
return newArray;
} | [
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array to the new array.
@param oldArray the old array, to be reallocated.
@param newSize the new array size.
@return A new array with the same contents. | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java#L734-L744 |
31,930 | biojava/biojava | biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java | WorkSheet.addCell | public void addCell(String row, String col, String value) throws Exception {
HeaderInfo rowIndex = rowLookup.get(row);
HeaderInfo colIndex = columnLookup.get(col);
if (rowIndex == null) {
throw new Exception("Row " + row + " not found in worksheet");
}
if (colIndex == null) {
throw new Exception("Column " + col + " not found in worksheet");
}
data[rowIndex.getIndex()][colIndex.getIndex()] = new CompactCharSequence(value);
} | java | public void addCell(String row, String col, String value) throws Exception {
HeaderInfo rowIndex = rowLookup.get(row);
HeaderInfo colIndex = columnLookup.get(col);
if (rowIndex == null) {
throw new Exception("Row " + row + " not found in worksheet");
}
if (colIndex == null) {
throw new Exception("Column " + col + " not found in worksheet");
}
data[rowIndex.getIndex()][colIndex.getIndex()] = new CompactCharSequence(value);
} | [
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@param row
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@param value
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31,931 | biojava/biojava | biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java | WorkSheet.getCell | public String getCell(String row, String col) throws Exception {
if (col.equals(this.getIndexColumnName())) {
return row;
}
HeaderInfo rowIndex = rowLookup.get(row);
HeaderInfo colIndex = columnLookup.get(col);
if (rowIndex == null) {
//allow for case insentive search
for (String rowtable : rowLookup.keySet()) {
if (row.equalsIgnoreCase(rowtable)) {
rowIndex = rowLookup.get(rowtable);
break;
}
}
if (rowIndex == null) {
throw new Exception("Row " + row + " not found in worksheet");
}
}
if (colIndex == null) {
//allow for case insentive search
for (String coltable : columnLookup.keySet()) {
if (col.equalsIgnoreCase(coltable)) {
colIndex = columnLookup.get(coltable);
break;
}
}
if (colIndex == null) {
throw new Exception("Column " + col + " not found in worksheet");
}
}
CompactCharSequence ccs = data[rowIndex.getIndex()][colIndex.getIndex()];
if (ccs != null) {
return ccs.toString();
} else {
return "";
}
// return .toString();
} | java | public String getCell(String row, String col) throws Exception {
if (col.equals(this.getIndexColumnName())) {
return row;
}
HeaderInfo rowIndex = rowLookup.get(row);
HeaderInfo colIndex = columnLookup.get(col);
if (rowIndex == null) {
//allow for case insentive search
for (String rowtable : rowLookup.keySet()) {
if (row.equalsIgnoreCase(rowtable)) {
rowIndex = rowLookup.get(rowtable);
break;
}
}
if (rowIndex == null) {
throw new Exception("Row " + row + " not found in worksheet");
}
}
if (colIndex == null) {
//allow for case insentive search
for (String coltable : columnLookup.keySet()) {
if (col.equalsIgnoreCase(coltable)) {
colIndex = columnLookup.get(coltable);
break;
}
}
if (colIndex == null) {
throw new Exception("Column " + col + " not found in worksheet");
}
}
CompactCharSequence ccs = data[rowIndex.getIndex()][colIndex.getIndex()];
if (ccs != null) {
return ccs.toString();
} else {
return "";
}
// return .toString();
} | [
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@param row
@param col
@return
@throws Exception | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java#L865-L905 |
31,932 | biojava/biojava | biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java | WorkSheet.changeColumnsHeaders | public void changeColumnsHeaders(LinkedHashMap<String, String> newColumnValues) throws Exception {
for (String oldColumn : newColumnValues.keySet()) {
String newColumn = newColumnValues.get(oldColumn);
changeColumnHeader(oldColumn, newColumn);
}
} | java | public void changeColumnsHeaders(LinkedHashMap<String, String> newColumnValues) throws Exception {
for (String oldColumn : newColumnValues.keySet()) {
String newColumn = newColumnValues.get(oldColumn);
changeColumnHeader(oldColumn, newColumn);
}
} | [
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@param newColumnValues
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31,933 | biojava/biojava | biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java | WorkSheet.getAllColumns | public ArrayList<String> getAllColumns() {
ArrayList<String> columns = new ArrayList<String>();
for (String col : columnLookup.keySet()) {
columns.add(col);
}
return columns;
} | java | public ArrayList<String> getAllColumns() {
ArrayList<String> columns = new ArrayList<String>();
for (String col : columnLookup.keySet()) {
columns.add(col);
}
return columns;
} | [
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@return | [
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31,934 | biojava/biojava | biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java | WorkSheet.getColumns | public ArrayList<String> getColumns() {
ArrayList<String> columns = new ArrayList<String>();
for (String col : columnLookup.keySet()) {
HeaderInfo hi = columnLookup.get(col);
if (!hi.isHide()) {
columns.add(col);
}
}
return columns;
} | java | public ArrayList<String> getColumns() {
ArrayList<String> columns = new ArrayList<String>();
for (String col : columnLookup.keySet()) {
HeaderInfo hi = columnLookup.get(col);
if (!hi.isHide()) {
columns.add(col);
}
}
return columns;
} | [
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31,935 | biojava/biojava | biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java | WorkSheet.getDiscreteColumnValues | public ArrayList<String> getDiscreteColumnValues(String column) throws Exception {
HashMap<String, String> hashMapValues = new HashMap<String, String>();
ArrayList<String> values = new ArrayList<String>();
ArrayList<String> rows = getDataRows();
for (String row : rows) {
String value = getCell(row, column);
if (!hashMapValues.containsKey(value)) {
hashMapValues.put(value, value);
values.add(value);
}
}
return values;
} | java | public ArrayList<String> getDiscreteColumnValues(String column) throws Exception {
HashMap<String, String> hashMapValues = new HashMap<String, String>();
ArrayList<String> values = new ArrayList<String>();
ArrayList<String> rows = getDataRows();
for (String row : rows) {
String value = getCell(row, column);
if (!hashMapValues.containsKey(value)) {
hashMapValues.put(value, value);
values.add(value);
}
}
return values;
} | [
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31,936 | biojava/biojava | biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java | WorkSheet.getDiscreteRowValues | public ArrayList<String> getDiscreteRowValues(String row) throws Exception {
HashMap<String, String> hashMapValues = new HashMap<String, String>();
ArrayList<String> values = new ArrayList<String>();
for (String column : getColumns()) {
String value = getCell(row, column);
if (!hashMapValues.containsKey(value)) {
hashMapValues.put(value, value);
values.add(value);
}
}
return values;
} | java | public ArrayList<String> getDiscreteRowValues(String row) throws Exception {
HashMap<String, String> hashMapValues = new HashMap<String, String>();
ArrayList<String> values = new ArrayList<String>();
for (String column : getColumns()) {
String value = getCell(row, column);
if (!hashMapValues.containsKey(value)) {
hashMapValues.put(value, value);
values.add(value);
}
}
return values;
} | [
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@param row
@return
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31,937 | biojava/biojava | biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java | WorkSheet.getAllRows | public ArrayList<String> getAllRows() {
ArrayList<String> rows = new ArrayList<String>();
for (String row : rowLookup.keySet()) {
rows.add(row);
}
return rows;
} | java | public ArrayList<String> getAllRows() {
ArrayList<String> rows = new ArrayList<String>();
for (String row : rowLookup.keySet()) {
rows.add(row);
}
return rows;
} | [
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... | Get all rows including those that may be hidden
@return | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java#L1123-L1130 |
31,938 | biojava/biojava | biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java | WorkSheet.getRows | public ArrayList<String> getRows() {
ArrayList<String> rows = new ArrayList<String>();
for (String row : rowLookup.keySet()) {
HeaderInfo hi = rowLookup.get(row);
if (!hi.isHide()) {
rows.add(row);
}
}
return rows;
} | java | public ArrayList<String> getRows() {
ArrayList<String> rows = new ArrayList<String>();
for (String row : rowLookup.keySet()) {
HeaderInfo hi = rowLookup.get(row);
if (!hi.isHide()) {
rows.add(row);
}
}
return rows;
} | [
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31,939 | biojava/biojava | biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java | WorkSheet.getDataRows | public ArrayList<String> getDataRows() {
ArrayList<String> rows = new ArrayList<String>();
for (String row : rowLookup.keySet()) {
if (this.isMetaDataRow(row)) {
continue;
}
HeaderInfo hi = rowLookup.get(row);
if (!hi.isHide()) {
rows.add(row);
}
}
return rows;
} | java | public ArrayList<String> getDataRows() {
ArrayList<String> rows = new ArrayList<String>();
for (String row : rowLookup.keySet()) {
if (this.isMetaDataRow(row)) {
continue;
}
HeaderInfo hi = rowLookup.get(row);
if (!hi.isHide()) {
rows.add(row);
}
}
return rows;
} | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java#L1153-L1165 |
31,940 | biojava/biojava | biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java | WorkSheet.getLogScale | public WorkSheet getLogScale(double base, double zeroValue) throws Exception {
WorkSheet workSheet = new WorkSheet(getRows(), getColumns());
workSheet.setIndexColumnName(this.getIndexColumnName());
ArrayList<String> rows = getRows();
ArrayList<String> columns = getColumns();
for (String row : rows) {
for (String col : columns) {
if (this.isMetaDataColumn(col) || this.isMetaDataRow(row)) {
String value = getCell(row, col);
workSheet.addCell(row, col, value);
} else {
String value = getCell(row, col);
try {
Double d = Double.parseDouble(value);
if (d == 0.0) {
d = zeroValue;
} else {
d = Math.log(d) / Math.log(base);
}
workSheet.addCell(row, col, d + "");
} catch (Exception e) {
workSheet.addCell(row, col, value);
}
}
}
}
ArrayList<String> metadataRows = this.getMetaDataRows();
ArrayList<String> metadataColumns = this.getMetaDataColumns();
workSheet.setMetaDataColumns(metadataColumns);
workSheet.setMetaDataRows(metadataRows);
return workSheet;
} | java | public WorkSheet getLogScale(double base, double zeroValue) throws Exception {
