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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32,100 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodFactory.java | EcodFactory.releaseReferences | private static void releaseReferences() {
synchronized(versionedEcodDBs) {
Iterator<Entry<String, SoftReference<EcodDatabase>>> it = versionedEcodDBs.entrySet().iterator();
while(it.hasNext()) {
Entry<String, SoftReference<EcodDatabase>> entry = it.next();
SoftReference<EcodDatabase> ref = entry.getValu... | java | private static void releaseReferences() {
synchronized(versionedEcodDBs) {
Iterator<Entry<String, SoftReference<EcodDatabase>>> it = versionedEcodDBs.entrySet().iterator();
while(it.hasNext()) {
Entry<String, SoftReference<EcodDatabase>> entry = it.next();
SoftReference<EcodDatabase> ref = entry.getValu... | [
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32,101 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/CasePreservingProteinSequenceCreator.java | CasePreservingProteinSequenceCreator.getSequence | @Override
public AbstractSequence<AminoAcidCompound> getSequence(
List<AminoAcidCompound> list) {
AbstractSequence<AminoAcidCompound> seq =super.getSequence(list);
Collection<Object> strCase = new ArrayList<Object>(seq.getLength());
for(int i=0;i<seq.getLength();i++) {
strCase.add(true);
}
seq.setUserC... | java | @Override
public AbstractSequence<AminoAcidCompound> getSequence(
List<AminoAcidCompound> list) {
AbstractSequence<AminoAcidCompound> seq =super.getSequence(list);
Collection<Object> strCase = new ArrayList<Object>(seq.getLength());
for(int i=0;i<seq.getLength();i++) {
strCase.add(true);
}
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32,102 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/CasePreservingProteinSequenceCreator.java | CasePreservingProteinSequenceCreator.getStringCase | private static List<Object> getStringCase(String str) {
List<Object> types = new ArrayList<Object>(str.length());
for(int i=0;i<str.length();i++) {
types.add(Character.isUpperCase(str.charAt(i)));
}
return types;
} | java | private static List<Object> getStringCase(String str) {
List<Object> types = new ArrayList<Object>(str.length());
for(int i=0;i<str.length();i++) {
types.add(Character.isUpperCase(str.charAt(i)));
}
return types;
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32,103 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/GetRepresentatives.java | GetRepresentatives.getAll | public static SortedSet<String> getAll() {
SortedSet<String> representatives = new TreeSet<String>();
try {
URL u = new URL(allUrl);
InputStream stream = URLConnectionTools.getInputStream(u, 60000);
if (stream != null) {
BufferedReader reader = new BufferedReader(
new InputStreamReader(stream... | java | public static SortedSet<String> getAll() {
SortedSet<String> representatives = new TreeSet<String>();
try {
URL u = new URL(allUrl);
InputStream stream = URLConnectionTools.getInputStream(u, 60000);
if (stream != null) {
BufferedReader reader = new BufferedReader(
new InputStreamReader(stream... | [
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32,104 | biojava/biojava | biojava-modfinder/src/main/java/org/biojava/nbio/protmod/Component.java | Component.lazyInit | private static void lazyInit() {
if (components==null) {
components = new HashSet<Component>();
nonTerminalComps = new HashMap<Set<String>, Component>();
nTerminalAminoAcids = new HashMap<Set<String>, Component>();
cTerminalAminoAcids = new HashMap<Set<String>, Component>();
}
} | java | private static void lazyInit() {
if (components==null) {
components = new HashSet<Component>();
nonTerminalComps = new HashMap<Set<String>, Component>();
nTerminalAminoAcids = new HashMap<Set<String>, Component>();
cTerminalAminoAcids = new HashMap<Set<String>, Component>();
}
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32,105 | biojava/biojava | biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/ElementTable.java | ElementTable.populateMaps | public void populateMaps(){
this.elementName2Element = new HashMap<String, Element>();
this.isotopeName2Isotope = new HashMap<String, Isotope>();
if(this.element != null){
for(Element e:this.element){
this.elementName2Element.put(e.getName(), e);
if(e.getIsotopes() != null){
for(Isotope i:e.getIso... | java | public void populateMaps(){
this.elementName2Element = new HashMap<String, Element>();
this.isotopeName2Isotope = new HashMap<String, Isotope>();
if(this.element != null){
for(Element e:this.element){
this.elementName2Element.put(e.getName(), e);
if(e.getIsotopes() != null){
for(Isotope i:e.getIso... | [
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32,106 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/contact/BoundingBox.java | BoundingBox.getDimensions | public double[] getDimensions(){
double[] dim = new double[3];
dim[0] = xmax-xmin;
dim[1] = ymax-ymin;
dim[2] = zmax-zmin;
return dim;
} | java | public double[] getDimensions(){
double[] dim = new double[3];
dim[0] = xmax-xmin;
dim[1] = ymax-ymin;
dim[2] = zmax-zmin;
return dim;
} | [
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32,107 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/contact/BoundingBox.java | BoundingBox.overlaps | public boolean overlaps(BoundingBox o, double cutoff) {
if (this==o) return true;
// x dimension
if (!areOverlapping(xmin,xmax,o.xmin,o.xmax,cutoff)) {
return false;
}
// y dimension
if (!areOverlapping(ymin,ymax,o.ymin,o.ymax,cutoff)) {
return false;
}
// z dimension
if (!areOverlapping(zmin,zm... | java | public boolean overlaps(BoundingBox o, double cutoff) {
if (this==o) return true;
// x dimension
if (!areOverlapping(xmin,xmax,o.xmin,o.xmax,cutoff)) {
return false;
}
// y dimension
if (!areOverlapping(ymin,ymax,o.ymin,o.ymax,cutoff)) {
return false;
}
// z dimension
if (!areOverlapping(zmin,zm... | [
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32,108 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/contact/BoundingBox.java | BoundingBox.contains | public boolean contains(Point3d atom) {
double x = atom.x;
double y = atom.y;
double z = atom.z;
return xmin <= x && x <= xmax
&& ymin <= y && y <= ymax
&& zmin <= z && z <= zmax;
} | java | public boolean contains(Point3d atom) {
double x = atom.x;
double y = atom.y;
double z = atom.z;
return xmin <= x && x <= xmax
&& ymin <= y && y <= ymax
&& zmin <= z && z <= zmax;
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32,109 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/contact/BoundingBox.java | BoundingBox.getMinMax | public double[] getMinMax(double[] array) {
double[] minmax = new double[2];
double max = Double.MIN_VALUE;
double min = Double.MAX_VALUE;
for(double value : array) {
if(value > max) max = value;
if(value < min) min = value;
}
minmax[0] = min;
minmax[1] = max;
return minmax;
} | java | public double[] getMinMax(double[] array) {
double[] minmax = new double[2];
double max = Double.MIN_VALUE;
double min = Double.MAX_VALUE;
for(double value : array) {
if(value > max) max = value;
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minmax[0] = min;
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32,110 | biojava/biojava | biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/color/LogColorMapper.java | LogColorMapper.transform | @Override
public double transform(double value) {
double logValue = Math.log(value>0?value:0)/Math.log(base);
return logValue;
} | java | @Override
public double transform(double value) {
double logValue = Math.log(value>0?value:0)/Math.log(base);
return logValue;
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32,111 | biojava/biojava | biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ProteinModificationRegistry.java | ProteinModificationRegistry.registerCommonProteinModifications | private static void registerCommonProteinModifications(InputStream inStream) {
try {
ProteinModificationXmlReader.registerProteinModificationFromXml(inStream);
} catch (Exception e) {
logger.error("Exception: ", e);
}
} | java | private static void registerCommonProteinModifications(InputStream inStream) {
try {
ProteinModificationXmlReader.registerProteinModificationFromXml(inStream);
} catch (Exception e) {
logger.error("Exception: ", e);
}
} | [
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32,112 | biojava/biojava | biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ProteinModificationRegistry.java | ProteinModificationRegistry.lazyInit | private static synchronized void lazyInit(InputStream inStream) {
if (registry==null) {
registry = new HashSet<ProteinModification>();
byId = new HashMap<String, ProteinModification>();
byResidId = new HashMap<String, Set<ProteinModification>>();
byPsimodId = new HashMap<String, Set<ProteinModification>... | java | private static synchronized void lazyInit(InputStream inStream) {
if (registry==null) {
registry = new HashSet<ProteinModification>();
byId = new HashMap<String, ProteinModification>();
byResidId = new HashMap<String, Set<ProteinModification>>();
byPsimodId = new HashMap<String, Set<ProteinModification>... | [
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32,113 | biojava/biojava | biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ProteinModificationRegistry.java | ProteinModificationRegistry.register | public static void register(final ProteinModification modification) {
if (modification==null) throw new IllegalArgumentException("modification == null!");
lazyInit();
String id = modification.getId();
if (byId.containsKey(id)) {
throw new IllegalArgumentException(id+" has already been registered.");
}
... | java | public static void register(final ProteinModification modification) {
if (modification==null) throw new IllegalArgumentException("modification == null!");
lazyInit();
String id = modification.getId();
if (byId.containsKey(id)) {
throw new IllegalArgumentException(id+" has already been registered.");
}
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ProteinModificationRegistry.java#L136-L205 |
32,114 | biojava/biojava | biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ProteinModificationRegistry.java | ProteinModificationRegistry.unregister | public static void unregister(ProteinModification modification) {
if (modification==null) throw new IllegalArgumentException("modification == null!");
registry.remove(modification);
byId.remove(modification.getId());
Set<ProteinModification> mods;
mods = byResidId.get(modification.getResidId());
if (mod... | java | public static void unregister(ProteinModification modification) {
if (modification==null) throw new IllegalArgumentException("modification == null!");
registry.remove(modification);
byId.remove(modification.getId());
Set<ProteinModification> mods;
mods = byResidId.get(modification.getResidId());
if (mod... | [
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32,115 | biojava/biojava | biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ProteinModificationRegistry.java | ProteinModificationRegistry.getByComponent | public static Set<ProteinModification> getByComponent(final Component comp1,
final Component... comps) {
lazyInit();
Set<ProteinModification> mods = byComponent.get(comp1);
if (mods==null) {
return Collections.emptySet();
}
if (comps.length==0) {
return Collections.unmodifiableSet(mods);
} else {
... | java | public static Set<ProteinModification> getByComponent(final Component comp1,
final Component... comps) {
lazyInit();
Set<ProteinModification> mods = byComponent.get(comp1);
if (mods==null) {
return Collections.emptySet();
}
if (comps.length==0) {
return Collections.unmodifiableSet(mods);
} else {
... | [
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@param comp1 a {@link Component}.
