try
{
- pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol);
+ pdb = ssm.setMapping(seq,
+ StructureSelectionManager.perChainList(chains),
+ pdbentry.getFile(), protocol);
if (protocol == DataSourceType.PASTE)
{
try
{
- pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol);
+ pdb = ssm.setMapping(seq,
+ StructureSelectionManager.perChainList(chains),
+ pdbentry.getFile(), protocol);
if (protocol.equals(jalview.io.DataSourceType.PASTE))
{
{
// register the association(s) and quit, don't create any windows.
if (StructureSelectionManager.getStructureSelectionManager(applet)
- .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
+ .setMapping(seqs,
+ StructureSelectionManager.perChainList(chains),
+ pdb.getFile(), protocol) == null)
{
System.err.println("Failed to map " + pdb.getFile() + " ("
+ protocol + ") to any sequences");
{
reader = StructureSelectionManager
.getStructureSelectionManager(ap.av.applet)
- .setMapping(seq, chains, pdbentry.getFile(), protocol);
+ .setMapping(seq,
+ StructureSelectionManager.perChainList(chains),
+ pdbentry.getFile(), protocol);
// PROMPT USER HERE TO ADD TO NEW OR EXISTING VIEW?
// FOR NOW, LETS JUST OPEN A NEW WINDOW
}
* If the PDB file is already loaded, the user may just choose to add to an
* existing viewer (or cancel)
*/
- if (addAlreadyLoadedFile(seq, chains, ap, pdbId))
+ if (addAlreadyLoadedFile(seq, ap, pdbId))
{
return;
}
* If the PDB file is already loaded, the user may just choose to add to an
* existing viewer (or cancel)
*/
- if (addAlreadyLoadedFile(seq, chains, ap, pdbId))
+ if (addAlreadyLoadedFile(seq, ap, pdbId))
{
return;
}
* and updates any viewers that have the PDB file
*
* @param seq
- * @param chains
* @param apanel
* @param pdbFilename
*/
protected void addSequenceMappingsToStructure(SequenceI[] seq,
- String[] chains, final AlignmentPanel apanel, String pdbFilename)
+ final AlignmentPanel apanel, String pdbFilename)
{
// TODO : Fix multiple seq to one chain issue here.
/*
* create the mappings
*/
- apanel.getStructureSelectionManager().setMapping(seq, chains,
+ apanel.getStructureSelectionManager().setMapping(seq, null,
pdbFilename, DataSourceType.FILE);
/*
* @param pdbId
* @return true if the user chooses to add to a viewer, or to cancel entirely
*/
- protected boolean addAlreadyLoadedFile(SequenceI[] seq, String[] chains,
+ protected boolean addAlreadyLoadedFile(SequenceI[] seq,
final AlignmentPanel apanel, String pdbId)
{
boolean finished = false;
}
else if (option == JvOptionPane.YES_OPTION)
{
- addSequenceMappingsToStructure(seq, chains, apanel, alreadyMapped);
+ addSequenceMappingsToStructure(seq, apanel, alreadyMapped);
finished = true;
}
}
* @return null or the structure data parsed as a pdb file
*/
synchronized public StructureFile setMapping(SequenceI[] sequence,
- String[] targetChains, String pdbFile, DataSourceType protocol)
+ List<String>[] targetChains, String pdbFile,
+ DataSourceType protocol)
{
return setMapping(true, sequence, targetChains, pdbFile, protocol);
}
* @return null or the structure data parsed as a pdb file
*/
synchronized public StructureFile setMapping(boolean forStructureView,
- SequenceI[] sequenceArray, String[] targetChainIds,
+ SequenceI[] sequenceArray, List<String>[] targetChainIds,
String pdbFile, DataSourceType sourceType)