WorkSheet workSheet = new WorkSheet(getRows(), getColumns());
workSheet.setIndexColumnName(this.getIndexColumnName());
ArrayList<String> rows = getRows();
ArrayList<String> columns = getColumns();
for (String row : rows) {
for (String col : columns) {
if (this.isMetaDataColumn(col) || this.isMetaDataRow(row)) {
String value = getCell(row, col);
workSheet.addCell(row, col, value);
} else {
String value = getCell(row, col);
try {
Double d = Double.parseDouble(value);
if (d == 0.0) {
d = zeroValue;
} else {
d = Math.log(d) / Math.log(base);
}
workSheet.addCell(row, col, d + "");
} catch (Exception e) {
workSheet.addCell(row, col, value);
}
}
}
}
ArrayList<String> metadataRows = this.getMetaDataRows();
ArrayList<String> metadataColumns = this.getMetaDataColumns();
workSheet.setMetaDataColumns(metadataColumns);
workSheet.setMetaDataRows(metadataRows);
return workSheet;
} | [
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@param base
@return
@throws Exception | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java#L1187-L1221 |
31,941 | biojava/biojava | biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java | WorkSheet.swapRowAndColumns | public WorkSheet swapRowAndColumns() throws Exception {
WorkSheet swappedWorkSheet = new WorkSheet(getColumns(), getRows());
for (String row : getRows()) {
for (String col : getColumns()) {
String value = getCell(row, col);
swappedWorkSheet.addCell(col, row, value);
}
}
ArrayList<String> metadataRows = this.getMetaDataRows();
ArrayList<String> metadataColumns = this.getMetaDataColumns();
swappedWorkSheet.setMetaDataColumns(metadataRows);
swappedWorkSheet.setMetaDataRows(metadataColumns);
return swappedWorkSheet;
} | java | public WorkSheet swapRowAndColumns() throws Exception {
WorkSheet swappedWorkSheet = new WorkSheet(getColumns(), getRows());
for (String row : getRows()) {
for (String col : getColumns()) {
String value = getCell(row, col);
swappedWorkSheet.addCell(col, row, value);
}
}
ArrayList<String> metadataRows = this.getMetaDataRows();
ArrayList<String> metadataColumns = this.getMetaDataColumns();
swappedWorkSheet.setMetaDataColumns(metadataRows);
swappedWorkSheet.setMetaDataRows(metadataColumns);
return swappedWorkSheet;
} | [
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@return
@throws Exception | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java#L1229-L1244 |
31,942 | biojava/biojava | biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java | WorkSheet.getAllValuesCompactCharSequence | static CompactCharSequence[][] getAllValuesCompactCharSequence(InputStream is, char delimiter) throws Exception {
// FileReader reader = new FileReader(fileName);
BufferedReader br = new BufferedReader(new InputStreamReader(is));
ArrayList<CompactCharSequence[]> rows = new ArrayList<CompactCharSequence[]>();
String line = br.readLine();
int numcolumns = -1;
while (line != null) {
String[] d = line.split(String.valueOf(delimiter));
if (numcolumns == -1) {
numcolumns = d.length;
}
CompactCharSequence[] ccs = new CompactCharSequence[d.length];
for (int i = 0; i < d.length; i++) {
ccs[i] = new CompactCharSequence(d[i]);
}
rows.add(ccs);
line = br.readLine();
}
br.close();
// reader.close();
CompactCharSequence[][] data = new CompactCharSequence[rows.size()][numcolumns];
for (int i = 0; i < rows.size(); i++) {
CompactCharSequence[] row = rows.get(i);
for (int j = 0; j < row.length; j++) { //
if (row[j].length() > 1 && row[j].charAt(0) == '"') {
// System.out.println(row[j]);
if (row[j].length() > 2) {
row[j] = new CompactCharSequence(row[j].subSequence(1, row[j].length() - 1).toString());
} else {
row[j] = new CompactCharSequence("");
}
}
if (j < row.length && j < data[0].length) {
data[i][j] = row[j];
}
}
}
return data;
} | java | static CompactCharSequence[][] getAllValuesCompactCharSequence(InputStream is, char delimiter) throws Exception {
// FileReader reader = new FileReader(fileName);
BufferedReader br = new BufferedReader(new InputStreamReader(is));
ArrayList<CompactCharSequence[]> rows = new ArrayList<CompactCharSequence[]>();
String line = br.readLine();
int numcolumns = -1;
while (line != null) {
String[] d = line.split(String.valueOf(delimiter));
if (numcolumns == -1) {
numcolumns = d.length;
}
CompactCharSequence[] ccs = new CompactCharSequence[d.length];
for (int i = 0; i < d.length; i++) {
ccs[i] = new CompactCharSequence(d[i]);
}
rows.add(ccs);
line = br.readLine();
}
br.close();
// reader.close();
CompactCharSequence[][] data = new CompactCharSequence[rows.size()][numcolumns];
for (int i = 0; i < rows.size(); i++) {
CompactCharSequence[] row = rows.get(i);
for (int j = 0; j < row.length; j++) { //
if (row[j].length() > 1 && row[j].charAt(0) == '"') {
// System.out.println(row[j]);
if (row[j].length() > 2) {
row[j] = new CompactCharSequence(row[j].subSequence(1, row[j].length() - 1).toString());
} else {
row[j] = new CompactCharSequence("");
}
}
if (j < row.length && j < data[0].length) {
data[i][j] = row[j];
}
}
}
return data;
} | [
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@param is
@param delimiter
@return
@throws Exception | [
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31,943 | biojava/biojava | biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java | WorkSheet.unionWorkSheetsRowJoin | static public WorkSheet unionWorkSheetsRowJoin(String w1FileName, String w2FileName, char delimitter, boolean secondSheetMetaData) throws Exception {
WorkSheet w1 = WorkSheet.readCSV(w1FileName, delimitter);
WorkSheet w2 = WorkSheet.readCSV(w2FileName, delimitter);
return unionWorkSheetsRowJoin(w1, w2, secondSheetMetaData);
} | java | static public WorkSheet unionWorkSheetsRowJoin(String w1FileName, String w2FileName, char delimitter, boolean secondSheetMetaData) throws Exception {
WorkSheet w1 = WorkSheet.readCSV(w1FileName, delimitter);
WorkSheet w2 = WorkSheet.readCSV(w2FileName, delimitter);
return unionWorkSheetsRowJoin(w1, w2, secondSheetMetaData);
} | [
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in one but not the other are removed. If the second sheet is meta data
then a meta data column will be added between the two joined columns
@param w1FileName
@param w2FileName
@param delimitter
@param secondSheetMetaData
@return
@throws Exception | [
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31,944 | biojava/biojava | biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java | WorkSheet.saveCSV | public void saveCSV(String fileName) throws Exception {
File f = new File(fileName);
File parentFile = f.getParentFile();
if (!parentFile.isDirectory()) {
parentFile.mkdirs();
}
FileOutputStream file = new FileOutputStream(fileName);
BufferedOutputStream bs = new BufferedOutputStream(file);
save(bs, ',', false);
bs.close();
file.close();
} | java | public void saveCSV(String fileName) throws Exception {
File f = new File(fileName);
File parentFile = f.getParentFile();
if (!parentFile.isDirectory()) {
parentFile.mkdirs();
}
FileOutputStream file = new FileOutputStream(fileName);
BufferedOutputStream bs = new BufferedOutputStream(file);
save(bs, ',', false);
bs.close();
file.close();
} | [
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@param fileName
@throws Exception | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java#L1489-L1500 |
31,945 | biojava/biojava | biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java | WorkSheet.appendWorkSheetColumns | public void appendWorkSheetColumns(WorkSheet worksheet) throws Exception {
ArrayList<String> newColumns = worksheet.getColumns();
this.addColumns(newColumns, "");
ArrayList<String> rows = this.getRows();
for (String row : rows) {
for (String col : newColumns) {
if (worksheet.isValidRow(row)) {
String value = worksheet.getCell(row, col);
this.addCell(row, col, value);
}
}
}
} | java | public void appendWorkSheetColumns(WorkSheet worksheet) throws Exception {
ArrayList<String> newColumns = worksheet.getColumns();
this.addColumns(newColumns, "");
ArrayList<String> rows = this.getRows();
for (String row : rows) {
for (String col : newColumns) {
if (worksheet.isValidRow(row)) {
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31,946 | biojava/biojava | biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java | WorkSheet.appendWorkSheetRows | public void appendWorkSheetRows(WorkSheet worksheet) throws Exception {
ArrayList<String> newRows = worksheet.getRows();
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31,947 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfActions.java | MmtfActions.readFromFile | public static Structure readFromFile(Path filePath) throws IOException {
// Get the reader - this is the bit that people need to implement.
MmtfStructureReader mmtfStructureReader = new MmtfStructureReader();
// Do the inflation
new StructureDataToAdapter(new GenericDecoder(ReaderUtils.getDataFromFile(filePath)), mmtfStructureReader);
// Get the structue
return mmtfStructureReader.getStructure();
} | java | public static Structure readFromFile(Path filePath) throws IOException {
// Get the reader - this is the bit that people need to implement.
MmtfStructureReader mmtfStructureReader = new MmtfStructureReader();
// Do the inflation
new StructureDataToAdapter(new GenericDecoder(ReaderUtils.getDataFromFile(filePath)), mmtfStructureReader);
// Get the structue
return mmtfStructureReader.getStructure();
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31,948 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfActions.java | MmtfActions.writeToFile | public static void writeToFile(Structure structure, Path path) throws IOException {
// Set up this writer
AdapterToStructureData writerToEncoder = new AdapterToStructureData();
// Get the writer - this is what people implement
new MmtfStructureWriter(structure, writerToEncoder);
// Now write this data to file
WriterUtils.writeDataToFile(writerToEncoder, path);
} | java | public static void writeToFile(Structure structure, Path path) throws IOException {
// Set up this writer
AdapterToStructureData writerToEncoder = new AdapterToStructureData();
// Get the writer - this is what people implement
new MmtfStructureWriter(structure, writerToEncoder);
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31,949 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfActions.java | MmtfActions.readFromWeb | public static Structure readFromWeb(String pdbId) throws IOException {
// Get the reader - this is the bit that people need to implement.
MmtfStructureReader mmtfStructureReader = new MmtfStructureReader();
// Do the inflation
new StructureDataToAdapter(new GenericDecoder(ReaderUtils.getDataFromUrl(pdbId)), mmtfStructureReader);
// Get the structue
return mmtfStructureReader.getStructure();
} | java | public static Structure readFromWeb(String pdbId) throws IOException {
// Get the reader - this is the bit that people need to implement.