@param comps other {@link Component}s.
@return a set of ProteinModifications that involves all the components. | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/ProteinModificationRegistry.java#L300-L323 |
32,116 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/scop/Astral.java | Astral.getRepresentatives | public static Set<String> getRepresentatives(AstralSet cutoff) {
if (instances.containsKey(cutoff.getId()) && instances.get(cutoff.getId()).get() != null) {
return instances.get(cutoff.getId()).get().getNames();
}
Astral astral = new Astral(cutoff);
instances.put(cutoff.getId(), new SoftReference<Astral>(ast... | java | public static Set<String> getRepresentatives(AstralSet cutoff) {
if (instances.containsKey(cutoff.getId()) && instances.get(cutoff.getId()).get() != null) {
return instances.get(cutoff.getId()).get().getNames();
}
Astral astral = new Astral(cutoff);
instances.put(cutoff.getId(), new SoftReference<Astral>(ast... | [
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32,117 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/scop/Astral.java | Astral.init | private void init(Reader reader) {
names = new TreeSet<String>();
failedLines = new LinkedHashMap<Integer,String>();
BufferedReader br = null;
try {
br = new BufferedReader(reader);
logger.info("Reading ASTRAL file...");
String line = "";
int i = 0;
while ((line = br.readLine()) != null) {
... | java | private void init(Reader reader) {
names = new TreeSet<String>();
failedLines = new LinkedHashMap<Integer,String>();
BufferedReader br = null;
try {
br = new BufferedReader(reader);
logger.info("Reading ASTRAL file...");
String line = "";
int i = 0;
while ((line = br.readLine()) != null) {
... | [
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32,118 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/contact/Grid.java | Grid.getAtomContacts | public AtomContactSet getAtomContacts() {
AtomContactSet contacts = new AtomContactSet(cutoff);
List<Contact> list = getIndicesContacts();
if (jAtomObjects == null) {
for (Contact cont : list) {
contacts.add(new AtomContact(new Pair<Atom>(iAtomObjects[cont.getI()],iAtomObjects[cont.getJ()]),cont.getDist... | java | public AtomContactSet getAtomContacts() {
AtomContactSet contacts = new AtomContactSet(cutoff);
List<Contact> list = getIndicesContacts();
if (jAtomObjects == null) {
for (Contact cont : list) {
contacts.add(new AtomContact(new Pair<Atom>(iAtomObjects[cont.getI()],iAtomObjects[cont.getJ()]),cont.getDist... | [
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If both iAtoms and jAtoms are defined then contacts are between iAtoms and jAtoms,
if jAtoms is null, then contacts are within the iAtoms.
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32,119 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/contact/Grid.java | Grid.getIndicesContacts | public List<Contact> getIndicesContacts() {
List<Contact> list = new ArrayList<>();
// if the 2 sets of atoms are not overlapping they are too far away and no need to calculate anything
// this won't apply if there's only one set of atoms (iAtoms), where we would want all-to-all contacts
if (noOverlap) return... | java | public List<Contact> getIndicesContacts() {
List<Contact> list = new ArrayList<>();
// if the 2 sets of atoms are not overlapping they are too far away and no need to calculate anything
// this won't apply if there's only one set of atoms (iAtoms), where we would want all-to-all contacts
if (noOverlap) return... | [
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If both iAtoms and jAtoms are defined then contacts are between iAtoms and jAtoms,
if jAtoms is null, then contacts are within the iAtoms.
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32,120 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/AFPTwister.java | AFPTwister.twistOptimized | public static Group[] twistOptimized(AFPChain afpChain, Atom[] ca1,
Atom[] ca2) throws StructureException {
Atom[] optTwistPdb = new Atom[ca2.length];
int gPos = -1;
for (Atom a : ca2) {
gPos++;
optTwistPdb[gPos] = a;
}
int blockNum = afpChain.getBlockNum();
int b2 = 0;
int e2 = 0;
int focu... | java | public static Group[] twistOptimized(AFPChain afpChain, Atom[] ca1,
Atom[] ca2) throws StructureException {
Atom[] optTwistPdb = new Atom[ca2.length];
int gPos = -1;
for (Atom a : ca2) {
gPos++;
optTwistPdb[gPos] = a;
}
int blockNum = afpChain.getBlockNum();
int b2 = 0;
int e2 = 0;
int focu... | [
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@param afpChain
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@return Group array twisted.
@throws StructureException | [
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32,121 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/AFPTwister.java | AFPTwister.getAtoms | private static Atom[] getAtoms(Atom[] ca, int[] positions, int length,
boolean clone) {
List<Atom> atoms = new ArrayList<Atom>();
for (int i = 0; i < length; i++) {
int p = positions[i];
Atom a;
if (clone) {
a = (Atom) ca[p].clone();
a.setGroup((Group) ca[p].getGroup().clone());
} else {
... | java | private static Atom[] getAtoms(Atom[] ca, int[] positions, int length,
boolean clone) {
List<Atom> atoms = new ArrayList<Atom>();
for (int i = 0; i < length; i++) {
int p = positions[i];
Atom a;
if (clone) {
a = (Atom) ca[p].clone();
a.setGroup((Group) ca[p].getGroup().clone());
} else {
... | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/align/AFPTwister.java#L297-L313 |
32,122 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/AFPTwister.java | AFPTwister.calCaRmsd | private static double calCaRmsd(Atom[] ca1, Atom[] pro, int resn,
int[] res1, int[] res2) throws StructureException {
Atom[] cod1 = getAtoms(ca1, res1, resn, false);
Atom[] cod2 = getAtoms(pro, res2, resn, false);
if (cod1.length == 0 || cod2.length == 0) {
logger.info("length of atoms == 0!");
return... | java | private static double calCaRmsd(Atom[] ca1, Atom[] pro, int resn,
int[] res1, int[] res2) throws StructureException {
Atom[] cod1 = getAtoms(ca1, res1, resn, false);
Atom[] cod2 = getAtoms(pro, res2, resn, false);
if (cod1.length == 0 || cod2.length == 0) {
logger.info("length of atoms == 0!");
return... | [
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Modifies the coordinates in the second set of Atoms (pro).
