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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
32,000 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/StructurePairAligner.java | StructurePairAligner.main | public static void main(String[] args) throws Exception {
// UPDATE THE FOLLOWING LINES TO MATCH YOUR SETUP
PDBFileReader pdbr = new PDBFileReader();
pdbr.setPath("/Users/andreas/WORK/PDB/");
// String pdb1 = "1crl";
// String pdb2 = "1ede";
String pdb1 = "1buz";
String pdb2 = "1ali";
String outputfile = "/tmp/alig_" + pdb1 + "_" + pdb2 + ".pdb";
// NO NEED TO DO CHANGE ANYTHING BELOW HERE...
StructurePairAligner sc = new StructurePairAligner();
// step1 : read molecules
logger.info("aligning {} vs. {}", pdb1, pdb2);
Structure s1 = pdbr.getStructureById(pdb1);
Structure s2 = pdbr.getStructureById(pdb2);
// step 2 : do the calculations
sc.align(s1, s2);
AlternativeAlignment[] aligs = sc.getAlignments();
// cluster similar results together
ClusterAltAligs.cluster(aligs);
// print the result:
// the AlternativeAlignment object gives also access to rotation
// matrices / shift vectors.
for (AlternativeAlignment aa : aligs) {
logger.info("Alternative Alignment: ", aa);
}
// convert AlternativeAlignemnt 1 to PDB file, so it can be opened with
// a viewer (e.g. Jmol, Rasmol)
if (aligs.length > 0) {
AlternativeAlignment aa1 = aligs[0];
String pdbstr = aa1.toPDB(s1, s2);
logger.info("writing alignment to {}", outputfile);
FileOutputStream out = new FileOutputStream(outputfile);
PrintStream p = new PrintStream(out);
p.println(pdbstr);
p.close();
out.close();
}
// display the alignment in Jmol
// only will work if Jmol is in the Classpath
if (aligs.length > 0) {
if (!GuiWrapper.isGuiModuleInstalled()) {
logger.error("Could not find structure-gui modules in classpath, please install first!");
}
}
} | java | public static void main(String[] args) throws Exception {
// UPDATE THE FOLLOWING LINES TO MATCH YOUR SETUP
PDBFileReader pdbr = new PDBFileReader();
pdbr.setPath("/Users/andreas/WORK/PDB/");
// String pdb1 = "1crl";
// String pdb2 = "1ede";
String pdb1 = "1buz";
String pdb2 = "1ali";
String outputfile = "/tmp/alig_" + pdb1 + "_" + pdb2 + ".pdb";
// NO NEED TO DO CHANGE ANYTHING BELOW HERE...
StructurePairAligner sc = new StructurePairAligner();
// step1 : read molecules
logger.info("aligning {} vs. {}", pdb1, pdb2);
Structure s1 = pdbr.getStructureById(pdb1);
Structure s2 = pdbr.getStructureById(pdb2);
// step 2 : do the calculations
sc.align(s1, s2);
AlternativeAlignment[] aligs = sc.getAlignments();
// cluster similar results together
ClusterAltAligs.cluster(aligs);
// print the result:
// the AlternativeAlignment object gives also access to rotation
// matrices / shift vectors.
for (AlternativeAlignment aa : aligs) {
logger.info("Alternative Alignment: ", aa);
}
// convert AlternativeAlignemnt 1 to PDB file, so it can be opened with
// a viewer (e.g. Jmol, Rasmol)
if (aligs.length > 0) {
AlternativeAlignment aa1 = aligs[0];
String pdbstr = aa1.toPDB(s1, s2);
logger.info("writing alignment to {}", outputfile);
FileOutputStream out = new FileOutputStream(outputfile);
PrintStream p = new PrintStream(out);
p.println(pdbstr);
p.close();
out.close();
}
// display the alignment in Jmol
// only will work if Jmol is in the Classpath
if (aligs.length > 0) {
if (!GuiWrapper.isGuiModuleInstalled()) {
logger.error("Could not find structure-gui modules in classpath, please install first!");
}
}
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32,001 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/StructurePairAligner.java | StructurePairAligner.align | public void align(Structure s1, Structure s2) throws StructureException {
align(s1, s2, params);
} | java | public void align(Structure s1, Structure s2) throws StructureException {
align(s1, s2, params);
} | [
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32,002 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/StructurePairAligner.java | StructurePairAligner.align | public void align(Structure s1, Structure s2, StrucAligParameters params)
throws StructureException {
// step 1 convert the structures to Atom Arrays
Atom[] ca1 = getAlignmentAtoms(s1);
Atom[] ca2 = getAlignmentAtoms(s2);
notifyStartingAlignment(s1.getName(), ca1, s2.getName(), ca2);
align(ca1, ca2, params);
} | java | public void align(Structure s1, Structure s2, StrucAligParameters params)
throws StructureException {
// step 1 convert the structures to Atom Arrays
Atom[] ca1 = getAlignmentAtoms(s1);
Atom[] ca2 = getAlignmentAtoms(s2);
notifyStartingAlignment(s1.getName(), ca1, s2.getName(), ca2);
align(ca1, ca2, params);
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32,003 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/StructurePairAligner.java | StructurePairAligner.align | public void align(Structure s1, String chainId1, Structure s2,
String chainId2) throws StructureException {
align(s1, chainId1, s2, chainId2, params);
} | java | public void align(Structure s1, String chainId1, Structure s2,
String chainId2) throws StructureException {
align(s1, chainId1, s2, chainId2, params);
} | [
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32,004 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/StructurePairAligner.java | StructurePairAligner.align | public void align(Structure s1, String chainId1, Structure s2,
String chainId2, StrucAligParameters params)
throws StructureException {
reset();
this.params = params;
Chain c1 = s1.getPolyChainByPDB(chainId1);
Chain c2 = s2.getPolyChainByPDB(chainId2);
Structure s3 = new StructureImpl();
s3.addChain(c1);
Structure s4 = new StructureImpl();
s4.addChain(c2);
Atom[] ca1 = getAlignmentAtoms(s3);
Atom[] ca2 = getAlignmentAtoms(s4);
notifyStartingAlignment(s1.getName(), ca1, s2.getName(), ca2);
align(ca1, ca2, params);
} | java | public void align(Structure s1, String chainId1, Structure s2,
String chainId2, StrucAligParameters params)
throws StructureException {
reset();
this.params = params;
Chain c1 = s1.getPolyChainByPDB(chainId1);
Chain c2 = s2.getPolyChainByPDB(chainId2);
Structure s3 = new StructureImpl();
s3.addChain(c1);
Structure s4 = new StructureImpl();
s4.addChain(c2);
Atom[] ca1 = getAlignmentAtoms(s3);
Atom[] ca2 = getAlignmentAtoms(s4);
notifyStartingAlignment(s1.getName(), ca1, s2.getName(), ca2);
align(ca1, ca2, params);
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32,005 | biojava/biojava | biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/JmolPanel.java | JmolPanel.jmolColorByChain | public void jmolColorByChain(){
String script =
"function color_by_chain(objtype, color_list) {"+ String.format("%n") +
""+ String.format("%n") +
" if (color_list) {"+ String.format("%n") +
" if (color_list.type == \"string\") {"+ String.format("%n") +
" color_list = color_list.split(\",\").trim();"+ String.format("%n") +
" }"+ String.format("%n") +
" } else {"+ String.format("%n") +
" color_list = [\"104BA9\",\"AA00A2\",\"C9F600\",\"FFA200\",\"284A7E\",\"7F207B\",\"9FB82E\",\"BF8B30\",\"052D6E\",\"6E0069\",\"83A000\",\"A66A00\",\"447BD4\",\"D435CD\",\"D8FA3F\",\"FFBA40\",\"6A93D4\",\"D460CF\",\"E1FA71\",\"FFCC73\"];"+ String.format("%n") +
" }"+ String.format("%n") +
" var cmd2 = \"\";"+ String.format("%n") +
" if (!objtype) {"+ String.format("%n") +
" var type_list = [ \"backbone\",\"cartoon\",\"dots\",\"halo\",\"label\",\"meshribbon\",\"polyhedra\",\"rocket\",\"star\",\"strand\",\"strut\",\"trace\"];"+ String.format("%n") +
" cmd2 = \"color \" + type_list.join(\" none; color \") + \" none;\";"+ String.format("%n") +
" objtype = \"atoms\";"+ String.format("%n") +
" }"+ String.format("%n") +
" var chain_list = script(\"show chain\").trim().lines;"+ String.format("%n") +
" var chain_count = chain_list.length;"+ String.format("%n") +
" var color_count = color_list.length;"+ String.format("%n") +
" var sel = {selected};"+ String.format("%n") +
" var cmds = \"\";"+ String.format("%n") +
" for (var chain_number=1; chain_number<=chain_count; chain_number++) {"+ String.format("%n") +
" // remember, Jmol arrays start with 1, but % can return 0"+ String.format("%n") +
" cmds += \"select sel and :\" + chain_list[chain_number] + \";color \" + objtype + \" [x\" + color_list[(chain_number-1) % color_count + 1] + \"];\" + cmd2;"+ String.format("%n") +
" }"+ String.format("%n") +
" script INLINE @{cmds + \"select sel\"}"+ String.format("%n") +
"}";
executeCmd(script);
} | java | public void jmolColorByChain(){
String script =
"function color_by_chain(objtype, color_list) {"+ String.format("%n") +
""+ String.format("%n") +
" if (color_list) {"+ String.format("%n") +
" if (color_list.type == \"string\") {"+ String.format("%n") +
" color_list = color_list.split(\",\").trim();"+ String.format("%n") +
" }"+ String.format("%n") +
" } else {"+ String.format("%n") +
" color_list = [\"104BA9\",\"AA00A2\",\"C9F600\",\"FFA200\",\"284A7E\",\"7F207B\",\"9FB82E\",\"BF8B30\",\"052D6E\",\"6E0069\",\"83A000\",\"A66A00\",\"447BD4\",\"D435CD\",\"D8FA3F\",\"FFBA40\",\"6A93D4\",\"D460CF\",\"E1FA71\",\"FFCC73\"];"+ String.format("%n") +
" }"+ String.format("%n") +
" var cmd2 = \"\";"+ String.format("%n") +
" if (!objtype) {"+ String.format("%n") +
" var type_list = [ \"backbone\",\"cartoon\",\"dots\",\"halo\",\"label\",\"meshribbon\",\"polyhedra\",\"rocket\",\"star\",\"strand\",\"strut\",\"trace\"];"+ String.format("%n") +
" cmd2 = \"color \" + type_list.join(\" none; color \") + \" none;\";"+ String.format("%n") +
" objtype = \"atoms\";"+ String.format("%n") +
" }"+ String.format("%n") +
" var chain_list = script(\"show chain\").trim().lines;"+ String.format("%n") +
" var chain_count = chain_list.length;"+ String.format("%n") +
" var color_count = color_list.length;"+ String.format("%n") +
" var sel = {selected};"+ String.format("%n") +
" var cmds = \"\";"+ String.format("%n") +
" for (var chain_number=1; chain_number<=chain_count; chain_number++) {"+ String.format("%n") +
" // remember, Jmol arrays start with 1, but % can return 0"+ String.format("%n") +
" cmds += \"select sel and :\" + chain_list[chain_number] + \";color \" + objtype + \" [x\" + color_list[(chain_number-1) % color_count + 1] + \"];\" + cmd2;"+ String.format("%n") +
" }"+ String.format("%n") +
" script INLINE @{cmds + \"select sel\"}"+ String.format("%n") +
"}";
executeCmd(script);
} | [
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32,006 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/compound/AminoAcidCompoundSet.java | AminoAcidCompoundSet.addAmbiguousEquivalents | private void addAmbiguousEquivalents(String one, String two, String either) {
Set<AminoAcidCompound> equivalents;
AminoAcidCompound cOne, cTwo, cEither;
equivalents = new HashSet<AminoAcidCompound>();
equivalents.add(cOne = aminoAcidCompoundCache.get(one));
equivalents.add(cTwo = aminoAcidCompoundCache.get(two));
equivalents.add(cEither = aminoAcidCompoundCache.get(either));
equivalentsCache.put(cEither, equivalents);
equivalents = new HashSet<AminoAcidCompound>();
equivalents.add(cOne);
equivalents.add(cEither);
equivalentsCache.put(cOne, equivalents);
equivalents = new HashSet<AminoAcidCompound>();
equivalents.add(cTwo);
equivalents.add(cEither);
equivalentsCache.put(cTwo, equivalents);
} | java | private void addAmbiguousEquivalents(String one, String two, String either) {
Set<AminoAcidCompound> equivalents;
AminoAcidCompound cOne, cTwo, cEither;
equivalents = new HashSet<AminoAcidCompound>();
equivalents.add(cOne = aminoAcidCompoundCache.get(one));
equivalents.add(cTwo = aminoAcidCompoundCache.get(two));
equivalents.add(cEither = aminoAcidCompoundCache.get(either));
equivalentsCache.put(cEither, equivalents);
equivalents = new HashSet<AminoAcidCompound>();
equivalents.add(cOne);
equivalents.add(cEither);
equivalentsCache.put(cOne, equivalents);
equivalents = new HashSet<AminoAcidCompound>();
equivalents.add(cTwo);
equivalents.add(cEither);
equivalentsCache.put(cTwo, equivalents);
} | [
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32,007 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.java | SimpleMMcifConsumer.getNewGroup | private Group getNewGroup(String recordName,Character aminoCode1, long seq_id,String groupCode3) {
Group g = ChemCompGroupFactory.getGroupFromChemCompDictionary(groupCode3);
if ( g != null && !g.getChemComp().isEmpty()) {
if ( g instanceof AminoAcidImpl) {
AminoAcidImpl aa = (AminoAcidImpl) g;
aa.setId(seq_id);
} else if ( g instanceof NucleotideImpl) {
NucleotideImpl nuc = (NucleotideImpl) g;
nuc.setId(seq_id);
} else if ( g instanceof HetatomImpl) {
HetatomImpl het = (HetatomImpl)g;
het.setId(seq_id);
}
return g;
}
Group group;
if ( recordName.equals("ATOM") ) {
if (StructureTools.isNucleotide(groupCode3)) {
// it is a nucleotide
NucleotideImpl nu = new NucleotideImpl();
group = nu;
nu.setId(seq_id);
} else if (aminoCode1==null || aminoCode1 == StructureTools.UNKNOWN_GROUP_LABEL){
HetatomImpl h = new HetatomImpl();
h.setId(seq_id);
group = h;
} else {
AminoAcidImpl aa = new AminoAcidImpl() ;
aa.setAminoType(aminoCode1);
aa.setId(seq_id);
group = aa ;
}
}
else {
if (StructureTools.isNucleotide(groupCode3)) {
// it is a nucleotide
NucleotideImpl nu = new NucleotideImpl();
group = nu;
nu.setId(seq_id);
}
else if (aminoCode1 != null ) {
AminoAcidImpl aa = new AminoAcidImpl() ;
aa.setAminoType(aminoCode1);
aa.setId(seq_id);
group = aa ;
} else {
HetatomImpl h = new HetatomImpl();
h.setId(seq_id);
group = h;
}
}
return group ;
} | java | private Group getNewGroup(String recordName,Character aminoCode1, long seq_id,String groupCode3) {
Group g = ChemCompGroupFactory.getGroupFromChemCompDictionary(groupCode3);
if ( g != null && !g.getChemComp().isEmpty()) {
if ( g instanceof AminoAcidImpl) {
AminoAcidImpl aa = (AminoAcidImpl) g;
aa.setId(seq_id);
} else if ( g instanceof NucleotideImpl) {
NucleotideImpl nuc = (NucleotideImpl) g;
nuc.setId(seq_id);
} else if ( g instanceof HetatomImpl) {
HetatomImpl het = (HetatomImpl)g;
het.setId(seq_id);
}
return g;
}
Group group;
if ( recordName.equals("ATOM") ) {
if (StructureTools.isNucleotide(groupCode3)) {
// it is a nucleotide
NucleotideImpl nu = new NucleotideImpl();
group = nu;
nu.setId(seq_id);
} else if (aminoCode1==null || aminoCode1 == StructureTools.UNKNOWN_GROUP_LABEL){
HetatomImpl h = new HetatomImpl();
h.setId(seq_id);
group = h;
} else {
