*/
package jalview.structure;
+import jalview.analysis.AlignSeq;
+import jalview.api.StructureSelectionManagerProvider;
+import jalview.commands.CommandI;
+import jalview.commands.EditCommand;
+import jalview.commands.OrderCommand;
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
+import jalview.util.MappingUtils;
+import jalview.util.MessageManager;
+import jalview.ws.sifts.SiftsClient;
+import jalview.ws.sifts.SiftsException;
+import jalview.ws.sifts.SiftsSettings;
+
import java.io.PrintStream;
import java.util.ArrayList;
import java.util.Arrays;
import MCview.PDBChain;
import MCview.PDBfile;
-import jalview.analysis.AlignSeq;
-import jalview.api.StructureSelectionManagerProvider;
-import jalview.commands.CommandI;
-import jalview.commands.EditCommand;
-import jalview.commands.OrderCommand;
-import jalview.datamodel.AlignedCodonFrame;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SearchResults;
-import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
-import jalview.util.MappingUtils;
-import jalview.util.MessageManager;
-
public class StructureSelectionManager
{
public final static String NEWLINE = System.lineSeparator();
/*
* Set of any registered mappings between (dataset) sequences.
*/
- Set<AlignedCodonFrame> seqmappings = new LinkedHashSet<AlignedCodonFrame>();
-
- /*
- * Reference counters for the above mappings. Remove mappings when ref count
- * goes to zero.
- */
- Map<AlignedCodonFrame, Integer> seqMappingRefCounts = new HashMap<AlignedCodonFrame, Integer>();
+ public Set<AlignedCodonFrame> seqmappings = new LinkedHashSet<AlignedCodonFrame>();
private List<CommandListener> commandListeners = new ArrayList<CommandListener>();
* @param forStructureView
* when true, record the mapping for use in mouseOvers
*
- * @param sequence
+ * @param sequenceArray
* - one or more sequences to be mapped to pdbFile
- * @param targetChains
+ * @param targetChainIds
* - optional chain specification for mapping each sequence to pdb
* (may be nill, individual elements may be nill)
* @param pdbFile
* @return null or the structure data parsed as a pdb file
*/
synchronized public PDBfile setMapping(boolean forStructureView,
- SequenceI[] sequence, String[] targetChains, String pdbFile,
+ SequenceI[] sequenceArray, String[] targetChainIds,
+ String pdbFile,
String protocol)
{
/*
boolean parseSecStr = processSecondaryStructure;
if (isPDBFileRegistered(pdbFile))
{
- for (SequenceI sq : sequence)
+ for (SequenceI sq : sequenceArray)
{
SequenceI ds = sq;
while (ds.getDatasetSequence() != null)
}
}
PDBfile pdb = null;
+ boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts();
+ SiftsClient siftsClient = null;
try
{
pdb = new PDBfile(addTempFacAnnot, parseSecStr, secStructServices,
pdbFile, protocol);
+
if (pdb.id != null && pdb.id.trim().length() > 0
&& AppletFormatAdapter.FILE.equals(protocol))
{
return null;
}
- String targetChain;
- for (int s = 0; s < sequence.length; s++)
+ try
+ {
+ if (isMapUsingSIFTs)
+ {
+ siftsClient = new SiftsClient(pdb);
+ }
+ } catch (SiftsException e)
+ {
+ isMapUsingSIFTs = false;
+ e.printStackTrace();
+ }
+
+ String targetChainId;
+ for (int s = 0; s < sequenceArray.length; s++)
{
boolean infChain = true;
- final SequenceI seq = sequence[s];
- if (targetChains != null && targetChains[s] != null)
+ final SequenceI seq = sequenceArray[s];
+ if (targetChainIds != null && targetChainIds[s] != null)
{
infChain = false;
- targetChain = targetChains[s];
+ targetChainId = targetChainIds[s];
}
else if (seq.getName().indexOf("|") > -1)
{
- targetChain = seq.getName().substring(
+ targetChainId = seq.getName().substring(
seq.getName().lastIndexOf("|") + 1);
- if (targetChain.length() > 1)
+ if (targetChainId.length() > 1)
{
- if (targetChain.trim().length() == 0)
+ if (targetChainId.trim().length() == 0)
{
- targetChain = " ";
+ targetChainId = " ";
}
else
{
// not a valid chain identifier
- targetChain = "";
+ targetChainId = "";
}
}
}
else
{
- targetChain = "";
+ targetChainId = "";
}
/*
boolean first = true;
for (PDBChain chain : pdb.chains)
{
- if (targetChain.length() > 0 && !targetChain.equals(chain.id)
+ if (targetChainId.length() > 0 && !targetChainId.equals(chain.id)
&& !infChain)
{
continue; // don't try to map chains don't match.