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32,123 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/AFPTwister.java | AFPTwister.afp2Res | public static int afp2Res(AFPChain afpChain, int afpn, int[] afpPositions,
int listStart) {
int[] res1 = afpChain.getFocusRes1();
int[] res2 = afpChain.getFocusRes2();
int minLen = afpChain.getMinLen();
int n = 0;
List<AFP> afpSet = afpChain.getAfpSet();
for (int i = listStart; i < listStart + afpn; i... | java | public static int afp2Res(AFPChain afpChain, int afpn, int[] afpPositions,
int listStart) {
int[] res1 = afpChain.getFocusRes1();
int[] res2 = afpChain.getFocusRes2();
int minLen = afpChain.getMinLen();
int n = 0;
List<AFP> afpSet = afpChain.getAfpSet();
for (int i = listStart; i < listStart + afpn; i... | [
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WARNING: changes the values for FocusRes1, focusRes2 and FocusResn in
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@param afpChain
the AFPChain to store resuts
@param afpn
nr of afp
@param afpPositions
@param listStart
@return nr of eq residues | [
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32,124 | biojava/biojava | biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/autosuggest/JAutoSuggest.java | JAutoSuggest.updateLocation | private void updateLocation() {
try {
location = getLocationOnScreen();
location.y += getHeight();
dialog.setLocation(location);
} catch (IllegalComponentStateException e) {
return; // might happen on window creation
}
} | java | private void updateLocation() {
try {
location = getLocationOnScreen();
location.y += getHeight();
dialog.setLocation(location);
} catch (IllegalComponentStateException e) {
return; // might happen on window creation
}
} | [
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32,125 | biojava/biojava | biojava-survival/src/main/java/org/biojava/nbio/survival/cox/matrix/StdArrayIO.java | StdArrayIO.print | public static void print(double[] a) {
int N = a.length;
System.out.println(N);
for (int i = 0; i < N; i++) {
// System.out.printf("%9.5f ", a[i]);
System.out.print(a[i] + " ");
}
System.out.println();
} | java | public static void print(double[] a) {
int N = a.length;
System.out.println(N);
for (int i = 0; i < N; i++) {
// System.out.printf("%9.5f ", a[i]);
System.out.print(a[i] + " ");
}
System.out.println();
} | [
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@param a | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-survival/src/main/java/org/biojava/nbio/survival/cox/matrix/StdArrayIO.java#L86-L94 |
32,126 | biojava/biojava | biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/SmallMap.java | SmallMap.removeMapping | private void removeMapping(int num) {
if (num < numMappings) {
System.arraycopy(mappings, num * 2, mappings, (num - 1) * 2, (numMappings - num) * 2);
}
mappings[numMappings * 2 - 1] = null;
mappings[numMappings * 2 - 2] = null;
numMappings--;
} | java | private void removeMapping(int num) {
if (num < numMappings) {
System.arraycopy(mappings, num * 2, mappings, (num - 1) * 2, (numMappings - num) * 2);
}
mappings[numMappings * 2 - 1] = null;
mappings[numMappings * 2 - 2] = null;
numMappings--;
} | [
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32,127 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SimpleSubstitutionMatrix.java | SimpleSubstitutionMatrix.getIndexOfCompound | private static <C extends Compound> int getIndexOfCompound(List<C> list, C compound) {
int index = list.indexOf(compound);
if (index == -1) {
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break;
}
}
}
return index;
} | java | private static <C extends Compound> int getIndexOfCompound(List<C> list, C compound) {
int index = list.indexOf(compound);
if (index == -1) {
for (int i = 0; i < list.size(); i++) {
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index = i;
break;
}
}
}
return index;
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32,128 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmetryAxes.java | SymmetryAxes.addAxis | public void addAxis(Matrix4d axis, int order, SymmetryType type) {
axes.add(new Axis(axis,order,type,axes.size(),0));
} | java | public void addAxis(Matrix4d axis, int order, SymmetryType type) {
axes.add(new Axis(axis,order,type,axes.size(),0));
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32,129 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmetryAxes.java | SymmetryAxes.updateAxis | public void updateAxis(Integer index, Matrix4d newAxis){
axes.get(index).setOperator(newAxis);
} | java | public void updateAxis(Integer index, Matrix4d newAxis){
axes.get(index).setOperator(newAxis);
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32,130 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmetryAxes.java | SymmetryAxes.getElementaryAxes | public List<Matrix4d> getElementaryAxes(){
List<Matrix4d> ops = new ArrayList<Matrix4d>(getNumLevels());
for(Axis axis : axes) {
ops.add(axis.getOperator());
}
return ops;
} | java | public List<Matrix4d> getElementaryAxes(){
List<Matrix4d> ops = new ArrayList<Matrix4d>(getNumLevels());
for(Axis axis : axes) {
ops.add(axis.getOperator());
}
return ops;
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32,131 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmetryAxes.java | SymmetryAxes.getRepeatTransform | public Matrix4d getRepeatTransform(int repeat){
Matrix4d transform = new Matrix4d();
transform.setIdentity();
int[] counts = getAxisCounts(repeat);
for(int t = counts.length-1; t>=0; t--) {
if( counts[t] == 0 )
continue;
Matrix4d axis = new Matrix4d(axes.get(t).getOperator());
for(int i=0;i<coun... | java | public Matrix4d getRepeatTransform(int repeat){
Matrix4d transform = new Matrix4d();
transform.setIdentity();
int[] counts = getAxisCounts(repeat);
for(int t = counts.length-1; t>=0; t--) {
if( counts[t] == 0 )
continue;
Matrix4d axis = new Matrix4d(axes.get(t).getOperator());
for(int i=0;i<coun... | [
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32,132 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmetryAxes.java | SymmetryAxes.getRepeatTransform | public Matrix4d getRepeatTransform(int x, int y){
Matrix4d transform = new Matrix4d();
transform.setIdentity();
int[] iCounts = getAxisCounts(x);
int[] jCounts = getAxisCounts(y);
int[] counts = new int[iCounts.length];
for (int k = 0; k < iCounts.length; k++)
counts[k] = iCounts[k] - jCounts[k];
f... | java | public Matrix4d getRepeatTransform(int x, int y){
Matrix4d transform = new Matrix4d();
transform.setIdentity();
int[] iCounts = getAxisCounts(x);
int[] jCounts = getAxisCounts(y);
int[] counts = new int[iCounts.length];
for (int k = 0; k < iCounts.length; k++)
counts[k] = iCounts[k] - jCounts[k];
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32,133 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmetryAxes.java | SymmetryAxes.getNumRepeats | private int getNumRepeats(int level) {
int size = 1;
// Return 1 for illegally high level
if(level < getNumLevels()) {
for(Axis axis : axes.subList(level, getNumLevels())) {
size *= axis.getOrder();
}
}
return size;
} | java | private int getNumRepeats(int level) {
int size = 1;
// Return 1 for illegally high level
if(level < getNumLevels()) {
for(Axis axis : axes.subList(level, getNumLevels())) {
size *= axis.getOrder();
}
}
return size;
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32,134 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmetryAxes.java | SymmetryAxes.getFirstRepeats | public List<Integer> getFirstRepeats(int level) {
List<Integer> firstRepeats = new ArrayList<Integer>();
int m = getNumRepeats(level+1); //size of the level
int d = axes.get(level).getOrder(); //degree of this level
int n = m*d; // number of repeats included in each axis
for (int firstRepeat = 0; firstRepeat ... | java | public List<Integer> getFirstRepeats(int level) {
List<Integer> firstRepeats = new ArrayList<Integer>();
int m = getNumRepeats(level+1); //size of the level
int d = axes.get(level).getOrder(); //degree of this level
int n = m*d; // number of repeats included in each axis
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32,135 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterface.java | StructureInterface.setAsas | void setAsas(double[] asas1, double[] asas2, int nSpherePoints, int nThreads, int cofactorSizeToUse) {
Atom[] atoms = getAtomsForAsa(cofactorSizeToUse);
AsaCalculator asaCalc = new AsaCalculator(atoms,
AsaCalculator.DEFAULT_PROBE_SIZE, nSpherePoints, nThreads);
double[] complexAsas = asaCalc.calculateAsas()... | java | void setAsas(double[] asas1, double[] asas2, int nSpherePoints, int nThreads, int cofactorSizeToUse) {
Atom[] atoms = getAtomsForAsa(cofactorSizeToUse);
AsaCalculator asaCalc = new AsaCalculator(atoms,
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double[] complexAsas = asaCalc.calculateAsas()... | [
