X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=e9aa575e1b76c402fe5a599f84fb5d0aa80eb88e;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=c0ab6f9b50b7ffc682c88f18dc0b423b56b79487;hpb=f72e829fdbcb33664d4fa687a8a5a6f66759d013;p=jalview.git
diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index c0ab6f9..e9aa575 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -1,47 +1,243 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
* You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.structure;
-import java.io.*;
-import java.util.*;
+import jalview.analysis.AlignSeq;
+import jalview.api.StructureSelectionManagerProvider;
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
+import jalview.util.MessageManager;
-import MCview.*;
-import jalview.analysis.*;
-import jalview.datamodel.*;
+import java.io.PrintStream;
+import java.util.Enumeration;
+import java.util.HashMap;
+import java.util.IdentityHashMap;
+import java.util.Vector;
+
+import MCview.Atom;
+import MCview.PDBChain;
public class StructureSelectionManager
{
- static StructureSelectionManager instance;
+ static IdentityHashMap instances;
+
StructureMapping[] mappings;
- Hashtable mappingData = new Hashtable();
- public static StructureSelectionManager getStructureSelectionManager()
+ private boolean processSecondaryStructure = false,
+ secStructServices = false, addTempFacAnnot = false;
+
+ /**
+ * @return true if will try to use external services for processing secondary
+ * structure
+ */
+ public boolean isSecStructServices()
{
- if (instance == null)
+ return secStructServices;
+ }
+
+ /**
+ * control use of external services for processing secondary structure
+ *
+ * @param secStructServices
+ */
+ public void setSecStructServices(boolean secStructServices)
+ {
+ this.secStructServices = secStructServices;
+ }
+
+ /**
+ * flag controlling addition of any kind of structural annotation
+ *
+ * @return true if temperature factor annotation will be added
+ */
+ public boolean isAddTempFacAnnot()
+ {
+ return addTempFacAnnot;
+ }
+
+ /**
+ * set flag controlling addition of structural annotation
+ *
+ * @param addTempFacAnnot
+ */
+ public void setAddTempFacAnnot(boolean addTempFacAnnot)
+ {
+ this.addTempFacAnnot = addTempFacAnnot;
+ }
+
+ /**
+ *
+ * @return if true, the structure manager will attempt to add secondary
+ * structure lines for unannotated sequences
+ */
+
+ public boolean isProcessSecondaryStructure()
+ {
+ return processSecondaryStructure;
+ }
+
+ /**
+ * Control whether structure manager will try to annotate mapped sequences
+ * with secondary structure from PDB data.
+ *
+ * @param enable
+ */
+ public void setProcessSecondaryStructure(boolean enable)
+ {
+ processSecondaryStructure = enable;
+ }
+
+ /**
+ * debug function - write all mappings to stdout
+ */
+ public void reportMapping()
+ {
+ if (mappings == null)
+ {
+ System.err.println("reportMapping: No PDB/Sequence mappings.");
+ }
+ else
{
- instance = new StructureSelectionManager();
+ System.err.println("reportMapping: There are " + mappings.length
+ + " mappings.");
+ for (int m = 0; m < mappings.length; m++)
+ {
+ System.err.println("mapping " + m + " : " + mappings[m].pdbfile);
+ }
}
+ }
+
+ /**
+ * map between the PDB IDs (or structure identifiers) used by Jalview and the
+ * absolute filenames for PDB data that corresponds to it
+ */
+ HashMap pdbIdFileName = new HashMap(),
+ pdbFileNameId = new HashMap();