{
/*
e.printStackTrace();
}
- String targetChainId;
+ List<String> targetChainId = new ArrayList();
+ String _targetChainId;
for (int s = 0; s < sequenceArray.length; s++)
{
boolean infChain = true;
}
else if (seq.getName().indexOf("|") > -1)
{
- targetChainId = seq.getName()
+ targetChainId = new ArrayList();
+ _targetChainId=seq.getName()
.substring(seq.getName().lastIndexOf("|") + 1);
- if (targetChainId.length() > 1)
+ if (_targetChainId.length() > 1)
{
- if (targetChainId.trim().length() == 0)
+ if (_targetChainId.trim().length() == 0)
{
- targetChainId = " ";
+ _targetChainId = " ";
}
else
{
// not a valid chain identifier
- targetChainId = "";
+ _targetChainId = "";
}
}
+ targetChainId.add(_targetChainId);
}
else
{
- targetChainId = "";
+ _targetChainId = "";
}
+
/*
* Attempt pairwise alignment of the sequence with each chain in the PDB,
List<String> maximalChainIds = new ArrayList<>();
for (PDBChain chain : pdb.getChains())
{
- if (targetChainId.length() > 0 && !targetChainId.equals(chain.id)
+ if (targetChainId.size() > 0 && !targetChainId.contains(chain.id)
&& !infChain)
{
continue; // don't try to map chains don't match.
// as.calcScoreMatrix();
// as.traceAlignment();
- if (targetChainId.length() > 0 && chain.id.equals(targetChainId))
+ if (targetChainId.size() > 0 && targetChainId.contains(chain.id))
{
// Don't care - just pick this chain as the mapping
maxChain = chain;
.getString("status.obtaining_mapping_with_sifts"));
jalview.datamodel.Mapping sqmpping = maxAlignseq
.getMappingFromS1(false);
- if (targetChainId != null && !targetChainId.trim().isEmpty())
+ if (targetChainId != null && !targetChainId.isEmpty())
{
- StructureMapping siftsMapping;
+ List<StructureMapping> siftsMappings;
try
{
- siftsMapping = getStructureMapping(seq, pdbFile, targetChainId,
+ siftsMappings = getStructureMapping(seq, pdbFile, targetChainId,
pdb, maxChain, sqmpping, maxAlignseq);
- seqToStrucMapping.add(siftsMapping);
+ for (StructureMapping siftsMapping : siftsMappings)
+ {
+ seqToStrucMapping.add(siftsMapping);
maxChain.makeExactMapping(maxAlignseq, seq);
maxChain.transferRESNUMFeatures(seq, null);// FIXME: is this
// "IEA:SIFTS" ?
maxChain.transferResidueAnnotation(siftsMapping, sqmpping);
ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
+ }
} catch (SiftsException e)
{
{
try
{
- StructureMapping siftsMapping = getStructureMapping(seq,
- pdbFile, chain.id, pdb, chain, sqmpping, maxAlignseq);
- foundSiftsMappings.add(siftsMapping);
+ foundSiftsMappings.addAll(getStructureMapping(seq, pdbFile,
+ Arrays.asList(new String[]
+ { chain.id }), pdb, chain, sqmpping, maxAlignseq));
} catch (SiftsException e)
{
System.err.println(e.getMessage());
* @return
* @throws SiftsException
*/
- private StructureMapping getStructureMapping(SequenceI seq,
- String pdbFile, String targetChainId, StructureFile pdb,
+ private List<StructureMapping> getStructureMapping(SequenceI seq,
+ String pdbFile, List<String> targetChainIdList, StructureFile pdb,
PDBChain maxChain, jalview.datamodel.Mapping sqmpping,
AlignSeq maxAlignseq) throws SiftsException
{
- StructureMapping curChainMapping = siftsClient
+ List<StructureMapping> currChainMappingList = new ArrayList();
+ int p = 0;
+ do
+ {
+ String targetChainId = (targetChainIdList == null