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32,136 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterface.java | StructureInterface.getAllNonHAtomArray | private static final Atom[] getAllNonHAtomArray(Atom[] m, int minSizeHetAtomToInclude) {
List<Atom> atoms = new ArrayList<>();
for (Atom a:m){
if (a.getElement()==Element.H) continue;
Group g = a.getGroup();
if (g.getType().equals(GroupType.HETATM) &&
!isInChain(g) &&
getSizeNoH(g)<minSizeHetAto... | java | private static final Atom[] getAllNonHAtomArray(Atom[] m, int minSizeHetAtomToInclude) {
List<Atom> atoms = new ArrayList<>();
for (Atom a:m){
if (a.getElement()==Element.H) continue;
Group g = a.getGroup();
if (g.getType().equals(GroupType.HETATM) &&
!isInChain(g) &&
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32,137 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterface.java | StructureInterface.getSizeNoH | private static int getSizeNoH(Group g) {
int size = 0;
for (Atom a:g.getAtoms()) {
if (a.getElement()!=Element.H)
size++;
}
return size;
} | java | private static int getSizeNoH(Group g) {
int size = 0;
for (Atom a:g.getAtoms()) {
if (a.getElement()!=Element.H)
size++;
}
return size;
} | [
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32,138 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterface.java | StructureInterface.isInChain | private static boolean isInChain(Group g) {
ChemComp chemComp = g.getChemComp();
if (chemComp==null) {
logger.warn("Warning: can't determine PolymerType for group "+g.getResidueNumber()+" ("+g.getPDBName()+"). Will consider it as non-nucleotide/non-protein type.");
return false;
}
PolymerType polyType =... | java | private static boolean isInChain(Group g) {
ChemComp chemComp = g.getChemComp();
if (chemComp==null) {
logger.warn("Warning: can't determine PolymerType for group "+g.getResidueNumber()+" ("+g.getPDBName()+"). Will consider it as non-nucleotide/non-protein type.");
return false;
}
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32,139 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterface.java | StructureInterface.getInterfacingResidues | public Pair<List<Group>> getInterfacingResidues(double minAsaForSurface) {
List<Group> interf1 = new ArrayList<Group>();
List<Group> interf2 = new ArrayList<Group>();
for (GroupAsa groupAsa:groupAsas1.values()) {
if (groupAsa.getAsaU()>minAsaForSurface && groupAsa.getBsa()>0) {
interf1.add(groupAsa.getG... | java | public Pair<List<Group>> getInterfacingResidues(double minAsaForSurface) {
List<Group> interf1 = new ArrayList<Group>();
List<Group> interf2 = new ArrayList<Group>();
for (GroupAsa groupAsa:groupAsas1.values()) {
if (groupAsa.getAsaU()>minAsaForSurface && groupAsa.getBsa()>0) {
interf1.add(groupAsa.getG... | [
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32,140 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterface.java | StructureInterface.getSurfaceResidues | public Pair<List<Group>> getSurfaceResidues(double minAsaForSurface) {
List<Group> surf1 = new ArrayList<Group>();
List<Group> surf2 = new ArrayList<Group>();
for (GroupAsa groupAsa:groupAsas1.values()) {
if (groupAsa.getAsaU()>minAsaForSurface) {
surf1.add(groupAsa.getGroup());
}
}
for (GroupAsa ... | java | public Pair<List<Group>> getSurfaceResidues(double minAsaForSurface) {
List<Group> surf1 = new ArrayList<Group>();
List<Group> surf2 = new ArrayList<Group>();
for (GroupAsa groupAsa:groupAsas1.values()) {
if (groupAsa.getAsaU()>minAsaForSurface) {
surf1.add(groupAsa.getGroup());
}
}
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32,141 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterface.java | StructureInterface.isIsologous | public boolean isIsologous() {
double scoreInverse = this.getContactOverlapScore(this, true);
logger.debug("Interface {} contact overlap score with itself inverted: {}",
getId(), scoreInverse);
return (scoreInverse>SELF_SCORE_FOR_ISOLOGOUS);
} | java | public boolean isIsologous() {
double scoreInverse = this.getContactOverlapScore(this, true);
logger.debug("Interface {} contact overlap score with itself inverted: {}",
getId(), scoreInverse);
return (scoreInverse>SELF_SCORE_FOR_ISOLOGOUS);
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32,142 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterface.java | StructureInterface.getParentChains | public Pair<Chain> getParentChains() {
Atom[] firstMol = this.molecules.getFirst();
Atom[] secondMol = this.molecules.getSecond();
if (firstMol.length==0 || secondMol.length==0) {
logger.warn("No atoms found in first or second molecule, can't get parent Chains");
return null;
}
return new Pair<Chain>(f... | java | public Pair<Chain> getParentChains() {
Atom[] firstMol = this.molecules.getFirst();
Atom[] secondMol = this.molecules.getSecond();
if (firstMol.length==0 || secondMol.length==0) {
logger.warn("No atoms found in first or second molecule, can't get parent Chains");
return null;
}
return new Pair<Chain>(f... | [
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32,143 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/contact/StructureInterface.java | StructureInterface.getParentCompounds | public Pair<EntityInfo> getParentCompounds() {
Pair<Chain> chains = getParentChains();
if (chains == null) {
logger.warn("Could not find parents chains, compounds will be null");
return null;
}
return new Pair<EntityInfo>(chains.getFirst().getEntityInfo(), chains.getSecond().getEntityInfo());
} | java | public Pair<EntityInfo> getParentCompounds() {
Pair<Chain> chains = getParentChains();
if (chains == null) {
logger.warn("Could not find parents chains, compounds will be null");
return null;
}
return new Pair<EntityInfo>(chains.getFirst().getEntityInfo(), chains.getSecond().getEntityInfo());
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32,144 | biojava/biojava | biojava-structure/src/main/java/demo/DemoMMCIFReader.java | DemoMMCIFReader.loadSimple | public void loadSimple(){
String pdbId = "4hhb";
AtomCache cache = new AtomCache();
cache.setUseMmCif(true);
StructureIO.setAtomCache(cache);
try {
Structure s = StructureIO.getStructure(pdbId);
System.out.println(pdbId + " has nr atoms: " + StructureTools.getNrAtoms(s));
} catch (Exception e){
... | java | public void loadSimple(){
String pdbId = "4hhb";
AtomCache cache = new AtomCache();
cache.setUseMmCif(true);
StructureIO.setAtomCache(cache);
try {
Structure s = StructureIO.getStructure(pdbId);
System.out.println(pdbId + " has nr atoms: " + StructureTools.getNrAtoms(s));
} catch (Exception e){
... | [
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32,145 | biojava/biojava | biojava-structure/src/main/java/demo/DemoMMCIFReader.java | DemoMMCIFReader.loadFromDirectAccess | public void loadFromDirectAccess(){
String pdbId = "1A4W";
StructureProvider pdbreader = new MMCIFFileReader();
try {
Structure s = pdbreader.getStructureById(pdbId);
System.out.println("Getting chain H of 1A4W");
List<Chain> hs = s.getNonPolyChainsByPDB("H");
Chain h = hs.get(0);
List<Group> ... | java | public void loadFromDirectAccess(){
String pdbId = "1A4W";
StructureProvider pdbreader = new MMCIFFileReader();
try {
Structure s = pdbreader.getStructureById(pdbId);
System.out.println("Getting chain H of 1A4W");
List<Chain> hs = s.getNonPolyChainsByPDB("H");
Chain h = hs.get(0);
List<Group> ... | [
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32,146 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPCalculator.java | AFPCalculator.getFragment | private static final Atom[] getFragment(Atom[] caall, int pos, int fragmentLength ,
boolean clone){
if ( pos+fragmentLength > caall.length)
return null;
Atom[] tmp = new Atom[fragmentLength];
for (int i=0;i< fragmentLength;i++){
if (clone){
tmp[i] = (Atom)caall[i+pos].clone();
} else {
tmp[... | java | private static final Atom[] getFragment(Atom[] caall, int pos, int fragmentLength ,
boolean clone){
if ( pos+fragmentLength > caall.length)
return null;
Atom[] tmp = new Atom[fragmentLength];
for (int i=0;i< fragmentLength;i++){
if (clone){
tmp[i] = (Atom)caall[i+pos].clone();
} else {
tmp[... | [
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32,147 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/fatcat/calc/AFPCalculator.java | AFPCalculator.scoreAfp | private static final double scoreAfp(AFP afp, double badRmsd, double fragScore)
{
//longer AFP with low rmsd is better
double s, w;
//s = (rmsdCut - afptmp.rmsd) * afptmp.len; //the same scroing strategy as that in the post-processing
w = afp.getRmsd() / badRmsd;
w = w * w;
s = fragScore * (1.0 - w);
re... | java | private static final double scoreAfp(AFP afp, double badRmsd, double fragScore)
{
//longer AFP with low rmsd is better
double s, w;
//s = (rmsdCut - afptmp.rmsd) * afptmp.len; //the same scroing strategy as that in the post-processing
w = afp.getRmsd() / badRmsd;
w = w * w;
s = fragScore * (1.0 - w);
re... | [
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32,148 | biojava/biojava | biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MenuCreator.java | MenuCreator.getAlignmentPanelMenu | public static JMenuBar getAlignmentPanelMenu(JFrame frame,