+ public void registerPDBFile(String idForFile, String absoluteFile)
+ {
+ pdbIdFileName.put(idForFile, absoluteFile);
+ pdbFileNameId.put(absoluteFile, idForFile);
+ }
+
+ public String findIdForPDBFile(String idOrFile)
+ {
+ String id = pdbFileNameId.get(idOrFile);
+ return id;
+ }
+
+ public String findFileForPDBId(String idOrFile)
+ {
+ String id = pdbIdFileName.get(idOrFile);
+ return id;
+ }
+
+ public boolean isPDBFileRegistered(String idOrFile)
+ {
+ return pdbFileNameId.containsKey(idOrFile)
+ || pdbIdFileName.containsKey(idOrFile);
+ }
+
+ private static StructureSelectionManager nullProvider = null;
+
+ public static StructureSelectionManager getStructureSelectionManager(
+ StructureSelectionManagerProvider context)
+ {
+ if (context == null)
+ {
+ if (nullProvider == null)
+ {
+ if (instances != null)
+ {
+ throw new Error(MessageManager.getString("error.implementation_error_structure_selection_manager_null"),
+ new NullPointerException(MessageManager.getString("exception.ssm_context_is_null")));
+ }
+ else
+ {
+ nullProvider = new StructureSelectionManager();
+ }
+ return nullProvider;
+ }
+ }
+ if (instances == null)
+ {
+ instances = new java.util.IdentityHashMap();
+ }
+ StructureSelectionManager instance = instances.get(context);
+ if (instance == null)
+ {
+ if (nullProvider != null)
+ {
+ instance = nullProvider;
+ }
+ else
+ {
+ instance = new StructureSelectionManager();
+ }
+ instances.put(context, instance);
+ }
return instance;
}
+ /**
+ * flag controlling whether SeqMappings are relayed from received sequence
+ * mouse over events to other sequences
+ */
+ boolean relaySeqMappings = true;
+
+ /**
+ * Enable or disable relay of seqMapping events to other sequences. You might
+ * want to do this if there are many sequence mappings and the host computer
+ * is slow
+ *
+ * @param relay
+ */
+ public void setRelaySeqMappings(boolean relay)
+ {
+ relaySeqMappings = relay;
+ }
+
+ /**
+ * get the state of the relay seqMappings flag.
+ *
+ * @return true if sequence mouse overs are being relayed to other mapped
+ * sequences
+ */
+ public boolean isRelaySeqMappingsEnabled()
+ {
+ return relaySeqMappings;
+ }
+
Vector listeners = new Vector();
+
+ /**
+ * register a listener for alignment sequence mouseover events
+ *
+ * @param svl
+ */
public void addStructureViewerListener(Object svl)
{
if (!listeners.contains(svl))
@@ -65,74 +261,177 @@ public class StructureSelectionManager
return null;
}
- /*
- There will be better ways of doing this in the future, for now we'll use
- the tried and tested MCview pdb mapping
+ /**
+ * Import structure data and register a structure mapping for broadcasting
+ * colouring, mouseovers and selection events (convenience wrapper).
+ *
+ * @param sequence
+ * - one or more sequences to be mapped to pdbFile
+ * @param targetChains
+ * - optional chain specification for mapping each sequence to pdb
+ * (may be nill, individual elements may be nill)
+ * @param pdbFile
+ * - structure data resource
+ * @param protocol
+ * - how to resolve data from resource
+ * @return null or the structure data parsed as a pdb file
*/
synchronized public MCview.PDBfile setMapping(SequenceI[] sequence,
- String pdbFile,
- String protocol)
+ String[] targetChains, String pdbFile, String protocol)
{
+ return setMapping(true, sequence, targetChains, pdbFile, protocol);
+ }
+
+ /**
+ * create sequence structure mappings between each sequence and the given
+ * pdbFile (retrieved via the given protocol).