AminoAcidImpl aa = new AminoAcidImpl() ;
aa.setAminoType(aminoCode1);
aa.setId(seq_id);
group = aa ;
}
}
else {
if (StructureTools.isNucleotide(groupCode3)) {
// it is a nucleotide
NucleotideImpl nu = new NucleotideImpl();
group = nu;
nu.setId(seq_id);
}
else if (aminoCode1 != null ) {
AminoAcidImpl aa = new AminoAcidImpl() ;
aa.setAminoType(aminoCode1);
aa.setId(seq_id);
group = aa ;
} else {
HetatomImpl h = new HetatomImpl();
h.setId(seq_id);
group = h;
}
}
return group ;
} | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.java#L250-L308 |
32,008 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.java | SimpleMMcifConsumer.isKnownChain | private static Chain isKnownChain(String asymId, List<Chain> chains){
for (int i = 0; i< chains.size();i++){
Chain testchain = chains.get(i);
//System.out.println("comparing chainID >"+chainID+"< against testchain " + i+" >" +testchain.getName()+"<");
if (asymId.equals(testchain.getId())) {
//System.out.println("chain "+ chainID+" already known ...");
return testchain;
}
}
return null;
} | java | private static Chain isKnownChain(String asymId, List<Chain> chains){
for (int i = 0; i< chains.size();i++){
Chain testchain = chains.get(i);
//System.out.println("comparing chainID >"+chainID+"< against testchain " + i+" >" +testchain.getName()+"<");
if (asymId.equals(testchain.getId())) {
//System.out.println("chain "+ chainID+" already known ...");
return testchain;
}
}
return null;
} | [
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32,009 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.java | SimpleMMcifConsumer.convertAtom | private Atom convertAtom(AtomSite atom){
Atom a = new AtomImpl();
a.setPDBserial(Integer.parseInt(atom.getId()));
a.setName(atom.getLabel_atom_id());
double x = Double.parseDouble (atom.getCartn_x());
double y = Double.parseDouble (atom.getCartn_y());
double z = Double.parseDouble (atom.getCartn_z());
a.setX(x);
a.setY(y);
a.setZ(z);
float occupancy = Float.parseFloat (atom.getOccupancy());
a.setOccupancy(occupancy);
float temp = Float.parseFloat (atom.getB_iso_or_equiv());
a.setTempFactor(temp);
String alt = atom.getLabel_alt_id();
if (( alt != null ) && ( alt.length() > 0) && (! alt.equals("."))){
a.setAltLoc(new Character(alt.charAt(0)));
} else {
a.setAltLoc(new Character(' '));
}
Element element = Element.R;
try {
element = Element.valueOfIgnoreCase(atom.getType_symbol());
} catch (IllegalArgumentException e) {
logger.info("Element {} was not recognised as a BioJava-known element, the element will be represented as the generic element {}", atom.getType_symbol(), Element.R.name());
}
a.setElement(element);
return a;
} | java | private Atom convertAtom(AtomSite atom){
Atom a = new AtomImpl();
a.setPDBserial(Integer.parseInt(atom.getId()));
a.setName(atom.getLabel_atom_id());
double x = Double.parseDouble (atom.getCartn_x());
double y = Double.parseDouble (atom.getCartn_y());
double z = Double.parseDouble (atom.getCartn_z());
a.setX(x);
a.setY(y);
a.setZ(z);
float occupancy = Float.parseFloat (atom.getOccupancy());
a.setOccupancy(occupancy);
float temp = Float.parseFloat (atom.getB_iso_or_equiv());
a.setTempFactor(temp);
String alt = atom.getLabel_alt_id();
if (( alt != null ) && ( alt.length() > 0) && (! alt.equals("."))){
a.setAltLoc(new Character(alt.charAt(0)));
} else {
a.setAltLoc(new Character(' '));
}
Element element = Element.R;
try {
element = Element.valueOfIgnoreCase(atom.getType_symbol());
} catch (IllegalArgumentException e) {
logger.info("Element {} was not recognised as a BioJava-known element, the element will be represented as the generic element {}", atom.getType_symbol(), Element.R.name());
}
a.setElement(element);
return a;
} | [
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@param atom the mmmcif AtomSite record
@return an Atom | [
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32,010 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.java | SimpleMMcifConsumer.documentStart | @Override
public void documentStart() {
structure = new StructureImpl();
currentChain = null;
currentGroup = null;
currentNmrModelNumber = null;
//atomCount = 0;
allModels = new ArrayList<List<Chain>>();
currentModel = new ArrayList<Chain>();
entities = new ArrayList<Entity>();
entityPolys = new ArrayList<>();
strucRefs = new ArrayList<StructRef>();
seqResChains = new ArrayList<Chain>();
entityChains = new ArrayList<Chain>();
structAsyms = new ArrayList<StructAsym>();
asymId2entityId = new HashMap<String,String>();
asymId2authorId = new HashMap<>();
structOpers = new ArrayList<PdbxStructOperList>();
strucAssemblies = new ArrayList<PdbxStructAssembly>();
strucAssemblyGens = new ArrayList<PdbxStructAssemblyGen>();
entitySrcGens = new ArrayList<EntitySrcGen>();
entitySrcNats = new ArrayList<EntitySrcNat>();
entitySrcSyns = new ArrayList<EntitySrcSyn>();
structConn = new ArrayList<StructConn>();
structNcsOper = new ArrayList<StructNcsOper>();
sequenceDifs = new ArrayList<StructRefSeqDif>();
structSiteGens = new ArrayList<StructSiteGen>();
} | java | @Override
public void documentStart() {
structure = new StructureImpl();
currentChain = null;
currentGroup = null;
currentNmrModelNumber = null;
//atomCount = 0;
allModels = new ArrayList<List<Chain>>();
currentModel = new ArrayList<Chain>();
entities = new ArrayList<Entity>();
entityPolys = new ArrayList<>();
strucRefs = new ArrayList<StructRef>();
seqResChains = new ArrayList<Chain>();
entityChains = new ArrayList<Chain>();
structAsyms = new ArrayList<StructAsym>();
asymId2entityId = new HashMap<String,String>();
asymId2authorId = new HashMap<>();
structOpers = new ArrayList<PdbxStructOperList>();
strucAssemblies = new ArrayList<PdbxStructAssembly>();
strucAssemblyGens = new ArrayList<PdbxStructAssemblyGen>();
entitySrcGens = new ArrayList<EntitySrcGen>();
entitySrcNats = new ArrayList<EntitySrcNat>();
entitySrcSyns = new ArrayList<EntitySrcSyn>();
structConn = new ArrayList<StructConn>();
structNcsOper = new ArrayList<StructNcsOper>();
sequenceDifs = new ArrayList<StructRefSeqDif>();
structSiteGens = new ArrayList<StructSiteGen>();
} | [
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32,011 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.java | SimpleMMcifConsumer.addAncilliaryEntityData | private void addAncilliaryEntityData(StructAsym asym, int entityId, Entity entity, EntityInfo entityInfo) {
// Loop through each of the entity types and add the corresponding data
// We're assuming if data is duplicated between sources it is consistent
// This is a potentially huge assumption...
for (EntitySrcGen esg : entitySrcGens) {
if (! esg.getEntity_id().equals(asym.getEntity_id()))
continue;
addInformationFromESG(esg, entityId, entityInfo);
}
for (EntitySrcNat esn : entitySrcNats) {
if (! esn.getEntity_id().equals(asym.getEntity_id()))
continue;
addInformationFromESN(esn, entityId, entityInfo);
}
for (EntitySrcSyn ess : entitySrcSyns) {
if (! ess.getEntity_id().equals(asym.getEntity_id()))
continue;
addInfoFromESS(ess, entityId, entityInfo);
}
} | java | private void addAncilliaryEntityData(StructAsym asym, int entityId, Entity entity, EntityInfo entityInfo) {
// Loop through each of the entity types and add the corresponding data
// We're assuming if data is duplicated between sources it is consistent
// This is a potentially huge assumption...
for (EntitySrcGen esg : entitySrcGens) {
if (! esg.getEntity_id().equals(asym.getEntity_id()))
continue;
addInformationFromESG(esg, entityId, entityInfo);
}
for (EntitySrcNat esn : entitySrcNats) {
if (! esn.getEntity_id().equals(asym.getEntity_id()))
continue;
addInformationFromESN(esn, entityId, entityInfo);
}
for (EntitySrcSyn ess : entitySrcSyns) {
if (! ess.getEntity_id().equals(asym.getEntity_id()))
continue;
addInfoFromESS(ess, entityId, entityInfo);
}
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32,012 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.java | SimpleMMcifConsumer.addInformationFromESG | private void addInformationFromESG(EntitySrcGen entitySrcInfo, int entityId, EntityInfo c) {
c.setAtcc(entitySrcInfo.getPdbx_gene_src_atcc());
c.setCell(entitySrcInfo.getPdbx_gene_src_cell());
c.setOrganismCommon(entitySrcInfo.getGene_src_common_name());
c.setOrganismScientific(entitySrcInfo.getPdbx_gene_src_scientific_name());
c.setOrganismTaxId(entitySrcInfo.getPdbx_gene_src_ncbi_taxonomy_id());
c.setExpressionSystemTaxId(entitySrcInfo.getPdbx_host_org_ncbi_taxonomy_id());
c.setExpressionSystem(entitySrcInfo.getPdbx_host_org_scientific_name());
} | java | private void addInformationFromESG(EntitySrcGen entitySrcInfo, int entityId, EntityInfo c) {
c.setAtcc(entitySrcInfo.getPdbx_gene_src_atcc());
c.setCell(entitySrcInfo.getPdbx_gene_src_cell());
c.setOrganismCommon(entitySrcInfo.getGene_src_common_name());
c.setOrganismScientific(entitySrcInfo.getPdbx_gene_src_scientific_name());
c.setOrganismTaxId(entitySrcInfo.getPdbx_gene_src_ncbi_taxonomy_id());
c.setExpressionSystemTaxId(entitySrcInfo.getPdbx_host_org_ncbi_taxonomy_id());
c.setExpressionSystem(entitySrcInfo.getPdbx_host_org_scientific_name());
} | [
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32,013 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.java | SimpleMMcifConsumer.addInformationFromESN | private void addInformationFromESN(EntitySrcNat esn, int eId, EntityInfo c) {
c.setAtcc(esn.getPdbx_atcc());
c.setCell(esn.getPdbx_cell());
c.setOrganismCommon(esn.getCommon_name());
c.setOrganismScientific(esn.getPdbx_organism_scientific());
c.setOrganismTaxId(esn.getPdbx_ncbi_taxonomy_id());
} | java | private void addInformationFromESN(EntitySrcNat esn, int eId, EntityInfo c) {
c.setAtcc(esn.getPdbx_atcc());
c.setCell(esn.getPdbx_cell());
c.setOrganismCommon(esn.getCommon_name());
c.setOrganismScientific(esn.getPdbx_organism_scientific());
c.setOrganismTaxId(esn.getPdbx_ncbi_taxonomy_id());
} | [
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32,014 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.java | SimpleMMcifConsumer.addInfoFromESS | private void addInfoFromESS(EntitySrcSyn ess, int eId, EntityInfo c) {
c.setOrganismCommon(ess.getOrganism_common_name());
c.setOrganismScientific(ess.getOrganism_scientific());
c.setOrganismTaxId(ess.getNcbi_taxonomy_id());
} | java | private void addInfoFromESS(EntitySrcSyn ess, int eId, EntityInfo c) {
c.setOrganismCommon(ess.getOrganism_common_name());
c.setOrganismScientific(ess.getOrganism_scientific());
c.setOrganismTaxId(ess.getNcbi_taxonomy_id());
} | [
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32,015 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.java | SimpleMMcifConsumer.addSites | private void addSites() {
List<Site> sites = structure.getSites();
if (sites == null) sites = new ArrayList<Site>();
for (StructSiteGen siteGen : structSiteGens) {
// For each StructSiteGen, find the residues involved, if they exist then
String site_id = siteGen.getSite_id(); // multiple could be in same site.
if (site_id == null) site_id = "";
String comp_id = siteGen.getLabel_comp_id(); // PDBName
// Assumption: the author chain ID and residue number for the site is consistent with the original
// author chain id and residue numbers.
String asymId = siteGen.getLabel_asym_id(); // chain name
String authId = siteGen.getAuth_asym_id(); // chain Id
String auth_seq_id = siteGen.getAuth_seq_id(); // Res num
String insCode = siteGen.getPdbx_auth_ins_code();
if ( insCode != null && insCode.equals("?"))
insCode = null;
// Look for asymID = chainID and seqID = seq_ID. Check that comp_id matches the resname.
Group g = null;
try {
Chain chain = structure.getChain(asymId);
if (null != chain) {
try {
Character insChar = null;
if (null != insCode && insCode.length() > 0) insChar = insCode.charAt(0);
g = chain.getGroupByPDB(new ResidueNumber(null, Integer.parseInt(auth_seq_id), insChar));
} catch (NumberFormatException e) {
logger.warn("Could not lookup residue : " + authId + auth_seq_id);
}
}
} catch (StructureException e) {
logger.warn("Problem finding residue in site entry " + siteGen.getSite_id() + " - " + e.getMessage(), e.getMessage());
}
if (g != null) {
// 2. find the site_id, if not existing, create anew.
Site site = null;
for (Site asite: sites) {
if (site_id.equals(asite.getSiteID())) site = asite;
}
boolean addSite = false;
// 3. add this residue to the site.
if (site == null) {
addSite = true;
site = new Site();
site.setSiteID(site_id);
}
List<Group> groups = site.getGroups();
if (groups == null) groups = new ArrayList<Group>();
// Check the self-consistency of the residue reference from auth_seq_id and chain_id
if (!comp_id.equals(g.getPDBName())) {
logger.warn("comp_id doesn't match the residue at " + authId + " " + auth_seq_id + " - skipping");
} else {
groups.add(g);
site.setGroups(groups);
}
if (addSite) sites.add(site);
}
}
structure.setSites(sites);
} | java | private void addSites() {
List<Site> sites = structure.getSites();
if (sites == null) sites = new ArrayList<Site>();
for (StructSiteGen siteGen : structSiteGens) {
// For each StructSiteGen, find the residues involved, if they exist then
String site_id = siteGen.getSite_id(); // multiple could be in same site.
if (site_id == null) site_id = "";
String comp_id = siteGen.getLabel_comp_id(); // PDBName
// Assumption: the author chain ID and residue number for the site is consistent with the original
// author chain id and residue numbers.
String asymId = siteGen.getLabel_asym_id(); // chain name
String authId = siteGen.getAuth_asym_id(); // chain Id
String auth_seq_id = siteGen.getAuth_seq_id(); // Res num
String insCode = siteGen.getPdbx_auth_ins_code();
if ( insCode != null && insCode.equals("?"))
insCode = null;
// Look for asymID = chainID and seqID = seq_ID. Check that comp_id matches the resname.
Group g = null;
try {
Chain chain = structure.getChain(asymId);
if (null != chain) {
try {
Character insChar = null;
if (null != insCode && insCode.length() > 0) insChar = insCode.charAt(0);
g = chain.getGroupByPDB(new ResidueNumber(null, Integer.parseInt(auth_seq_id), insChar));
} catch (NumberFormatException e) {
logger.warn("Could not lookup residue : " + authId + auth_seq_id);
}
}
} catch (StructureException e) {
logger.warn("Problem finding residue in site entry " + siteGen.getSite_id() + " - " + e.getMessage(), e.getMessage());
}
if (g != null) {
// 2. find the site_id, if not existing, create anew.