ActionListener actionListener, AFPChain afpChain,
MultipleAlignment msa){
JMenuBar menu = new JMenuBar();
JMenu file= new JMenu("File");
file.getAccessibleContext().setAccessibleDescription("File Menu");
menu.add(file);
ImageIcon saveicon = c... | java | public static JMenuBar getAlignmentPanelMenu(JFrame frame,
ActionListener actionListener, AFPChain afpChain,
MultipleAlignment msa){
JMenuBar menu = new JMenuBar();
JMenu file= new JMenu("File");
file.getAccessibleContext().setAccessibleDescription("File Menu");
menu.add(file);
ImageIcon saveicon = c... | [
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32,149 | biojava/biojava | biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/FeatureList.java | FeatureList.add | @Override
public boolean add(FeatureI feature) {
if (mLocation == null) {
mLocation = feature.location().plus();
} else if (null != feature.location()) {
mLocation = mLocation.union(feature.location().plus());
}
for (Entry<String, String> entry : feature.getAttributes().entrySet()){
if (featindex.cont... | java | @Override
public boolean add(FeatureI feature) {
if (mLocation == null) {
mLocation = feature.location().plus();
} else if (null != feature.location()) {
mLocation = mLocation.union(feature.location().plus());
}
for (Entry<String, String> entry : feature.getAttributes().entrySet()){
if (featindex.cont... | [
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32,150 | biojava/biojava | biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/FeatureList.java | FeatureList.hasGaps | public boolean hasGaps(int gapLength) {
Location last = null;
for (FeatureI f : this) {
if (last != null && gapLength <= f.location().distance(last)) {
return true;
} else {
last = f.location();
}
}
return false;
} | java | public boolean hasGaps(int gapLength) {
Location last = null;
for (FeatureI f : this) {
if (last != null && gapLength <= f.location().distance(last)) {
return true;
} else {
last = f.location();
}
}
return false;
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/FeatureList.java#L132-L143 |
32,151 | biojava/biojava | biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/FeatureList.java | FeatureList.splice | public String splice(DNASequence sequence) {
StringBuilder subData = new StringBuilder();
Location last = null;
for (FeatureI f : this) {
Location loc = f.location();
if (last == null || loc.startsAfter(last)) {
subData.append(sequence.getSubSequence(loc.start(), loc.end()).toString());
last = loc... | java | public String splice(DNASequence sequence) {
StringBuilder subData = new StringBuilder();
Location last = null;
for (FeatureI f : this) {
Location loc = f.location();
if (last == null || loc.startsAfter(last)) {
subData.append(sequence.getSubSequence(loc.start(), loc.end()).toString());
last = loc... | [
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32,152 | biojava/biojava | biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/FeatureList.java | FeatureList.selectByAttribute | public FeatureList selectByAttribute(String key) {
FeatureList list = new FeatureList();
if (featindex.containsKey(key)){
Map<String, List<FeatureI>> featsmap =featindex.get(key);
if(null != featsmap) {
for (List<FeatureI> feats: featsmap.values()){
list.addAll(Collections.unmodifiableCollection(feat... | java | public FeatureList selectByAttribute(String key) {
FeatureList list = new FeatureList();
if (featindex.containsKey(key)){
Map<String, List<FeatureI>> featsmap =featindex.get(key);
if(null != featsmap) {
for (List<FeatureI> feats: featsmap.values()){
list.addAll(Collections.unmodifiableCollection(feat... | [
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32,153 | biojava/biojava | biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/FeatureList.java | FeatureList.selectOverlapping | public FeatureList selectOverlapping(String seqname, Location location, boolean useBothStrands)
throws Exception {
FeatureList list = new FeatureList();
for (FeatureI feature : this) {
boolean overlaps = false;
if (feature.seqname().equals(seqname)) {
if (location.isSameStrand(feature.location())) {
... | java | public FeatureList selectOverlapping(String seqname, Location location, boolean useBothStrands)
throws Exception {
FeatureList list = new FeatureList();
for (FeatureI feature : this) {
boolean overlaps = false;
if (feature.seqname().equals(seqname)) {
if (location.isSameStrand(feature.location())) {
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32,154 | biojava/biojava | biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/FeatureList.java | FeatureList.hasAttribute | public boolean hasAttribute(String key) {
if (featindex.containsKey(key)){
Map<String, List<FeatureI>> mappa = featindex.get(key);
if (mappa!= null && mappa.size()>0)return true;
return false;
}
for (FeatureI f : this) {
if (f.hasAttribute(key)) {
return true;
}
}
return false;
} | java | public boolean hasAttribute(String key) {
if (featindex.containsKey(key)){
Map<String, List<FeatureI>> mappa = featindex.get(key);
if (mappa!= null && mappa.size()>0)return true;
return false;
}
for (FeatureI f : this) {
if (f.hasAttribute(key)) {
return true;
}
}
return false;
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32,155 | biojava/biojava | biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/FeatureList.java | FeatureList.sortByStart | public FeatureList sortByStart() {
FeatureI[] array = toArray(new FeatureI[1]);
Arrays.sort(array, new FeatureComparator());
return new FeatureList(Arrays.asList(array));
} | java | public FeatureList sortByStart() {
FeatureI[] array = toArray(new FeatureI[1]);
Arrays.sort(array, new FeatureComparator());
return new FeatureList(Arrays.asList(array));
} | [
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32,156 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.java | SimpleMMcifParser.processLine | private List<String> processLine(String line,
BufferedReader buf,
int fieldLength)
throws IOException{
//System.out.println("XX processLine " + fieldLength + " " + line);
// go through the line and process each character
List<String> lineData = new ArrayList<String>();
boolean inString = false;
... | java | private List<String> processLine(String line,
BufferedReader buf,
int fieldLength)
throws IOException{
//System.out.println("XX processLine " + fieldLength + " " + line);
// go through the line and process each character
List<String> lineData = new ArrayList<String>();
boolean inString = false;
... | [
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32,157 | biojava/biojava | biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/BiojavaJmol.java | BiojavaJmol.jmolInClassPath | public static boolean jmolInClassPath(){
try {
Class.forName(viewer);
} catch (ClassNotFoundException e){
e.printStackTrace();
return false;
}
return true;
} | java | public static boolean jmolInClassPath(){
try {
Class.forName(viewer);
} catch (ClassNotFoundException e){
e.printStackTrace();
return false;
}
return true;
} | [
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32,158 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/util/InputStreamProvider.java | InputStreamProvider.getInputStream | public InputStream getInputStream(String pathToFile)
throws IOException
{
File f = new File(pathToFile);
return getInputStream(f);
} | java | public InputStream getInputStream(String pathToFile)
throws IOException
{
File f = new File(pathToFile);
return getInputStream(f);
} | [
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32,159 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/util/InputStreamProvider.java | InputStreamProvider.getMagicNumber | private int getMagicNumber(InputStream in)
throws IOException {
int t = in.read();
if (t < 0) throw new EOFException("Failed to read magic number");
int magic = (t & 0xff) << 8;
t = in.read();
if (t < 0) throw new EOFException("Failed to read magic number");
magic += t & 0xff;
return magic;
} | java | private int getMagicNumber(InputStream in)
throws IOException {
int t = in.read();
if (t < 0) throw new EOFException("Failed to read magic number");
int magic = (t & 0xff) << 8;
t = in.read();
if (t < 0) throw new EOFException("Failed to read magic number");
magic += t & 0xff;
return magic;
} | [
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32,160 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/util/InputStreamProvider.java | InputStreamProvider.getInputStream | public InputStream getInputStream(File f)
throws IOException
{
// use the magic numbers to determine the compression type,
// use file extension only as 2nd choice
int magic = 0;
InputStream test = getInputStreamFromFile(f);
magic = getMagicNumber(test);
test.close();
InputStream inputStream = nu... | java | public InputStream getInputStream(File f)
throws IOException
{
// use the magic numbers to determine the compression type,