+ *
+ * @param forStructureView
+ * when true, record the mapping for use in mouseOvers
+ *
+ * @param sequence
+ * - one or more sequences to be mapped to pdbFile
+ * @param targetChains
+ * - optional chain specification for mapping each sequence to pdb
+ * (may be nill, individual elements may be nill)
+ * @param pdbFile
+ * - structure data resource
+ * @param protocol
+ * - how to resolve data from resource
+ * @return null or the structure data parsed as a pdb file
+ */
+ synchronized public MCview.PDBfile setMapping(boolean forStructureView,
+ SequenceI[] sequence,
+ String[] targetChains, String pdbFile, String protocol)
+ {
+ /*
+ * There will be better ways of doing this in the future, for now we'll use
+ * the tried and tested MCview pdb mapping
+ */
MCview.PDBfile pdb = null;
- try
+ boolean parseSecStr = processSecondaryStructure;
+ if (isPDBFileRegistered(pdbFile))
{
- pdb = new MCview.PDBfile(pdbFile, protocol);
+ for (SequenceI sq : sequence)
+ {
+ SequenceI ds = sq;
+ while (ds.getDatasetSequence() != null)
+ {
+ ds = ds.getDatasetSequence();
+ }
+ ;
+ if (ds.getAnnotation() != null)
+ {
+ for (AlignmentAnnotation ala : ds.getAnnotation())
+ {
+ // false if any annotation present from this structure
+ // JBPNote this fails for jmol/chimera view because the *file* is
+ // passed, not the structure data ID -
+ if (MCview.PDBfile.isCalcIdForFile(ala,
+ findIdForPDBFile(pdbFile)))
+ {
+ parseSecStr = false;
+ }
+ }
+ }
+ }
}
- catch (Exception ex)
+ try
+ {
+ pdb = new MCview.PDBfile(addTempFacAnnot, parseSecStr,
+ secStructServices, pdbFile, protocol);
+ if (pdb.id != null && pdb.id.trim().length() > 0
+ && AppletFormatAdapter.FILE.equals(protocol))
+ {
+ registerPDBFile(pdb.id.trim(), pdbFile);
+ }
+ } catch (Exception ex)
{
ex.printStackTrace();
return null;
}
+ String targetChain;
for (int s = 0; s < sequence.length; s++)
{
- String targetChain = "";
-
- if (sequence[s].getName().indexOf("|") > -1)
+ boolean infChain = true;
+ if (targetChains != null && targetChains[s] != null)
+ {
+ infChain = false;
+ targetChain = targetChains[s];
+ }
+ else if (sequence[s].getName().indexOf("|") > -1)
{
targetChain = sequence[s].getName().substring(
- sequence[s].getName().lastIndexOf("|") + 1);
+ sequence[s].getName().lastIndexOf("|") + 1);
+ if (targetChain.length() > 1)
+ {
+ if (targetChain.trim().length() == 0)
+ {
+ targetChain = " ";
+ }
+ else
+ {
+ // not a valid chain identifier
+ targetChain = "";
+ }
+ }
+ }
+ else
+ {
+ targetChain = "";
}
int max = -10;
AlignSeq maxAlignseq = null;
String maxChainId = " ";
PDBChain maxChain = null;
-
+ boolean first = true;
for (int i = 0; i < pdb.chains.size(); i++)
{
+ PDBChain chain = (pdb.chains.elementAt(i));
+ if (targetChain.length() > 0 && !targetChain.equals(chain.id)
+ && !infChain)
+ {
+ continue; // don't try to map chains don't match.
+ }
+ // TODO: correctly determine sequence type for mixed na/peptide
+ // structures
AlignSeq as = new AlignSeq(sequence[s],
- ( (PDBChain) pdb.chains.elementAt(i)).
- sequence,
- AlignSeq.PEP);
+ pdb.chains.elementAt(i).sequence,
+ pdb.chains.elementAt(i).isNa ? AlignSeq.DNA
+ : AlignSeq.PEP);
as.calcScoreMatrix();
as.traceAlignment();
- PDBChain chain = ( (PDBChain) pdb.chains.elementAt(i));
- if (as.maxscore > max
- || (as.maxscore == max && chain.id.equals(targetChain)))
+ if (first || as.maxscore > max
+ || (as.maxscore == max && chain.id.equals(targetChain)))
{
+ first = false;
maxChain = chain;
max = as.maxscore;
maxAlignseq = as;
maxChainId = chain.id;
}
}
-
+ if (maxChain == null)
+ {
+ continue;
+ }
final StringBuffer mappingDetails = new StringBuffer();
- mappingDetails.append("\n\nPDB Sequence is :\nSequence = " +
- maxChain.sequence.getSequenceAsString());
- mappingDetails.append("\nNo of residues = " +
- maxChain.residues.