Site site = null;
for (Site asite: sites) {
if (site_id.equals(asite.getSiteID())) site = asite;
}
boolean addSite = false;
// 3. add this residue to the site.
if (site == null) {
addSite = true;
site = new Site();
site.setSiteID(site_id);
}
List<Group> groups = site.getGroups();
if (groups == null) groups = new ArrayList<Group>();
// Check the self-consistency of the residue reference from auth_seq_id and chain_id
if (!comp_id.equals(g.getPDBName())) {
logger.warn("comp_id doesn't match the residue at " + authId + " " + auth_seq_id + " - skipping");
} else {
groups.add(g);
site.setGroups(groups);
}
if (addSite) sites.add(site);
}
}
structure.setSites(sites);
} | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.java#L2097-L2166 |
32,016 | biojava/biojava | biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/JMatrixPanel.java | JMatrixPanel.drawPairs | public void drawPairs(Graphics g){
if ( aligs == null)
return;
int nr = aligs.length;
Graphics2D g2D = (Graphics2D)g;
Stroke oldStroke = g2D.getStroke();
g2D.setStroke(stroke);
Color color;
float hue;
int width = Math.round(scale);
int w2 = width / 2 ;
for (int i = 0; i < aligs.length; i++) {
AlternativeAlignment a = aligs[i];
int[] idx1 = a.getIdx1();
int[] idx2 = a.getIdx2();
int xold = -1;
int yold = -1;
boolean start = true;
if ( (selectedAlignmentPos != -1 ) &&
( selectedAlignmentPos == i)){
color = Color.white;
} else {
hue = i * (1/ (float)nr);
color = Color.getHSBColor(hue,1.0f,1.0f);
}
g.setColor(color);
for (int j = 0; j < idx1.length; j++) {
int x1 = Math.round(idx1[j]*scale) ;
int y1 = Math.round(idx2[j]*scale) ;
if ( ! start){
//g.drawLine(xold+1,yold,x1+1,y1);
//g2D.draw(new Line2D.Double(xold,yold,x1,y1));
g.fillRect(xold,yold,2,2);
} else {
g.fillRect(x1,y1, w2, w2);
start =false;
}
xold = x1;
yold = y1;
}
if ( ! start)
g.fillRect(xold,yold,w2,w2);
}
g2D.setStroke(oldStroke);
} | java | public void drawPairs(Graphics g){
if ( aligs == null)
return;
int nr = aligs.length;
Graphics2D g2D = (Graphics2D)g;
Stroke oldStroke = g2D.getStroke();
g2D.setStroke(stroke);
Color color;
float hue;
int width = Math.round(scale);
int w2 = width / 2 ;
for (int i = 0; i < aligs.length; i++) {
AlternativeAlignment a = aligs[i];
int[] idx1 = a.getIdx1();
int[] idx2 = a.getIdx2();
int xold = -1;
int yold = -1;
boolean start = true;
if ( (selectedAlignmentPos != -1 ) &&
( selectedAlignmentPos == i)){
color = Color.white;
} else {
hue = i * (1/ (float)nr);
color = Color.getHSBColor(hue,1.0f,1.0f);
}
g.setColor(color);
for (int j = 0; j < idx1.length; j++) {
int x1 = Math.round(idx1[j]*scale) ;
int y1 = Math.round(idx2[j]*scale) ;
if ( ! start){
//g.drawLine(xold+1,yold,x1+1,y1);
//g2D.draw(new Line2D.Double(xold,yold,x1,y1));
g.fillRect(xold,yold,2,2);
} else {
g.fillRect(x1,y1, w2, w2);
start =false;
}
xold = x1;
yold = y1;
}
if ( ! start)
g.fillRect(xold,yold,w2,w2);
}
g2D.setStroke(oldStroke);
} | [
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@param g | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/JMatrixPanel.java#L176-L234 |
32,017 | biojava/biojava | biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/JMatrixPanel.java | JMatrixPanel.drawBoxes | public void drawBoxes(Graphics g){
if ( fragmentPairs == null )
return;
g.setColor(Color.yellow);
for (int i = 0; i < fragmentPairs.length; i++) {
FragmentPair fp =fragmentPairs[i];
int xp = fp.getPos1();
int yp = fp.getPos2();
int width = Math.round(scale);
g.drawRect(Math.round(xp*scale),Math.round(yp*scale),width, width);
}
} | java | public void drawBoxes(Graphics g){
if ( fragmentPairs == null )
return;
g.setColor(Color.yellow);
for (int i = 0; i < fragmentPairs.length; i++) {
FragmentPair fp =fragmentPairs[i];
int xp = fp.getPos1();
int yp = fp.getPos2();
int width = Math.round(scale);
g.drawRect(Math.round(xp*scale),Math.round(yp*scale),width, width);
}
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32,018 | biojava/biojava | biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/JMatrixPanel.java | JMatrixPanel.drawDistances | public void drawDistances(Graphics g1){
Graphics2D g = (Graphics2D)g1;
int c = matrix.getRowDimension();
int d = matrix.getColumnDimension();
float scale = getScale();
int width = Math.round(scale);
for (int i = 0; i < c; i++) {
int ipaint = Math.round(i*scale);
for (int j = 0; j < d; j++) {
double val = matrix.get(i,j);
int jpaint = Math.round(j*scale);
Color color = cellColor.getColor(val);
g.setColor(color);
g.fillRect(ipaint,jpaint,width,width);
}
}
} | java | public void drawDistances(Graphics g1){
Graphics2D g = (Graphics2D)g1;
int c = matrix.getRowDimension();
int d = matrix.getColumnDimension();
float scale = getScale();
int width = Math.round(scale);
for (int i = 0; i < c; i++) {
int ipaint = Math.round(i*scale);
for (int j = 0; j < d; j++) {
double val = matrix.get(i,j);
int jpaint = Math.round(j*scale);
Color color = cellColor.getColor(val);
g.setColor(color);
g.fillRect(ipaint,jpaint,width,width);
}
}
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32,019 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ABITrace.java | ABITrace.ABITraceInit | private void ABITraceInit(BufferedInputStream bis) throws IOException{
byte[] bytes = null;
ByteArrayOutputStream baos = new ByteArrayOutputStream();
int b;
while ((b = bis.read()) >= 0)
{
baos.write(b);
}
bis.close(); baos.close();
bytes = baos.toByteArray();
initData(bytes);
} | java | private void ABITraceInit(BufferedInputStream bis) throws IOException{
byte[] bytes = null;
ByteArrayOutputStream baos = new ByteArrayOutputStream();
int b;
while ((b = bis.read()) >= 0)
{
baos.write(b);
}
bis.close(); baos.close();
bytes = baos.toByteArray();
initData(bytes);
} | [
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@param bis - BufferedInputStream
@throws IOException if there is a problem reading from the BufferedInputStream | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ABITrace.java#L112-L123 |
32,020 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ABITrace.java | ABITrace.getTrace | public int[] getTrace (String base) throws CompoundNotFoundException {
if (base.equals("A")) {
return A;
} else if (base.equals("C")) {
return C;
} else if (base.equals("G")) {
return G;
} else if (base.equals("T")) {
return T;
} else {
throw new CompoundNotFoundException("Don't know base: " + base);
}
} | java | public int[] getTrace (String base) throws CompoundNotFoundException {
if (base.equals("A")) {
return A;
} else if (base.equals("C")) {
return C;
} else if (base.equals("G")) {
return G;
} else if (base.equals("T")) {
return T;
} else {
throw new CompoundNotFoundException("Don't know base: " + base);
}
} | [
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each of which correspond to a single x-coordinate relative to the
position in the array, so that if element 4 in the array is 972, then
x is 4 and y is 972 for that point.
@param base - the DNA String to retrieve the trace values for
@return an array of ints giving the entire trace for that base
@throws CompoundNotFoundException if the base is not valid | [
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32,021 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ABITrace.java | ABITrace.calculateScale | private double calculateScale(int height) {
double newScale = 0.0;
double max = (double) getMaximum();
double ht = (double) height;
newScale = ((ht - 50.0)) / max;
return newScale;
} | java | private double calculateScale(int height) {
double newScale = 0.0;
double max = (double) getMaximum();
double ht = (double) height;
newScale = ((ht - 50.0)) / max;
return newScale;
} | [
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@param height - required height in pixels
@return - scaling factor | [
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32,022 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ABITrace.java | ABITrace.getMaximum | private int getMaximum() {
int max = 0;
for (int x = 0; x <= T.length - 1; x++) {
if (T[x] > max) max = T[x];
if (A[x] > max) max = A[x];
if (C[x] > max) max = C[x];
if (G[x] > max) max = G[x];
}
return max;
} | java | private int getMaximum() {
int max = 0;
for (int x = 0; x <= T.length - 1; x++) {
if (T[x] > max) max = T[x];
if (A[x] > max) max = A[x];
if (C[x] > max) max = C[x];
if (G[x] > max) max = G[x];
}
return max;
} | [
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in the event of multiple calls, but it initialized lazily.
@return - maximum height of any of the traces | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ABITrace.java#L336-L345 |
32,023 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ABITrace.java | ABITrace.initData | private void initData(byte[] fileData) {
traceData = fileData;
if (isABI()) {
setIndex();
setBasecalls();
setQcalls();
setSeq();
setTraces();
} else throw new IllegalArgumentException("Not a valid ABI file.");
} | java | private void initData(byte[] fileData) {
traceData = fileData;
if (isABI()) {
setIndex();
setBasecalls();
setQcalls();
setSeq();
setTraces();
} else throw new IllegalArgumentException("Not a valid ABI file.");
} | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ABITrace.java#L353-L362 |
32,024 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ABITrace.java | ABITrace.setTraces | private void setTraces() {
int pointers[] = new int[4]; //alphabetical, 0=A, 1=C, 2=G, 3=T
int datas[] = new int[4];
char order[] = new char[4];
datas[0] = DATA9;
datas[1] = DATA10;
datas[2] = DATA11;
datas[3] = DATA12;
for (int i = 0; i <= 3; i++) {
order[i] = (char) traceData[FWO + i];
}
for (int i = 0; i <= 3; i++) {
switch (order[i]) {
case 'A':
case 'a':
pointers[0] = datas[i];
break;
case 'C':
case 'c':
pointers[1] = datas[i];
break;
case 'G':
case 'g':
pointers[2] = datas[i];
break;
case 'T':
case 't':
pointers[3] = datas[i];
break;
default:
throw new IllegalArgumentException("Trace contains illegal values.");
}
}
A = new int[traceLength];
C = new int[traceLength];
G = new int[traceLength];
T = new int[traceLength];
for (int i = 0; i <= 3; i++) {
byte[] qq = new byte[traceLength * 2];
getSubArray(qq, pointers[i]);
DataInputStream dis = new DataInputStream(new ByteArrayInputStream(qq));
for (int x = 0; x <= traceLength - 1; x++) {
try {
if (i == 0) A[x] = (int) dis.readShort();
if (i == 1) C[x] = (int) dis.readShort();
if (i == 2) G[x] = (int) dis.readShort();
if (i == 3) T[x] = (int) dis.readShort();
} catch (IOException e)//This shouldn't happen. If it does something must be seriously wrong.
{
throw new IllegalStateException("Unexpected IOException encountered while manipulating internal streams.");
}
}
}
return;
} | java | private void setTraces() {
int pointers[] = new int[4]; //alphabetical, 0=A, 1=C, 2=G, 3=T
int datas[] = new int[4];
char order[] = new char[4];
datas[0] = DATA9;
datas[1] = DATA10;
datas[2] = DATA11;
datas[3] = DATA12;
for (int i = 0; i <= 3; i++) {
order[i] = (char) traceData[FWO + i];
}
for (int i = 0; i <= 3; i++) {
switch (order[i]) {
case 'A':
case 'a':
pointers[0] = datas[i];
break;
case 'C':
case 'c':
pointers[1] = datas[i];
break;
case 'G':
case 'g':
pointers[2] = datas[i];
break;
case 'T':
case 't':
pointers[3] = datas[i];
break;
default:
throw new IllegalArgumentException("Trace contains illegal values.");
}
}
A = new int[traceLength];
C = new int[traceLength];
G = new int[traceLength];
T = new int[traceLength];
for (int i = 0; i <= 3; i++) {
byte[] qq = new byte[traceLength * 2];
getSubArray(qq, pointers[i]);
DataInputStream dis = new DataInputStream(new ByteArrayInputStream(qq));
for (int x = 0; x <= traceLength - 1; x++) {
try {
if (i == 0) A[x] = (int) dis.readShort();
if (i == 1) C[x] = (int) dis.readShort();
if (i == 2) G[x] = (int) dis.readShort();
if (i == 3) T[x] = (int) dis.readShort();
} catch (IOException e)//This shouldn't happen. If it does something must be seriously wrong.
{
throw new IllegalStateException("Unexpected IOException encountered while manipulating internal streams.");
}
}
}
return;
} | [
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32,025 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ABITrace.java | ABITrace.setSeq | private void setSeq() {
char tempseq[] = new char[seqLength];
for (int x = 0; x <= seqLength - 1; ++x) {
tempseq[x] = (char) traceData[PBAS2 + x];
}
sequence = new String(tempseq);
} | java | private void setSeq() {
char tempseq[] = new char[seqLength];
for (int x = 0; x <= seqLength - 1; ++x) {
tempseq[x] = (char) traceData[PBAS2 + x];
}
sequence = new String(tempseq);
} | [
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"... | Fetch the sequence from the trace data. | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ABITrace.java#L432-L438 |
32,026 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ABITrace.java | ABITrace.setQcalls | private void setQcalls() {
qCalls = new int[seqLength];
byte[] qq = new byte[seqLength];
getSubArray(qq, PCON);
DataInputStream dis = new DataInputStream(new ByteArrayInputStream(qq));
for (int i = 0; i <= seqLength - 1; ++i) {
try {
qCalls[i] = (int) dis.readByte();
} catch (IOException e)//This shouldn't happen. If it does something must be seriously wrong.
{
throw new IllegalStateException("Unexpected IOException encountered while manipulating internal streams.");
}
}
} | java | private void setQcalls() {
qCalls = new int[seqLength];
byte[] qq = new byte[seqLength];
getSubArray(qq, PCON);
DataInputStream dis = new DataInputStream(new ByteArrayInputStream(qq));
for (int i = 0; i <= seqLength - 1; ++i) {
try {
qCalls[i] = (int) dis.readByte();
} catch (IOException e)//This shouldn't happen. If it does something must be seriously wrong.
{
throw new IllegalStateException("Unexpected IOException encountered while manipulating internal streams.");
}
}
} | [
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32,027 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ABITrace.java | ABITrace.setBasecalls | private void setBasecalls() {
baseCalls = new int[seqLength];
byte[] qq = new byte[seqLength * 2];
getSubArray(qq, PLOC);
DataInputStream dis = new DataInputStream(new ByteArrayInputStream(qq));
for (int i = 0; i <= seqLength - 1; ++i) {
try {
baseCalls[i] = (int) dis.readShort();
} catch (IOException e)//This shouldn't happen. If it does something must be seriously wrong.
{
throw new IllegalStateException("Unexpected IOException encountered while manipulating internal streams.");
}
}
} | java | private void setBasecalls() {
baseCalls = new int[seqLength];
byte[] qq = new byte[seqLength * 2];
getSubArray(qq, PLOC);
DataInputStream dis = new DataInputStream(new ByteArrayInputStream(qq));
for (int i = 0; i <= seqLength - 1; ++i) {
try {
baseCalls[i] = (int) dis.readShort();
} catch (IOException e)//This shouldn't happen. If it does something must be seriously wrong.
{
throw new IllegalStateException("Unexpected IOException encountered while manipulating internal streams.");
}
}
} | [
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32,028 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ABITrace.java | ABITrace.setIndex | private void setIndex() {
int DataCounter, PBASCounter, PLOCCounter, PCONCounter, NumRecords, indexBase;
byte[] RecNameArray = new byte[4];
String RecName;
DataCounter = 0;
PBASCounter = 0;
PLOCCounter = 0;
PCONCounter = 0;
indexBase = getIntAt(absIndexBase + macJunk);
NumRecords = getIntAt(absIndexBase - 8 + macJunk);
for (int record = 0; record <= NumRecords - 1; record++) {
getSubArray(RecNameArray, (indexBase + (record * 28)));
RecName = new String(RecNameArray);
if (RecName.equals("FWO_"))
FWO = indexBase + (record * 28) + 20;
if (RecName.equals("DATA")) {
++DataCounter;
if (DataCounter == 9)
DATA9 = indexBase + (record * 28) + 20;
if (DataCounter == 10)
DATA10 = indexBase + (record * 28) + 20;
if (DataCounter == 11)
DATA11 = indexBase + (record * 28) + 20;
if (DataCounter == 12)
DATA12 = indexBase + (record * 28) + 20;
}
if (RecName.equals("PBAS")) {
++PBASCounter;
if (PBASCounter == 2)
PBAS2 = indexBase + (record * 28) + 20;
}
if (RecName.equals("PLOC")) {
++PLOCCounter;
if (PLOCCounter == 2)
PLOC = indexBase + (record * 28) + 20;
}
if (RecName.equals("PCON")) {
++PCONCounter;
if (PCONCounter == 2)
PCON = indexBase + (record * 28) + 20;
}
} //next record
traceLength = getIntAt(DATA12 - 8);
seqLength = getIntAt(PBAS2 - 4);
PLOC = getIntAt(PLOC) + macJunk;
DATA9 = getIntAt(DATA9) + macJunk;
DATA10 = getIntAt(DATA10) + macJunk;
DATA11 = getIntAt(DATA11) + macJunk;
DATA12 = getIntAt(DATA12) + macJunk;
PBAS2 = getIntAt(PBAS2) + macJunk;
PCON = getIntAt(PCON) + macJunk;
} | java | private void setIndex() {
int DataCounter, PBASCounter, PLOCCounter, PCONCounter, NumRecords, indexBase;
byte[] RecNameArray = new byte[4];
String RecName;
DataCounter = 0;
PBASCounter = 0;
PLOCCounter = 0;
PCONCounter = 0;
indexBase = getIntAt(absIndexBase + macJunk);
NumRecords = getIntAt(absIndexBase - 8 + macJunk);
for (int record = 0; record <= NumRecords - 1; record++) {
getSubArray(RecNameArray, (indexBase + (record * 28)));
RecName = new String(RecNameArray);
if (RecName.equals("FWO_"))
FWO = indexBase + (record * 28) + 20;
if (RecName.equals("DATA")) {
++DataCounter;
if (DataCounter == 9)
DATA9 = indexBase + (record * 28) + 20;
if (DataCounter == 10)
DATA10 = indexBase + (record * 28) + 20;
if (DataCounter == 11)
DATA11 = indexBase + (record * 28) + 20;
if (DataCounter == 12)
DATA12 = indexBase + (record * 28) + 20;
}
if (RecName.equals("PBAS")) {
++PBASCounter;
if (PBASCounter == 2)
PBAS2 = indexBase + (record * 28) + 20;
}
if (RecName.equals("PLOC")) {
++PLOCCounter;
if (PLOCCounter == 2)
PLOC = indexBase + (record * 28) + 20;
}
if (RecName.equals("PCON")) {
++PCONCounter;
if (PCONCounter == 2)
PCON = indexBase + (record * 28) + 20;
}
} //next record
traceLength = getIntAt(DATA12 - 8);
seqLength = getIntAt(PBAS2 - 4);
PLOC = getIntAt(PLOC) + macJunk;
DATA9 = getIntAt(DATA9) + macJunk;
DATA10 = getIntAt(DATA10) + macJunk;
DATA11 = getIntAt(DATA11) + macJunk;
DATA12 = getIntAt(DATA12) + macJunk;
PBAS2 = getIntAt(PBAS2) + macJunk;
PCON = getIntAt(PCON) + macJunk;
} | [
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32,029 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ABITrace.java | ABITrace.getSubArray | private void getSubArray(byte[] b, int traceDataOffset) {
for (int x = 0; x <= b.length - 1; x++) {
b[x] = traceData[traceDataOffset + x];
}
} | java | private void getSubArray(byte[] b, int traceDataOffset) {
for (int x = 0; x <= b.length - 1; x++) {
b[x] = traceData[traceDataOffset + x];
}
} | [
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@param b - trace byte array
@param traceDataOffset - starting point | [
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32,030 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/ABITrace.java | ABITrace.isABI | private boolean isABI() {
char ABI[] = new char[4];
for (int i = 0; i <= 2; i++) {
ABI[i] = (char) traceData[i];
}
if (ABI[0] == 'A' && (ABI[1] == 'B' && ABI[2] == 'I')) {
return true;
} else {
for (int i = 128; i <= 130; i++) {
ABI[i-128] = (char) traceData[i];
}
if (ABI[0] == 'A' && (ABI[1] == 'B' && ABI[2] == 'I')) {
macJunk = 128;
return true;
} else
return false;
}
} | java | private boolean isABI() {
char ABI[] = new char[4];
for (int i = 0; i <= 2; i++) {
ABI[i] = (char) traceData[i];
}
if (ABI[0] == 'A' && (ABI[1] == 'B' && ABI[2] == 'I')) {
return true;
} else {
for (int i = 128; i <= 130; i++) {
ABI[i-128] = (char) traceData[i];
}
if (ABI[0] == 'A' && (ABI[1] == 'B' && ABI[2] == 'I')) {
macJunk = 128;
return true;
} else
return false;
}
} | [
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are "ABI". Also handle the special case where 128 bytes were prepended to the file
due to binary FTP from an older macintosh system.