// use file extension only as 2nd choice
int magic = 0;
InputStream test = getInputStreamFromFile(f);
magic = getMagicNumber(test);
test.close();
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32,161 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/util/InputStreamProvider.java | InputStreamProvider.getInputStreamFromFile | private InputStream getInputStreamFromFile(File f) throws FileNotFoundException{
InputStream stream = null;
if ( cacheRawFiles ){
stream = FlatFileCache.getInputStream(f.getAbsolutePath());
if ( stream == null){
FlatFileCache.addToCache(f.getAbsolutePath(),f);
stream = FlatFileCache.getInputStream... | java | private InputStream getInputStreamFromFile(File f) throws FileNotFoundException{
InputStream stream = null;
if ( cacheRawFiles ){
stream = FlatFileCache.getInputStream(f.getAbsolutePath());
if ( stream == null){
FlatFileCache.addToCache(f.getAbsolutePath(),f);
stream = FlatFileCache.getInputStream... | [
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32,162 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java | AFPChain.getNrEQR | public int getNrEQR(){
if (myResultsEQR < 0){
if ( optLen == null) {
myResultsEQR = 0;
return 0;
}
int nrEqr = 0;
for(int bk = 0; bk < blockNum; bk ++) {
for ( int i=0;i< optLen[bk];i++){
nrEqr++;
}
}
myResultsEQR = nrEqr;
}
return myResultsEQR;
} | java | public int getNrEQR(){
if (myResultsEQR < 0){
if ( optLen == null) {
myResultsEQR = 0;
return 0;
}
int nrEqr = 0;
for(int bk = 0; bk < blockNum; bk ++) {
for ( int i=0;i< optLen[bk];i++){
nrEqr++;
}
}
myResultsEQR = nrEqr;
}
return myResultsEQR;
} | [
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32,163 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java | AFPChain.getCoverage1 | public int getCoverage1(){
if ( myResultsSimilarity1 < 0 ) {
int distance = ca1Length + ca2Length - 2 * getNrEQR();
int similarity = (ca1Length + ca2Length - distance ) / 2;
myResultsSimilarity1 = Math.round(similarity /(float) ca1Length * 100);
}
return myResultsSimilarity1;
} | java | public int getCoverage1(){
if ( myResultsSimilarity1 < 0 ) {
int distance = ca1Length + ca2Length - 2 * getNrEQR();
int similarity = (ca1Length + ca2Length - distance ) / 2;
myResultsSimilarity1 = Math.round(similarity /(float) ca1Length * 100);
}
return myResultsSimilarity1;
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java#L326-L335 |
32,164 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AFPChain.java | AFPChain.getCoverage2 | public int getCoverage2(){
if ( myResultsSimilarity2 < 0 ) {
int distance = ca1Length + ca2Length - 2 * getNrEQR();
int similarity = (ca1Length + ca2Length - distance ) / 2;
myResultsSimilarity2 = Math.round(similarity /(float) ca2Length * 100);
}
return myResultsSimilarity2;
} | java | public int getCoverage2(){
if ( myResultsSimilarity2 < 0 ) {
int distance = ca1Length + ca2Length - 2 * getNrEQR();
int similarity = (ca1Length + ca2Length - distance ) / 2;
myResultsSimilarity2 = Math.round(similarity /(float) ca2Length * 100);
}
return myResultsSimilarity2;
} | [
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32,165 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/PDBStatus.java | PDBStatus.getStatus | public static Status getStatus(String pdbId) {
Status[] statuses = getStatus(new String[] {pdbId});
if(statuses != null) {
assert(statuses.length == 1);
return statuses[0];
} else {
return null;
}
} | java | public static Status getStatus(String pdbId) {
Status[] statuses = getStatus(new String[] {pdbId});
if(statuses != null) {
assert(statuses.length == 1);
return statuses[0];
} else {
return null;
}
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32,166 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/PDBStatus.java | PDBStatus.getStatus | public static Status[] getStatus(String[] pdbIds) {
Status[] statuses = new Status[pdbIds.length];
List<Map<String,String>> attrList = getStatusIdRecords(pdbIds);
//Expect a single record
if(attrList == null || attrList.size() != pdbIds.length) {
logger.error("Error getting Status for {} from the PDB websit... | java | public static Status[] getStatus(String[] pdbIds) {
Status[] statuses = new Status[pdbIds.length];
List<Map<String,String>> attrList = getStatusIdRecords(pdbIds);
//Expect a single record
if(attrList == null || attrList.size() != pdbIds.length) {
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32,167 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/PDBStatus.java | PDBStatus.mergeReversed | private static void mergeReversed(List<String> merged,
final List<String> other) {
if(other.isEmpty())
return;
if(merged.isEmpty()) {
merged.addAll(other);
return;
}
ListIterator<String> m = merged.listIterator();
ListIterator<String> o = other.listIterator();
... | java | private static void mergeReversed(List<String> merged,
final List<String> other) {
if(other.isEmpty())
return;
if(merged.isEmpty()) {
merged.addAll(other);
return;
}
ListIterator<String> m = merged.listIterator();
ListIterator<String> o = other.listIterator();
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32,168 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/PDBStatus.java | PDBStatus.getReplaces | public static List<String> getReplaces(String newPdbId, boolean recurse) {
List<Map<String,String>> attrList = getStatusIdRecords(new String[] {newPdbId});
//Expect a single record
if(attrList == null || attrList.size() != 1) {
//TODO Is it possible to have multiple record per ID?
// They seem to be combine... | java | public static List<String> getReplaces(String newPdbId, boolean recurse) {
List<Map<String,String>> attrList = getStatusIdRecords(new String[] {newPdbId});
//Expect a single record
if(attrList == null || attrList.size() != 1) {
//TODO Is it possible to have multiple record per ID?
// They seem to be combine... | [
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32,169 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/PDBStatus.java | PDBStatus.getStatusIdRecords | private static List<Map<String, String>> getStatusIdRecords(String[] pdbIDs) {
List<Map<String,String>> result = new ArrayList<Map<String,String>>(pdbIDs.length);
String serverName = System.getProperty(PDB_SERVER_PROPERTY);
if ( serverName == null)
serverName = DEFAULT_PDB_SERVER;
else
logger.info(Stri... | java | private static List<Map<String, String>> getStatusIdRecords(String[] pdbIDs) {
List<Map<String,String>> result = new ArrayList<Map<String,String>>(pdbIDs.length);
String serverName = System.getProperty(PDB_SERVER_PROPERTY);
if ( serverName == null)
serverName = DEFAULT_PDB_SERVER;
else
logger.info(Stri... | [
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32,170 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/PDBStatus.java | PDBStatus.getCurrentPDBIds | public static SortedSet<String> getCurrentPDBIds() throws IOException {
SortedSet<String> allPDBs = new TreeSet<String>();
String serverName = System.getProperty(PDB_SERVER_PROPERTY);
if ( serverName == null)
serverName = DEFAULT_PDB_SERVER;
else
logger.info(String.format("Got System property %s=%s",PDB... | java | public static SortedSet<String> getCurrentPDBIds() throws IOException {
SortedSet<String> allPDBs = new TreeSet<String>();
String serverName = System.getProperty(PDB_SERVER_PROPERTY);
if ( serverName == null)
serverName = DEFAULT_PDB_SERVER;
else
logger.info(String.format("Got System property %s=%s",PDB... | [
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32,171 | biojava/biojava | biojava-protein-disorder/src/main/java/org/biojava/nbio/data/sequence/FastaSequence.java | FastaSequence.getFormatedSequence | public String getFormatedSequence(final int width) {
if (sequence == null) {
return "";
}
assert width >= 0 : "Wrong width parameter ";
final StringBuilder sb = new StringBuilder(sequence);
int nchunks = sequence.length() / width;
// add up inserted new line chars
nchunks = (nchunks + sequence.length()) / wi... | java | public String getFormatedSequence(final int width) {
if (sequence == null) {
return "";
}
assert width >= 0 : "Wrong width parameter ";
final StringBuilder sb = new StringBuilder(sequence);
int nchunks = sequence.length() / width;
// add up inserted new line chars
nchunks = (nchunks + sequence.length()) / wi... | [
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32,172 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/PermutationGroup.java | PermutationGroup.completeGroup | public void completeGroup() {
// Copy initial set to allow permutations to grow
List<List<Integer>> gens = new ArrayList<List<Integer>>(permutations);
// Keep HashSet version of permutations for fast lookup.
Set<List<Integer>> known = new HashSet<List<Integer>>(permutations);
//breadth-first search through th... | java | public void completeGroup() {
// Copy initial set to allow permutations to grow
List<List<Integer>> gens = new ArrayList<List<Integer>>(permutations);
// Keep HashSet version of permutations for fast lookup.