// as.traceAlignment();
if (first || as.maxscore > max
- || (as.maxscore == max && chain.id.equals(targetChain)))
+ || (as.maxscore == max && chain.id.equals(targetChainId)))
{
first = false;
maxChain = chain;
{
continue;
}
- final StringBuilder mappingDetails = new StringBuilder(128);
- mappingDetails.append(NEWLINE).append("PDB Sequence is :")
- .append(NEWLINE).append("Sequence = ")
- .append(maxChain.sequence.getSequenceAsString());
- mappingDetails.append(NEWLINE).append("No of residues = ")
- .append(maxChain.residues.size()).append(NEWLINE)
- .append(NEWLINE);
- PrintStream ps = new PrintStream(System.out)
+
+ if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
{
- @Override
- public void print(String x)
- {
- mappingDetails.append(x);
- }
+ pdbFile = "INLINE" + pdb.id;
+ }
- @Override
- public void println()
- {
- mappingDetails.append(NEWLINE);
- }
- };
-
- maxAlignseq.printAlignment(ps);
-
- mappingDetails.append(NEWLINE).append("PDB start/end ");
- mappingDetails.append(String.valueOf(maxAlignseq.seq2start)).append(
- " ");
- mappingDetails.append(String.valueOf(maxAlignseq.seq2end));
-
- mappingDetails.append(NEWLINE).append("SEQ start/end ");
- mappingDetails.append(
- String.valueOf(maxAlignseq.seq1start + seq.getStart() - 1))
- .append(" ");
- mappingDetails.append(String.valueOf(maxAlignseq.seq1end
- + seq.getEnd() - 1));
-
- maxChain.makeExactMapping(maxAlignseq, seq);
- jalview.datamodel.Mapping sqmpping = maxAlignseq
- .getMappingFromS1(false);
- jalview.datamodel.Mapping omap = new jalview.datamodel.Mapping(
- sqmpping.getMap().getInverse());
- maxChain.transferRESNUMFeatures(seq, null);
-
- // allocate enough slots to store the mapping from positions in
- // sequence[s] to the associated chain
- int[][] mapping = new int[seq.findPosition(seq.getLength()) + 2][2];
- int resNum = -10000;
- int index = 0;
-
- do
+ ArrayList<StructureMapping> seqToStrucMapping = null;
+ if (isMapUsingSIFTs)
{
- Atom tmp = maxChain.atoms.elementAt(index);
- if (resNum != tmp.resNumber && tmp.alignmentMapping != -1)
+ try
+ {
+ jalview.datamodel.Mapping sqmpping = maxAlignseq
+ .getMappingFromS1(false);
+ seqToStrucMapping = new ArrayList<StructureMapping>();
+ if (targetChainId != null && !targetChainId.trim().isEmpty())
+ {
+ StructureMapping curChainMapping = siftsClient
+ .getSiftsStructureMapping(seq, pdbFile, targetChainId);
+ seqToStrucMapping.add(curChainMapping);
+ maxChainId = targetChainId;
+ PDBChain chain = pdb.findChain(targetChainId);
+ if (chain != null)
+ {
+ chain.transferResidueAnnotation(curChainMapping, sqmpping);
+ }
+ }
+ else
+ {
+ for (PDBChain chain : pdb.chains)
+ {
+ StructureMapping curChainMapping = siftsClient
+ .getSiftsStructureMapping(seq, pdbFile, chain.id);
+ seqToStrucMapping.add(curChainMapping);
+ maxChainId = chain.id;
+ chain.transferResidueAnnotation(curChainMapping, sqmpping);
+ }
+ }
+ } catch (SiftsException e)
{
- resNum = tmp.resNumber;
- mapping[tmp.alignmentMapping + 1][0] = tmp.resNumber;
- mapping[tmp.alignmentMapping + 1][1] = tmp.atomIndex;
+ e.printStackTrace();
+ System.err
+ .println(">>>>>>> SIFTs mapping could not be obtained... Now mapping with NW alignment");
+ seqToStrucMapping = getNWMappings(seq, pdbFile, maxChainId,
+ maxChain, pdb, maxAlignseq);
}
-
- index++;
- } while (index < maxChain.atoms.size());
-
- if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