@return - if format of ABI file is correct | [
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32,031 | biojava/biojava | biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/GeneNamesParser.java | GeneNamesParser.main | public static void main(String[] args) {
try {
List<GeneName> geneNames = getGeneNames();
logger.info("got {} gene names", geneNames.size());
for ( GeneName g : geneNames){
if ( g.getApprovedSymbol().equals("FOLH1"))
logger.info("Gene Name: {}", g);
}
// and returns a list of beans that contains key-value pairs for each gene name
} catch (Exception e) {
// TODO Auto-generated catch block
logger.error("Exception: ", e);
}
} | java | public static void main(String[] args) {
try {
List<GeneName> geneNames = getGeneNames();
logger.info("got {} gene names", geneNames.size());
for ( GeneName g : geneNames){
if ( g.getApprovedSymbol().equals("FOLH1"))
logger.info("Gene Name: {}", g);
}
// and returns a list of beans that contains key-value pairs for each gene name
} catch (Exception e) {
// TODO Auto-generated catch block
logger.error("Exception: ", e);
}
} | [
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@param args | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/GeneNamesParser.java#L55-L74 |
32,032 | biojava/biojava | biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/GeneNamesParser.java | GeneNamesParser.getGeneNames | public static List<GeneName> getGeneNames(InputStream inStream) throws IOException{
ArrayList<GeneName> geneNames = new ArrayList<GeneName>();
BufferedReader reader = new BufferedReader(new InputStreamReader(inStream));
// skip reading first line (it is the legend)
String line = reader.readLine();
while ((line = reader.readLine()) != null) {
// process line...
//System.out.println(Arrays.toString(line.split("\t")));
GeneName geneName = getGeneName(line);
if ( geneName != null)
geneNames.add(geneName);
//System.out.println(geneName);
}
// since this is a large list, let's free up unused space...
geneNames.trimToSize();
return geneNames;
} | java | public static List<GeneName> getGeneNames(InputStream inStream) throws IOException{
ArrayList<GeneName> geneNames = new ArrayList<GeneName>();
BufferedReader reader = new BufferedReader(new InputStreamReader(inStream));
// skip reading first line (it is the legend)
String line = reader.readLine();
while ((line = reader.readLine()) != null) {
// process line...
//System.out.println(Arrays.toString(line.split("\t")));
GeneName geneName = getGeneName(line);
if ( geneName != null)
geneNames.add(geneName);
//System.out.println(geneName);
}
// since this is a large list, let's free up unused space...
geneNames.trimToSize();
return geneNames;
} | [
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@param inStream
@return list of geneNames
@throws IOException | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/genename/GeneNamesParser.java#L93-L115 |
32,033 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/GeneSequence.java | GeneSequence.addIntronsUsingExons | public void addIntronsUsingExons() throws Exception {
if (intronAdded) { //going to assume introns are correct
return;
}
if (exonSequenceList.size() == 0) {
return;
}
ExonComparator exonComparator = new ExonComparator();
//sort based on start position and sense;
Collections.sort(exonSequenceList, exonComparator);
int shift = -1;
if (getStrand() == Strand.NEGATIVE) {
shift = 1;
}
//ExonSequence firstExonSequence = exonSequenceList.get(0);
int intronIndex = 1;
// if (firstExonSequence.getBioBegin().intValue() != getBioBegin().intValue()) {
// this.addIntron(new AccessionID(this.getAccession().getID() + "-" + "intron" + intronIndex), getBioBegin(), firstExonSequence.getBioBegin() + shift);
// intronIndex++;
// }
for (int i = 0; i < exonSequenceList.size() - 1; i++) {
ExonSequence exon1 = exonSequenceList.get(i);
ExonSequence exon2 = exonSequenceList.get(i + 1);
this.addIntron(new AccessionID(this.getAccession().getID() + "-" + "intron" + intronIndex), exon1.getBioEnd() - shift, exon2.getBioBegin() + shift);
intronIndex++;
}
// ExonSequence lastExonSequence = exonSequenceList.get(exonSequenceList.size() - 1);
// if (lastExonSequence.getBioEnd().intValue() != getBioEnd().intValue()) {
// this.addIntron(new AccessionID(this.getAccession().getID() + "-" + "intron" + intronIndex), lastExonSequence.getBioEnd() - shift, getBioEnd());
// intronIndex++;
// }
// log.severe("Add in support for building introns based on added exons");
} | java | public void addIntronsUsingExons() throws Exception {
if (intronAdded) { //going to assume introns are correct
return;
}
if (exonSequenceList.size() == 0) {
return;
}
ExonComparator exonComparator = new ExonComparator();
//sort based on start position and sense;
Collections.sort(exonSequenceList, exonComparator);
int shift = -1;
if (getStrand() == Strand.NEGATIVE) {
shift = 1;
}
//ExonSequence firstExonSequence = exonSequenceList.get(0);
int intronIndex = 1;
// if (firstExonSequence.getBioBegin().intValue() != getBioBegin().intValue()) {
// this.addIntron(new AccessionID(this.getAccession().getID() + "-" + "intron" + intronIndex), getBioBegin(), firstExonSequence.getBioBegin() + shift);
// intronIndex++;
// }
for (int i = 0; i < exonSequenceList.size() - 1; i++) {
ExonSequence exon1 = exonSequenceList.get(i);
ExonSequence exon2 = exonSequenceList.get(i + 1);
this.addIntron(new AccessionID(this.getAccession().getID() + "-" + "intron" + intronIndex), exon1.getBioEnd() - shift, exon2.getBioBegin() + shift);
intronIndex++;
}
// ExonSequence lastExonSequence = exonSequenceList.get(exonSequenceList.size() - 1);
// if (lastExonSequence.getBioEnd().intValue() != getBioEnd().intValue()) {
// this.addIntron(new AccessionID(this.getAccession().getID() + "-" + "intron" + intronIndex), lastExonSequence.getBioEnd() - shift, getBioEnd());
// intronIndex++;
// }
// log.severe("Add in support for building introns based on added exons");
} | [
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can infer the intron sequences and add them. You may also have the case where you only added one or more
TranscriptSequences and from that you can infer the exon sequences and intron sequences.
Currently not implement | [
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32,034 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/GeneSequence.java | GeneSequence.addTranscript | public TranscriptSequence addTranscript(AccessionID accession, int begin, int end) throws Exception {
if (transcriptSequenceHashMap.containsKey(accession.getID())) {
throw new Exception("Duplicate accesion id " + accession.getID());
}
TranscriptSequence transcriptSequence = new TranscriptSequence(this, begin, end);
transcriptSequence.setAccession(accession);
transcriptSequenceHashMap.put(accession.getID(), transcriptSequence);
return transcriptSequence;
} | java | public TranscriptSequence addTranscript(AccessionID accession, int begin, int end) throws Exception {
if (transcriptSequenceHashMap.containsKey(accession.getID())) {
throw new Exception("Duplicate accesion id " + accession.getID());
}
TranscriptSequence transcriptSequence = new TranscriptSequence(this, begin, end);
transcriptSequence.setAccession(accession);
transcriptSequenceHashMap.put(accession.getID(), transcriptSequence);
return transcriptSequence;
} | [
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32,035 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/GeneSequence.java | GeneSequence.removeIntron | public IntronSequence removeIntron(String accession) {
for (IntronSequence intronSequence : intronSequenceList) {
if (intronSequence.getAccession().getID().equals(accession)) {
intronSequenceList.remove(intronSequence);
intronSequenceHashMap.remove(accession);
return intronSequence;
}
}
return null;
} | java | public IntronSequence removeIntron(String accession) {
for (IntronSequence intronSequence : intronSequenceList) {
if (intronSequence.getAccession().getID().equals(accession)) {
intronSequenceList.remove(intronSequence);
intronSequenceHashMap.remove(accession);
return intronSequence;
}
}
return null;
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@return intron sequence | [
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32,036 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/GeneSequence.java | GeneSequence.addIntron | public IntronSequence addIntron(AccessionID accession, int begin, int end) throws Exception {
if (intronSequenceHashMap.containsKey(accession.getID())) {
throw new Exception("Duplicate accesion id " + accession.getID());
}
intronAdded = true;
IntronSequence intronSequence = new IntronSequence(this, begin, end); // working off the assumption that intron frame is always 0 or doesn't matter and same sense as parent
intronSequence.setAccession(accession);
intronSequenceList.add(intronSequence);
intronSequenceHashMap.put(accession.getID(), intronSequence);
return intronSequence;
} | java | public IntronSequence addIntron(AccessionID accession, int begin, int end) throws Exception {
if (intronSequenceHashMap.containsKey(accession.getID())) {
throw new Exception("Duplicate accesion id " + accession.getID());
}
intronAdded = true;
IntronSequence intronSequence = new IntronSequence(this, begin, end); // working off the assumption that intron frame is always 0 or doesn't matter and same sense as parent
intronSequence.setAccession(accession);
intronSequenceList.add(intronSequence);
intronSequenceHashMap.put(accession.getID(), intronSequence);
return intronSequence;
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32,037 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/GeneSequence.java | GeneSequence.removeExon | public ExonSequence removeExon(String accession) {
for (ExonSequence exonSequence : exonSequenceList) {
if (exonSequence.getAccession().getID().equals(accession)) {
exonSequenceList.remove(exonSequence);
exonSequenceHashMap.remove(accession);
// we now have a new gap which creates an intron
intronSequenceList.clear();
intronSequenceHashMap.clear();
intronAdded = false;
try{
addIntronsUsingExons();
} catch(Exception e){
logger.error("Remove Exon validate() error " + e.getMessage());
}
return exonSequence;
}
}
return null;
} | java | public ExonSequence removeExon(String accession) {
for (ExonSequence exonSequence : exonSequenceList) {
if (exonSequence.getAccession().getID().equals(accession)) {
exonSequenceList.remove(exonSequence);
exonSequenceHashMap.remove(accession);
// we now have a new gap which creates an intron
intronSequenceList.clear();
intronSequenceHashMap.clear();
intronAdded = false;
try{
addIntronsUsingExons();
} catch(Exception e){
logger.error("Remove Exon validate() error " + e.getMessage());
}
return exonSequence;
}
}
return null;
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32,038 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/GeneSequence.java | GeneSequence.addExon | public ExonSequence addExon(AccessionID accession, int begin, int end) throws Exception {
if (exonSequenceHashMap.containsKey(accession.getID())) {
throw new Exception("Duplicate accesion id " + accession.getID());
}
ExonSequence exonSequence = new ExonSequence(this, begin, end); //sense should be the same as parent
exonSequence.setAccession(accession);
exonSequenceList.add(exonSequence);
exonSequenceHashMap.put(accession.getID(), exonSequence);
return exonSequence;
} | java | public ExonSequence addExon(AccessionID accession, int begin, int end) throws Exception {
if (exonSequenceHashMap.containsKey(accession.getID())) {
throw new Exception("Duplicate accesion id " + accession.getID());
}
ExonSequence exonSequence = new ExonSequence(this, begin, end); //sense should be the same as parent
exonSequence.setAccession(accession);
exonSequenceList.add(exonSequence);
exonSequenceHashMap.put(accession.getID(), exonSequence);
return exonSequence;
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32,039 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/GeneSequence.java | GeneSequence.getSequence5PrimeTo3Prime | public DNASequence getSequence5PrimeTo3Prime() {
String sequence = getSequenceAsString(this.getBioBegin(), this.getBioEnd(), this.getStrand());
if (getStrand() == Strand.NEGATIVE) {
//need to take complement of sequence because it is negative and we are returning the gene sequence from the opposite strand
StringBuilder b = new StringBuilder(getLength());
CompoundSet<NucleotideCompound> compoundSet = this.getCompoundSet();
for (int i = 0; i < sequence.length(); i++) {
String nucleotide = String.valueOf(sequence.charAt(i));
NucleotideCompound nucleotideCompound = compoundSet.getCompoundForString(nucleotide);
b.append(nucleotideCompound.getComplement().getShortName());
}
sequence = b.toString();
}
DNASequence dnaSequence = null;
try {
dnaSequence = new DNASequence(sequence.toUpperCase());
} catch (CompoundNotFoundException e) {
// this should not happen, the sequence is DNA originally, if it does, there's a bug somewhere
logger.error("Could not create new DNA sequence in getSequence5PrimeTo3Prime(). Error: {}",e.getMessage());
}
dnaSequence.setAccession(new AccessionID(this.getAccession().getID()));
return dnaSequence;
} | java | public DNASequence getSequence5PrimeTo3Prime() {
String sequence = getSequenceAsString(this.getBioBegin(), this.getBioEnd(), this.getStrand());
if (getStrand() == Strand.NEGATIVE) {
//need to take complement of sequence because it is negative and we are returning the gene sequence from the opposite strand
StringBuilder b = new StringBuilder(getLength());
CompoundSet<NucleotideCompound> compoundSet = this.getCompoundSet();
for (int i = 0; i < sequence.length(); i++) {
String nucleotide = String.valueOf(sequence.charAt(i));
NucleotideCompound nucleotideCompound = compoundSet.getCompoundForString(nucleotide);
b.append(nucleotideCompound.getComplement().getShortName());
}
sequence = b.toString();
}
DNASequence dnaSequence = null;
try {
dnaSequence = new DNASequence(sequence.toUpperCase());
} catch (CompoundNotFoundException e) {
// this should not happen, the sequence is DNA originally, if it does, there's a bug somewhere
logger.error("Could not create new DNA sequence in getSequence5PrimeTo3Prime(). Error: {}",e.getMessage());
}
dnaSequence.setAccession(new AccessionID(this.getAccession().getID()));
return dnaSequence;
} | [
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Returns the DNASequence representative of the 5' and 3' reading based on strand
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32,040 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/PDBHeader.java | PDBHeader.toPDB | @Override
public void toPDB(StringBuffer buf){
// 1 2 3 4 5 6 7
//01234567890123456789012345678901234567890123456789012345678901234567890123456789
//HEADER COMPLEX (SERINE PROTEASE/INHIBITORS) 06-FEB-98 1A4W
//TITLE CRYSTAL STRUCTURES OF THROMBIN WITH THIAZOLE-CONTAINING
//TITLE 2 INHIBITORS: PROBES OF THE S1' BINDING SITE
printHeader(buf);
printTitle(buf);
printExpdata(buf);
printAuthors(buf);
printResolution(buf);
} | java | @Override
public void toPDB(StringBuffer buf){
// 1 2 3 4 5 6 7
//01234567890123456789012345678901234567890123456789012345678901234567890123456789
//HEADER COMPLEX (SERINE PROTEASE/INHIBITORS) 06-FEB-98 1A4W
//TITLE CRYSTAL STRUCTURES OF THROMBIN WITH THIAZOLE-CONTAINING
//TITLE 2 INHIBITORS: PROBES OF THE S1' BINDING SITE
printHeader(buf);
printTitle(buf);
printExpdata(buf);
printAuthors(buf);
printResolution(buf);
} | [
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32,041 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/PDBHeader.java | PDBHeader.setExperimentalTechnique | public boolean setExperimentalTechnique(String techniqueStr) {
ExperimentalTechnique et = ExperimentalTechnique.getByName(techniqueStr);
if (et==null) return false;
if (techniques==null) {
techniques = EnumSet.of(et);
return true;
} else {
return techniques.add(et);
}
} | java | public boolean setExperimentalTechnique(String techniqueStr) {
ExperimentalTechnique et = ExperimentalTechnique.getByName(techniqueStr);
if (et==null) return false;
if (techniques==null) {
techniques = EnumSet.of(et);
return true;
} else {