- size() +
- "\n\n");
+ mappingDetails.append("\n\nPDB Sequence is :\nSequence = "
+ + maxChain.sequence.getSequenceAsString());
+ mappingDetails.append("\nNo of residues = "
+ + maxChain.residues.size() + "\n\n");
PrintStream ps = new PrintStream(System.out)
{
+ @Override
public void print(String x)
{
mappingDetails.append(x);
}
+ @Override
public void println()
{
mappingDetails.append("\n");
@@ -141,85 +440,118 @@ public class StructureSelectionManager
maxAlignseq.printAlignment(ps);
- mappingDetails.append("\nPDB start/end " + maxAlignseq.seq2start + " " +
- maxAlignseq.seq2end);
+ mappingDetails.append("\nPDB start/end " + maxAlignseq.seq2start
+ + " " + maxAlignseq.seq2end);
mappingDetails.append("\nSEQ start/end "
- + (maxAlignseq.seq1start + sequence[s].getStart() - 1) +
- " "
- + (maxAlignseq.seq1end + sequence[s].getEnd() - 1));
+ + (maxAlignseq.seq1start + sequence[s].getStart() - 1) + " "
+ + (maxAlignseq.seq1end + sequence[s].getEnd() - 1));
maxChain.makeExactMapping(maxAlignseq, sequence[s]);
-
+ jalview.datamodel.Mapping sqmpping = maxAlignseq
+ .getMappingFromS1(false);
+ jalview.datamodel.Mapping omap = new jalview.datamodel.Mapping(
+ sqmpping.getMap().getInverse());
maxChain.transferRESNUMFeatures(sequence[s], null);
- int[][] mapping = new int[sequence[s].getEnd() + 2][2];
+ // allocate enough slots to store the mapping from positions in
+ // sequence[s] to the associated chain
+ int[][] mapping = new int[sequence[s].findPosition(sequence[s]
+ .getLength()) + 2][2];
int resNum = -10000;
int index = 0;
-
do
{
Atom tmp = (Atom) maxChain.atoms.elementAt(index);
if (resNum != tmp.resNumber && tmp.alignmentMapping != -1)
{
resNum = tmp.resNumber;
- mapping[tmp.alignmentMapping+1][0] = tmp.resNumber;
- mapping[tmp.alignmentMapping+1][1] = tmp.atomIndex;
+ mapping[tmp.alignmentMapping + 1][0] = tmp.resNumber;
+ mapping[tmp.alignmentMapping + 1][1] = tmp.atomIndex;
}
index++;
- }
- while(index < maxChain.atoms.size());
+ } while (index < maxChain.atoms.size());
- if (mappings == null)
+ if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
{
- mappings = new StructureMapping[1];
+ pdbFile = "INLINE" + pdb.id;
}
- else
+ StructureMapping newMapping = new StructureMapping(sequence[s],
+ pdbFile, pdb.id, maxChainId, mapping,
+ mappingDetails.toString());
+ if (forStructureView)
{
- StructureMapping[] tmp = new StructureMapping[mappings.length + 1];
- System.arraycopy(mappings, 0, tmp, 0, mappings.length);
- mappings = tmp;
- }
- if(protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
- pdbFile = "INLINE"+pdb.id;
+ if (mappings == null)
+ {
+ mappings = new StructureMapping[1];
+ }
+ else
+ {
+ StructureMapping[] tmp = new StructureMapping[mappings.length + 1];
+ System.arraycopy(mappings, 0, tmp, 0, mappings.length);
+ mappings = tmp;
+ }
- mappings[mappings.length - 1]
- = new StructureMapping(sequence[s], pdbFile, pdb.id, maxChainId,
- mapping, mappingDetails.toString());
+ mappings[mappings.length - 1] = newMapping;
+ }
+ maxChain.transferResidueAnnotation(newMapping, sqmpping);
}
- /////////
+ // ///////
return pdb;
}
- public void removeStructureViewerListener(Object svl, String pdbfile)
+ public void removeStructureViewerListener(Object svl, String[] pdbfiles)
{
listeners.removeElement(svl);
+ if (svl instanceof SequenceListener)
+ {
+ for (int i = 0; i < listeners.size(); i++)
+ {
+ if (listeners.elementAt(i) instanceof StructureListener)