+ }
+ else
{
- pdbFile = "INLINE" + pdb.id;
+ seqToStrucMapping = getNWMappings(seq, pdbFile,
+ maxChainId, maxChain, pdb,
+ maxAlignseq);
}
- StructureMapping newMapping = new StructureMapping(seq, pdbFile,
- pdb.id, maxChainId, mapping, mappingDetails.toString());
+
if (forStructureView)
{
- mappings.add(newMapping);
+ // mappings.add(seqToStrucMapping);
+ mappings.addAll(seqToStrucMapping);
}
- maxChain.transferResidueAnnotation(newMapping, sqmpping);
}
- // ///////
-
return pdb;
}
+ private ArrayList<StructureMapping> getNWMappings(SequenceI seq,
+ String pdbFile,
+ String maxChainId, PDBChain maxChain, PDBfile pdb,
+ AlignSeq maxAlignseq)
+ {
+ final StringBuilder mappingDetails = new StringBuilder(128);
+ mappingDetails.append(NEWLINE).append(
+ "Sequence \u27f7 Structure mapping details");
+ mappingDetails.append(NEWLINE);
+ mappingDetails
+ .append("Method: inferred with Needleman & Wunsch alignment");
+ mappingDetails.append(NEWLINE).append("PDB Sequence is :")
+ .append(NEWLINE).append("Sequence = ")
+ .append(maxChain.sequence.getSequenceAsString());
+ mappingDetails.append(NEWLINE).append("No of residues = ")
+ .append(maxChain.residues.size()).append(NEWLINE)
+ .append(NEWLINE);
+ PrintStream ps = new PrintStream(System.out)
+ {
+ @Override
+ public void print(String x)
+ {
+ mappingDetails.append(x);
+ }
+
+ @Override
+ public void println()
+ {
+ mappingDetails.append(NEWLINE);
+ }
+ };
+
+ maxAlignseq.printAlignment(ps);
+
+ mappingDetails.append(NEWLINE).append("PDB start/end ");
+ mappingDetails.append(String.valueOf(maxAlignseq.seq2start))
+ .append(" ");
+ mappingDetails.append(String.valueOf(maxAlignseq.seq2end));
+ mappingDetails.append(NEWLINE).append("SEQ start/end ");
+ mappingDetails.append(
+ String.valueOf(maxAlignseq.seq1start + (seq.getStart() - 1)))
+ .append(" ");
+ mappingDetails.append(String.valueOf(maxAlignseq.seq1end
+ + (seq.getStart() - 1)));
+ mappingDetails.append(NEWLINE);
+ maxChain.makeExactMapping(maxAlignseq, seq);
+ jalview.datamodel.Mapping sqmpping = maxAlignseq
+ .getMappingFromS1(false);
+ maxChain.transferRESNUMFeatures(seq, null);
+
+ HashMap<Integer, int[]> mapping = new HashMap<Integer, int[]>();
+ int resNum = -10000;
+ int index = 0;
+
+ do
+ {
+ Atom tmp = maxChain.atoms.elementAt(index);
+ if (resNum != tmp.resNumber && tmp.alignmentMapping != -1)
+ {
+ resNum = tmp.resNumber;
+ if (tmp.alignmentMapping >= -1)
+ {
+ // TODO (JAL-1836) address root cause: negative residue no in PDB
+ // file
+ mapping.put(tmp.alignmentMapping + 1, new int[] { tmp.resNumber,
+ tmp.atomIndex });
+ }
+ }
+
+ index++;
+ } while (index < maxChain.atoms.size());
+
+ StructureMapping nwMapping = new StructureMapping(seq, pdbFile,
+ pdb.id, maxChainId, mapping, mappingDetails.toString());
+ maxChain.transferResidueAnnotation(nwMapping, sqmpping);
+ ArrayList<StructureMapping> mappings = new ArrayList<StructureMapping>();
+ mappings.add(nwMapping);
+ return mappings;
+ }
+
public void removeStructureViewerListener(Object svl, String[] pdbfiles)
{
listeners.removeElement(svl);
results.addResult(seq, index, index);
}
- seqListener.highlightSequence(results);
+ if (!results.isEmpty())
+ {
+ seqListener.highlightSequence(results);
+ }
}
}
}
}
/**
- * Decrement the reference counter for each of the given mappings, and remove
- * it entirely if its reference counter reduces to zero.