return techniques.add(et);
}
} | [
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32,042 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/ChargeAdder.java | ChargeAdder.addCharges | public static void addCharges(Structure structure) {
// Loop through the models
for(int i=0; i<structure.nrModels(); i++){
for(Chain c: structure.getChains(i)){
for(Group g: c.getAtomGroups()){
ChemComp thisChemComp = ChemCompGroupFactory.getChemComp(g.getPDBName());
List<ChemCompAtom> chemAtoms = thisChemComp.getAtoms();
for(ChemCompAtom chemCompAtom : chemAtoms) {
Atom atom = g.getAtom(chemCompAtom.getAtom_id());
String stringCharge = chemCompAtom.getCharge();
short shortCharge = 0;
if (stringCharge!=null){
if(!stringCharge.equals("?")){
try{
shortCharge = Short.parseShort(stringCharge);
}
catch(NumberFormatException e){
logger.warn("Number format exception. Parsing '"+stringCharge+"' to short");
}
}
else{
logger.warn("? charge on atom "+chemCompAtom.getAtom_id()+" in group "+thisChemComp.getId());
}
}
else{
logger.warn("Null charge on atom "+chemCompAtom.getAtom_id()+" in group "+thisChemComp.getId());
}
if(atom!=null){
atom.setCharge(shortCharge);
}
// Now do the same for alt locs
for (Group altLoc : g.getAltLocs()) {
Atom altAtom = altLoc.getAtom(chemCompAtom.getAtom_id());
if(altAtom!=null){
altAtom.setCharge(shortCharge);
}
}
}
}
}
}
} | java | public static void addCharges(Structure structure) {
// Loop through the models
for(int i=0; i<structure.nrModels(); i++){
for(Chain c: structure.getChains(i)){
for(Group g: c.getAtomGroups()){
ChemComp thisChemComp = ChemCompGroupFactory.getChemComp(g.getPDBName());
List<ChemCompAtom> chemAtoms = thisChemComp.getAtoms();
for(ChemCompAtom chemCompAtom : chemAtoms) {
Atom atom = g.getAtom(chemCompAtom.getAtom_id());
String stringCharge = chemCompAtom.getCharge();
short shortCharge = 0;
if (stringCharge!=null){
if(!stringCharge.equals("?")){
try{
shortCharge = Short.parseShort(stringCharge);
}
catch(NumberFormatException e){
logger.warn("Number format exception. Parsing '"+stringCharge+"' to short");
}
}
else{
logger.warn("? charge on atom "+chemCompAtom.getAtom_id()+" in group "+thisChemComp.getId());
}
}
else{
logger.warn("Null charge on atom "+chemCompAtom.getAtom_id()+" in group "+thisChemComp.getId());
}
if(atom!=null){
atom.setCharge(shortCharge);
}
// Now do the same for alt locs
for (Group altLoc : g.getAltLocs()) {
Atom altAtom = altLoc.getAtom(chemCompAtom.getAtom_id());
if(altAtom!=null){
altAtom.setCharge(shortCharge);
}
}
}
}
}
}
} | [
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32,043 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmOptimizer.java | SymmOptimizer.updateMultipleAlignment | private void updateMultipleAlignment() throws StructureException,
RefinerFailedException {
msa.clear();
// Override the alignment with the new information
Block b = msa.getBlock(0);
b.setAlignRes(block);
repeatCore = b.getCoreLength();
if (repeatCore < 1)
throw new RefinerFailedException(
"Optimization converged to length 0");
SymmetryTools.updateSymmetryTransformation(axes, msa);
} | java | private void updateMultipleAlignment() throws StructureException,
RefinerFailedException {
msa.clear();
// Override the alignment with the new information
Block b = msa.getBlock(0);
b.setAlignRes(block);
repeatCore = b.getCoreLength();
if (repeatCore < 1)
throw new RefinerFailedException(
"Optimization converged to length 0");
SymmetryTools.updateSymmetryTransformation(axes, msa);
} | [
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32,044 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmOptimizer.java | SymmOptimizer.shrinkBlock | private boolean shrinkBlock() throws StructureException,
RefinerFailedException {
// Let shrink moves only if the repeat is larger enough
if (repeatCore <= Lmin)
return false;
// Select column by maximum distance
updateMultipleAlignment();
Matrix residueDistances = MultipleAlignmentTools
.getAverageResidueDistances(msa);
double maxDist = Double.MIN_VALUE;
double[] colDistances = new double[length];
int res = 0;
for (int col = 0; col < length; col++) {
int normalize = 0;
for (int s = 0; s < order; s++) {
if (residueDistances.get(s, col) != -1) {
colDistances[col] += residueDistances.get(s, col);
normalize++;
}
}
colDistances[col] /= normalize;
if (colDistances[col] > maxDist) {
// geometric distribution
if (rnd.nextDouble() > 0.5) {
maxDist = colDistances[col];
res = col;
}
}
}
for (int su = 0; su < order; su++) {
Integer residue = block.get(su).get(res);
block.get(su).remove(res);
if (residue != null)
freePool.add(residue);
Collections.sort(freePool);
}
length--;
checkGaps();
return true;
} | java | private boolean shrinkBlock() throws StructureException,
RefinerFailedException {
// Let shrink moves only if the repeat is larger enough
if (repeatCore <= Lmin)
return false;
// Select column by maximum distance
updateMultipleAlignment();
Matrix residueDistances = MultipleAlignmentTools
.getAverageResidueDistances(msa);
double maxDist = Double.MIN_VALUE;
double[] colDistances = new double[length];
int res = 0;
for (int col = 0; col < length; col++) {
int normalize = 0;
for (int s = 0; s < order; s++) {
if (residueDistances.get(s, col) != -1) {
colDistances[col] += residueDistances.get(s, col);
normalize++;
}
}
colDistances[col] /= normalize;
if (colDistances[col] > maxDist) {
// geometric distribution
if (rnd.nextDouble() > 0.5) {
maxDist = colDistances[col];
res = col;
}
}
}
for (int su = 0; su < order; su++) {
Integer residue = block.get(su).get(res);
block.get(su).remove(res);
if (residue != null)
freePool.add(residue);
Collections.sort(freePool);
}
length--;
checkGaps();
return true;
} | [
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32,045 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/SymmOptimizer.java | SymmOptimizer.saveHistory | private void saveHistory(String folder) throws IOException {
String name = msa.getStructureIdentifier(0).getIdentifier();
FileWriter writer = new FileWriter(folder + name
+ "-symm_opt.csv");
writer.append("Step,Time,RepeatLength,RMSD,TMscore,MCscore\n");
for (int i = 0; i < lengthHistory.size(); i++) {
writer.append(i * saveStep + ",");
writer.append(timeHistory.get(i) + ",");
writer.append(lengthHistory.get(i) + ",");
writer.append(rmsdHistory.get(i) + ",");
writer.append(tmScoreHistory.get(i) + ",");
writer.append(mcScoreHistory.get(i) + "\n");
}
writer.flush();
writer.close();
} | java | private void saveHistory(String folder) throws IOException {
String name = msa.getStructureIdentifier(0).getIdentifier();
FileWriter writer = new FileWriter(folder + name
+ "-symm_opt.csv");
writer.append("Step,Time,RepeatLength,RMSD,TMscore,MCscore\n");
for (int i = 0; i < lengthHistory.size(); i++) {
writer.append(i * saveStep + ",");
writer.append(timeHistory.get(i) + ",");
writer.append(lengthHistory.get(i) + ",");
writer.append(rmsdHistory.get(i) + ",");
writer.append(tmScoreHistory.get(i) + ",");
writer.append(mcScoreHistory.get(i) + "\n");
}
writer.flush();
writer.close();
} | [
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32,046 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureWriter.java | MmtfStructureWriter.addBonds | private void addBonds(Atom atom, List<Atom> atomsInGroup, List<Atom> allAtoms) {
if(atom.getBonds()==null){
return;
}
for(Bond bond : atom.getBonds()) {
// Now set the bonding information.
Atom other = bond.getOther(atom);
// If both atoms are in the group
if (atomsInGroup.indexOf(other)!=-1){
Integer firstBondIndex = atomsInGroup.indexOf(atom);
Integer secondBondIndex = atomsInGroup.indexOf(other);
// Don't add the same bond twice
if(firstBondIndex>secondBondIndex){
int bondOrder = bond.getBondOrder();
mmtfDecoderInterface.setGroupBond(firstBondIndex, secondBondIndex, bondOrder);
}
}
// Otherwise it's an inter group bond - so add it here
else {
Integer firstBondIndex = allAtoms.indexOf(atom);
Integer secondBondIndex = allAtoms.indexOf(other);
if(firstBondIndex>secondBondIndex){
// Don't add the same bond twice
int bondOrder = bond.getBondOrder();
mmtfDecoderInterface.setInterGroupBond(firstBondIndex, secondBondIndex, bondOrder);
}
}
}
} | java | private void addBonds(Atom atom, List<Atom> atomsInGroup, List<Atom> allAtoms) {
if(atom.getBonds()==null){
return;
}
for(Bond bond : atom.getBonds()) {
// Now set the bonding information.
Atom other = bond.getOther(atom);
// If both atoms are in the group
if (atomsInGroup.indexOf(other)!=-1){
Integer firstBondIndex = atomsInGroup.indexOf(atom);
Integer secondBondIndex = atomsInGroup.indexOf(other);
// Don't add the same bond twice
if(firstBondIndex>secondBondIndex){
int bondOrder = bond.getBondOrder();
mmtfDecoderInterface.setGroupBond(firstBondIndex, secondBondIndex, bondOrder);
}
}
// Otherwise it's an inter group bond - so add it here
else {
Integer firstBondIndex = allAtoms.indexOf(atom);
Integer secondBondIndex = allAtoms.indexOf(other);
if(firstBondIndex>secondBondIndex){
// Don't add the same bond twice
int bondOrder = bond.getBondOrder();
mmtfDecoderInterface.setInterGroupBond(firstBondIndex, secondBondIndex, bondOrder);
}
}
}
} | [
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@param allAtoms the list of atoms in the whole structure | [
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32,047 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureWriter.java | MmtfStructureWriter.storeEntityInformation | private void storeEntityInformation(List<Chain> allChains, List<EntityInfo> entityInfos) {
for (EntityInfo entityInfo : entityInfos) {
String description = entityInfo.getDescription();
String type;
if (entityInfo.getType()==null){
type = null;
}
else{
type = entityInfo.getType().getEntityType();
}
List<Chain> entityChains = entityInfo.getChains();
if (entityChains.isEmpty()){
// Error mapping chain to entity
System.err.println("ERROR MAPPING CHAIN TO ENTITY: "+description);
mmtfDecoderInterface.setEntityInfo(new int[0], "", description, type);
continue;
}
else{
int[] chainIndices = new int[entityChains.size()];
for (int i=0; i<entityChains.size(); i++) {
chainIndices[i] = allChains.indexOf(entityChains.get(i));
}
Chain chain = entityChains.get(0);
ChainImpl chainImpl;
if (chain instanceof ChainImpl){
chainImpl = (ChainImpl) entityChains.get(0);
}
else{
throw new RuntimeException();
}
String sequence = chainImpl.getSeqResOneLetterSeq();
mmtfDecoderInterface.setEntityInfo(chainIndices, sequence, description, type);
}
}
} | java | private void storeEntityInformation(List<Chain> allChains, List<EntityInfo> entityInfos) {
for (EntityInfo entityInfo : entityInfos) {
String description = entityInfo.getDescription();
String type;
if (entityInfo.getType()==null){
type = null;
}
else{
type = entityInfo.getType().getEntityType();
}
List<Chain> entityChains = entityInfo.getChains();
if (entityChains.isEmpty()){
// Error mapping chain to entity
System.err.println("ERROR MAPPING CHAIN TO ENTITY: "+description);
mmtfDecoderInterface.setEntityInfo(new int[0], "", description, type);
continue;
}
else{
int[] chainIndices = new int[entityChains.size()];
for (int i=0; i<entityChains.size(); i++) {
chainIndices[i] = allChains.indexOf(entityChains.get(i));
}
Chain chain = entityChains.get(0);
ChainImpl chainImpl;
if (chain instanceof ChainImpl){
chainImpl = (ChainImpl) entityChains.get(0);
}
else{
throw new RuntimeException();
}
String sequence = chainImpl.getSeqResOneLetterSeq();
mmtfDecoderInterface.setEntityInfo(chainIndices, sequence, description, type);
}
}
} | [
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@param allChains a list of all the chains in a structure
@param entityInfos a list of the entity information | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureWriter.java#L168-L202 |
32,048 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureWriter.java | MmtfStructureWriter.storeBioassemblyInformation | private void storeBioassemblyInformation(Map<String, Integer> chainIdToIndexMap, Map<Integer, BioAssemblyInfo> inputBioAss) {
int bioAssemblyIndex = 0;
for (Entry<Integer, BioAssemblyInfo> entry : inputBioAss.entrySet()) {
Map<double[], int[]> transformMap = MmtfUtils.getTransformMap(entry.getValue(), chainIdToIndexMap);
for(Entry<double[], int[]> transformEntry : transformMap.entrySet()) {
mmtfDecoderInterface.setBioAssemblyTrans(bioAssemblyIndex, transformEntry.getValue(), transformEntry.getKey(), entry.getKey().toString());
}
bioAssemblyIndex++;
}
} | java | private void storeBioassemblyInformation(Map<String, Integer> chainIdToIndexMap, Map<Integer, BioAssemblyInfo> inputBioAss) {
int bioAssemblyIndex = 0;
for (Entry<Integer, BioAssemblyInfo> entry : inputBioAss.entrySet()) {
Map<double[], int[]> transformMap = MmtfUtils.getTransformMap(entry.getValue(), chainIdToIndexMap);
for(Entry<double[], int[]> transformEntry : transformMap.entrySet()) {
mmtfDecoderInterface.setBioAssemblyTrans(bioAssemblyIndex, transformEntry.getValue(), transformEntry.getKey(), entry.getKey().toString());
}
bioAssemblyIndex++;
}
} | [
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@param bioJavaStruct the Biojava structure
@param header the header | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureWriter.java#L210-L219 |
32,049 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/TranscriptSequence.java | TranscriptSequence.removeCDS | public CDSSequence removeCDS(String accession) {
for (CDSSequence cdsSequence : cdsSequenceList) {
if (cdsSequence.getAccession().getID().equals(accession)) {
cdsSequenceList.remove(cdsSequence);
cdsSequenceHashMap.remove(accession);
return cdsSequence;
}
}
return null;
} | java | public CDSSequence removeCDS(String accession) {
for (CDSSequence cdsSequence : cdsSequenceList) {
if (cdsSequence.getAccession().getID().equals(accession)) {
cdsSequenceList.remove(cdsSequence);
cdsSequenceHashMap.remove(accession);
return cdsSequence;
}
}
return null;
} | [
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@param accession
@return | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-core/src/main/java/org/biojava/nbio/core/sequence/TranscriptSequence.java#L82-L91 |
32,050 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/TranscriptSequence.java | TranscriptSequence.addCDS | public CDSSequence addCDS(AccessionID accession, int begin, int end, int phase) throws Exception {
if (cdsSequenceHashMap.containsKey(accession.getID())) {
throw new Exception("Duplicate accesion id " + accession.getID());
}
CDSSequence cdsSequence = new CDSSequence(this, begin, end, phase); //sense should be the same as parent
cdsSequence.setAccession(accession);
cdsSequenceList.add(cdsSequence);
Collections.sort(cdsSequenceList, new CDSComparator());
cdsSequenceHashMap.put(accession.getID(), cdsSequence);
return cdsSequence;
} | java | public CDSSequence addCDS(AccessionID accession, int begin, int end, int phase) throws Exception {
if (cdsSequenceHashMap.containsKey(accession.getID())) {
throw new Exception("Duplicate accesion id " + accession.getID());
}
CDSSequence cdsSequence = new CDSSequence(this, begin, end, phase); //sense should be the same as parent
cdsSequence.setAccession(accession);
cdsSequenceList.add(cdsSequence);
Collections.sort(cdsSequenceList, new CDSComparator());
cdsSequenceHashMap.put(accession.getID(), cdsSequence);
return cdsSequence;
} | [
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@param accession
@param begin
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@param phase 0,1,2
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32,051 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/TranscriptSequence.java | TranscriptSequence.getDNACodingSequence | public DNASequence getDNACodingSequence() {
StringBuilder sb = new StringBuilder();
for (CDSSequence cdsSequence : cdsSequenceList) {
sb.append(cdsSequence.getCodingSequence());
}
DNASequence dnaSequence = null;
try {
dnaSequence = new DNASequence(sb.toString().toUpperCase());
} catch (CompoundNotFoundException e) {
// if I understand this should not happen, please correct if I'm wrong - JD 2014-10-24
logger.error("Could not create DNA coding sequence, {}. This is most likely a bug.", e.getMessage());
}