+ || p >= targetChainIdList.size()) ? null
+ : targetChainIdList.get(p);
+ StructureMapping curChainMapping = siftsClient
+
.getSiftsStructureMapping(seq, pdbFile, targetChainId);
try
{
if (chain != null)
{
chain.transferResidueAnnotation(curChainMapping, sqmpping);
+ currChainMappingList.add(curChainMapping);
}
} catch (Exception e)
{
e.printStackTrace();
}
- return curChainMapping;
+ } while (targetChainIdList != null && ++p < targetChainIdList.size());
+ return currChainMappingList;
}
private List<StructureMapping> getNWMappings(SequenceI seq,
private SequenceI[][] sequence;
/*
- * array of target chains for sequences - tied to pdbentry and sequence[]
+ * array of list of target chains for sequences - tied to pdbentry and sequence[]
*/
- private String[][] chains;
+ private List<String>[][] chains;
/*
* datasource protocol for access to PDBEntrylatest
int chainmaps = 0;
// JBPNote: JAL-2693 - this should be a list of chain mappings per
// [pdbentry][sequence]
- String[][] newchains = new String[pdbEntry.length][];
+ List<String>[][] newchains = new List[pdbEntry.length][];
int pe = 0;
for (PDBEntry pdb : pdbEntry)
{
SequenceI[] seqsForPdb = sequence[pe];
if (seqsForPdb != null)
{
- newchains[pe] = new String[seqsForPdb.length];
+ newchains[pe] = new List[seqsForPdb.length];
int se = 0;
for (SequenceI asq : seqsForPdb)
{
- String chain = (chains != null && chains[pe] != null)
+ List<String> chain = (chains != null && chains[pe] != null)
? chains[pe][se]
: null;
+ if (chain == null)
+ {
+ chain = new ArrayList<>();
+ }
+ newchains[pe][se] = chain;
+
SequenceI sq = (asq.getDatasetSequence() == null) ? asq
: asq.getDatasetSequence();
if (sq.getAllPDBEntries() != null)
String chaincode = pdbentry.getChainCode();
if (chaincode != null && chaincode.length() > 0)
{
- chain = chaincode;
+ newchains[pe][se].add(chaincode);
chainmaps++;
- break;
}
}
}
}
- newchains[pe][se] = chain;
se++;
}
pe++;
return sequence;
}
- public String[][] getChains()
+ public List<String>[][] getChains()
{
return chains;
}
this.sequence = sequence;
}
- protected void setChains(String[][] chains)
+ protected void setChains(List<String>[][] chains)
{
this.chains = chains;
}
new Object[]
{ Integer.valueOf(pe).toString() }));
}
- final String nullChain = "TheNullChain";
- List<SequenceI> s = new ArrayList<SequenceI>();
- List<String> c = new ArrayList<String>();
+ List<SequenceI> s = new ArrayList<>();
+ List<List<String>> c = new ArrayList<>();
if (getChains() == null)
{
- setChains(new String[getPdbCount()][]);
+ setChains(new List[getPdbCount()][]);
}
if (getSequence()[pe] != null)
{
}
else
{
- c.add(nullChain);
+ c.add(new ArrayList());
}
}
else
{
if (tchain != null && tchain.length > 0)
{
- c.add(nullChain);
+ c.add(new ArrayList());
}
}
}
s.add(seq[i]);
if (tchain != null && i < tchain.length)
{
- c.add(tchain[i] == null ? nullChain : tchain[i]);
+ List<String> clist = new ArrayList();
+ c.add(clist);
+ if (tchain[i] != null)
+ {
+ clist.add(tchain[i]);
+ }
}
}
}
getSequence()[pe] = tmp;
if (c.size() > 0)
{
- String[] tch = c.toArray(new String[c.size()]);
- for (int i = 0; i < tch.length; i++)
- {
- if (tch[i] == nullChain)
- {
- tch[i] = null;
- }
- }
+ List<String>[] tch = c.toArray(new List[c.size()]);
getChains()[pe] = tch;
}
else