MmtfStructureReader mmtfStructureReader = new MmtfStructureReader();
// Do the inflation
new StructureDataToAdapter(new GenericDecoder(ReaderUtils.getDataFromUrl(pdbId)), mmtfStructureReader);
// Get the structue
return mmtfStructureReader.getStructure();
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31,950 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentEnsembleImpl.java | MultipleAlignmentEnsembleImpl.updateDistanceMatrix | public void updateDistanceMatrix() {
// Reset the distance Matrix variable
distanceMatrix = new ArrayList<Matrix>();
for (int s = 0; s < size(); s++) {
Atom[] ca = atomArrays.get(s);
Matrix distMat = AlignUtils.getDistanceMatrix(ca, ca);
distanceMatrix.add(distMat);
}
} | java | public void updateDistanceMatrix() {
// Reset the distance Matrix variable
distanceMatrix = new ArrayList<Matrix>();
for (int s = 0; s < size(); s++) {
Atom[] ca = atomArrays.get(s);
Matrix distMat = AlignUtils.getDistanceMatrix(ca, ca);
distanceMatrix.add(distMat);
}
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31,951 | biojava/biojava | biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java | ProfeatProperties.getComposition | public static double getComposition(ProteinSequence sequence, ATTRIBUTE attribute, GROUPING group) throws Exception{
return new ProfeatPropertiesImpl().getComposition(sequence, attribute, group);
} | java | public static double getComposition(ProteinSequence sequence, ATTRIBUTE attribute, GROUPING group) throws Exception{
return new ProfeatPropertiesImpl().getComposition(sequence, attribute, group);
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31,952 | biojava/biojava | biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java | ProfeatProperties.getTransition | public static double getTransition(ProteinSequence sequence, ATTRIBUTE attribute, TRANSITION transition) throws Exception{
return new ProfeatPropertiesImpl().getTransition(sequence, attribute, transition);
} | java | public static double getTransition(ProteinSequence sequence, ATTRIBUTE attribute, TRANSITION transition) throws Exception{
return new ProfeatPropertiesImpl().getTransition(sequence, attribute, transition);
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31,953 | biojava/biojava | biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractMatrixAligner.java | AbstractMatrixAligner.getScoreMatrix | @Override
public int[][][] getScoreMatrix() {
boolean tempStoringScoreMatrix = storingScoreMatrix;
if (scores == null) {
storingScoreMatrix = true;
align();
if (scores == null) {
return null;
}
}
int[][][] copy = scores;
if (tempStoringScoreMatrix) {
copy = new int[scores.length][scores[0].length][];
for (int i = 0; i < copy.length; i++) {
for (int j = 0; j < copy[0].length; j++) {
copy[i][j] = Arrays.copyOf(scores[i][j], scores[i][j].length);
}
}
}
setStoringScoreMatrix(tempStoringScoreMatrix);
return copy;
} | java | @Override
public int[][][] getScoreMatrix() {
boolean tempStoringScoreMatrix = storingScoreMatrix;
if (scores == null) {
storingScoreMatrix = true;
align();
if (scores == null) {
return null;
}
}
int[][][] copy = scores;
if (tempStoringScoreMatrix) {
copy = new int[scores.length][scores[0].length][];
for (int i = 0; i < copy.length; i++) {
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copy[i][j] = Arrays.copyOf(scores[i][j], scores[i][j].length);
}
}
}
setStoringScoreMatrix(tempStoringScoreMatrix);
return copy;
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31,954 | biojava/biojava | biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractMatrixAligner.java | AbstractMatrixAligner.getSubstitutionScoreVector | protected int[] getSubstitutionScoreVector(int queryColumn, Subproblem subproblem) {
int[] subs = new int[subproblem.getTargetEndIndex() + 1];
if (queryColumn > 0) {
for (int y = Math.max(1, subproblem.getTargetStartIndex()); y <= subproblem.getTargetEndIndex(); y++) {
subs[y] = getSubstitutionScore(queryColumn, y);
}
}
return subs;
} | java | protected int[] getSubstitutionScoreVector(int queryColumn, Subproblem subproblem) {
int[] subs = new int[subproblem.getTargetEndIndex() + 1];
if (queryColumn > 0) {
for (int y = Math.max(1, subproblem.getTargetStartIndex()); y <= subproblem.getTargetEndIndex(); y++) {
subs[y] = getSubstitutionScore(queryColumn, y);
}
}
return subs;
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31,955 | biojava/biojava | biojava-alignment/src/main/java/org/biojava/nbio/alignment/template/AbstractMatrixAligner.java | AbstractMatrixAligner.reset | protected void reset() {
xyMax = new int[] {0, 0};
xyStart = new int[] {0, 0};
scores = null;
types = (gapPenalty == null || gapPenalty.getType() == GapPenalty.Type.LINEAR) ? new String[] { null } :
new String[] { "Substitution", "Deletion", "Insertion" };
time = -1;
profile = null;
} | java | protected void reset() {
xyMax = new int[] {0, 0};
xyStart = new int[] {0, 0};
scores = null;
types = (gapPenalty == null || gapPenalty.getType() == GapPenalty.Type.LINEAR) ? new String[] { null } :
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profile = null;
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31,956 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/UnitQuaternions.java | UnitQuaternions.angle | public static double angle(Quat4d q) {
AxisAngle4d axis = new AxisAngle4d();
axis.set(q);
return axis.angle;
} | java | public static double angle(Quat4d q) {
AxisAngle4d axis = new AxisAngle4d();
axis.set(q);
return axis.angle;
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31,957 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/UnitQuaternions.java | UnitQuaternions.relativeOrientation | public static Quat4d relativeOrientation(Point3d[] fixed, Point3d[] moved) {
Matrix m = CalcPoint.formMatrix(moved, fixed); // inverse
EigenvalueDecomposition eig = m.eig();
double[][] v = eig.getV().getArray();
Quat4d q = new Quat4d(v[1][3], v[2][3], v[3][3], v[0][3]);
q.normalize();
q.conjugate();
return q;
} | java | public static Quat4d relativeOrientation(Point3d[] fixed, Point3d[] moved) {
Matrix m = CalcPoint.formMatrix(moved, fixed); // inverse
EigenvalueDecomposition eig = m.eig();
double[][] v = eig.getV().getArray();
Quat4d q = new Quat4d(v[1][3], v[2][3], v[3][3], v[0][3]);
q.normalize();
q.conjugate();
return q;
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/UnitQuaternions.java#L199-L207 |
31,958 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/AbstractLocation.java | AbstractLocation.iterator | @Override
public Iterator<Location> iterator() {
List<Location> list;
if(isComplex()) {
list = getSubLocations();
}
else {
list = new ArrayList<Location>();
list.add(this);
}
return list.iterator();
} | java | @Override
public Iterator<Location> iterator() {
List<Location> list;
if(isComplex()) {
list = getSubLocations();
}
else {
list = new ArrayList<Location>();
list.add(this);
}
return list.iterator();
} | [
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31,959 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/AbstractLocation.java | AbstractLocation.getAllSubLocations | private List<Location> getAllSubLocations(Location location) {
List<Location> flatSubLocations = new ArrayList<Location>();
for (Location l : location.getSubLocations()) {
if (l.isComplex()) {
flatSubLocations.addAll(getAllSubLocations(l));
}
else {
flatSubLocations.add(l);
}
}
return flatSubLocations;
} | java | private List<Location> getAllSubLocations(Location location) {
List<Location> flatSubLocations = new ArrayList<Location>();
for (Location l : location.getSubLocations()) {
if (l.isComplex()) {
flatSubLocations.addAll(getAllSubLocations(l));
}
else {
flatSubLocations.add(l);
}
}
return flatSubLocations;
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31,960 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/AbstractLocation.java | AbstractLocation.getSubSequence | @Override
public <C extends Compound> Sequence<C> getSubSequence(Sequence<C> sequence) {
if(isCircular()) {
List<Sequence<C>> sequences = new ArrayList<Sequence<C>>();
for(Location l: this) {
sequences.add(l.getSubSequence(sequence));
}
return new JoiningSequenceReader<C>(sequence.getCompoundSet(), sequences);
}
return reverseSequence(sequence.getSubSequence(
getStart().getPosition(), getEnd().getPosition()));
} | java | @Override
public <C extends Compound> Sequence<C> getSubSequence(Sequence<C> sequence) {
if(isCircular()) {
List<Sequence<C>> sequences = new ArrayList<Sequence<C>>();
for(Location l: this) {
sequences.add(l.getSubSequence(sequence));
}
return new JoiningSequenceReader<C>(sequence.getCompoundSet(), sequences);
}
return reverseSequence(sequence.getSubSequence(
getStart().getPosition(), getEnd().getPosition()));
} | [
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31,961 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/AbstractLocation.java | AbstractLocation.canComplement | protected <C extends Compound> boolean canComplement(Sequence<C> sequence) {
CompoundSet<C> compoundSet = sequence.getCompoundSet();
Compound c = compoundSet.getAllCompounds().iterator().next();
return ComplementCompound.class.isAssignableFrom(c.getClass());
} | java | protected <C extends Compound> boolean canComplement(Sequence<C> sequence) {
CompoundSet<C> compoundSet = sequence.getCompoundSet();
Compound c = compoundSet.getAllCompounds().iterator().next();
return ComplementCompound.class.isAssignableFrom(c.getClass());
} | [
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31,962 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java | AFPChainer.getRmsd | private static double getRmsd(int focusResn, int[] focusRes1, int[] focusRes2, AFPChain afpChain, Atom[] ca1, Atom[] ca2){
Atom[] tmp1 = new Atom[focusResn];
Atom[] tmp2 = new Atom[focusResn];
for ( int i =0 ; i< focusResn;i++){
tmp1[i] = ca1[focusRes1[i]];
tmp2[i] = (Atom)ca2[focusRes2[i]].clone();
if (tmp1[i].getCoords() == null){
System.err.println("tmp1 got null: " +i + " pos: " + focusRes1[i]);
}
if (tmp2[i].getCoords() == null){
System.err.println("tmp1 got null: " +i + " pos: " + focusRes2[i]);
}
//XX
//tmp2[i].setParent((Group) ca2[focusRes2[i]].getParent().clone());
}
double rmsd = 99;
try {
rmsd = getRmsd(tmp1,tmp2);
} catch (Exception e){
e.printStackTrace();
}
return rmsd;
} | java | private static double getRmsd(int focusResn, int[] focusRes1, int[] focusRes2, AFPChain afpChain, Atom[] ca1, Atom[] ca2){
Atom[] tmp1 = new Atom[focusResn];
Atom[] tmp2 = new Atom[focusResn];
for ( int i =0 ; i< focusResn;i++){
tmp1[i] = ca1[focusRes1[i]];
tmp2[i] = (Atom)ca2[focusRes2[i]].clone();
if (tmp1[i].getCoords() == null){
System.err.println("tmp1 got null: " +i + " pos: " + focusRes1[i]);
}
if (tmp2[i].getCoords() == null){
System.err.println("tmp1 got null: " +i + " pos: " + focusRes2[i]);
}
//XX
//tmp2[i].setParent((Group) ca2[focusRes2[i]].getParent().clone());
}
double rmsd = 99;
try {
rmsd = getRmsd(tmp1,tmp2);
} catch (Exception e){
e.printStackTrace();
}
return rmsd;
} | [
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31,963 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPChainer.java | AFPChainer.getRmsd | private static double getRmsd(Atom[] catmp1, Atom[] catmp2) throws StructureException{
Matrix4d trans = SuperPositions.superpose(Calc.atomsToPoints(catmp1),
Calc.atomsToPoints(catmp2));
Calc.transform(catmp2, trans);
// if ( showAlig) {
// StructureAlignmentJmol jmol = new StructureAlignmentJmol();
// jmol.setTitle("AFPCHainer: getRmsd" + rmsd);
//
// Chain c1 = new ChainImpl();
// c1.setName("A");
// for ( Atom a : catmp1){
// c1.addGroup(a.getParent());
// }
//
// Chain c2 = new ChainImpl();
// c2.setName("B");
// for ( Atom a : catmp2){
// c2.addGroup(a.getParent());
// }
//
// Structure fake = new StructureImpl();
// fake.setPDBCode("AFPCHainer: getRmsd" + rmsd);
// List<Chain> model1 = new ArrayList<Chain>();
// model1.add(c1);
// List<Chain> model2 = new ArrayList<Chain>();
// model2.add(c2);
// fake.addModel(model1);
// fake.addModel(model2);
// fake.setNmr(true);
//
// jmol.setStructure(fake);
// jmol.evalString("select *; backbone 0.4; wireframe off; spacefill off; " +
// "select not protein and not solvent; spacefill on;");
// jmol.evalString("select */1 ; color red; model 1; ");
//
// // now show both models again.