dnaSequence.setAccession(new AccessionID(this.getAccession().getID()));
return dnaSequence;
} | java | public DNASequence getDNACodingSequence() {
StringBuilder sb = new StringBuilder();
for (CDSSequence cdsSequence : cdsSequenceList) {
sb.append(cdsSequence.getCodingSequence());
}
DNASequence dnaSequence = null;
try {
dnaSequence = new DNASequence(sb.toString().toUpperCase());
} catch (CompoundNotFoundException e) {
// if I understand this should not happen, please correct if I'm wrong - JD 2014-10-24
logger.error("Could not create DNA coding sequence, {}. This is most likely a bug.", e.getMessage());
}
dnaSequence.setAccession(new AccessionID(this.getAccession().getID()));
return dnaSequence;
} | [
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32,052 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/TranscriptSequence.java | TranscriptSequence.getProteinSequence | public ProteinSequence getProteinSequence(TranscriptionEngine engine) {
DNASequence dnaCodingSequence = getDNACodingSequence();
RNASequence rnaCodingSequence = dnaCodingSequence.getRNASequence(engine);
ProteinSequence proteinSequence = rnaCodingSequence.getProteinSequence(engine);
proteinSequence.setAccession(new AccessionID(this.getAccession().getID()));
return proteinSequence;
} | java | public ProteinSequence getProteinSequence(TranscriptionEngine engine) {
DNASequence dnaCodingSequence = getDNACodingSequence();
RNASequence rnaCodingSequence = dnaCodingSequence.getRNASequence(engine);
ProteinSequence proteinSequence = rnaCodingSequence.getProteinSequence(engine);
proteinSequence.setAccession(new AccessionID(this.getAccession().getID()));
return proteinSequence;
} | [
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@param engine
@return | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-core/src/main/java/org/biojava/nbio/core/sequence/TranscriptSequence.java#L232-L239 |
32,053 | biojava/biojava | biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SequenceScalePanel.java | SequenceScalePanel.setPaintDefaults | protected void setPaintDefaults(Graphics2D g2D){
g2D.setRenderingHint(RenderingHints.KEY_TEXT_ANTIALIASING,
RenderingHints.VALUE_TEXT_ANTIALIAS_ON);
g2D.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
RenderingHints.VALUE_ANTIALIAS_ON);
g2D.setFont(seqFont);
} | java | protected void setPaintDefaults(Graphics2D g2D){
g2D.setRenderingHint(RenderingHints.KEY_TEXT_ANTIALIASING,
RenderingHints.VALUE_TEXT_ANTIALIAS_ON);
g2D.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
RenderingHints.VALUE_ANTIALIAS_ON);
g2D.setFont(seqFont);
} | [
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32,054 | biojava/biojava | biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SequenceScalePanel.java | SequenceScalePanel.drawSequence | protected int drawSequence(Graphics2D g2D, int y){
//g2D.drawString(panelName,10,10);
g2D.setColor(SEQUENCE_COLOR);
int aminosize = Math.round(1*scale);
if ( aminosize < 1)
aminosize = 1;
// only draw within the ranges of the Clip
Rectangle drawHere = g2D.getClipBounds();
int startpos = coordManager.getSeqPos(drawHere.x);
//int endpos = coordManager.getSeqPos(drawHere.x+drawHere.width-2);
Composite oldComp = g2D.getComposite();
g2D.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER,0.8f));
//logger.info("paint l " + l + " length " + length );
if ( startpos < 0)
startpos = 999;
if ( scale > SEQUENCE_SHOW){
g2D.setColor(Color.black);
//g2D.setColor(SCALE_COLOR);
int i = startpos;
// display the actual sequence!;
for ( int gap = startpos ; gap < apos.size() ;gap++){
int xpos = coordManager.getPanelPos(gap) ;
AlignedPosition m = apos.get(gap);
if (m.getPos(position) == -1){
// a gap position
g2D.drawString("-",xpos+1,y+2+DEFAULT_Y_STEP);
continue;
}
i = m.getPos(position);
// TODO:
// color amino acids by hydrophobicity
g2D.drawString(seqArr[i].toString(),xpos+1,y+2+DEFAULT_Y_STEP);
}
// in full sequence mode we need abit more space to look nice
y+=2;
}
g2D.setComposite(oldComp);
y+= DEFAULT_Y_STEP + 2;
return y;
} | java | protected int drawSequence(Graphics2D g2D, int y){
//g2D.drawString(panelName,10,10);
g2D.setColor(SEQUENCE_COLOR);
int aminosize = Math.round(1*scale);
if ( aminosize < 1)
aminosize = 1;
// only draw within the ranges of the Clip
Rectangle drawHere = g2D.getClipBounds();
int startpos = coordManager.getSeqPos(drawHere.x);
//int endpos = coordManager.getSeqPos(drawHere.x+drawHere.width-2);
Composite oldComp = g2D.getComposite();
g2D.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER,0.8f));
//logger.info("paint l " + l + " length " + length );
if ( startpos < 0)
startpos = 999;
if ( scale > SEQUENCE_SHOW){
g2D.setColor(Color.black);
//g2D.setColor(SCALE_COLOR);
int i = startpos;
// display the actual sequence!;
for ( int gap = startpos ; gap < apos.size() ;gap++){
int xpos = coordManager.getPanelPos(gap) ;
AlignedPosition m = apos.get(gap);
if (m.getPos(position) == -1){
// a gap position
g2D.drawString("-",xpos+1,y+2+DEFAULT_Y_STEP);
continue;
}
i = m.getPos(position);
// TODO:
// color amino acids by hydrophobicity
g2D.drawString(seqArr[i].toString(),xpos+1,y+2+DEFAULT_Y_STEP);
}
// in full sequence mode we need abit more space to look nice
y+=2;
}
g2D.setComposite(oldComp);
y+= DEFAULT_Y_STEP + 2;
return y;
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/SequenceScalePanel.java#L422-L477 |
32,055 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/CalcPoint.java | CalcPoint.centroid | public static Point3d centroid(Point3d[] x) {
Point3d center = new Point3d();
for (Point3d p : x) {
center.add(p);
}
center.scale(1.0 / x.length);
return center;
} | java | public static Point3d centroid(Point3d[] x) {
Point3d center = new Point3d();
for (Point3d p : x) {
center.add(p);
}
center.scale(1.0 / x.length);
return center;
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@return centroid as Point3d | [
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32,056 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/CalcPoint.java | CalcPoint.transform | public static void transform(Matrix4d rotTrans, Point3d[] x) {
for (Point3d p : x) {
rotTrans.transform(p);
}
} | java | public static void transform(Matrix4d rotTrans, Point3d[] x) {
for (Point3d p : x) {
rotTrans.transform(p);
}
} | [
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32,057 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/CalcPoint.java | CalcPoint.translate | public static void translate(Vector3d trans, Point3d[] x) {
for (Point3d p : x) {
p.add(trans);
}
} | java | public static void translate(Vector3d trans, Point3d[] x) {
for (Point3d p : x) {
p.add(trans);
}
} | [
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32,058 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/CalcPoint.java | CalcPoint.clonePoint3dArray | public static Point3d[] clonePoint3dArray(Point3d[] x) {
Point3d[] clone = new Point3d[x.length];
for (int i = 0; i < x.length; i++) {
clone[i] = new Point3d(x[i]);
}
return clone;
} | java | public static Point3d[] clonePoint3dArray(Point3d[] x) {
Point3d[] clone = new Point3d[x.length];
for (int i = 0; i < x.length; i++) {
clone[i] = new Point3d(x[i]);
}
return clone;
} | [
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@return new array of points, identical clone of x | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/CalcPoint.java#L106-L112 |
32,059 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/CalcPoint.java | CalcPoint.rmsd | public static double rmsd(Point3d[] x, Point3d[] y) {
if (x.length != y.length) {
throw new IllegalArgumentException(
"Point arrays are not of the same length.");
}
double sum = 0.0;
for (int i = 0; i < x.length; i++) {
sum += x[i].distanceSquared(y[i]);
}
return Math.sqrt(sum / x.length);
} | java | public static double rmsd(Point3d[] x, Point3d[] y) {
if (x.length != y.length) {
throw new IllegalArgumentException(
"Point arrays are not of the same length.");
}
double sum = 0.0;
for (int i = 0; i < x.length; i++) {
sum += x[i].distanceSquared(y[i]);
}
return Math.sqrt(sum / x.length);
} | [
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array of points superposed to x
@return RMSD | [
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32,060 | biojava/biojava | biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/MenuCreator.java | MenuCreator.initMenu | public static JMenuBar initMenu(){
// show a menu
JMenuBar menu = new JMenuBar();
JMenu file= new JMenu("File");
file.getAccessibleContext().setAccessibleDescription("File Menu");
JMenuItem openI = new JMenuItem("Open");
openI.setMnemonic(KeyEvent.VK_O);
openI.addActionListener(new ActionListener(){
@Override
public void actionPerformed(ActionEvent e) {
String cmd = e.getActionCommand();
if ( cmd.equals("Open")){
final JFileChooser fc = new JFileChooser();
// In response to a button click:
int returnVal = fc.showOpenDialog(null);
if ( returnVal == JFileChooser.APPROVE_OPTION) {
File file = fc.getSelectedFile();
PDBFileReader reader = new PDBFileReader();
try {
Structure s = reader.getStructure(file);
BiojavaJmol jmol = new BiojavaJmol();
jmol.setStructure(s);
jmol.evalString("select * ; color chain;");
jmol.evalString("select *; spacefill off; wireframe off; backbone 0.4; ");
} catch (Exception ex){
ex.printStackTrace();
}
}
}
}
});
file.add(openI);
JMenuItem exitI = new JMenuItem("Exit");
exitI.setMnemonic(KeyEvent.VK_X);
exitI.addActionListener(new ActionListener(){
@Override
public void actionPerformed(ActionEvent e) {
String cmd = e.getActionCommand();
if ( cmd.equals("Exit")){
System.exit(0);
}
}
});
file.add(exitI);
menu.add(file);
JMenu align = new JMenu("Align");
JMenuItem pairI = new JMenuItem("2 protein structures");
pairI.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
String cmd = e.getActionCommand();
if ( cmd.equals("2 protein structures")){
MenuCreator.showPairDialog();
}
}
});
align.add(pairI);
menu.add(align);
JMenu about = new JMenu("About");
JMenuItem aboutI = new JMenuItem("PDBview");
aboutI.addActionListener(new ActionListener(){
@Override
public void actionPerformed(ActionEvent e) {
String cmd = e.getActionCommand();
if ( cmd.equals("PDBview")){
MenuCreator.showAboutDialog();
}
}
});
about.add(aboutI);
menu.add(Box.createGlue());
menu.add(about);
return menu;
} | java | public static JMenuBar initMenu(){
// show a menu
JMenuBar menu = new JMenuBar();
JMenu file= new JMenu("File");
file.getAccessibleContext().setAccessibleDescription("File Menu");
JMenuItem openI = new JMenuItem("Open");
openI.setMnemonic(KeyEvent.VK_O);
openI.addActionListener(new ActionListener(){
@Override
public void actionPerformed(ActionEvent e) {
String cmd = e.getActionCommand();
if ( cmd.equals("Open")){
final JFileChooser fc = new JFileChooser();
// In response to a button click:
int returnVal = fc.showOpenDialog(null);
if ( returnVal == JFileChooser.APPROVE_OPTION) {
File file = fc.getSelectedFile();
PDBFileReader reader = new PDBFileReader();
try {
Structure s = reader.getStructure(file);
BiojavaJmol jmol = new BiojavaJmol();
jmol.setStructure(s);
jmol.evalString("select * ; color chain;");
jmol.evalString("select *; spacefill off; wireframe off; backbone 0.4; ");
} catch (Exception ex){
ex.printStackTrace();
}
}
}
}
});
file.add(openI);
JMenuItem exitI = new JMenuItem("Exit");
exitI.setMnemonic(KeyEvent.VK_X);
exitI.addActionListener(new ActionListener(){
@Override
public void actionPerformed(ActionEvent e) {
String cmd = e.getActionCommand();
if ( cmd.equals("Exit")){
System.exit(0);
}
}
});
file.add(exitI);
menu.add(file);
JMenu align = new JMenu("Align");
JMenuItem pairI = new JMenuItem("2 protein structures");
pairI.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
String cmd = e.getActionCommand();
if ( cmd.equals("2 protein structures")){
MenuCreator.showPairDialog();
}
}
});
align.add(pairI);
menu.add(align);
JMenu about = new JMenu("About");
JMenuItem aboutI = new JMenuItem("PDBview");
aboutI.addActionListener(new ActionListener(){
@Override
public void actionPerformed(ActionEvent e) {
String cmd = e.getActionCommand();
if ( cmd.equals("PDBview")){
MenuCreator.showAboutDialog();
}
}
});
about.add(aboutI);
menu.add(Box.createGlue());
menu.add(about);
return menu;
} | [
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32,061 | biojava/biojava | biojava-structure-gui/src/main/java/org/biojava/nbio/structure/gui/util/MenuCreator.java | MenuCreator.showAboutDialog | private static void showAboutDialog(){
JDialog dialog = new JDialog();
dialog.setSize(new Dimension(300,300));
String msg = "This viewer is based on <b>BioJava</b> and <b>Jmol</>. <br>Author: Andreas Prlic <br> ";
msg += "Structure Alignment algorithm based on a variation of the PSC++ algorithm by Peter Lackner.";
JEditorPane txt = new JEditorPane("text/html", msg);
txt.setEditable(false);
JScrollPane scroll = new JScrollPane(txt);
Box vBox = Box.createVerticalBox();
vBox.add(scroll);
JButton close = new JButton("Close");
close.addActionListener(new ActionListener(){
@Override
public void actionPerformed(ActionEvent event) {
Object source = event.getSource();
JButton but = (JButton)source;
Container parent = but.getParent().getParent().getParent().getParent().getParent().getParent() ;
JDialog dia = (JDialog) parent;
dia.dispose();
}
});
Box hBoxb = Box.createHorizontalBox();
hBoxb.add(Box.createGlue());
hBoxb.add(close,BorderLayout.EAST);
vBox.add(hBoxb);
dialog.getContentPane().add(vBox);
dialog.setVisible(true);
} | java | private static void showAboutDialog(){
JDialog dialog = new JDialog();
dialog.setSize(new Dimension(300,300));
String msg = "This viewer is based on <b>BioJava</b> and <b>Jmol</>. <br>Author: Andreas Prlic <br> ";
msg += "Structure Alignment algorithm based on a variation of the PSC++ algorithm by Peter Lackner.";
JEditorPane txt = new JEditorPane("text/html", msg);
txt.setEditable(false);
JScrollPane scroll = new JScrollPane(txt);
Box vBox = Box.createVerticalBox();
vBox.add(scroll);
JButton close = new JButton("Close");
close.addActionListener(new ActionListener(){
@Override
public void actionPerformed(ActionEvent event) {
Object source = event.getSource();
JButton but = (JButton)source;
Container parent = but.getParent().getParent().getParent().getParent().getParent().getParent() ;
JDialog dia = (JDialog) parent;
dia.dispose();
}
});
Box hBoxb = Box.createHorizontalBox();
hBoxb.add(Box.createGlue());
hBoxb.add(close,BorderLayout.EAST);
vBox.add(hBoxb);
dialog.getContentPane().add(vBox);
dialog.setVisible(true);
} | [
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32,062 | biojava/biojava | biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java | AnchoredPairwiseSequenceAligner.getAnchors | public int[] getAnchors() {
int[] anchor = new int[getScoreMatrixDimensions()[0] - 1];
for (int i = 0; i < anchor.length; i++) {
anchor[i] = -1;
}
for (int i = 0; i < anchors.size(); i++) {
anchor[anchors.get(i).getQueryIndex()] = anchors.get(i).getTargetIndex();
}
return anchor;
} | java | public int[] getAnchors() {
int[] anchor = new int[getScoreMatrixDimensions()[0] - 1];
for (int i = 0; i < anchor.length; i++) {
anchor[i] = -1;
}
for (int i = 0; i < anchors.size(); i++) {
anchor[anchors.get(i).getQueryIndex()] = anchors.get(i).getTargetIndex();
}
return anchor;
} | [
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32,063 | biojava/biojava | biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java | AnchoredPairwiseSequenceAligner.setAnchors | public void setAnchors(int[] anchors) {
super.anchors = new ArrayList<Anchor>();
if (anchors != null) {
for (int i = 0; i < anchors.length; i++) {
if (anchors[i] >= 0) {
addAnchor(i, anchors[i]);
}
}
}
} | java | public void setAnchors(int[] anchors) {
super.anchors = new ArrayList<Anchor>();
if (anchors != null) {
for (int i = 0; i < anchors.length; i++) {
if (anchors[i] >= 0) {
addAnchor(i, anchors[i]);
}
}
}
} | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AnchoredPairwiseSequenceAligner.java#L113-L122 |
32,064 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReaderHelper.java | GenbankReaderHelper.readGenbankProteinSequence | public static LinkedHashMap<String, ProteinSequence> readGenbankProteinSequence(