Set<List<Integer>> known = new HashSet<List<Integer>>(permutations);
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32,173 | biojava/biojava | biojava-alignment/src/main/java/org/biojava/nbio/alignment/GuideTree.java | GuideTree.getDistanceMatrix | public double[][] getDistanceMatrix() {
double[][] matrix = new double[distances.getSize()][distances.getSize()];
for (int i = 0; i < matrix.length; i++) {
for (int j = i+1; j < matrix.length; j++) {
matrix[i][j] = matrix[j][i] = distances.getValue(i, j);
}
}
return matrix;
} | java | public double[][] getDistanceMatrix() {
double[][] matrix = new double[distances.getSize()][distances.getSize()];
for (int i = 0; i < matrix.length; i++) {
for (int j = i+1; j < matrix.length; j++) {
matrix[i][j] = matrix[j][i] = distances.getValue(i, j);
}
}
return matrix;
} | [
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32,174 | biojava/biojava | biojava-alignment/src/main/java/org/biojava/nbio/alignment/GuideTree.java | GuideTree.getScoreMatrix | public double[][] getScoreMatrix() {
double[][] matrix = new double[sequences.size()][sequences.size()];
for (int i = 0, n = 0; i < matrix.length; i++) {
matrix[i][i] = scorers.get(i).getMaxScore();
for (int j = i+1; j < matrix.length; j++) {
matrix[i][j] = matrix[j][i] = scorers.get(n++).getScore();
}... | java | public double[][] getScoreMatrix() {
double[][] matrix = new double[sequences.size()][sequences.size()];
for (int i = 0, n = 0; i < matrix.length; i++) {
matrix[i][i] = scorers.get(i).getMaxScore();
for (int j = i+1; j < matrix.length; j++) {
matrix[i][j] = matrix[j][i] = scorers.get(n++).getScore();
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32,175 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.java | BiologicalAssemblyBuilder.orderTransformationsByChainId | private void orderTransformationsByChainId(Structure asymUnit, List<BiologicalAssemblyTransformation> transformations) {
final List<String> chainIds = getChainIds(asymUnit);
Collections.sort(transformations, new Comparator<BiologicalAssemblyTransformation>() {
@Override
public int compare(BiologicalAssemblyTr... | java | private void orderTransformationsByChainId(Structure asymUnit, List<BiologicalAssemblyTransformation> transformations) {
final List<String> chainIds = getChainIds(asymUnit);
Collections.sort(transformations, new Comparator<BiologicalAssemblyTransformation>() {
@Override
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32,176 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.java | BiologicalAssemblyBuilder.getChainIds | private List<String> getChainIds(Structure asymUnit) {
List<String> chainIds = new ArrayList<String>();
for ( Chain c : asymUnit.getChains()){
String intChainID = c.getId();
chainIds.add(intChainID);
}
return chainIds;
} | java | private List<String> getChainIds(Structure asymUnit) {
List<String> chainIds = new ArrayList<String>();
for ( Chain c : asymUnit.getChains()){
String intChainID = c.getId();
chainIds.add(intChainID);
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.java#L186-L193 |
32,177 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.java | BiologicalAssemblyBuilder.addChainMultiModel | private void addChainMultiModel(Structure s, Chain newChain, String transformId) {
// multi-model bioassembly
if ( modelIndex.size() == 0)
modelIndex.add("PLACEHOLDER FOR ASYM UNIT");
int modelCount = modelIndex.indexOf(transformId);
if ( modelCount == -1) {
modelIndex.add(transformId);
modelCount ... | java | private void addChainMultiModel(Structure s, Chain newChain, String transformId) {
// multi-model bioassembly
if ( modelIndex.size() == 0)
modelIndex.add("PLACEHOLDER FOR ASYM UNIT");
int modelCount = modelIndex.indexOf(transformId);
if ( modelCount == -1) {
modelIndex.add(transformId);
modelCount ... | [
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32,178 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/quaternary/BiologicalAssemblyBuilder.java | BiologicalAssemblyBuilder.getBioUnitTransformationList | public ArrayList<BiologicalAssemblyTransformation> getBioUnitTransformationList(PdbxStructAssembly psa, List<PdbxStructAssemblyGen> psags, List<PdbxStructOperList> operators) {
init();
// first we populate the list of all operators from pdbx_struct_oper_list so that we can then
// get them from getBioUnitTransfo... | java | public ArrayList<BiologicalAssemblyTransformation> getBioUnitTransformationList(PdbxStructAssembly psa, List<PdbxStructAssemblyGen> psags, List<PdbxStructOperList> operators) {
init();
// first we populate the list of all operators from pdbx_struct_oper_list so that we can then
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32,179 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java | StructureTools.getNrAtoms | public static final int getNrAtoms(Structure s) {
int nrAtoms = 0;
Iterator<Group> iter = new GroupIterator(s);
while (iter.hasNext()) {
Group g = iter.next();
nrAtoms += g.size();
}
return nrAtoms;
} | java | public static final int getNrAtoms(Structure s) {
int nrAtoms = 0;
Iterator<Group> iter = new GroupIterator(s);
while (iter.hasNext()) {
Group g = iter.next();
nrAtoms += g.size();
}
return nrAtoms;
} | [
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32,180 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java | StructureTools.getNrGroups | public static final int getNrGroups(Structure s) {
int nrGroups = 0;
List<Chain> chains = s.getChains(0);
for (Chain c : chains) {
nrGroups += c.getAtomLength();
}
return nrGroups;
} | java | public static final int getNrGroups(Structure s) {
int nrGroups = 0;
List<Chain> chains = s.getChains(0);
for (Chain c : chains) {
nrGroups += c.getAtomLength();
}
return nrGroups;
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32,181 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java | StructureTools.getLigandsByProximity | public static List<Group> getLigandsByProximity(Collection<Group> target, Atom[] query, double cutoff) {
// Geometric hashing of the reduced structure
Grid grid = new Grid(cutoff);
grid.addAtoms(query);
List<Group> ligands = new ArrayList<>();
for(Group g :target ) {
// don't worry about waters
if(g.is... | java | public static List<Group> getLigandsByProximity(Collection<Group> target, Atom[] query, double cutoff) {
// Geometric hashing of the reduced structure
Grid grid = new Grid(cutoff);
grid.addAtoms(query);
List<Group> ligands = new ArrayList<>();
for(Group g :target ) {
// don't worry about waters
if(g.is... | [
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32,182 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java | StructureTools.addGroupToStructure | public static Chain addGroupToStructure(Structure s, Group g, int model, Chain chainGuess, boolean clone ) {
synchronized(s) {
// Find or create the chain
String chainId = g.getChainId();
assert !chainId.isEmpty();
Chain chain;
if(chainGuess != null && chainGuess.getId() == chainId) {
// previously... | java | public static Chain addGroupToStructure(Structure s, Group g, int model, Chain chainGuess, boolean clone ) {
synchronized(s) {
// Find or create the chain
String chainId = g.getChainId();
assert !chainId.isEmpty();
Chain chain;
if(chainGuess != null && chainGuess.getId() == chainId) {
// previously... | [
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32,183 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java | StructureTools.addGroupsToStructure | public static void addGroupsToStructure(Structure s, Collection<Group> groups, int model, boolean clone) {
Chain chainGuess = null;
for(Group g : groups) {
chainGuess = addGroupToStructure(s, g, model, chainGuess, clone);
}
} | java | public static void addGroupsToStructure(Structure s, Collection<Group> groups, int model, boolean clone) {
Chain chainGuess = null;
for(Group g : groups) {
chainGuess = addGroupToStructure(s, g, model, chainGuess, clone);
}
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32,184 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java | StructureTools.getAllGroupsFromSubset | public static Set<Group> getAllGroupsFromSubset(Atom[] atoms,GroupType types) {
// Get the full structure
Structure s = null;
if (atoms.length > 0) {
Group g = atoms[0].getGroup();
if (g != null) {
Chain c = g.getChain();
if (c != null) {
s = c.getStructure();
}
}
}
// Collect all gr... | java | public static Set<Group> getAllGroupsFromSubset(Atom[] atoms,GroupType types) {
// Get the full structure
Structure s = null;
if (atoms.length > 0) {
Group g = atoms[0].getGroup();
if (g != null) {
Chain c = g.getChain();
if (c != null) {
s = c.getStructure();
}
}
}
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32,185 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java | StructureTools.getAllNonHAtomArray | public static final Atom[] getAllNonHAtomArray(Structure s, boolean hetAtoms) {
AtomIterator iter = new AtomIterator(s);
return getAllNonHAtomArray(s, hetAtoms, iter);
} | java | public static final Atom[] getAllNonHAtomArray(Structure s, boolean hetAtoms) {
AtomIterator iter = new AtomIterator(s);
return getAllNonHAtomArray(s, hetAtoms, iter);
} | [
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32,186 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java | StructureTools.getAllNonHAtomArray | public static final Atom[] getAllNonHAtomArray(Chain c, boolean hetAtoms) {
List<Atom> atoms = new ArrayList<Atom>();
for (Group g : c.getAtomGroups()) {
if (g.isWater())
continue;
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continue;
if (!hetAtoms && g.getType().equals(... | java | public static final Atom[] getAllNonHAtomArray(Chain c, boolean hetAtoms) {
List<Atom> atoms = new ArrayList<Atom>();
for (Group g : c.getAtomGroups()) {
if (g.isWater())
continue;
for (Atom a : g.getAtoms()) {
if (a.getElement() == Element.H)
continue;
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32,187 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java | StructureTools.extractAtoms | private static void extractAtoms(String[] atomNames, List<Chain> chains,
List<Atom> atoms) {
for (Chain c : chains) {
for (Group g : c.getAtomGroups()) {
// a temp container for the atoms of this group
List<Atom> thisGroupAtoms = new ArrayList<Atom>();
// flag to check if this group contains all ... | java | private static void extractAtoms(String[] atomNames, List<Chain> chains,
List<Atom> atoms) {
for (Chain c : chains) {
for (Group g : c.getAtomGroups()) {
// a temp container for the atoms of this group
List<Atom> thisGroupAtoms = new ArrayList<Atom>();
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32,188 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java | StructureTools.getAtomArray | public static final Atom[] getAtomArray(Chain c, String[] atomNames) {
List<Atom> atoms = new ArrayList<Atom>();
for (Group g : c.getAtomGroups()) {
// a temp container for the atoms of this group
List<Atom> thisGroupAtoms = new ArrayList<Atom>();
// flag to check if this group contains all the requeste... | java | public static final Atom[] getAtomArray(Chain c, String[] atomNames) {
List<Atom> atoms = new ArrayList<Atom>();
for (Group g : c.getAtomGroups()) {
// a temp container for the atoms of this group
List<Atom> thisGroupAtoms = new ArrayList<Atom>();
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... | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java#L825-L859 |
32,189 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java | StructureTools.cloneAtomArray | public static final Atom[] cloneAtomArray(Atom[] ca) {
Atom[] newCA = new Atom[ca.length];
List<Chain> model = new ArrayList<Chain>();
int apos = -1;
for (Atom a : ca) {
apos++;
Group parentG = a.getGroup();
Chain parentC = parentG.getChain();
Chain newChain = null;
for (Chain c : model) {
... | java | public static final Atom[] cloneAtomArray(Atom[] ca) {
Atom[] newCA = new Atom[ca.length];
List<Chain> model = new ArrayList<Chain>();
int apos = -1;
for (Atom a : ca) {
apos++;
Group parentG = a.getGroup();
Chain parentC = parentG.getChain();
Chain newChain = null;
for (Chain c : model) {
... | [
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starting with parent groups and chains. The chain will only contain
groups that are part of the input array.