// jmol.evalString("model 0;");
// }
return Calc.rmsd(catmp1,catmp2);
} | java | private static double getRmsd(Atom[] catmp1, Atom[] catmp2) throws StructureException{
Matrix4d trans = SuperPositions.superpose(Calc.atomsToPoints(catmp1),
Calc.atomsToPoints(catmp2));
Calc.transform(catmp2, trans);
// if ( showAlig) {
// StructureAlignmentJmol jmol = new StructureAlignmentJmol();
// jmol.setTitle("AFPCHainer: getRmsd" + rmsd);
//
// Chain c1 = new ChainImpl();
// c1.setName("A");
// for ( Atom a : catmp1){
// c1.addGroup(a.getParent());
// }
//
// Chain c2 = new ChainImpl();
// c2.setName("B");
// for ( Atom a : catmp2){
// c2.addGroup(a.getParent());
// }
//
// Structure fake = new StructureImpl();
// fake.setPDBCode("AFPCHainer: getRmsd" + rmsd);
// List<Chain> model1 = new ArrayList<Chain>();
// model1.add(c1);
// List<Chain> model2 = new ArrayList<Chain>();
// model2.add(c2);
// fake.addModel(model1);
// fake.addModel(model2);
// fake.setNmr(true);
//
// jmol.setStructure(fake);
// jmol.evalString("select *; backbone 0.4; wireframe off; spacefill off; " +
// "select not protein and not solvent; spacefill on;");
// jmol.evalString("select */1 ; color red; model 1; ");
//
// // now show both models again.
// jmol.evalString("model 0;");
// }
return Calc.rmsd(catmp1,catmp2);
} | [
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31,964 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/SphereSampler.java | SphereSampler.pind | private static double pind(double ind, double delta, double sigma) {
return (sigma == 0) ? ind * delta : Math.sinh(sigma * ind * delta)
/ sigma;
} | java | private static double pind(double ind, double delta, double sigma) {
return (sigma == 0) ? ind * delta : Math.sinh(sigma * ind * delta)
/ sigma;
} | [
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31,965 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/MultipleSequenceAlignment.java | MultipleSequenceAlignment.addAlignedSequence | public void addAlignedSequence(S sequence){
if(length == null){
length = sequence.getLength();
}
if(sequence.getLength() != length){
throw new IllegalArgumentException(sequence.getAccession() + " length = " + sequence.getLength() +
" not equal to MSA length = " + length);
}
sequences.add(sequence);
} | java | public void addAlignedSequence(S sequence){
if(length == null){
length = sequence.getLength();
}
if(sequence.getLength() != length){
throw new IllegalArgumentException(sequence.getAccession() + " length = " + sequence.getLength() +
" not equal to MSA length = " + length);
}
sequences.add(sequence);
} | [
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31,966 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/MultipleSequenceAlignment.java | MultipleSequenceAlignment.getCompoundsAt | @Override
public List<C> getCompoundsAt(int alignmentIndex) {
List<C> column = new ArrayList<C>();
for (S s : sequences) {
column.add(s.getCompoundAt(alignmentIndex));
}
return Collections.unmodifiableList(column);
} | java | @Override
public List<C> getCompoundsAt(int alignmentIndex) {
List<C> column = new ArrayList<C>();
for (S s : sequences) {
column.add(s.getCompoundAt(alignmentIndex));
}
return Collections.unmodifiableList(column);
} | [
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... | Get a list of compounds at a sequence position
@param alignmentIndex
@return compounds | [
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31,967 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/SubstructureIdentifier.java | SubstructureIdentifier.getIdentifier | @Override
public String getIdentifier() {
if (ranges.isEmpty()) return pdbId;
return pdbId + "." + ResidueRange.toString(ranges);
} | java | @Override
public String getIdentifier() {
if (ranges.isEmpty()) return pdbId;
return pdbId + "." + ResidueRange.toString(ranges);
} | [
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This provides the canonical form for a StructureIdentifier and has
all the information needed to recreate a particular substructure.
Example: 3iek.A_17-28,A_56-294
@return The String form of this identifier | [
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31,968 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/cluster/SubunitExtractor.java | SubunitExtractor.calcAdjustedMinimumSequenceLength | private static int calcAdjustedMinimumSequenceLength(
List<Subunit> subunits, int absMinLen, double fraction, int minLen) {
int maxLength = Integer.MIN_VALUE;
int minLength = Integer.MAX_VALUE;
// Extract the length List, the min and the max
List<Integer> lengths = new ArrayList<Integer>();
for (int i = 0; i < subunits.size(); i++) {
if (subunits.get(i).size() >= absMinLen) {
maxLength = Math.max(subunits.get(i).size(), maxLength);
minLength = Math.min(subunits.get(i).size(), minLength);
lengths.add(subunits.get(i).size());
}
}
int adjustedMinimumSequenceLength = minLen;
if (lengths.size() < 2)
return adjustedMinimumSequenceLength;
// Calculate the median of the lengths
double median = 0;
Collections.sort(lengths);
if (lengths.size() % 2 == 1) {
int middle = (lengths.size() - 1) / 2;
median = lengths.get(middle);
} else {
int middle2 = lengths.size() / 2;
int middle1 = middle2 - 1;
median = 0.5 * (lengths.get(middle1) + lengths.get(middle2));
}
// If the median * fraction is lower than the minLength
if (minLength >= median * fraction) {
adjustedMinimumSequenceLength = Math.min(minLength, minLen);
}
return adjustedMinimumSequenceLength;
} | java | private static int calcAdjustedMinimumSequenceLength(
List<Subunit> subunits, int absMinLen, double fraction, int minLen) {
int maxLength = Integer.MIN_VALUE;
int minLength = Integer.MAX_VALUE;
// Extract the length List, the min and the max
List<Integer> lengths = new ArrayList<Integer>();
for (int i = 0; i < subunits.size(); i++) {
if (subunits.get(i).size() >= absMinLen) {
maxLength = Math.max(subunits.get(i).size(), maxLength);
minLength = Math.min(subunits.get(i).size(), minLength);
lengths.add(subunits.get(i).size());
}
}
int adjustedMinimumSequenceLength = minLen;
if (lengths.size() < 2)
return adjustedMinimumSequenceLength;
// Calculate the median of the lengths
double median = 0;
Collections.sort(lengths);
if (lengths.size() % 2 == 1) {
int middle = (lengths.size() - 1) / 2;
median = lengths.get(middle);
} else {
int middle2 = lengths.size() / 2;
int middle1 = middle2 - 1;
median = 0.5 * (lengths.get(middle1) + lengths.get(middle2));
}
// If the median * fraction is lower than the minLength
if (minLength >= median * fraction) {
adjustedMinimumSequenceLength = Math.min(minLength, minLen);
}
return adjustedMinimumSequenceLength;
} | [
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31,969 | biojava/biojava | biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convertor.java | Convertor.convert | public String convert(ProteinSequence sequence){
String convertedSequence = "";
String uppercaseSequence = sequence.getSequenceAsString().toUpperCase();
for(int x = 0; x < uppercaseSequence.length(); x++){
convertedSequence += String.valueOf(convert(uppercaseSequence.charAt(x)));
}
return convertedSequence;
} | java | public String convert(ProteinSequence sequence){
String convertedSequence = "";
String uppercaseSequence = sequence.getSequenceAsString().toUpperCase();
for(int x = 0; x < uppercaseSequence.length(); x++){
convertedSequence += String.valueOf(convert(uppercaseSequence.charAt(x)));
}
return convertedSequence;
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The sequence argument must be a protein sequence consisting of preferably non-ambiguous characters only.
Standard amino acids will be converted to '1', '2' or '3' depending on its grouping
Non-standard amino acids are simply converted to '0'.