+ {
+ ((StructureListener) listeners.elementAt(i))
+ .releaseReferences(svl);
+ }
+ }
+ }
- boolean removeMapping = true;
-
+ if (pdbfiles == null)
+ {
+ return;
+ }
+ String[] handlepdbs;
+ Vector pdbs = new Vector();
+ for (int i = 0; i < pdbfiles.length; pdbs.addElement(pdbfiles[i++]))
+ {
+ ;
+ }
StructureListener sl;
for (int i = 0; i < listeners.size(); i++)
{
if (listeners.elementAt(i) instanceof StructureListener)
{
sl = (StructureListener) listeners.elementAt(i);
- if (sl.getPdbFile().equals(pdbfile))
+ handlepdbs = sl.getPdbFile();
+ for (int j = 0; j < handlepdbs.length; j++)
{
- removeMapping = false;
- break;
+ if (pdbs.contains(handlepdbs[j]))
+ {
+ pdbs.removeElement(handlepdbs[j]);
+ }
}
+
}
}
- if (removeMapping && mappings!=null)
+ if (pdbs.size() > 0 && mappings != null)
{
Vector tmp = new Vector();
for (int i = 0; i < mappings.length; i++)
{
- if (!mappings[i].pdbfile.equals(pdbfile))
+ if (!pdbs.contains(mappings[i].pdbfile))
{
tmp.addElement(mappings[i]);
}
@@ -232,126 +564,250 @@ public class StructureSelectionManager
public void mouseOverStructure(int pdbResNum, String chain, String pdbfile)
{
- SequenceListener sl;
+ if (listeners == null)
+ {
+ // old or prematurely sent event
+ return;
+ }
+ boolean hasSequenceListeners = handlingVamsasMo || seqmappings != null;
+ SearchResults results = null;
+ SequenceI lastseq = null;
+ int lastipos = -1, indexpos;
for (int i = 0; i < listeners.size(); i++)
{
if (listeners.elementAt(i) instanceof SequenceListener)
{
- sl = (SequenceListener) listeners.elementAt(i);
-
- for (int j = 0; j < mappings.length; j++)
+ if (results == null)
{
- if (mappings[j].pdbfile.equals(pdbfile) &&
- mappings[j].pdbchain.equals(chain))
+ results = new SearchResults();
+ }
+ if (mappings != null)
+ {
+ for (int j = 0; j < mappings.length; j++)
{
- sl.highlightSequence(mappings[j].sequence,
- mappings[j].getSeqPos(pdbResNum));
+ if (mappings[j].pdbfile.equals(pdbfile)
+ && mappings[j].pdbchain.equals(chain))
+ {
+ indexpos = mappings[j].getSeqPos(pdbResNum);
+ if (lastipos != indexpos && lastseq != mappings[j].sequence)
+ {
+ results.addResult(mappings[j].sequence, indexpos, indexpos);
+ lastipos = indexpos;
+ lastseq = mappings[j].sequence;
+ // construct highlighted sequence list
+ if (seqmappings != null)
+ {
+
+ Enumeration e = seqmappings.elements();
+ while (e.hasMoreElements())
+
+ {
+ ((AlignedCodonFrame) e.nextElement()).markMappedRegion(
+ mappings[j].sequence, indexpos, results);
+ }
+ }
+ }
+
+ }
}
}
-
- sl.highlightSequence(null, pdbResNum);
+ }
+ }
+ if (results != null)
+ {
+ for (int i = 0; i < listeners.size(); i++)
+ {
+ Object li = listeners.elementAt(i);
+ if (li instanceof SequenceListener)
+ {
+ ((SequenceListener) li).highlightSequence(results);
+ }
}
}
}
- public void mouseOverSequence(SequenceI seq, int index)
+ Vector seqmappings = null; // should be a simpler list of mapped seuqence
+
+ /**
+ * highlight regions associated with a position (indexpos) in seq
+ *
+ * @param seq
+ * the sequeence that the mouse over occured on
+ * @param indexpos
+ * the absolute position being mouseovered in seq (0 to seq.length())
+ * @param index
+ * the sequence position (if -1, seq.findPosition is called to
+ * resolve the residue number)
+ */
+ public void mouseOverSequence(SequenceI seq, int indexpos, int index,
+ VamsasSource source)
{
+ boolean hasSequenceListeners = handlingVamsasMo || seqmappings != null;
