-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.structure;\r
-\r
-import java.io.*;\r
-import java.util.*;\r
-\r
-import MCview.*;\r
-import jalview.analysis.*;\r
-import jalview.datamodel.*;\r
-\r
-public class StructureSelectionManager\r
-{\r
- static StructureSelectionManager instance;\r
- StructureMapping[] mappings;\r
- Hashtable mappingData = new Hashtable();\r
-\r
- public static StructureSelectionManager getStructureSelectionManager()\r
- {\r
- if (instance == null)\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * 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.
+ *
+ * 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ */
+package jalview.structure;
+
+import java.io.*;
+import java.util.*;
+
+import MCview.*;
+import jalview.analysis.*;
+import jalview.api.AlignmentViewPanel;
+import jalview.api.StructureSelectionManagerProvider;
+import jalview.datamodel.*;
+
+public class StructureSelectionManager
+{
+ static IdentityHashMap<StructureSelectionManagerProvider,StructureSelectionManager> instances;
+
+ StructureMapping[] mappings;
+
+ /**
+ * debug function - write all mappings to stdout
+ */
+ public void reportMapping() {\r
+ if (mappings==null)\r
{\r
- instance = new StructureSelectionManager();\r
- }\r
-\r
- return instance;\r
- }\r
-\r
- Vector listeners = new Vector();\r
- public void addStructureViewerListener(Object svl)\r
- {\r
- if (!listeners.contains(svl))\r
- {\r
- listeners.addElement(svl);\r
- }\r
- }\r
-\r
- public String alreadyMappedToFile(String pdbid)\r
- {\r
- if (mappings != null)\r
- {\r
- for (int i = 0; i < mappings.length; i++)\r
- {\r
- if (mappings[i].getPdbId().equals(pdbid))\r
- {\r
- return mappings[i].pdbfile;\r
- }\r
- }\r
- }\r
- return null;\r
- }\r
-\r
- /*\r
- There will be better ways of doing this in the future, for now we'll use\r
- the tried and tested MCview pdb mapping\r
- */\r
- public MCview.PDBfile setMapping(SequenceI[] sequence,\r
- String pdbFile,\r
- String protocol)\r
- {\r
- MCview.PDBfile pdb = null;\r
- try\r
- {\r
- pdb = new MCview.PDBfile(pdbFile, protocol);\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- return null;\r
- }\r
-\r
- for (int s = 0; s < sequence.length; s++)\r
- {\r
- String targetChain = "";\r
-\r
- if (sequence[s].getName().indexOf("|") > -1)\r
- {\r
- targetChain = sequence[s].getName().substring(\r
- sequence[s].getName().lastIndexOf("|") + 1);\r
- }\r
-\r
- int max = -10;\r
- AlignSeq maxAlignseq = null;\r
- String maxChainId = " ";\r
- PDBChain maxChain = null;\r
-\r
- for (int i = 0; i < pdb.chains.size(); i++)\r
- {\r
- AlignSeq as = new AlignSeq(sequence[s],\r
- ( (PDBChain) pdb.chains.elementAt(i)).\r
- sequence,\r
- AlignSeq.PEP);\r
- as.calcScoreMatrix();\r
- as.traceAlignment();\r
- PDBChain chain = ( (PDBChain) pdb.chains.elementAt(i));\r
-\r
- if (as.maxscore > max\r
- || (as.maxscore == max && chain.id.equals(targetChain)))\r
- {\r
- maxChain = chain;\r
- max = as.maxscore;\r
- maxAlignseq = as;\r
- maxChainId = chain.id;\r
- }\r
- }\r
-\r
- final StringBuffer mappingDetails = new StringBuffer();\r
- mappingDetails.append("\n\nPDB Sequence is :\nSequence = " +\r
- maxChain.sequence.getSequenceAsString());\r