@param sequence
a protein sequence consisting of preferably non-ambiguous characters only
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31,970 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/SeqRes2AtomAligner.java | SeqRes2AtomAligner.mapSeqresRecords | public void mapSeqresRecords(Chain atomRes, Chain seqRes) {
List<Group> seqResGroups = seqRes.getAtomGroups();
List<Group> atmResGroups = atomRes.getAtomGroups();
logger.debug("Comparing ATOM {} ({} groups) to SEQRES {} ({} groups) ",
atomRes.getId(), atmResGroups.size(), seqRes.getId(), seqResGroups.size());
List<Group> matchedGroups = trySimpleMatch(seqResGroups, atmResGroups);
if ( matchedGroups != null) {
// update the new SEQRES list
atomRes.setSeqResGroups(matchedGroups);
return;
}
logger.debug("Could not map SEQRES to ATOM records easily, need to align...");
int numAminosSeqres = seqRes.getAtomGroups(GroupType.AMINOACID).size();
int numNucleotidesSeqres = seqRes.getAtomGroups(GroupType.NUCLEOTIDE).size();
if ( numAminosSeqres < 1) {
if ( numNucleotidesSeqres > 1) {
logger.debug("SEQRES chain {} is a nucleotide chain ({} nucleotides), aligning nucleotides...", seqRes.getId(), numNucleotidesSeqres);
alignNucleotideChains(seqRes,atomRes);
return;
} else {
logger.debug("SEQRES chain {} contains {} amino acids and {} nucleotides, ignoring...", seqRes.getId(),numAminosSeqres,numNucleotidesSeqres);
return;
}
}
if ( atomRes.getAtomGroups(GroupType.AMINOACID).size() < 1) {
logger.debug("ATOM chain {} does not contain amino acids, ignoring...", atomRes.getId());
return;
}
logger.debug("Proceeding to do protein alignment for chain {}", atomRes.getId() );
boolean noMatchFound = alignProteinChains(seqResGroups,atomRes.getAtomGroups());
if ( ! noMatchFound){
atomRes.setSeqResGroups(seqResGroups);
}
} | java | public void mapSeqresRecords(Chain atomRes, Chain seqRes) {
List<Group> seqResGroups = seqRes.getAtomGroups();
List<Group> atmResGroups = atomRes.getAtomGroups();
logger.debug("Comparing ATOM {} ({} groups) to SEQRES {} ({} groups) ",
atomRes.getId(), atmResGroups.size(), seqRes.getId(), seqResGroups.size());
List<Group> matchedGroups = trySimpleMatch(seqResGroups, atmResGroups);
if ( matchedGroups != null) {
// update the new SEQRES list
atomRes.setSeqResGroups(matchedGroups);
return;
}
logger.debug("Could not map SEQRES to ATOM records easily, need to align...");
int numAminosSeqres = seqRes.getAtomGroups(GroupType.AMINOACID).size();
int numNucleotidesSeqres = seqRes.getAtomGroups(GroupType.NUCLEOTIDE).size();
if ( numAminosSeqres < 1) {
if ( numNucleotidesSeqres > 1) {
logger.debug("SEQRES chain {} is a nucleotide chain ({} nucleotides), aligning nucleotides...", seqRes.getId(), numNucleotidesSeqres);
alignNucleotideChains(seqRes,atomRes);
return;
} else {
logger.debug("SEQRES chain {} contains {} amino acids and {} nucleotides, ignoring...", seqRes.getId(),numAminosSeqres,numNucleotidesSeqres);
return;
}
}
if ( atomRes.getAtomGroups(GroupType.AMINOACID).size() < 1) {
logger.debug("ATOM chain {} does not contain amino acids, ignoring...", atomRes.getId());
return;
}
logger.debug("Proceeding to do protein alignment for chain {}", atomRes.getId() );
boolean noMatchFound = alignProteinChains(seqResGroups,atomRes.getAtomGroups());
if ( ! noMatchFound){
atomRes.setSeqResGroups(seqResGroups);
}
} | [
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Updates the atomRes chain object with the mapped data
The seqRes chain should not be needed after this and atomRes should be further used.
@param atomRes the chain containing ATOM groups (in atomGroups slot). This chain
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@param seqRes the chain containing SEQRES groups (in atomGroups slot). This chain
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31,971 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/SeqRes2AtomAligner.java | SeqRes2AtomAligner.getFullAtomSequence | public static String getFullAtomSequence(List<Group> groups, Map<Integer, Integer> positionIndex, boolean isNucleotideChain){
StringBuffer sequence = new StringBuffer() ;
int seqIndex = 0; // track sequence.length()
for ( int i=0 ; i< groups.size(); i++){
Group g = groups.get(i);
if ( g instanceof AminoAcid ){
AminoAcid a = (AminoAcid)g;
char oneLetter =a.getAminoType();
if ( oneLetter == '?')
oneLetter = 'X';
positionIndex.put(seqIndex,i);
sequence.append(oneLetter );
seqIndex++;
} else {
// exclude solvents
if ( g.isWater())
continue;
// exclude metals
if ( g.size() == 1 ) {
Atom a = g.getAtom(0);
if ( a == null)
continue;
if (a.getElement().isMetal())
continue;
}
ChemComp cc = g.getChemComp();
if ( cc == null) {
logger.debug("No chem comp available for group {}",g.toString());
// not sure what to do in that case!
continue;
}
if (
ResidueType.lPeptideLinking.equals(cc.getResidueType()) ||
PolymerType.PROTEIN_ONLY.contains(cc.getPolymerType()) ||
PolymerType.POLYNUCLEOTIDE_ONLY.contains(cc.getPolymerType())
) {
//System.out.println(cc.getOne_letter_code());
String c = cc.getOne_letter_code();
if ( c.equals("?")) {
if (isNucleotideChain && PolymerType.POLYNUCLEOTIDE_ONLY.contains(cc.getPolymerType())) {
// the way to represent unknown nucleotides is with 'N', see https://en.wikipedia.org/wiki/Nucleic_acid_notation
c = "N";
} else {
c = "X";
}
}
// For some unusual cases the het residue can map to 2 or more standard aas and thus give an
// insertion of length >1.
// e.g. 1: SUI maps to DG (in 1oew,A)
// e.g. 2: NRQ maps to MYG (in 3cfh,A)
if (c.length()>1) {
logger.info("Group '{}' maps to more than 1 standard aminoacid: {}.",
g.toString(), c);
}
// because of the mapping to more than 1 aminoacid, we have
// to loop through it (99% of cases c will have length 1 anyway)
for (int cIdx=0;cIdx<c.length();cIdx++) {
positionIndex.put(seqIndex,i);
sequence.append(c.charAt(cIdx));
seqIndex++;
}
} else {
logger.debug("Group {} is not lPeptideLinked, nor PROTEIN_ONLY, nor POLYNUCLEOTIDE_ONLY",g.toString());
continue;
}
//sequence.append("X");
}
}
return sequence.toString();
} | java | public static String getFullAtomSequence(List<Group> groups, Map<Integer, Integer> positionIndex, boolean isNucleotideChain){
StringBuffer sequence = new StringBuffer() ;
int seqIndex = 0; // track sequence.length()
for ( int i=0 ; i< groups.size(); i++){
Group g = groups.get(i);
if ( g instanceof AminoAcid ){
AminoAcid a = (AminoAcid)g;
char oneLetter =a.getAminoType();
if ( oneLetter == '?')
oneLetter = 'X';
positionIndex.put(seqIndex,i);
sequence.append(oneLetter );
seqIndex++;
} else {
// exclude solvents
if ( g.isWater())
continue;
// exclude metals
if ( g.size() == 1 ) {
Atom a = g.getAtom(0);
if ( a == null)
continue;
if (a.getElement().isMetal())
continue;
}
ChemComp cc = g.getChemComp();
if ( cc == null) {
logger.debug("No chem comp available for group {}",g.toString());
// not sure what to do in that case!
continue;
}
if (
ResidueType.lPeptideLinking.equals(cc.getResidueType()) ||
PolymerType.PROTEIN_ONLY.contains(cc.getPolymerType()) ||
PolymerType.POLYNUCLEOTIDE_ONLY.contains(cc.getPolymerType())
) {
//System.out.println(cc.getOne_letter_code());
String c = cc.getOne_letter_code();
if ( c.equals("?")) {
if (isNucleotideChain && PolymerType.POLYNUCLEOTIDE_ONLY.contains(cc.getPolymerType())) {
// the way to represent unknown nucleotides is with 'N', see https://en.wikipedia.org/wiki/Nucleic_acid_notation
c = "N";
} else {
c = "X";
}
}
// For some unusual cases the het residue can map to 2 or more standard aas and thus give an
// insertion of length >1.
// e.g. 1: SUI maps to DG (in 1oew,A)
// e.g. 2: NRQ maps to MYG (in 3cfh,A)
if (c.length()>1) {
logger.info("Group '{}' maps to more than 1 standard aminoacid: {}.",
g.toString(), c);
}
// because of the mapping to more than 1 aminoacid, we have
// to loop through it (99% of cases c will have length 1 anyway)
for (int cIdx=0;cIdx<c.length();cIdx++) {
positionIndex.put(seqIndex,i);
sequence.append(c.charAt(cIdx));
seqIndex++;
}
} else {
logger.debug("Group {} is not lPeptideLinked, nor PROTEIN_ONLY, nor POLYNUCLEOTIDE_ONLY",g.toString());
continue;
}
//sequence.append("X");
}
}
return sequence.toString();
} | [
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with X instead of HETATMSs. The advantage of this is
that it allows us to also align HETATM groups back to the SEQRES.
@param groups the list of groups in a parent
@param positionIndex a Map to keep track of which group is at which sequence position
@param isNucleotideChain whether the atom groups are predominantly nucleotides (the groups represent a nucleotide chain), if true
non-standard nucleotides will be represented with ambiguous letter 'N' instead of 'X', if false all non-standard residues will be 'X'
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31,972 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/SeqRes2AtomAligner.java | SeqRes2AtomAligner.storeUnAlignedSeqRes | public static void storeUnAlignedSeqRes(Structure structure, List<Chain> seqResChains, boolean headerOnly) {
if (headerOnly) {
List<Chain> atomChains = new ArrayList<>();
for (Chain seqRes: seqResChains) {
// In header-only mode skip ATOM records.
// Here we store chains with SEQRES instead of AtomGroups.
seqRes.setSeqResGroups(seqRes.getAtomGroups());
seqRes.setAtomGroups(new ArrayList<>()); // clear out the atom groups.
atomChains.add(seqRes);
}
structure.setChains(0, atomChains);
} else {
for (int i = 0; i < structure.nrModels(); i++) {
List<Chain> atomChains = structure.getModel(i);
for (Chain seqRes: seqResChains){
Chain atomRes;
// Otherwise, we find a chain with AtomGroups
// and set this as SEQRES groups.