File file) throws Exception {
FileInputStream inStream = new FileInputStream(file);
LinkedHashMap<String, ProteinSequence> proteinSequences = readGenbankProteinSequence(inStream);
inStream.close();
return proteinSequences;
} | java | public static LinkedHashMap<String, ProteinSequence> readGenbankProteinSequence(
File file) throws Exception {
FileInputStream inStream = new FileInputStream(file);
LinkedHashMap<String, ProteinSequence> proteinSequences = readGenbankProteinSequence(inStream);
inStream.close();
return proteinSequences;
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32,065 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReaderHelper.java | GenbankReaderHelper.readGenbankProteinSequence | public static LinkedHashMap<String, ProteinSequence> readGenbankProteinSequence(
InputStream inStream) throws Exception {
GenbankReader<ProteinSequence, AminoAcidCompound> GenbankReader = new GenbankReader<ProteinSequence, AminoAcidCompound>(
inStream,
new GenericGenbankHeaderParser<ProteinSequence, AminoAcidCompound>(),
new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
return GenbankReader.process();
} | java | public static LinkedHashMap<String, ProteinSequence> readGenbankProteinSequence(
InputStream inStream) throws Exception {
GenbankReader<ProteinSequence, AminoAcidCompound> GenbankReader = new GenbankReader<ProteinSequence, AminoAcidCompound>(
inStream,
new GenericGenbankHeaderParser<ProteinSequence, AminoAcidCompound>(),
new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
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32,066 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReaderHelper.java | GenbankReaderHelper.readGenbankDNASequence | public static LinkedHashMap<String, DNASequence> readGenbankDNASequence(
InputStream inStream) throws Exception {
GenbankReader<DNASequence, NucleotideCompound> GenbankReader = new GenbankReader<DNASequence, NucleotideCompound>(
inStream,
new GenericGenbankHeaderParser<DNASequence, NucleotideCompound>(),
new DNASequenceCreator(DNACompoundSet.getDNACompoundSet()));
return GenbankReader.process();
} | java | public static LinkedHashMap<String, DNASequence> readGenbankDNASequence(
InputStream inStream) throws Exception {
GenbankReader<DNASequence, NucleotideCompound> GenbankReader = new GenbankReader<DNASequence, NucleotideCompound>(
inStream,
new GenericGenbankHeaderParser<DNASequence, NucleotideCompound>(),
new DNASequenceCreator(DNACompoundSet.getDNACompoundSet()));
return GenbankReader.process();
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32,067 | biojava/biojava | biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReaderHelper.java | GenbankReaderHelper.readGenbankRNASequence | public static LinkedHashMap<String, RNASequence> readGenbankRNASequence(
InputStream inStream) throws Exception {
GenbankReader<RNASequence, NucleotideCompound> GenbankReader = new GenbankReader<RNASequence, NucleotideCompound>(
inStream,
new GenericGenbankHeaderParser<RNASequence, NucleotideCompound>(),
new RNASequenceCreator(RNACompoundSet.getRNACompoundSet()));
return GenbankReader.process();
} | java | public static LinkedHashMap<String, RNASequence> readGenbankRNASequence(
InputStream inStream) throws Exception {
GenbankReader<RNASequence, NucleotideCompound> GenbankReader = new GenbankReader<RNASequence, NucleotideCompound>(
inStream,
new GenericGenbankHeaderParser<RNASequence, NucleotideCompound>(),
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return GenbankReader.process();
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32,068 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/scop/CachedRemoteScopInstallation.java | CachedRemoteScopInstallation.loadRepresentativeDomains | private void loadRepresentativeDomains() throws IOException {
URL u = null;
try {
u = new URL(RemoteScopInstallation.DEFAULT_SERVER + "getRepresentativeScopDomains");
} catch (MalformedURLException e) {
throw new IOException("URL " + RemoteScopInstallation.DEFAULT_SERVER + "getRepresentativeScopDomains" + " is wrong", e);
}
logger.info("Using " + u + " to download representative domains");
InputStream response = URLConnectionTools.getInputStream(u);
String xml = JFatCatClient.convertStreamToString(response);
ScopDomains results = ScopDomains.fromXML(xml);
logger.info("got " + results.getScopDomain().size() + " domain ranges for Scop domains from server.");
for (ScopDomain dom : results.getScopDomain()){
String scopId = dom.getScopId();
serializedCache.put(scopId, dom);
}
} | java | private void loadRepresentativeDomains() throws IOException {
URL u = null;
try {
u = new URL(RemoteScopInstallation.DEFAULT_SERVER + "getRepresentativeScopDomains");
} catch (MalformedURLException e) {
throw new IOException("URL " + RemoteScopInstallation.DEFAULT_SERVER + "getRepresentativeScopDomains" + " is wrong", e);
}
logger.info("Using " + u + " to download representative domains");
InputStream response = URLConnectionTools.getInputStream(u);
String xml = JFatCatClient.convertStreamToString(response);
ScopDomains results = ScopDomains.fromXML(xml);
logger.info("got " + results.getScopDomain().size() + " domain ranges for Scop domains from server.");
for (ScopDomain dom : results.getScopDomain()){
String scopId = dom.getScopId();
serializedCache.put(scopId, dom);
}
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32,069 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java | Calc.getDistance | public static final double getDistance(Atom a, Atom b) {
double x = a.getX() - b.getX();
double y = a.getY() - b.getY();
double z = a.getZ() - b.getZ();
double s = x * x + y * y + z * z;
return Math.sqrt(s);
} | java | public static final double getDistance(Atom a, Atom b) {
double x = a.getX() - b.getX();
double y = a.getY() - b.getY();
double z = a.getZ() - b.getZ();
double s = x * x + y * y + z * z;
return Math.sqrt(s);
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32,070 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java | Calc.angle | public static final double angle(Atom a, Atom b){
Vector3d va = new Vector3d(a.getCoordsAsPoint3d());
Vector3d vb = new Vector3d(b.getCoordsAsPoint3d());
return Math.toDegrees(va.angle(vb));
} | java | public static final double angle(Atom a, Atom b){
Vector3d va = new Vector3d(a.getCoordsAsPoint3d());
Vector3d vb = new Vector3d(b.getCoordsAsPoint3d());
return Math.toDegrees(va.angle(vb));
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@return Angle between a and b in degrees, in range [0,180]. If either
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32,071 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java | Calc.unitVector | public static final Atom unitVector(Atom a) {
double amount = amount(a) ;
double[] coords = new double[3];
coords[0] = a.getX() / amount ;
coords[1] = a.getY() / amount ;
coords[2] = a.getZ() / amount ;
a.setCoords(coords);
return a;
} | java | public static final Atom unitVector(Atom a) {
double amount = amount(a) ;
double[] coords = new double[3];
coords[0] = a.getX() / amount ;
coords[1] = a.getY() / amount ;
coords[2] = a.getZ() / amount ;
a.setCoords(coords);
return a;
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32,072 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java | Calc.getPhi | public static final double getPhi(AminoAcid a, AminoAcid b)
throws StructureException {
if ( ! isConnected(a,b)){
throw new StructureException(
"can not calc Phi - AminoAcids are not connected!");
}
Atom a_C = a.getC();
Atom b_N = b.getN();
Atom b_CA = b.getCA();
Atom b_C = b.getC();
// C and N were checked in isConnected already
if (b_CA == null)
throw new StructureException(
"Can not calculate Phi, CA atom is missing");
return torsionAngle(a_C,b_N,b_CA,b_C);
} | java | public static final double getPhi(AminoAcid a, AminoAcid b)
throws StructureException {
if ( ! isConnected(a,b)){
throw new StructureException(
"can not calc Phi - AminoAcids are not connected!");
}
Atom a_C = a.getC();
Atom b_N = b.getN();
Atom b_CA = b.getCA();
Atom b_C = b.getC();
// C and N were checked in isConnected already
if (b_CA == null)
throw new StructureException(
"Can not calculate Phi, CA atom is missing");
return torsionAngle(a_C,b_N,b_CA,b_C);
} | [
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32,073 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java | Calc.getPsi | public static final double getPsi(AminoAcid a, AminoAcid b)
throws StructureException {
if ( ! isConnected(a,b)) {
throw new StructureException(
"can not calc Psi - AminoAcids are not connected!");
}
Atom a_N = a.getN();
Atom a_CA = a.getCA();
Atom a_C = a.getC();
Atom b_N = b.getN();
// C and N were checked in isConnected already
if (a_CA == null)
throw new StructureException(
"Can not calculate Psi, CA atom is missing");
return torsionAngle(a_N,a_CA,a_C,b_N);
} | java | public static final double getPsi(AminoAcid a, AminoAcid b)
throws StructureException {
if ( ! isConnected(a,b)) {
throw new StructureException(
"can not calc Psi - AminoAcids are not connected!");
}
Atom a_N = a.getN();
Atom a_CA = a.getCA();
Atom a_C = a.getC();
Atom b_N = b.getN();
// C and N were checked in isConnected already
if (a_CA == null)
throw new StructureException(
"Can not calculate Psi, CA atom is missing");
return torsionAngle(a_N,a_CA,a_C,b_N);
} | [
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32,074 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java | Calc.isConnected | public static final boolean isConnected(AminoAcid a, AminoAcid b) {
Atom C = null ;
Atom N = null;
C = a.getC();
N = b.getN();
if ( C == null || N == null)
return false;
// one could also check if the CA atoms are < 4 A...
double distance = getDistance(C,N);
return distance < 2.5;
} | java | public static final boolean isConnected(AminoAcid a, AminoAcid b) {
Atom C = null ;
Atom N = null;
C = a.getC();
N = b.getN();
if ( C == null || N == null)
return false;
// one could also check if the CA atoms are < 4 A...
double distance = getDistance(C,N);
return distance < 2.5;
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32,075 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java | Calc.rotate | public static final void rotate(Atom atom, double[][] m){
double x = atom.getX();
double y = atom.getY() ;
double z = atom.getZ();
double nx = m[0][0] * x + m[0][1] * y + m[0][2] * z ;
double ny = m[1][0] * x + m[1][1] * y + m[1][2] * z ;
double nz = m[2][0] * x + m[2][1] * y + m[2][2] * z ;
atom.setX(nx);
atom.setY(ny);
atom.setZ(nz);
} | java | public static final void rotate(Atom atom, double[][] m){
double x = atom.getX();
double y = atom.getY() ;
double z = atom.getZ();
double nx = m[0][0] * x + m[0][1] * y + m[0][2] * z ;
double ny = m[1][0] * x + m[1][1] * y + m[1][2] * z ;
double nz = m[2][0] * x + m[2][1] * y + m[2][2] * z ;
atom.setX(nx);
atom.setY(ny);
atom.setZ(nz);
} | [
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"z",... | Rotate a single Atom aroud a rotation matrix. The rotation Matrix must be
a pre-multiplication 3x3 Matrix.
If the matrix is indexed m[row][col], then the matrix will be
pre-multiplied (y=atom*M)
@param atom
atom to be rotated
@param m
a rotation matrix represented as a double[3][3] array | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java#L368-L381 |
32,076 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java | Calc.rotate | public static final void rotate(Structure structure,
double[][] rotationmatrix) throws StructureException {
if ( rotationmatrix.length != 3 ) {
throw new StructureException ("matrix does not have size 3x3 !");
}
AtomIterator iter = new AtomIterator(structure) ;
while (iter.hasNext()) {
Atom atom = iter.next() ;
Calc.rotate(atom,rotationmatrix);
}
} | java | public static final void rotate(Structure structure,
double[][] rotationmatrix) throws StructureException {
if ( rotationmatrix.length != 3 ) {
throw new StructureException ("matrix does not have size 3x3 !");
}
AtomIterator iter = new AtomIterator(structure) ;
while (iter.hasNext()) {
Atom atom = iter.next() ;
Calc.rotate(atom,rotationmatrix);
}
} | [
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@param structure
a Structure object
@param rotationmatrix
an array (3x3) of double representing the rotation matrix.
@throws StructureException
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32,077 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java | Calc.rotate | public static final void rotate(Group group, double[][] rotationmatrix)
throws StructureException {
if ( rotationmatrix.length != 3 ) {
throw new StructureException ("matrix does not have size 3x3 !");
}
AtomIterator iter = new AtomIterator(group) ;
while (iter.hasNext()) {
Atom atom = null ;
atom = iter.next() ;
rotate(atom,rotationmatrix);
}
} | java | public static final void rotate(Group group, double[][] rotationmatrix)
throws StructureException {
if ( rotationmatrix.length != 3 ) {
throw new StructureException ("matrix does not have size 3x3 !");
}
AtomIterator iter = new AtomIterator(group) ;
while (iter.hasNext()) {
Atom atom = null ;
atom = iter.next() ;
rotate(atom,rotationmatrix);
}
} | [
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@param rotationmatrix
an array (3x3) of double representing the rotation matrix.
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32,078 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java | Calc.rotate | public static final void rotate(Atom atom, Matrix m){
double x = atom.getX();
double y = atom.getY();
double z = atom.getZ();
double[][] ad = new double[][]{{x,y,z}};
Matrix am = new Matrix(ad);
Matrix na = am.times(m);
atom.setX(na.get(0,0));
atom.setY(na.get(0,1));
atom.setZ(na.get(0,2));
} | java | public static final void rotate(Atom atom, Matrix m){
double x = atom.getX();
double y = atom.getY();
double z = atom.getZ();
double[][] ad = new double[][]{{x,y,z}};
Matrix am = new Matrix(ad);
Matrix na = am.times(m);
atom.setX(na.get(0,0));
atom.setY(na.get(0,1));
atom.setZ(na.get(0,2));
} | [
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@param atom
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@param m
rotation matrix to be applied to the atom | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java#L442-L456 |
32,079 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java | Calc.rotate | public static final void rotate(Group group, Matrix m){
AtomIterator iter = new AtomIterator(group) ;
while (iter.hasNext()) {
Atom atom = iter.next() ;
rotate(atom,m);
}
} | java | public static final void rotate(Group group, Matrix m){
AtomIterator iter = new AtomIterator(group) ;
while (iter.hasNext()) {
Atom atom = iter.next() ;
rotate(atom,m);
}
} | [
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... | Rotate a group object. The rotation Matrix must be a pre-multiplication
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@param group
a group to be rotated
@param m
a Matrix object representing the rotation matrix | [
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32,080 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java | Calc.rotate | public static final void rotate(Structure structure, Matrix m){
AtomIterator iter = new AtomIterator(structure) ;
while (iter.hasNext()) {
Atom atom = iter.next() ;
rotate(atom,m);
}
} | java | public static final void rotate(Structure structure, Matrix m){
AtomIterator iter = new AtomIterator(structure) ;
while (iter.hasNext()) {
Atom atom = iter.next() ;
rotate(atom,m);
}
} | [
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@param structure
the structure to be rotated
@param m
rotation matrix to be applied | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java#L488-L498 |
32,081 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java | Calc.transform | public static void transform(Atom[] ca, Matrix4d t) {
for (Atom atom : ca)
Calc.transform(atom, t);
} | java | public static void transform(Atom[] ca, Matrix4d t) {
for (Atom atom : ca)
Calc.transform(atom, t);
} | [
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] | Transform an array of atoms at once. The transformation Matrix must be a
post-multiplication Matrix.