- mappingDetails.append("\nNo of residues = " +\r
- maxChain.residues.\r
- size() +\r
- "\n\n");\r
- PrintStream ps = new PrintStream(System.out)\r
- {\r
- public void print(String x)\r
- {\r
- mappingDetails.append(x);\r
- }\r
-\r
- public void println()\r
- {\r
- mappingDetails.append("\n");\r
- }\r
- };\r
-\r
- maxAlignseq.printAlignment(ps);\r
-\r
- mappingDetails.append("\nPDB start/end " + maxAlignseq.seq2start + " " +\r
- maxAlignseq.seq2end);\r
- mappingDetails.append("\nSEQ start/end "\r
- + (maxAlignseq.seq1start + sequence[s].getStart() - 1) +\r
- " "\r
- + (maxAlignseq.seq1end + sequence[s].getEnd() - 1));\r
-\r
- maxChain.makeExactMapping(maxAlignseq, sequence[s]);\r
-\r
- // maxChain.transferRESNUMFeatures(sequence[s], null);\r
-\r
- int[][] mapping = new int[sequence[s].getEnd() + 2][2];\r
- int resNum = -10000;\r
- int index = 0;\r
-\r
-\r
- do\r
- {\r
- Atom tmp = (Atom) maxChain.atoms.elementAt(index);\r
- if (resNum != tmp.resNumber && tmp.alignmentMapping != -1)\r
- {\r
- resNum = tmp.resNumber;\r
- mapping[tmp.alignmentMapping+1][0] = tmp.resNumber;\r
- mapping[tmp.alignmentMapping+1][1] = tmp.atomIndex;\r
- }\r
-\r
- index++;\r
- }\r
- while(index < maxChain.atoms.size());\r
-\r
- if (mappings == null)\r
- {\r
- mappings = new StructureMapping[1];\r
- }\r
- else\r
- {\r
- StructureMapping[] tmp = new StructureMapping[mappings.length + 1];\r
- System.arraycopy(mappings, 0, tmp, 0, mappings.length);\r
- mappings = tmp;\r
- }\r
-\r
- if(protocol.equals(jalview.io.AppletFormatAdapter.PASTE))\r
- pdbFile = "INLINE"+pdb.id;\r
-\r
- mappings[mappings.length - 1]\r
- = new StructureMapping(sequence[s], pdbFile, pdb.id, maxChainId,\r
- mapping, mappingDetails.toString());\r
- }\r
- /////////\r
-\r
- return pdb;\r
- }\r
-\r
- public void removeStructureViewerListener(Object svl, String pdbfile)\r
- {\r
- listeners.removeElement(svl);\r
-\r
- boolean removeMapping = true;\r
-\r
- StructureListener sl;\r
- for (int i = 0; i < listeners.size(); i++)\r
- {\r
- if (listeners.elementAt(i) instanceof StructureListener)\r
- {\r
- sl = (StructureListener) listeners.elementAt(i);\r
- if (sl.getPdbFile().equals(pdbfile))\r
- {\r
- removeMapping = false;\r
- break;\r
- }\r
- }\r
- }\r
-\r
- if (removeMapping && mappings!=null)\r
- {\r
- Vector tmp = new Vector();\r
- for (int i = 0; i < mappings.length; i++)\r
- {\r
- if (!mappings[i].pdbfile.equals(pdbfile))\r
- {\r
- tmp.addElement(mappings[i]);\r
- }\r
- }\r
-\r
- mappings = new StructureMapping[tmp.size()];\r
- tmp.copyInto(mappings);\r
- }\r
- }\r
-\r
- public void mouseOverStructure(int pdbResNum, String chain, String pdbfile)\r
- {\r
- SequenceListener sl;\r
- for (int i = 0; i < listeners.size(); i++)\r
- {\r
- if (listeners.elementAt(i) instanceof SequenceListener)\r
- {\r
- sl = (SequenceListener) listeners.elementAt(i);\r
-\r
- for (int j = 0; j < mappings.length; j++)\r
- {\r
- if (mappings[j].pdbfile.equals(pdbfile) &&\r
- mappings[j].pdbchain.equals(chain))\r
- {\r
- sl.highlightSequence(mappings[j].sequence,\r
- mappings[j].getSeqPos(pdbResNum));\r
- }\r
- }\r
-\r
- sl.highlightSequence(null, pdbResNum);\r
- }\r
- }\r
- }\r
-\r
- public void mouseOverSequence(SequenceI seq, int index)\r