+ * Remove the given mapping
*
- * @param set
+ * @param acf
*/
- public void removeMappings(Set<AlignedCodonFrame> set)
+ public void deregisterMapping(AlignedCodonFrame acf)
{
- if (set != null)
+ if (acf != null)
{
- for (AlignedCodonFrame acf : set)
- {
- removeMapping(acf);
+ boolean removed = seqmappings.remove(acf);
+ if (removed && seqmappings.isEmpty())
+ { // debug
+ System.out.println("All mappings removed");
}
}
}
/**
- * Decrement the reference counter for the given mapping, and remove it
- * entirely if its reference counter reduces to zero.
+ * Add each of the given codonFrames to the stored set, if not aready present.
*
- * @param acf
+ * @param set
*/
- public void removeMapping(AlignedCodonFrame acf)
+ public void registerMappings(Set<AlignedCodonFrame> set)
{
- if (acf != null && seqmappings.contains(acf))
+ if (set != null)
{
- int count = seqMappingRefCounts.get(acf);
- count--;
- if (count > 0)
- {
- seqMappingRefCounts.put(acf, count);
- }
- else
+ for (AlignedCodonFrame acf : set)
{
- seqmappings.remove(acf);
- seqMappingRefCounts.remove(acf);
+ registerMapping(acf);
}
}
}
/**
- * Add each of the given codonFrames to the stored set. If not aready present,
- * increments its reference count instead.
- *
- * @param set
+ * Add the given mapping to the stored set, unless already stored.
*/
- public void addMappings(Set<AlignedCodonFrame> set)
+ public void registerMapping(AlignedCodonFrame acf)
{
- if (set != null)
+ if (acf != null)
{
- for (AlignedCodonFrame acf : set)
+ if (!seqmappings.contains(acf))
{
- addMapping(acf);
+ seqmappings.add(acf);
}
}
}
/**
- * Add the given mapping to the stored set, or if already stored, increment
- * its reference counter.
+ * Resets this object to its initial state by removing all registered
+ * listeners, codon mappings, PDB file mappings
*/
- public void addMapping(AlignedCodonFrame acf)
+ public void resetAll()
{
- if (acf != null)
+ if (mappings != null)
{
- if (seqmappings.contains(acf))
- {
- seqMappingRefCounts.put(acf, seqMappingRefCounts.get(acf) + 1);
- }
- else
- {
- seqmappings.add(acf);
- seqMappingRefCounts.put(acf, 1);
- }
+ mappings.clear();
+ }
+ if (seqmappings != null)
+ {
+ seqmappings.clear();
+ }
+ if (sel_listeners != null)
+ {
+ sel_listeners.clear();
+ }
+ if (listeners != null)
+ {
+ listeners.clear();
+ }
+ if (commandListeners != null)
+ {
+ commandListeners.clear();
+ }
+ if (view_listeners != null)
+ {
+ view_listeners.clear();
+ }
+ if (pdbFileNameId != null)
+ {
+ pdbFileNameId.clear();
+ }
+ if (pdbIdFileName != null)
+ {
+ pdbIdFileName.clear();
}
}
git://source.jalview.org / jalview.git / blobdiff