@param ca
array of Atoms to shift
@param t
transformation Matrix4d | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java#L509-L512 |
32,082 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java | Calc.plus | public static final void plus(Structure s, Matrix matrix){
AtomIterator iter = new AtomIterator(s) ;
Atom oldAtom = null;
Atom rotOldAtom = null;
while (iter.hasNext()) {
Atom atom = null ;
atom = iter.next() ;
try {
if ( oldAtom != null){
logger.debug("before {}", getDistance(oldAtom,atom));
}
} catch (Exception e){
logger.error("Exception: ", e);
}
oldAtom = (Atom)atom.clone();
double x = atom.getX();
double y = atom.getY() ;
double z = atom.getZ();
double[][] ad = new double[][]{{x,y,z}};
Matrix am = new Matrix(ad);
Matrix na = am.plus(matrix);
double[] coords = new double[3] ;
coords[0] = na.get(0,0);
coords[1] = na.get(0,1);
coords[2] = na.get(0,2);
atom.setCoords(coords);
try {
if ( rotOldAtom != null){
logger.debug("after {}", getDistance(rotOldAtom,atom));
}
} catch (Exception e){
logger.error("Exception: ", e);
}
rotOldAtom = (Atom) atom.clone();
}
} | java | public static final void plus(Structure s, Matrix matrix){
AtomIterator iter = new AtomIterator(s) ;
Atom oldAtom = null;
Atom rotOldAtom = null;
while (iter.hasNext()) {
Atom atom = null ;
atom = iter.next() ;
try {
if ( oldAtom != null){
logger.debug("before {}", getDistance(oldAtom,atom));
}
} catch (Exception e){
logger.error("Exception: ", e);
}
oldAtom = (Atom)atom.clone();
double x = atom.getX();
double y = atom.getY() ;
double z = atom.getZ();
double[][] ad = new double[][]{{x,y,z}};
Matrix am = new Matrix(ad);
Matrix na = am.plus(matrix);
double[] coords = new double[3] ;
coords[0] = na.get(0,0);
coords[1] = na.get(0,1);
coords[2] = na.get(0,2);
atom.setCoords(coords);
try {
if ( rotOldAtom != null){
logger.debug("after {}", getDistance(rotOldAtom,atom));
}
} catch (Exception e){
logger.error("Exception: ", e);
}
rotOldAtom = (Atom) atom.clone();
}
} | [
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... | calculate structure + Matrix coodinates ...
@param s
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@param matrix
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java#L649-L689 |
32,083 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java | Calc.shift | public static final void shift(Structure structure, Atom a ){
AtomIterator iter = new AtomIterator(structure) ;
while (iter.hasNext() ) {
Atom atom = null ;
atom = iter.next() ;
Atom natom = add(atom,a);
double x = natom.getX();
double y = natom.getY() ;
double z = natom.getZ();
atom.setX(x);
atom.setY(y);
atom.setZ(z);
}
} | java | public static final void shift(Structure structure, Atom a ){
AtomIterator iter = new AtomIterator(structure) ;
while (iter.hasNext() ) {
Atom atom = null ;
atom = iter.next() ;
Atom natom = add(atom,a);
double x = natom.getX();
double y = natom.getY() ;
double z = natom.getZ();
atom.setX(x);
atom.setY(y);
atom.setZ(z);
}
} | [
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@param a
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java#L699-L716 |
32,084 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java | Calc.shift | public static final void shift(Atom a, Atom b){
Atom natom = add(a,b);
double x = natom.getX();
double y = natom.getY() ;
double z = natom.getZ();
a.setX(x);
a.setY(y);
a.setZ(z);
} | java | public static final void shift(Atom a, Atom b){
Atom natom = add(a,b);
double x = natom.getX();
double y = natom.getY() ;
double z = natom.getZ();
a.setX(x);
a.setY(y);
a.setZ(z);
} | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java#L726-L735 |
32,085 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java | Calc.getCentroid | public static final Atom getCentroid(Atom[] atomSet){
// if we don't catch this case, the centroid returned is (NaN,NaN,NaN), which can cause lots of problems down the line
if (atomSet.length==0)
throw new IllegalArgumentException("Atom array has length 0, can't calculate centroid!");
double[] coords = new double[3];
coords[0] = 0;
coords[1] = 0;
coords[2] = 0 ;
for (Atom a : atomSet) {
coords[0] += a.getX();
coords[1] += a.getY();
coords[2] += a.getZ();
}
int n = atomSet.length;
coords[0] = coords[0] / n;
coords[1] = coords[1] / n;
coords[2] = coords[2] / n;
Atom vec = new AtomImpl();
vec.setCoords(coords);
return vec;
} | java | public static final Atom getCentroid(Atom[] atomSet){
// if we don't catch this case, the centroid returned is (NaN,NaN,NaN), which can cause lots of problems down the line
if (atomSet.length==0)
throw new IllegalArgumentException("Atom array has length 0, can't calculate centroid!");
double[] coords = new double[3];
coords[0] = 0;
coords[1] = 0;
coords[2] = 0 ;
for (Atom a : atomSet) {
coords[0] += a.getX();
coords[1] += a.getY();
coords[2] += a.getZ();
}
int n = atomSet.length;
coords[0] = coords[0] / n;
coords[1] = coords[1] / n;
coords[2] = coords[2] / n;
Atom vec = new AtomImpl();
vec.setCoords(coords);
return vec;
} | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java#L771-L799 |
32,086 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java | Calc.centerOfMass | public static Atom centerOfMass(Atom[] points) {
Atom center = new AtomImpl();
float totalMass = 0.0f;
for (Atom a : points) {
float mass = a.getElement().getAtomicMass();
totalMass += mass;
center = scaleAdd(mass, a, center);
}
center = scaleEquals(center, 1.0f/totalMass);
return center;
} | java | public static Atom centerOfMass(Atom[] points) {
Atom center = new AtomImpl();
float totalMass = 0.0f;
for (Atom a : points) {
float mass = a.getElement().getAtomicMass();
totalMass += mass;
center = scaleAdd(mass, a, center);
}
center = scaleEquals(center, 1.0f/totalMass);
return center;
} | [
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@param points
a set of Atoms
@return an Atom representing the center of mass | [
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32,087 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java | Calc.scale | public static Atom scale(Atom a, double s) {
double x = a.getX();
double y = a.getY();
double z = a.getZ();
Atom b = new AtomImpl();
b.setX(x*s);
b.setY(y*s);
b.setZ(z*s);
return b;
} | java | public static Atom scale(Atom a, double s) {
double x = a.getX();
double y = a.getY();
double z = a.getZ();
Atom b = new AtomImpl();
b.setX(x*s);
b.setY(y*s);
b.setZ(z*s);
return b;
} | [
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32,088 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java | Calc.getCenterVector | public static final Atom getCenterVector(Atom[] atomSet){
Atom centroid = getCentroid(atomSet);
return getCenterVector(atomSet,centroid);
} | java | public static final Atom getCenterVector(Atom[] atomSet){
Atom centroid = getCentroid(atomSet);
return getCenterVector(atomSet,centroid);
} | [
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32,089 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java | Calc.getCenterVector | public static final Atom getCenterVector(Atom[] atomSet, Atom centroid){
double[] coords = new double[3];
coords[0] = 0 - centroid.getX();
coords[1] = 0 - centroid.getY();
coords[2] = 0 - centroid.getZ();
Atom shiftVec = new AtomImpl();
shiftVec.setCoords(coords);
return shiftVec;
} | java | public static final Atom getCenterVector(Atom[] atomSet, Atom centroid){
double[] coords = new double[3];
coords[0] = 0 - centroid.getX();
coords[1] = 0 - centroid.getY();
coords[2] = 0 - centroid.getZ();
Atom shiftVec = new AtomImpl();
shiftVec.setCoords(coords);
return shiftVec;
} | [
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32,090 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java | Calc.centerAtoms | public static final Atom[] centerAtoms(Atom[] atomSet)
throws StructureException {
Atom centroid = getCentroid(atomSet);
return centerAtoms(atomSet, centroid);
} | java | public static final Atom[] centerAtoms(Atom[] atomSet)
throws StructureException {
Atom centroid = getCentroid(atomSet);
return centerAtoms(atomSet, centroid);
} | [
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32,091 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java | Calc.centerAtoms | public static final Atom[] centerAtoms(Atom[] atomSet, Atom centroid)
throws StructureException {
Atom shiftVector = getCenterVector(atomSet, centroid);
Atom[] newAtoms = new AtomImpl[atomSet.length];
for (int i =0 ; i < atomSet.length; i++){
Atom a = atomSet[i];
Atom n = add(a,shiftVector);
newAtoms[i] = n ;
}
return newAtoms;
} | java | public static final Atom[] centerAtoms(Atom[] atomSet, Atom centroid)
throws StructureException {
Atom shiftVector = getCenterVector(atomSet, centroid);
Atom[] newAtoms = new AtomImpl[atomSet.length];
for (int i =0 ; i < atomSet.length; i++){
Atom a = atomSet[i];
Atom n = add(a,shiftVector);
newAtoms[i] = n ;
}
return newAtoms;
} | [
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32,092 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java | Calc.createVirtualCBAtom | public static final Atom createVirtualCBAtom(AminoAcid amino)
throws StructureException{
AminoAcid ala = StandardAminoAcid.getAminoAcid("ALA");
Atom aN = ala.getN();
Atom aCA = ala.getCA();
Atom aC = ala.getC();
Atom aCB = ala.getCB();
Atom[] arr1 = new Atom[3];
arr1[0] = aN;
arr1[1] = aCA;
arr1[2] = aC;
Atom[] arr2 = new Atom[3];
arr2[0] = amino.getN();
arr2[1] = amino.getCA();
arr2[2] = amino.getC();
// ok now we got the two arrays, do a Superposition:
SuperPositionSVD svd = new SuperPositionSVD(false);
Matrix4d transform = svd.superpose(Calc.atomsToPoints(arr1), Calc.atomsToPoints(arr2));
Matrix rotMatrix = Matrices.getRotationJAMA(transform);
Atom tranMatrix = getTranslationVector(transform);
Calc.rotate(aCB,rotMatrix);
Atom virtualCB = Calc.add(aCB,tranMatrix);
virtualCB.setName("CB");
return virtualCB;
} | java | public static final Atom createVirtualCBAtom(AminoAcid amino)
throws StructureException{
AminoAcid ala = StandardAminoAcid.getAminoAcid("ALA");
Atom aN = ala.getN();
Atom aCA = ala.getCA();
Atom aC = ala.getC();
Atom aCB = ala.getCB();
Atom[] arr1 = new Atom[3];
arr1[0] = aN;
arr1[1] = aCA;
arr1[2] = aC;
Atom[] arr2 = new Atom[3];
arr2[0] = amino.getN();
arr2[1] = amino.getCA();
arr2[2] = amino.getC();
// ok now we got the two arrays, do a Superposition:
SuperPositionSVD svd = new SuperPositionSVD(false);
Matrix4d transform = svd.superpose(Calc.atomsToPoints(arr1), Calc.atomsToPoints(arr2));
Matrix rotMatrix = Matrices.getRotationJAMA(transform);
Atom tranMatrix = getTranslationVector(transform);
Calc.rotate(aCB,rotMatrix);
Atom virtualCB = Calc.add(aCB,tranMatrix);
virtualCB.setName("CB");
return virtualCB;
} | [
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@return a "virtual" CB atom
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32,093 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java | Calc.calcRotationAngleInDegrees | public static double calcRotationAngleInDegrees(Atom centerPt, Atom targetPt) {
// calculate the angle theta from the deltaY and deltaX values
// (atan2 returns radians values from [-PI,PI])
// 0 currently points EAST.
// NOTE: By preserving Y and X param order to atan2, we are expecting
// a CLOCKWISE angle direction.
double theta = Math.atan2(targetPt.getY() - centerPt.getY(),
targetPt.getX() - centerPt.getX());
// rotate the theta angle clockwise by 90 degrees
// (this makes 0 point NORTH)
// NOTE: adding to an angle rotates it clockwise.
// subtracting would rotate it counter-clockwise
theta += Math.PI/2.0;
// convert from radians to degrees
// this will give you an angle from [0->270],[-180,0]
double angle = Math.toDegrees(theta);
// convert to positive range [0-360)
// since we want to prevent negative angles, adjust them now.
// we can assume that atan2 will not return a negative value
// greater than one partial rotation
if (angle < 0) {
angle += 360;
}
return angle;
} | java | public static double calcRotationAngleInDegrees(Atom centerPt, Atom targetPt) {
// calculate the angle theta from the deltaY and deltaX values
// (atan2 returns radians values from [-PI,PI])
// 0 currently points EAST.
// NOTE: By preserving Y and X param order to atan2, we are expecting
// a CLOCKWISE angle direction.
double theta = Math.atan2(targetPt.getY() - centerPt.getY(),
targetPt.getX() - centerPt.getX());
// rotate the theta angle clockwise by 90 degrees
// (this makes 0 point NORTH)
// NOTE: adding to an angle rotates it clockwise.
// subtracting would rotate it counter-clockwise
theta += Math.PI/2.0;
// convert from radians to degrees
// this will give you an angle from [0->270],[-180,0]
double angle = Math.toDegrees(theta);
// convert to positive range [0-360)
// since we want to prevent negative angles, adjust them now.
// we can assume that atan2 will not return a negative value
// greater than one partial rotation
if (angle < 0) {
angle += 360;
}
return angle;
} | [
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Assumes all points are in the same coordinate space. If they are not, you
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32,094 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java | Calc.shift | public static void shift(Atom[] ca, Atom b) {
for (Atom atom : ca)
Calc.shift(atom, b);
} | java | public static void shift(Atom[] ca, Atom b) {
for (Atom atom : ca)
Calc.shift(atom, b);
} | [
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32,095 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java | Calc.getTransformation | public static Matrix4d getTransformation(Matrix rot, Atom trans) {
return new Matrix4d(new Matrix3d(rot.getColumnPackedCopy()),
new Vector3d(trans.getCoordsAsPoint3d()), 1.0);
} | java | public static Matrix4d getTransformation(Matrix rot, Atom trans) {
return new Matrix4d(new Matrix3d(rot.getColumnPackedCopy()),
new Vector3d(trans.getCoordsAsPoint3d()), 1.0);
} | [
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@param rot
3x3 Rotation matrix
@param trans
3x1 translation vector in Atom coordinates
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32,096 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java | Calc.getTranslationVector | public static Atom getTranslationVector(Matrix4d transform){
Atom transl = new AtomImpl();
double[] coords = {transform.m03, transform.m13, transform.m23};
transl.setCoords(coords);
return transl;
} | java | public static Atom getTranslationVector(Matrix4d transform){
Atom transl = new AtomImpl();
double[] coords = {transform.m03, transform.m13, transform.m23};
transl.setCoords(coords);
return transl;
} | [
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32,097 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java | Calc.rmsd | public static double rmsd(Atom[] x, Atom[] y) {
return CalcPoint.rmsd(atomsToPoints(x), atomsToPoints(y));
} | java | public static double rmsd(Atom[] x, Atom[] y) {
return CalcPoint.rmsd(atomsToPoints(x), atomsToPoints(y));
} | [
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32,098 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/CliTools.java | CliTools.getEnumValuesAsString | public static <T extends Enum<?>> String getEnumValuesAsString(Class<T> enumClass) {
//ScoringStrategy[] vals = ScoringStrategy.values();
T[] vals = enumClass.getEnumConstants();
StringBuilder str = new StringBuilder();
if(vals.length == 1) {
str.append(vals[0].name());
} else if(vals.length > 1 ) {
for(int i=0;i<vals.length-1;i++) {
str.append(vals[i].name());
str.append(", ");
}
str.append("or ");
str.append(vals[vals.length-1].name());
}
return str.toString();
} | java | public static <T extends Enum<?>> String getEnumValuesAsString(Class<T> enumClass) {
//ScoringStrategy[] vals = ScoringStrategy.values();
T[] vals = enumClass.getEnumConstants();
StringBuilder str = new StringBuilder();
if(vals.length == 1) {
str.append(vals[0].name());
} else if(vals.length > 1 ) {
for(int i=0;i<vals.length-1;i++) {
str.append(vals[i].name());
str.append(", ");
}
str.append("or ");
str.append(vals[vals.length-1].name());
}
return str.toString();
} | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/CliTools.java#L340-L357 |
32,099 | biojava/biojava | biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/UnitCellBoundingBox.java | UnitCellBoundingBox.getTranslatedBbs | public UnitCellBoundingBox getTranslatedBbs(Vector3d translation) {
UnitCellBoundingBox translatedBbs = new UnitCellBoundingBox(numOperatorsSg, numPolyChainsAu);
for (int i=0; i<numOperatorsSg; i++) {
for (int j = 0;j<numPolyChainsAu; j++) {
translatedBbs.chainBbs[i][j] = new BoundingBox(this.chainBbs[i][j]);
translatedBbs.chainBbs[i][j].translate(translation);
}
translatedBbs.auBbs[i] = new BoundingBox(translatedBbs.chainBbs[i]);
}
return translatedBbs;
} | java | public UnitCellBoundingBox getTranslatedBbs(Vector3d translation) {
UnitCellBoundingBox translatedBbs = new UnitCellBoundingBox(numOperatorsSg, numPolyChainsAu);
for (int i=0; i<numOperatorsSg; i++) {
for (int j = 0;j<numPolyChainsAu; j++) {
translatedBbs.chainBbs[i][j] = new BoundingBox(this.chainBbs[i][j]);
translatedBbs.chainBbs[i][j].translate(translation);
}
translatedBbs.auBbs[i] = new BoundingBox(translatedBbs.chainBbs[i]);
}
return translatedBbs;
} | [
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... | Returns a new BoundingBoxes object containing the same bounds as this
BoundingBoxes object translated by the given translation
@param translation
@return | [
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] | a1c71a8e3d40cc32104b1d387a3d3b560b43356e | https://github.com/biojava/biojava/blob/a1c71a8e3d40cc32104b1d387a3d3b560b43356e/biojava-structure/src/main/java/org/biojava/nbio/structure/xtal/UnitCellBoundingBox.java#L114-L126 |
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