- {\r
- StructureListener sl;\r
- int atomNo = 0;\r
- for (int i = 0; i < listeners.size(); i++)\r
- {\r
- if (listeners.elementAt(i) instanceof StructureListener)\r
- {\r
- sl = (StructureListener) listeners.elementAt(i);\r
-\r
- for (int j = 0; j < mappings.length; j++)\r
- {\r
- if (mappings[j].sequence == seq)\r
- {\r
- atomNo = mappings[j].getAtomNum(index);\r
-\r
- if (atomNo > 0)\r
- {\r
- sl.highlightAtom(atomNo,\r
- mappings[j].getPDBResNum(index),\r
- mappings[j].pdbchain,\r
- mappings[j].pdbfile);\r
- }\r
- }\r
- }\r
- }\r
- }\r
- }\r
-\r
- public void structureSelectionChanged()\r
- {\r
- StructureListener svl;\r
- for (int i = 0; i < listeners.size(); i++)\r
- {\r
- svl = (StructureListener) listeners.elementAt(i);\r
- }\r
- }\r
-\r
- public void sequenceSelectionChanged()\r
- {\r
- StructureListener svl;\r
- for (int i = 0; i < listeners.size(); i++)\r
- {\r
- svl = (StructureListener) listeners.elementAt(i);\r
- }\r
- }\r
-\r
- public void sequenceColoursChanged(Object source)\r
- {\r
- StructureListener sl;\r
- for (int i = 0; i < listeners.size(); i++)\r
- {\r
- if (listeners.elementAt(i) instanceof StructureListener)\r
- {\r
- sl = (StructureListener) listeners.elementAt(i);\r
- sl.updateColours(source);\r
- }\r
- }\r
- }\r
-\r
- public StructureMapping[] getMapping(String pdbfile)\r
- {\r
- Vector tmp = new Vector();\r
- for (int i = 0; i < mappings.length; i++)\r
- {\r
- if (mappings[i].pdbfile.equals(pdbfile))\r
- {\r
- tmp.addElement(mappings[i]);\r
- }\r
- }\r
-\r
- StructureMapping[] ret = new StructureMapping[tmp.size()];\r
- for (int i = 0; i < tmp.size(); i++)\r
- {\r
- ret[i] = (StructureMapping) tmp.elementAt(i);\r
- }\r
-\r
- return ret;\r
- }\r
-\r
- public String printMapping(String pdbfile)\r
- {\r
- StringBuffer sb = new StringBuffer();\r
- for (int i = 0; i < mappings.length; i++)\r
- {\r
- if (mappings[i].pdbfile.equals(pdbfile))\r
+ System.err.println("reportMapping: No PDB/Sequence mappings.");\r
+ }else{\r
+ System.err.println("reportMapping: There are "+mappings.length+" mappings.");\r
+ for (int m=0;m<mappings.length;m++)\r
{\r
- sb.append(mappings[i].mappingDetails);\r
+ System.err.println("mapping "+m+" : "+mappings[m].pdbfile);\r
}\r
}\r
-\r
- return sb.toString();\r
}\r
-}\r
+ Hashtable mappingData = new Hashtable();
+
+ public static StructureSelectionManager getStructureSelectionManager(StructureSelectionManagerProvider context)
+ {
+ if (instances == null)
+ {
+ instances = new java.util.IdentityHashMap<StructureSelectionManagerProvider,StructureSelectionManager>();
+ }
+ StructureSelectionManager instance=instances.get(context);
+ if (instance==null)
+ {
+ instances.put(context, instance=new StructureSelectionManager());
+ }
+ 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))
+ {
+ listeners.addElement(svl);
+ }
+ }
+
+ public String alreadyMappedToFile(String pdbid)
+ {
+ if (mappings != null)
+ {
+ for (int i = 0; i < mappings.length; i++)
+ {
+ if (mappings[i].getPdbId().equals(pdbid))
+ {
+ return mappings[i].pdbfile;
+ }
+ }
+ }
+ return null;
+ }
+
+ /**
+ * create sequence structure mappings between each sequence and the given
+ * pdbFile (retrieved via the given protocol).