@param ca
array of representative atoms, e.g. CA atoms
@return Atom array
@since Biojava 4.1.0 | [
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32,190 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java | StructureTools.cloneGroups | public static Group[] cloneGroups(Atom[] ca) {
Group[] newGroup = new Group[ca.length];
List<Chain> model = new ArrayList<Chain>();
int apos = -1;
for (Atom a : ca) {
apos++;
Group parentG = a.getGroup();
Chain parentC = parentG.getChain();
Chain newChain = null;
for (Chain c : model) {
if ... | java | public static Group[] cloneGroups(Atom[] ca) {
Group[] newGroup = new Group[ca.length];
List<Chain> model = new ArrayList<Chain>();
int apos = -1;
for (Atom a : ca) {
apos++;
Group parentG = a.getGroup();
Chain parentC = parentG.getChain();
Chain newChain = null;
for (Chain c : model) {
if ... | [
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@param ca
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@return Group array | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java#L979-L1007 |
32,191 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java | StructureTools.duplicateCA2 | public static Atom[] duplicateCA2(Atom[] ca2) {
// we don't want to rotate input atoms, do we?
Atom[] ca2clone = new Atom[ca2.length * 2];
int pos = 0;
Chain c = null;
String prevChainId = "";
for (Atom a : ca2) {
Group g = (Group) a.getGroup().clone(); // works because each group
// has only a sing... | java | public static Atom[] duplicateCA2(Atom[] ca2) {
// we don't want to rotate input atoms, do we?
Atom[] ca2clone = new Atom[ca2.length * 2];
int pos = 0;
Chain c = null;
String prevChainId = "";
for (Atom a : ca2) {
Group g = (Group) a.getGroup().clone(); // works because each group
// has only a sing... | [
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... | Utility method for working with circular permutations. Creates a
duplicated and cloned set of Calpha atoms from the input array.
@param ca2
atom array
@return cloned and duplicated set of input array | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java#L1017-L1077 |
32,192 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java | StructureTools.getAtomCAArray | public static Atom[] getAtomCAArray(Structure s) {
List<Atom> atoms = new ArrayList<Atom>();
for (Chain c : s.getChains()) {
for (Group g : c.getAtomGroups()) {
if (g.hasAtom(CA_ATOM_NAME)
&& g.getAtom(CA_ATOM_NAME).getElement() == Element.C) {
atoms.add(g.getAtom(CA_ATOM_NAME));
}
}
}
... | java | public static Atom[] getAtomCAArray(Structure s) {
List<Atom> atoms = new ArrayList<Atom>();
for (Chain c : s.getChains()) {
for (Group g : c.getAtomGroups()) {
if (g.hasAtom(CA_ATOM_NAME)
&& g.getAtom(CA_ATOM_NAME).getElement() == Element.C) {
atoms.add(g.getAtom(CA_ATOM_NAME));
}
}
}
... | [
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... | Return an Atom array of the C-alpha atoms. Any atom that is a carbon and
has CA name will be returned.
@param s
the structure object
@return an Atom[] array
@see #getRepresentativeAtomArray(Structure) | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java#L1088-L1102 |
32,193 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java | StructureTools.isNucleotide | public static final boolean isNucleotide(String groupCode3) {
String code = groupCode3.trim();
return nucleotides30.containsKey(code)
|| nucleotides23.containsKey(code);
} | java | public static final boolean isNucleotide(String groupCode3) {
String code = groupCode3.trim();
return nucleotides30.containsKey(code)
|| nucleotides23.containsKey(code);
} | [
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"cont... | Test if the three-letter code of an ATOM entry corresponds to a
nucleotide or to an aminoacid.
@param groupCode3
3-character code for a group. | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java#L1267-L1271 |
32,194 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java | StructureTools.getReducedStructure | @Deprecated
public static final Structure getReducedStructure(Structure s,
String chainId) throws StructureException {
// since we deal here with structure alignments,
// only use Model 1...
Structure newS = new StructureImpl();
newS.setPDBCode(s.getPDBCode());
newS.setPDBHeader(s.getPDBHeader());
newS... | java | @Deprecated
public static final Structure getReducedStructure(Structure s,
String chainId) throws StructureException {
// since we deal here with structure alignments,
// only use Model 1...
Structure newS = new StructureImpl();
newS.setPDBCode(s.getPDBCode());
newS.setPDBHeader(s.getPDBHeader());
newS... | [
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structure containing that Chain ID. Converts lower case chain IDs to
upper case if structure does not contain a chain with that ID.
@param s
@param chainId
@return Structure
@sin... | [
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32,195 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java | StructureTools.getGroupByPDBResidueNumber | public static final Group getGroupByPDBResidueNumber(Structure struc,
ResidueNumber pdbResNum) throws StructureException {
if (struc == null || pdbResNum == null) {
throw new IllegalArgumentException("Null argument(s).");
}
Chain chain = struc.getPolyChainByPDB(pdbResNum.getChainName());
return chain.ge... | java | public static final Group getGroupByPDBResidueNumber(Structure struc,
ResidueNumber pdbResNum) throws StructureException {
if (struc == null || pdbResNum == null) {
throw new IllegalArgumentException("Null argument(s).");
}
Chain chain = struc.getPolyChainByPDB(pdbResNum.getChainName());
return chain.ge... | [
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@param struc
a {@link Structure}
@param pdbResNum
a {@link ResidueNumber}
@return a group in the structure that is represented by the pdbResNum.
@throws StructureException
if the group cannot be found. | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java#L1377-L1386 |
32,196 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java | StructureTools.removeModels | public static Structure removeModels(Structure s) {
if (s.nrModels() == 1)
return s;
Structure n = new StructureImpl();
// go through whole substructure and clone ...
// copy structure data
n.setPDBCode(s.getPDBCode());
n.setName(s.getName());
// TODO: do deep copying of data!
n.setPDBHeader(s.ge... | java | public static Structure removeModels(Structure s) {
if (s.nrModels() == 1)
return s;
Structure n = new StructureImpl();
// go through whole substructure and clone ...
// copy structure data
n.setPDBCode(s.getPDBCode());
n.setName(s.getName());
// TODO: do deep copying of data!
n.setPDBHeader(s.ge... | [
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@param s
original Structure
@return a structure that contains only the first model
@since 3.0.5 | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java#L1715-L1737 |
32,197 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java | StructureTools.filterLigands | public static List<Group> filterLigands(List<Group> allGroups) {
List<Group> groups = new ArrayList<Group>();
for (Group g : allGroups) {
if ( g.isPolymeric())
continue;
if (!g.isWater()) {
groups.add(g);
}
}
return groups;
} | java | public static List<Group> filterLigands(List<Group> allGroups) {
List<Group> groups = new ArrayList<Group>();
for (Group g : allGroups) {
if ( g.isPolymeric())
continue;
if (!g.isWater()) {
groups.add(g);
}
}
return groups;
} | [
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32,198 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java | StructureTools.hasNonDeuteratedEquiv | public static boolean hasNonDeuteratedEquiv(Atom atom, Group currentGroup) {
if(atom.getElement()==Element.D && currentGroup.hasAtom(replaceFirstChar(atom.getName(),'D', 'H'))) {
// If it's deuterated and has a non-deuterated brother
return true;
}
return false;
} | java | public static boolean hasNonDeuteratedEquiv(Atom atom, Group currentGroup) {
if(atom.getElement()==Element.D && currentGroup.hasAtom(replaceFirstChar(atom.getName(),'D', 'H'))) {
// If it's deuterated and has a non-deuterated brother
return true;
}
return false;
} | [
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@param atom the input atom that is putatively deuterium
@param currentGroup the group the atom is in
@return true if the atom is deuterated and it's hydrogen equive exists. | [
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32,199 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java | StructureTools.hasDeuteratedEquiv | public static boolean hasDeuteratedEquiv(Atom atom, Group currentGroup) {
if(atom.getElement()==Element.H && currentGroup.hasAtom(replaceFirstChar(atom.getName(),'H', 'D'))) {
// If it's hydrogen and has a deuterated brother
return true;
}
return false;
} | java | public static boolean hasDeuteratedEquiv(Atom atom, Group currentGroup) {
if(atom.getElement()==Element.H && currentGroup.hasAtom(replaceFirstChar(atom.getName(),'H', 'D'))) {
// If it's hydrogen and has a deuterated brother
return true;
}
return false;
} | [
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@return true if the atom is hydrogen and it's Deuterium equiv exists. | [
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