// TODO no idea if new parameter useChainId should be false or true here, used true as a guess - JD 2016-05-09
atomRes = SeqRes2AtomAligner.getMatchingAtomRes(seqRes,atomChains,true);
if ( atomRes != null)
atomRes.setSeqResGroups(seqRes.getAtomGroups());
else
logger.warn("Could not find atom records for chain " + seqRes.getId());
}
}
}
} | java | public static void storeUnAlignedSeqRes(Structure structure, List<Chain> seqResChains, boolean headerOnly) {
if (headerOnly) {
List<Chain> atomChains = new ArrayList<>();
for (Chain seqRes: seqResChains) {
// In header-only mode skip ATOM records.
// Here we store chains with SEQRES instead of AtomGroups.
seqRes.setSeqResGroups(seqRes.getAtomGroups());
seqRes.setAtomGroups(new ArrayList<>()); // clear out the atom groups.
atomChains.add(seqRes);
}
structure.setChains(0, atomChains);
} else {
for (int i = 0; i < structure.nrModels(); i++) {
List<Chain> atomChains = structure.getModel(i);
for (Chain seqRes: seqResChains){
Chain atomRes;
// Otherwise, we find a chain with AtomGroups
// and set this as SEQRES groups.
// TODO no idea if new parameter useChainId should be false or true here, used true as a guess - JD 2016-05-09
atomRes = SeqRes2AtomAligner.getMatchingAtomRes(seqRes,atomChains,true);
if ( atomRes != null)
atomRes.setSeqResGroups(seqRes.getAtomGroups());
else
logger.warn("Could not find atom records for chain " + seqRes.getId());
}
}
}
} | [
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@param structure
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/io/SeqRes2AtomAligner.java#L820-L858 |
31,973 | biojava/biojava | biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/AbstractAlignmentJmol.java | AbstractAlignmentJmol.setAtoms | public void setAtoms(Atom[] atoms){
Structure s = new StructureImpl();
Chain c = new ChainImpl();
c.setId("A");
for (Atom a: atoms){
c.addGroup(a.getGroup());
}
s.addChain(c);
setStructure(s);
} | java | public void setAtoms(Atom[] atoms){
Structure s = new StructureImpl();
Chain c = new ChainImpl();
c.setId("A");
for (Atom a: atoms){
c.addGroup(a.getGroup());
}
s.addChain(c);
setStructure(s);
} | [
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31,974 | biojava/biojava | biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/AbstractAlignmentJmol.java | AbstractAlignmentJmol.evalString | public void evalString(String rasmolScript){
if ( jmolPanel == null ){
logger.error("please install Jmol first");
return;
}
jmolPanel.evalString(rasmolScript);
} | java | public void evalString(String rasmolScript){
if ( jmolPanel == null ){
logger.error("please install Jmol first");
return;
}
jmolPanel.evalString(rasmolScript);
} | [
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31,975 | biojava/biojava | biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/AbstractAlignmentJmol.java | AbstractAlignmentJmol.setStructure | public void setStructure(Structure s) {
if (jmolPanel == null){
logger.error("please install Jmol first");
return;
}
setTitle(s.getPDBCode());
jmolPanel.setStructure(s);
// actually this is very simple
// just convert the structure to a PDB file
//String pdb = s.toPDB();
//System.out.println(s.isNmr());
//System.out.println(pdb);
// Jmol could also read the file directly from your file system
//viewer.openFile("/Path/To/PDB/1tim.pdb");
//System.out.println(pdb);
//jmolPanel.openStringInline(pdb);
// send the PDB file to Jmol.
// there are also other ways to interact with Jmol,
// e.g make it directly
// access the biojava structure object, but they require more
// code. See the SPICE code repository for how to do this.
structure = s;
} | java | public void setStructure(Structure s) {
if (jmolPanel == null){
logger.error("please install Jmol first");
return;
}
setTitle(s.getPDBCode());
jmolPanel.setStructure(s);
// actually this is very simple
// just convert the structure to a PDB file
//String pdb = s.toPDB();
//System.out.println(s.isNmr());
//System.out.println(pdb);
// Jmol could also read the file directly from your file system
//viewer.openFile("/Path/To/PDB/1tim.pdb");
//System.out.println(pdb);
//jmolPanel.openStringInline(pdb);
// send the PDB file to Jmol.
// there are also other ways to interact with Jmol,
// e.g make it directly
// access the biojava structure object, but they require more
// code. See the SPICE code repository for how to do this.
structure = s;
} | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/AbstractAlignmentJmol.java#L152-L181 |
31,976 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterfaceCluster.java | StructureInterfaceCluster.getTotalArea | public double getTotalArea() {
double area = 0;
for (StructureInterface interf:members) {
area+=interf.getTotalArea();
}
return area/members.size();
} | java | public double getTotalArea() {
double area = 0;
for (StructureInterface interf:members) {
area+=interf.getTotalArea();
}
return area/members.size();
} | [
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31,977 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java | MmtfUtils.calculateDsspSecondaryStructure | public static void calculateDsspSecondaryStructure(Structure bioJavaStruct) {
SecStrucCalc ssp = new SecStrucCalc();
try{
ssp.calculate(bioJavaStruct, true);
}
catch(StructureException e) {
LOGGER.warn("Could not calculate secondary structure (error {}). Will try to get a DSSP file from the RCSB web server instead.", e.getMessage());
try {
DSSPParser.fetch(bioJavaStruct.getPDBCode(), bioJavaStruct, true); //download from PDB the DSSP result
} catch(Exception bige){
LOGGER.warn("Could not get a DSSP file from RCSB web server. There will not be secondary structure assignment for this structure ({}). Error: {}", bioJavaStruct.getPDBCode(), bige.getMessage());
}
}
} | java | public static void calculateDsspSecondaryStructure(Structure bioJavaStruct) {
SecStrucCalc ssp = new SecStrucCalc();
try{
ssp.calculate(bioJavaStruct, true);
}
catch(StructureException e) {
LOGGER.warn("Could not calculate secondary structure (error {}). Will try to get a DSSP file from the RCSB web server instead.", e.getMessage());
try {
DSSPParser.fetch(bioJavaStruct.getPDBCode(), bioJavaStruct, true); //download from PDB the DSSP result
} catch(Exception bige){
LOGGER.warn("Could not get a DSSP file from RCSB web server. There will not be secondary structure assignment for this structure ({}). Error: {}", bioJavaStruct.getPDBCode(), bige.getMessage());
}
}
} | [
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31,978 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java | MmtfUtils.getUnitCellAsArray | public static float[] getUnitCellAsArray(PDBCrystallographicInfo xtalInfo) {
CrystalCell xtalCell = xtalInfo.getCrystalCell();
if(xtalCell==null){
return null;
}else{
float[] inputUnitCell = new float[6];
inputUnitCell[0] = (float) xtalCell.getA();
inputUnitCell[1] = (float) xtalCell.getB();
inputUnitCell[2] = (float) xtalCell.getC();
inputUnitCell[3] = (float) xtalCell.getAlpha();
inputUnitCell[4] = (float) xtalCell.getBeta();
inputUnitCell[5] = (float) xtalCell.getGamma();
return inputUnitCell;
}
} | java | public static float[] getUnitCellAsArray(PDBCrystallographicInfo xtalInfo) {
CrystalCell xtalCell = xtalInfo.getCrystalCell();
if(xtalCell==null){
return null;
}else{
float[] inputUnitCell = new float[6];
inputUnitCell[0] = (float) xtalCell.getA();
inputUnitCell[1] = (float) xtalCell.getB();
inputUnitCell[2] = (float) xtalCell.getC();
inputUnitCell[3] = (float) xtalCell.getAlpha();
inputUnitCell[4] = (float) xtalCell.getBeta();
inputUnitCell[5] = (float) xtalCell.getGamma();
return inputUnitCell;
}
} | [
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31,979 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java | MmtfUtils.techniquesToStringArray | public static String[] techniquesToStringArray(Set<ExperimentalTechnique> experimentalTechniques) {
if(experimentalTechniques==null){
return new String[0];
}
String[] outArray = new String[experimentalTechniques.size()];
int index = 0;
for (ExperimentalTechnique experimentalTechnique : experimentalTechniques) {
outArray[index] = experimentalTechnique.getName();
index++;
}
return outArray;
} | java | public static String[] techniquesToStringArray(Set<ExperimentalTechnique> experimentalTechniques) {
if(experimentalTechniques==null){
return new String[0];
}
String[] outArray = new String[experimentalTechniques.size()];
int index = 0;
for (ExperimentalTechnique experimentalTechnique : experimentalTechniques) {
outArray[index] = experimentalTechnique.getName();
index++;
}
return outArray;
} | [
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@param experimentalTechniques the input set of experimental techniques
@return the array of strings describing the methods used. | [
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31,980 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java | MmtfUtils.dateToIsoString | public static String dateToIsoString(Date inputDate) {
DateFormat dateStringFormat = new SimpleDateFormat("yyyy-MM-dd");
return dateStringFormat.format(inputDate);
} | java | public static String dateToIsoString(Date inputDate) {
DateFormat dateStringFormat = new SimpleDateFormat("yyyy-MM-dd");
return dateStringFormat.format(inputDate);
} | [
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@param inputDate The input date object
@return the time in ISO time format | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java#L234-L237 |
31,981 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java | MmtfUtils.getTransformMap | public static Map<double[], int[]> getTransformMap(BioAssemblyInfo bioassemblyInfo, Map<String, Integer> chainIdToIndexMap) {
Map<Matrix4d, List<Integer>> matMap = new LinkedHashMap<>();
List<BiologicalAssemblyTransformation> transforms = bioassemblyInfo.getTransforms();
for (BiologicalAssemblyTransformation transformation : transforms) {
Matrix4d transMatrix = transformation.getTransformationMatrix();
String transChainId = transformation.getChainId();
if (!chainIdToIndexMap.containsKey(transChainId)){
continue;
}
int chainIndex = chainIdToIndexMap.get(transformation.getChainId());
if(matMap.containsKey(transMatrix)){
matMap.get(transMatrix).add(chainIndex);
}
else{
List<Integer> chainIdList = new ArrayList<>();
chainIdList.add(chainIndex);
matMap.put(transMatrix, chainIdList);
}
}
Map<double[], int[]> outMap = new LinkedHashMap<>();
for (Entry<Matrix4d, List<Integer>> entry : matMap.entrySet()) {
outMap.put(convertToDoubleArray(entry.getKey()), CodecUtils.convertToIntArray(entry.getValue()));
}
return outMap;
} | java | public static Map<double[], int[]> getTransformMap(BioAssemblyInfo bioassemblyInfo, Map<String, Integer> chainIdToIndexMap) {
Map<Matrix4d, List<Integer>> matMap = new LinkedHashMap<>();
List<BiologicalAssemblyTransformation> transforms = bioassemblyInfo.getTransforms();
for (BiologicalAssemblyTransformation transformation : transforms) {
Matrix4d transMatrix = transformation.getTransformationMatrix();
String transChainId = transformation.getChainId();
if (!chainIdToIndexMap.containsKey(transChainId)){
continue;
}
int chainIndex = chainIdToIndexMap.get(transformation.getChainId());
if(matMap.containsKey(transMatrix)){
matMap.get(transMatrix).add(chainIndex);
}
else{
List<Integer> chainIdList = new ArrayList<>();
chainIdList.add(chainIndex);
matMap.put(transMatrix, chainIdList);
}
}
Map<double[], int[]> outMap = new LinkedHashMap<>();
for (Entry<Matrix4d, List<Integer>> entry : matMap.entrySet()) {
outMap.put(convertToDoubleArray(entry.getKey()), CodecUtils.convertToIntArray(entry.getValue()));
}
return outMap;
} | [
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@param chainIdToIndexMap the map of chain ids to the index that chain corresponds to.