+ SearchResults results = null;
+ if (index == -1)
+ {
+ index = seq.findPosition(indexpos);
+ }
StructureListener sl;
int atomNo = 0;
for (int i = 0; i < listeners.size(); i++)
{
- if (listeners.elementAt(i) instanceof StructureListener)
+ Object listener = listeners.elementAt(i);
+ if (listener == source)
{
- sl = (StructureListener) listeners.elementAt(i);
-
+ continue;
+ }
+ if (listener instanceof StructureListener)
+ {
+ sl = (StructureListener) listener;
+ if (mappings == null)
+ {
+ continue;
+ }
for (int j = 0; j < mappings.length; j++)
{
- if (mappings[j].sequence == seq)
+ if (mappings[j].sequence == seq
+ || mappings[j].sequence == seq.getDatasetSequence())
{
atomNo = mappings[j].getAtomNum(index);
if (atomNo > 0)
{
- sl.highlightAtom(atomNo,
- mappings[j].getPDBResNum(index),
- mappings[j].pdbchain,
- mappings[j].pdbfile);
+ sl.highlightAtom(atomNo, mappings[j].getPDBResNum(index),
+ mappings[j].pdbchain, mappings[j].pdbfile);
}
}
}
}
- }
- }
-
- public Annotation[] colourSequenceFromStructure(SequenceI seq, String pdbid)
- {
- Annotation [] annotations = new Annotation[seq.getLength()];
-
- StructureListener sl;
- int atomNo = 0;
- for (int i = 0; i < listeners.size(); i++)
- {
- if (listeners.elementAt(i) instanceof StructureListener)
+ else
{
- sl = (StructureListener) listeners.elementAt(i);
-
- for (int j = 0; j < mappings.length; j++)
+ if (relaySeqMappings && hasSequenceListeners
+ && listener instanceof SequenceListener)
{
+ // DEBUG
+ // System.err.println("relay Seq " + seq.getDisplayId(false) + " " +
+ // index);
- if (mappings[j].sequence == seq
- && mappings[j].getPdbId().equals(pdbid)
- && mappings[j].pdbfile.equals(sl.getPdbFile()))
+ if (results == null)
{
- System.out.println(pdbid+" "+mappings[j].getPdbId()
- +" "+mappings[j].pdbfile);
-
- java.awt.Color col;
- for(int index=0; index= seq.getStart() && index <= seq.getEnd())
{
- if(jalview.util.Comparison.isGap(seq.getCharAt(index)))
- continue;
+ // construct highlighted sequence list
- atomNo = mappings[j].getAtomNum(seq.findPosition(index));
- col = java.awt.Color.white;
- if (atomNo > 0)
+ if (seqmappings != null)
{
- col = sl.getColour(atomNo,
- mappings[j].getPDBResNum(index),
- mappings[j].pdbchain,
- mappings[j].pdbfile);
+ Enumeration e = seqmappings.elements();
+ while (e.hasMoreElements())
- // System.out.println(atomNo+" "+mappings[j].getPDBResNum(index)
- // +" "+index+" "+col);
+ {
+ ((AlignedCodonFrame) e.nextElement()).markMappedRegion(
+ seq, index, results);
+ }
+ }
+ // hasSequenceListeners = results.getSize() > 0;
+ if (handlingVamsasMo)
+ {
+ // maybe have to resolve seq to a dataset seqeunce...
+ // add in additional direct sequence and/or dataset sequence
+ // highlighting
+ results.addResult(seq, index, index);
}
-
- annotations[index] = new Annotation("X",null,' ',0,col);
}
- return annotations;
}
+ if (hasSequenceListeners)
+ {
+ ((SequenceListener) listener).highlightSequence(results);
+ }
+ }
+ else if (listener instanceof VamsasListener && !handlingVamsasMo)
+ {
+ // DEBUG
+ // System.err.println("Vamsas from Seq " + seq.getDisplayId(false) + "
+ // " +
+ // index);
+ // pass the mouse over and absolute position onto the
+ // VamsasListener(s)
+ ((VamsasListener) listener).mouseOver(seq, indexpos, source);
+ }
+ else if (listener instanceof SecondaryStructureListener)
+ {
+ ((SecondaryStructureListener) listener).mouseOverSequence(seq,
