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 |
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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 requestRepresen... | 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 requestRepresen... | [
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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,
Attribut... | 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,
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@param url Eg "http://www.rcsb.org/pdb/rest/representativeDomains"
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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
SAXPars... | 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
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@param url REST request
@param handler SAX XML parser
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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++){
dou... | 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++){
dou... | [
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@param ca1subset
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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... | 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... | [
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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
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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(orde... | 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(orde... | [
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@param strategy
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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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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 se... | 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 se... | [
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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... | 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... | [
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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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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 alignmen... | 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 alignmen... | [
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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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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... | 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) {
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return 11;
case megablast:
return 28... | [
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@return int value of WORD_SIZE used by this search
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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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@param gapCreation integer to use as gap creation value
@param gapExtension integer to use as gap extension value | [
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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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@param d
@param pad
@return | [
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] | 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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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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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(ro... | 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(ro... | [
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a way to duplicate original worksheet
@param copyWorkSheet
@param rows
@return
@throws Exception | [
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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... | 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... | [
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... | Randomly shuffle the columns and rows. Should be constrained to the same
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@param columns
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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++) {
... | 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++) {
... | [
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@param columns
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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);
}
Collect... | 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);
}
Collect... | [
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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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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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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, oldrowl... | 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, oldrowl... | [
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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, d... | 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, d... | [
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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(
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int preserveLength = Math.min(oldSize, new... | 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(
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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... | 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");
}
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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 : rowLooku... | 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
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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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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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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);
... | 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);
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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(val... | 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);
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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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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()) {
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}
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return rows;
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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 ... | 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) {
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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> metadat... | 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);
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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));
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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);
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WorkSheet w2 = WorkSheet.readCSV(w2FileName, delimitter);
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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()) {
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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 {
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ArrayList<String> newColumns = worksheet.getColumns();
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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 {
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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)... | 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
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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
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// Now write this data to file... | 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();
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// 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)), mmt... | [
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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{
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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{
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} | java | public static double getTransition(ProteinSequence sequence, ATTRIBUTE attribute, TRANSITION transition) throws Exception{
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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]... | java | @Override
public int[][][] getScoreMatrix() {
boolean tempStoringScoreMatrix = storingScoreMatrix;
if (scores == null) {
storingScoreMatrix = true;
align();
if (scores == null) {
return null;
}
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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];
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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 } :
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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();
retur... | 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();
retur... | [
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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 flatSu... | 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));
}
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flatSubLocations.add(l);
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}
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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(), s... | 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(), s... | [
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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(... | 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(... | [
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@param focusResn
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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()... | 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()... | [
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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() +
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}
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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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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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 = ... | 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 = ... | [
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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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Standard amino acids will be converted to '1', '2' or '3' depending on its grouping
Non-standard amino acids are simply converted to '0'.
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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(... | 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(... | [
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Updates the atomRes chain object with the mapped data
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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 AminoAc... | 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 AminoAc... | [
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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 AtomGr... | 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 AtomGr... | [
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@param structure
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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.... | 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.... | [
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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 serv... | 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 serv... | [
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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();
inputU... | 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();
inputU... | [
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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 : experimentalTechniqu... | 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 : experimentalTechniqu... | [
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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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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 t... | 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 t... | [
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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);
... | 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);
... | [
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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... | 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... | [
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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 gr... | 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 gr... | [
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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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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<>... | 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<>... | [
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@param structure the structure for which to get the information. | [
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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#L410-L445 |
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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@param chain the chain to add the seq res group to
@param group the group to add
@param sequenceIndexId the index to add it in | [
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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(seqResGroup... | 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(seqResGroup... | [
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@param modelChain the chain to add the information for
@param sequence the sequence of the construct | [
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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,Loc... | 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,Loc... | [
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@param feature
@param record_length | [
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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>();
C... | 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>();
C... | [
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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 = no... | 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 = no... | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/ProteinModificationXmlReader.java#L341-L364 |
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 (isSt... | 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 (isSt... | [
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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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@param alignRes
the alignment block, will be modified. | [
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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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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.... | 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.... | [
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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
... | 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
... | [
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")... | Load the sequence
@return | [
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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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