@return the bioassembly information (as primitive types). | [
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31,982 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java | MmtfUtils.convertToDoubleArray | public static double[] convertToDoubleArray(Matrix4d transformationMatrix) {
// Initialise the output array
double[] outArray = new double[16];
// Iterate over the matrix
for(int i=0; i<4; i++){
for(int j=0; j<4; j++){
// Now set this element
outArray[i*4+j] = transformationMatrix.getElement(i,j);
}
}
return outArray;
} | java | public static double[] convertToDoubleArray(Matrix4d transformationMatrix) {
// Initialise the output array
double[] outArray = new double[16];
// Iterate over the matrix
for(int i=0; i<4; i++){
for(int j=0; j<4; j++){
// Now set this element
outArray[i*4+j] = transformationMatrix.getElement(i,j);
}
}
return outArray;
} | [
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31,983 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java | MmtfUtils.getNumGroups | public static int getNumGroups(Structure structure) {
int count = 0;
for(int i=0; i<structure.nrModels(); i++) {
for(Chain chain : structure.getChains(i)){
count+= chain.getAtomGroups().size();
}
}
return count;
} | java | public static int getNumGroups(Structure structure) {
int count = 0;
for(int i=0; i<structure.nrModels(); i++) {
for(Chain chain : structure.getChains(i)){
count+= chain.getAtomGroups().size();
}
}
return count;
} | [
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31,984 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java | MmtfUtils.getAtomsForGroup | public static List<Atom> getAtomsForGroup(Group inputGroup) {
Set<Atom> uniqueAtoms = new HashSet<Atom>();
List<Atom> theseAtoms = new ArrayList<Atom>();
for(Atom a: inputGroup.getAtoms()){
theseAtoms.add(a);
uniqueAtoms.add(a);
}
List<Group> altLocs = inputGroup.getAltLocs();
for(Group thisG: altLocs){
for(Atom a: thisG.getAtoms()){
if(uniqueAtoms.contains(a)){
continue;
}
theseAtoms.add(a);
}
}
return theseAtoms;
} | java | public static List<Atom> getAtomsForGroup(Group inputGroup) {
Set<Atom> uniqueAtoms = new HashSet<Atom>();
List<Atom> theseAtoms = new ArrayList<Atom>();
for(Atom a: inputGroup.getAtoms()){
theseAtoms.add(a);
uniqueAtoms.add(a);
}
List<Group> altLocs = inputGroup.getAltLocs();
for(Group thisG: altLocs){
for(Atom a: thisG.getAtoms()){
if(uniqueAtoms.contains(a)){
continue;
}
theseAtoms.add(a);
}
}
return theseAtoms;
} | [
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31,985 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java | MmtfUtils.getNumBondsInGroup | public static int getNumBondsInGroup(List<Atom> atomsInGroup) {
int bondCounter = 0;
for(Atom atom : atomsInGroup) {
if(atom.getBonds()==null){
continue;
}
for(Bond bond : atom.getBonds()) {
// Now set the bonding information.
Atom other = bond.getOther(atom);
// If both atoms are in the group
if (atomsInGroup.indexOf(other)!=-1){
Integer firstBondIndex = atomsInGroup.indexOf(atom);
Integer secondBondIndex = atomsInGroup.indexOf(other);
// Don't add the same bond twice
if (firstBondIndex<secondBondIndex){
bondCounter++;
}
}
}
}
return bondCounter;
} | java | public static int getNumBondsInGroup(List<Atom> atomsInGroup) {
int bondCounter = 0;
for(Atom atom : atomsInGroup) {
if(atom.getBonds()==null){
continue;
}
for(Bond bond : atom.getBonds()) {
// Now set the bonding information.
Atom other = bond.getOther(atom);
// If both atoms are in the group
if (atomsInGroup.indexOf(other)!=-1){
Integer firstBondIndex = atomsInGroup.indexOf(atom);
Integer secondBondIndex = atomsInGroup.indexOf(other);
// Don't add the same bond twice
if (firstBondIndex<secondBondIndex){
bondCounter++;
}
}
}
}
return bondCounter;
} | [
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31,986 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java | MmtfUtils.getSecStructTypeFromDsspIndex | public static SecStrucType getSecStructTypeFromDsspIndex(int dsspIndex) {
String dsspType = DsspType.dsspTypeFromInt(dsspIndex).getDsspType();
for(SecStrucType secStrucType : SecStrucType.values())
{
if(dsspType==secStrucType.name)
{
return secStrucType;
}
}
// Return a null entry.
return null;
} | java | public static SecStrucType getSecStructTypeFromDsspIndex(int dsspIndex) {
String dsspType = DsspType.dsspTypeFromInt(dsspIndex).getDsspType();
for(SecStrucType secStrucType : SecStrucType.values())
{
if(dsspType==secStrucType.name)
{
return secStrucType;
}
}
// Return a null entry.
return null;
} | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java#L393-L404 |
31,987 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java | MmtfUtils.getStructureInfo | public static MmtfSummaryDataBean getStructureInfo(Structure structure) {
MmtfSummaryDataBean mmtfSummaryDataBean = new MmtfSummaryDataBean();
// Get all the atoms
List<Atom> theseAtoms = new ArrayList<>();
List<Chain> allChains = new ArrayList<>();
Map<String, Integer> chainIdToIndexMap = new LinkedHashMap<>();
int chainCounter = 0;
int bondCount = 0;
mmtfSummaryDataBean.setAllAtoms(theseAtoms);
mmtfSummaryDataBean.setAllChains(allChains);
mmtfSummaryDataBean.setChainIdToIndexMap(chainIdToIndexMap);
for (int i=0; i<structure.nrModels(); i++){
List<Chain> chains = structure.getModel(i);
allChains.addAll(chains);
for (Chain chain : chains) {
String idOne = chain.getId();
if (!chainIdToIndexMap.containsKey(idOne)) {
chainIdToIndexMap.put(idOne, chainCounter);
}
chainCounter++;
for (Group g : chain.getAtomGroups()) {
for(Atom atom: getAtomsForGroup(g)){
theseAtoms.add(atom);
// If both atoms are in the group
if (atom.getBonds()!=null){
bondCount+=atom.getBonds().size();
}
}
}
}
}
// Assumes all bonds are referenced twice
mmtfSummaryDataBean.setNumBonds(bondCount/2);
return mmtfSummaryDataBean;
} | java | public static MmtfSummaryDataBean getStructureInfo(Structure structure) {
MmtfSummaryDataBean mmtfSummaryDataBean = new MmtfSummaryDataBean();
// Get all the atoms
List<Atom> theseAtoms = new ArrayList<>();
List<Chain> allChains = new ArrayList<>();
Map<String, Integer> chainIdToIndexMap = new LinkedHashMap<>();
int chainCounter = 0;
int bondCount = 0;
mmtfSummaryDataBean.setAllAtoms(theseAtoms);
mmtfSummaryDataBean.setAllChains(allChains);
mmtfSummaryDataBean.setChainIdToIndexMap(chainIdToIndexMap);
for (int i=0; i<structure.nrModels(); i++){
List<Chain> chains = structure.getModel(i);
allChains.addAll(chains);
for (Chain chain : chains) {
String idOne = chain.getId();
if (!chainIdToIndexMap.containsKey(idOne)) {
chainIdToIndexMap.put(idOne, chainCounter);
}
chainCounter++;
for (Group g : chain.getAtomGroups()) {
for(Atom atom: getAtomsForGroup(g)){
theseAtoms.add(atom);
// If both atoms are in the group
if (atom.getBonds()!=null){
bondCount+=atom.getBonds().size();
}
}
}
}
}
// Assumes all bonds are referenced twice
mmtfSummaryDataBean.setNumBonds(bondCount/2);
return mmtfSummaryDataBean;
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31,988 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java | MmtfUtils.insertSeqResGroup | public static void insertSeqResGroup(Chain chain, Group group, int sequenceIndexId) {
List<Group> seqResGroups = chain.getSeqResGroups();
addGroupAtId(seqResGroups, group, sequenceIndexId);
} | java | public static void insertSeqResGroup(Chain chain, Group group, int sequenceIndexId) {
List<Group> seqResGroups = chain.getSeqResGroups();
addGroupAtId(seqResGroups, group, sequenceIndexId);
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31,989 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java | MmtfUtils.addSeqRes | public static void addSeqRes(Chain modelChain, String sequence) {
List<Group> seqResGroups = modelChain.getSeqResGroups();
GroupType chainType = getChainType(modelChain.getAtomGroups());
for(int i=0; i<sequence.length(); i++){
char singleLetterCode = sequence.charAt(i);
Group group = null;
if(seqResGroups.size()<=i){
}
else{
group=seqResGroups.get(i);
}
if(group!=null){
continue;
}
group = getSeqResGroup(modelChain, singleLetterCode, chainType);
addGroupAtId(seqResGroups, group, i);
seqResGroups.set(i, group);
}
} | java | public static void addSeqRes(Chain modelChain, String sequence) {
List<Group> seqResGroups = modelChain.getSeqResGroups();
GroupType chainType = getChainType(modelChain.getAtomGroups());
for(int i=0; i<sequence.length(); i++){
char singleLetterCode = sequence.charAt(i);
Group group = null;
if(seqResGroups.size()<=i){
}
else{
group=seqResGroups.get(i);
}
if(group!=null){
continue;
}
group = getSeqResGroup(modelChain, singleLetterCode, chainType);
addGroupAtId(seqResGroups, group, i);
seqResGroups.set(i, group);
}
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31,990 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericInsdcHeaderFormat.java | GenericInsdcHeaderFormat._write_feature | protected String _write_feature(FeatureInterface<AbstractSequence<C>, C> feature, int record_length) {
String location = _insdc_feature_location_string(feature, record_length);
String f_type = feature.getType().replace(" ", "_");
StringBuilder sb = new StringBuilder();
Formatter formatter = new Formatter(sb,Locale.US);
formatter.format(QUALIFIER_INDENT_TMP, f_type);
String line = formatter.toString().substring(0, QUALIFIER_INDENT) + _wrap_location(location) + lineSep;
formatter.close();
//Now the qualifiers...