+ indexpos);
}
}
}
-
- return annotations;
}
+ /**
+ * true if a mouse over event from an external (ie Vamsas) source is being
+ * handled
+ */
+ boolean handlingVamsasMo = false;
- public void structureSelectionChanged()
+ long lastmsg = 0;
+
+ /**
+ * as mouseOverSequence but only route event to SequenceListeners
+ *
+ * @param sequenceI
+ * @param position
+ * in an alignment sequence
+ */
+ public void mouseOverVamsasSequence(SequenceI sequenceI, int position,
+ VamsasSource source)
{
- StructureListener svl;
- for (int i = 0; i < listeners.size(); i++)
+ handlingVamsasMo = true;
+ long msg = sequenceI.hashCode() * (1 + position);
+ if (lastmsg != msg)
{
- svl = (StructureListener) listeners.elementAt(i);
+ lastmsg = msg;
+ mouseOverSequence(sequenceI, position, -1, source);
}
+ handlingVamsasMo = false;
+ }
+
+ public Annotation[] colourSequenceFromStructure(SequenceI seq,
+ String pdbid)
+ {
+ return null;
+ // THIS WILL NOT BE AVAILABLE IN JALVIEW 2.3,
+ // UNTIL THE COLOUR BY ANNOTATION IS REWORKED
+ /*
+ * Annotation [] annotations = new Annotation[seq.getLength()];
+ *
+ * StructureListener sl; int atomNo = 0; for (int i = 0; i <
+ * listeners.size(); i++) { if (listeners.elementAt(i) instanceof
+ * StructureListener) { sl = (StructureListener) listeners.elementAt(i);
+ *
+ * for (int j = 0; j < mappings.length; j++) {
+ *
+ * if (mappings[j].sequence == seq && mappings[j].getPdbId().equals(pdbid)
+ * && mappings[j].pdbfile.equals(sl.getPdbFile())) {
+ * System.out.println(pdbid+" "+mappings[j].getPdbId() +"
+ * "+mappings[j].pdbfile);
+ *
+ * java.awt.Color col; for(int index=0; index 0) { col = sl.getColour(atomNo,
+ * mappings[j].getPDBResNum(index), mappings[j].pdbchain,
+ * mappings[j].pdbfile); }
+ *
+ * annotations[index] = new Annotation("X",null,' ',0,col); } return
+ * annotations; } } } }
+ *
+ * return annotations;
+ */
+ }
+
+ public void structureSelectionChanged()
+ {
}
public void sequenceSelectionChanged()
{
- StructureListener svl;
- for (int i = 0; i < listeners.size(); i++)
- {
- svl = (StructureListener) listeners.elementAt(i);
- }
}
public void sequenceColoursChanged(Object source)
@@ -370,14 +826,16 @@ public class StructureSelectionManager
public StructureMapping[] getMapping(String pdbfile)
{
Vector tmp = new Vector();
- for (int i = 0; i < mappings.length; i++)
+ if (mappings != null)
{
- if (mappings[i].pdbfile.equals(pdbfile))
+ for (int i = 0; i < mappings.length; i++)
{
- tmp.addElement(mappings[i]);
+ if (mappings[i].pdbfile.equals(pdbfile))
+ {
+ tmp.addElement(mappings[i]);
+ }
}
}
-
StructureMapping[] ret = new StructureMapping[tmp.size()];
for (int i = 0; i < tmp.size(); i++)
{
@@ -400,4 +858,201 @@ public class StructureSelectionManager
return sb.toString();
}
+
+ private int[] seqmappingrefs = null; // refcount for seqmappings elements
+
+ private synchronized void modifySeqMappingList(boolean add,
+ AlignedCodonFrame[] codonFrames)
+ {
+ if (!add && (seqmappings == null || seqmappings.size() == 0))
+ {
+ return;
+ }
+ if (seqmappings == null)
+ {
+ seqmappings = new Vector();
+ }
+ if (codonFrames != null && codonFrames.length > 0)
+ {
+ for (int cf = 0; cf < codonFrames.length; cf++)
+ {
+ if (seqmappings.contains(codonFrames[cf]))
+ {
+ if (add)
+ {
+ seqmappingrefs[seqmappings.indexOf(codonFrames[cf])]++;
+ }
+ else
+ {
+ if (--seqmappingrefs[seqmappings.indexOf(codonFrames[cf])] <= 0)
+ {