public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe,
SequenceI[][] seq, String[][] chns)
{
- List<PDBEntry> v = new ArrayList<PDBEntry>();
- List<int[]> rtn = new ArrayList<int[]>();
+ List<PDBEntry> v = new ArrayList<>();
+ List<int[]> rtn = new ArrayList<>();
for (int i = 0; i < getPdbCount(); i++)
{
v.add(getPdbEntry(i));
{
// expand the tied sequence[] and string[] arrays
SequenceI[][] sqs = new SequenceI[getPdbCount()][];
- String[][] sch = new String[getPdbCount()][];
+ List<String>[][] sch = new List[getPdbCount()][];
System.arraycopy(getSequence(), 0, sqs, 0, getSequence().length);
System.arraycopy(getChains(), 0, sch, 0, this.getChains().length);
setSequence(sqs);
import jalview.io.FileLoader;
import jalview.io.StructureFile;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
import org.testng.Assert;
import org.testng.AssertJUnit;
import org.testng.annotations.BeforeClass;
StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
StructureFile pmap = ssm.setMapping(true, new SequenceI[] { uprot },
- new String[] { "A" }, "test/jalview/ext/jmol/1QCF.pdb",
+ new List[]
+ { Arrays.asList(new String[] { "A" }) },
+ "test/jalview/ext/jmol/1QCF.pdb",
DataSourceType.FILE);
assertTrue(pmap != null);
SequenceI protseq = pmap.getSeqsAsArray()[0];
// Associate the 1GAQ pdb file with the subsequence 'imported' from another
// source
StructureFile pde = ssm.setMapping(true, new SequenceI[] { sq },
- new String[]
- { "A" }, inFile = "examples/1gaq.txt", DataSourceType.FILE);
+ new List[]
+ { Arrays.asList(new String[] { "A" }) },
+ inFile = "examples/1gaq.txt", DataSourceType.FILE);
assertTrue("PDB File couldn't be found", pde != null);
StructureMapping[] mp = ssm.getMapping(inFile);
assertTrue("No mappings made.", mp != null && mp.length > 0);
SequenceI newseq = seqf.getViewport().getAlignment().getSequenceAt(0);
StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
StructureFile pmap = ssm.setMapping(true, new SequenceI[] { newseq },
- new String[] { null }, "examples/3W5V.pdb",
+ new List[]
+ { Arrays.asList(new String[0]) }, "examples/3W5V.pdb",
DataSourceType.FILE);
if (pmap == null)
{
ssm.setProcessSecondaryStructure(true);
ssm.setAddTempFacAnnot(true);
StructureFile pmap = ssm.setMapping(true, new SequenceI[] { newseq },
- new String[] { null }, "test/jalview/ext/jmol/1QCF.pdb",
+ new List[]
+ { new ArrayList() }, "test/jalview/ext/jmol/1QCF.pdb",
DataSourceType.FILE);
assertTrue(pmap != null);
assertEquals("Original and copied sequence of different lengths.",
sm.setProcessSecondaryStructure(true);
sm.setAddTempFacAnnot(true);
StructureFile pmap = sm.setMapping(true, new SequenceI[] { seq },
- new String[] { null }, "examples/1gaq.txt", DataSourceType.FILE);
+ null, "examples/1gaq.txt", DataSourceType.FILE);
assertTrue(pmap != null);
assertEquals(3, pmap.getSeqs().size());
}
};
- String[][] chains = binder.getChains();
+ List<String>[][] chains = binder.getChains();
assertFalse(chains == null || chains[0] == null,
"No chains discovered by binding");
assertEquals(2, chains[0].length);
- assertEquals("A", chains[0][0]);
- assertEquals("B", chains[0][1]);
+ assertEquals("A", chains[0][0].get(0));
+ assertEquals("B", chains[0][1].get(0));
}
AAStructureBindingModel testee;
git://source.jalview.org / jalview.git / commitdiff