for(List<Qualifier> qualifiers : feature.getQualifiers().values()) {
for(Qualifier q : qualifiers){
line += _write_feature_qualifier(q.getName(), q.getValue(), q.needsQuotes());
}
}
return line;
/*
self.handle.write(line)
#Now the qualifiers...
for key, values in feature.qualifiers.items():
if isinstance(values, list) or isinstance(values, tuple):
for value in values:
self._write_feature_qualifier(key, value)
elif values:
#String, int, etc
self._write_feature_qualifier(key, values)
else:
#e.g. a /psuedo entry
self._write_feature_qualifier(key)
*/
} | java | protected String _write_feature(FeatureInterface<AbstractSequence<C>, C> feature, int record_length) {
String location = _insdc_feature_location_string(feature, record_length);
String f_type = feature.getType().replace(" ", "_");
StringBuilder sb = new StringBuilder();
Formatter formatter = new Formatter(sb,Locale.US);
formatter.format(QUALIFIER_INDENT_TMP, f_type);
String line = formatter.toString().substring(0, QUALIFIER_INDENT) + _wrap_location(location) + lineSep;
formatter.close();
//Now the qualifiers...
for(List<Qualifier> qualifiers : feature.getQualifiers().values()) {
for(Qualifier q : qualifiers){
line += _write_feature_qualifier(q.getName(), q.getValue(), q.needsQuotes());
}
}
return line;
/*
self.handle.write(line)
#Now the qualifiers...
for key, values in feature.qualifiers.items():
if isinstance(values, list) or isinstance(values, tuple):
for value in values:
self._write_feature_qualifier(key, value)
elif values:
#String, int, etc
self._write_feature_qualifier(key, values)
else:
#e.g. a /psuedo entry
self._write_feature_qualifier(key)
*/
} | [
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31,991 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenericInsdcHeaderFormat.java | GenericInsdcHeaderFormat._split_multi_line | protected ArrayList<String> _split_multi_line(String text, int max_len) {
// TODO Auto-generated method stub
ArrayList<String> output = new ArrayList<String>();
text = text.trim();
if(text.length() <= max_len) {
output.add(text);
return output;
}
ArrayList<String> words = new ArrayList<String>();
Collections.addAll(words, text.split("\\s+"));
while(!words.isEmpty()) {
text = words.remove(0);
while(!words.isEmpty() && (text.length() + 1 + words.get(0).length()) <= max_len) {
text += " " + words.remove(0);
text = text.trim();
}
output.add(text);
}
assert words.isEmpty();
return output;
} | java | protected ArrayList<String> _split_multi_line(String text, int max_len) {
// TODO Auto-generated method stub
ArrayList<String> output = new ArrayList<String>();
text = text.trim();
if(text.length() <= max_len) {
output.add(text);
return output;
}
ArrayList<String> words = new ArrayList<String>();
Collections.addAll(words, text.split("\\s+"));
while(!words.isEmpty()) {
text = words.remove(0);
while(!words.isEmpty() && (text.length() + 1 + words.get(0).length()) <= max_len) {
text += " " + words.remove(0);
text = text.trim();
}
output.add(text);
}
assert words.isEmpty();
return output;
} | [
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31,992 | biojava/biojava | biojava-alignment/src/main/java/org/biojava/nbio/alignment/SimpleGapPenalty.java | SimpleGapPenalty.setType | private void setType() {
type = (gop == 0) ? GapPenalty.Type.LINEAR : ((gep == 0) ? GapPenalty.Type.CONSTANT : GapPenalty.Type.AFFINE);
} | java | private void setType() {
type = (gop == 0) ? GapPenalty.Type.LINEAR : ((gep == 0) ? GapPenalty.Type.CONSTANT : GapPenalty.Type.AFFINE);
} | [
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31,993 | biojava/biojava | biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/ProteinModificationXmlReader.java | ProteinModificationXmlReader.getChildNodes | private static Map<String,List<Node>> getChildNodes(Node parent) {
if (parent==null)
return Collections.emptyMap();
Map<String,List<Node>> children = new HashMap<String,List<Node>>();
NodeList nodes = parent.getChildNodes();
int nNodes = nodes.getLength();
for (int i=0; i<nNodes; i++) {
Node node = nodes.item(i);
if (node.getNodeType()!=Node.ELEMENT_NODE)
continue;
String name = node.getNodeName();
List<Node> namesakes = children.get(name);
if (namesakes==null) {
namesakes = new ArrayList<Node>();
children.put(name, namesakes);
}
namesakes.add(node);
}
return children;
} | java | private static Map<String,List<Node>> getChildNodes(Node parent) {
if (parent==null)
return Collections.emptyMap();
Map<String,List<Node>> children = new HashMap<String,List<Node>>();
NodeList nodes = parent.getChildNodes();
int nNodes = nodes.getLength();
for (int i=0; i<nNodes; i++) {
Node node = nodes.item(i);
if (node.getNodeType()!=Node.ELEMENT_NODE)
continue;
String name = node.getNodeName();
List<Node> namesakes = children.get(name);
if (namesakes==null) {
namesakes = new ArrayList<Node>();
children.put(name, namesakes);
}
namesakes.add(node);
}
return children;
} | [
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31,994 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/RNAToAminoAcidTranslator.java | RNAToAminoAcidTranslator.postProcessCompoundLists | @Override
protected void postProcessCompoundLists(
List<List<AminoAcidCompound>> compoundLists) {
for (List<AminoAcidCompound> compounds : compoundLists) {
if (trimStops) {
trimStop(compounds);
}
}
} | java | @Override
protected void postProcessCompoundLists(
List<List<AminoAcidCompound>> compoundLists) {
for (List<AminoAcidCompound> compounds : compoundLists) {
if (trimStops) {
trimStop(compounds);
}
}
} | [
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31,995 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/transcription/RNAToAminoAcidTranslator.java | RNAToAminoAcidTranslator.trimStop | protected void trimStop(List<AminoAcidCompound> sequence) {
AminoAcidCompound stop = sequence.get(sequence.size() - 1);
boolean isStop = false;
if (aminoAcidToCodon.containsKey(stop)) {
for (Codon c : aminoAcidToCodon.get(stop)) {
if (c.isStop()) {
isStop = true;
break;
}
}
}
if (isStop) {
sequence.remove(sequence.size() - 1);
}
} | java | protected void trimStop(List<AminoAcidCompound> sequence) {
AminoAcidCompound stop = sequence.get(sequence.size() - 1);
boolean isStop = false;
if (aminoAcidToCodon.containsKey(stop)) {
for (Codon c : aminoAcidToCodon.get(stop)) {
if (c.isStop()) {
isStop = true;
break;
}
}
}
if (isStop) {
sequence.remove(sequence.size() - 1);
}
} | [
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31,996 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/ResidueGroup.java | ResidueGroup.combineWith | public void combineWith(List<List<Integer>> alignRes) {
for (int i = 0; i < order(); i++)
alignRes.get(i).add(residues.get(i));
} | java | public void combineWith(List<List<Integer>> alignRes) {
for (int i = 0; i < order(); i++)
alignRes.get(i).add(residues.get(i));
} | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/ResidueGroup.java#L110-L113 |
31,997 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/AllChemCompProvider.java | AllChemCompProvider.downloadFile | public static void downloadFile() throws IOException {
initPath();
initServerName();
String localName = getLocalFileName();
String u = serverName + "/" + COMPONENTS_FILE_LOCATION;
downloadFileFromRemote(new URL(u), new File(localName));
} | java | public static void downloadFile() throws IOException {
initPath();
initServerName();
String localName = getLocalFileName();
String u = serverName + "/" + COMPONENTS_FILE_LOCATION;
downloadFileFromRemote(new URL(u), new File(localName));
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"... | Downloads the components.cif.gz file from the wwPDB site. | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/AllChemCompProvider.java#L119-L132 |
31,998 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/AllChemCompProvider.java | AllChemCompProvider.run | @Override
public void run() {
long timeS = System.currentTimeMillis();
initPath();
ensureFileExists();
try {
loadAllChemComps();
long timeE = System.currentTimeMillis();
logger.debug("Time to init chem comp dictionary: " + (timeE - timeS) / 1000 + " sec.");
} catch (IOException e) {
logger.error("Could not load chemical components definition file {}. Error: {}", getLocalFileName(), e.getMessage());
} finally {
loading.set(false);
isInitialized.set(true);
}
} | java | @Override
public void run() {
long timeS = System.currentTimeMillis();
initPath();
ensureFileExists();
try {
loadAllChemComps();
long timeE = System.currentTimeMillis();
logger.debug("Time to init chem comp dictionary: " + (timeE - timeS) / 1000 + " sec.");
} catch (IOException e) {
logger.error("Could not load chemical components definition file {}. Error: {}", getLocalFileName(), e.getMessage());
} finally {
loading.set(false);
isInitialized.set(true);
}
} | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/AllChemCompProvider.java#L222-L244 |
31,999 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/SequenceFileProxyLoader.java | SequenceFileProxyLoader.init | private boolean init() throws IOException, CompoundNotFoundException {
BufferedReader br = new BufferedReader(new FileReader(file));
br.skip(sequenceStartIndex);
String sequence = sequenceParser.getSequence(br, sequenceLength);
setContents(sequence);
br.close(); // close file to prevent too many being open
return true;
} | java | private boolean init() throws IOException, CompoundNotFoundException {
BufferedReader br = new BufferedReader(new FileReader(file));
br.skip(sequenceStartIndex);
String sequence = sequenceParser.getSequence(br, sequenceLength);
setContents(sequence);
br.close(); // close file to prevent too many being open
return true;
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/SequenceFileProxyLoader.java#L100-L109 |
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