+ int pos = seqmappings.indexOf(codonFrames[cf]);
+ int[] nr = new int[seqmappingrefs.length - 1];
+ if (pos > 0)
+ {
+ System.arraycopy(seqmappingrefs, 0, nr, 0, pos);
+ }
+ if (pos < seqmappingrefs.length - 1)
+ {
+ System.arraycopy(seqmappingrefs, pos + 1, nr, 0,
+ seqmappingrefs.length - pos - 2);
+ }
+ }
+ }
+ }
+ else
+ {
+ if (add)
+ {
+ seqmappings.addElement(codonFrames[cf]);
+
+ int[] nsr = new int[(seqmappingrefs == null) ? 1
+ : seqmappingrefs.length + 1];
+ if (seqmappingrefs != null && seqmappingrefs.length > 0)
+ {
+ System.arraycopy(seqmappingrefs, 0, nsr, 0,
+ seqmappingrefs.length);
+ }
+ nsr[(seqmappingrefs == null) ? 0 : seqmappingrefs.length] = 1;
+ seqmappingrefs = nsr;
+ }
+ }
+ }
+ }
+ }
+
+ public void removeMappings(AlignedCodonFrame[] codonFrames)
+ {
+ modifySeqMappingList(false, codonFrames);
+ }
+
+ public void addMappings(AlignedCodonFrame[] codonFrames)
+ {
+ modifySeqMappingList(true, codonFrames);
+ }
+
+ Vector sel_listeners = new Vector();
+
+ public void addSelectionListener(SelectionListener selecter)
+ {
+ if (!sel_listeners.contains(selecter))
+ {
+ sel_listeners.addElement(selecter);
+ }
+ }
+
+ public void removeSelectionListener(SelectionListener toremove)
+ {
+ if (sel_listeners.contains(toremove))
+ {
+ sel_listeners.removeElement(toremove);
+ }
+ }
+
+ public synchronized void sendSelection(
+ jalview.datamodel.SequenceGroup selection,
+ jalview.datamodel.ColumnSelection colsel, SelectionSource source)
+ {
+ if (sel_listeners != null && sel_listeners.size() > 0)
+ {
+ Enumeration listeners = sel_listeners.elements();
+ while (listeners.hasMoreElements())
+ {
+ SelectionListener slis = ((SelectionListener) listeners
+ .nextElement());
+ if (slis != source)
+ {
+ slis.selection(selection, colsel, source);
+ }
+ ;
+ }
+ }
+ }
+
+ Vector view_listeners = new Vector();
+
+ public synchronized void sendViewPosition(
+ jalview.api.AlignmentViewPanel source, int startRes, int endRes,
+ int startSeq, int endSeq)
+ {
+
+ if (view_listeners != null && view_listeners.size() > 0)
+ {
+ Enumeration listeners = view_listeners
+ .elements();
+ while (listeners.hasMoreElements())
+ {
+ AlignmentViewPanelListener slis = listeners.nextElement();
+ if (slis != source)
+ {
+ slis.viewPosition(startRes, endRes, startSeq, endSeq, source);
+ }
+ ;
+ }
+ }
+ }
+
+ public void finalize() throws Throwable
+ {
+ if (listeners != null)
+ {
+ listeners.clear();
+ listeners = null;
+ }
+ if (pdbIdFileName != null)
+ {
+ pdbIdFileName.clear();
+ pdbIdFileName = null;
+ }
+ if (sel_listeners != null)
+ {
+ sel_listeners.clear();
+ sel_listeners = null;
+ }
+ if (view_listeners != null)
+ {
+ view_listeners.clear();
+ view_listeners = null;
+ }
+ mappings = null;
+ seqmappingrefs = null;
+ }
+
+ /**
+ * release all references associated with this manager provider
+ *
+ * @param jalviewLite
+ */
+ public static void release(StructureSelectionManagerProvider jalviewLite)
+ {
+ // synchronized (instances)
+ {
+ if (instances == null)
+ {
+ return;
+ }
+ StructureSelectionManager mnger = (instances.get(jalviewLite));
+ if (mnger != null)
+ {
+ instances.remove(jalviewLite);
+ try
+ {
+ mnger.finalize();
+ } catch (Throwable x)
+ {
+ }
+ ;
+ }
+ }
+ }
+
+ public void registerPDBEntry(PDBEntry pdbentry)
+ {
+ if (pdbentry.getFile() != null
+ && pdbentry.getFile().trim().length() > 0)
+ {
+ registerPDBFile(pdbentry.getId(), pdbentry.getFile());
+ }
+ }
+
}