+ *
+ * @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[] 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
+ {
+ pdb = new MCview.PDBfile(pdbFile, protocol);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ return null;
+ }
+
+ String targetChain;
+ for (int s = 0; s < sequence.length; s++)
+ {
+ if (targetChains != null && targetChains[s] != null)
+ targetChain = targetChains[s];
+ else if (sequence[s].getName().indexOf("|") > -1)
+ {
+ targetChain = sequence[s].getName().substring(
+ sequence[s].getName().lastIndexOf("|") + 1);
+ }
+ 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++)
+ {
+ // TODO: re http://issues.jalview.org/browse/JAL-583 : this patch may
+ // need to be revoked
+ PDBChain chain = ((PDBChain) pdb.chains.elementAt(i));
+ if (targetChain.length() > 0 && !targetChain.equals(chain.id))
+ {
+ continue; // don't try to map chains don't match.
+ }
+ // end of patch for limiting computed mappings
+ // TODO: correctly determine sequence type for mixed na/peptide
+ // structures
+ AlignSeq as = new AlignSeq(sequence[s],
+ ((PDBChain) pdb.chains.elementAt(i)).sequence,
+ ((PDBChain) pdb.chains.elementAt(i)).isNa ? AlignSeq.DNA
+ : AlignSeq.PEP);
+ as.calcScoreMatrix();
+ as.traceAlignment();
+
+ 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");
+ PrintStream ps = new PrintStream(System.out)
+ {
+ public void print(String x)
+ {
+ mappingDetails.append(x);
+ }
+
+ public void println()
+ {
+ mappingDetails.append("\n");
+ }
+ };
+
+ maxAlignseq.printAlignment(ps);
+
+ 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));
+
+ maxChain.makeExactMapping(maxAlignseq, sequence[s]);
+
+ maxChain.transferRESNUMFeatures(sequence[s], null);
+
+ // 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;
+ }
+
+ index++;
+ } while (index < maxChain.atoms.size());
+
+ 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;
+ }
+
+ if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
+ pdbFile = "INLINE" + pdb.id;
+
+ mappings[mappings.length - 1] = new StructureMapping(sequence[s],
+ pdbFile, pdb.id, maxChainId, mapping,
+ mappingDetails.toString());
+ maxChain.transferResidueAnnotation(mappings[mappings.length - 1]);
+ }
+ // ///////
+
+ return pdb;
+ }
+
+ 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);
+ }
+ }
+ }
+
+ if (pdbfiles == null)
+ {
+ return;
+ }
+ boolean removeMapping = true;
+ 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);
+ handlepdbs = sl.getPdbFile();
+ for (int j = 0; j < handlepdbs.length; j++)
+ {
+ if (pdbs.contains(handlepdbs[j]))
+ {
+ pdbs.removeElement(handlepdbs[j]);
+ }
+ }
+
+ }
+ }
+
+ if (pdbs.size() > 0 && mappings != null)
+ {
+ Vector tmp = new Vector();
+ for (int i = 0; i < mappings.length; i++)
+ {
+ if (!pdbs.contains(mappings[i].pdbfile))
+ {
+ tmp.addElement(mappings[i]);
+ }
+ }
+
+ mappings = new StructureMapping[tmp.size()];
+ tmp.copyInto(mappings);
+ }
+ }
+
+ public void mouseOverStructure(int pdbResNum, String chain, String pdbfile)
+ {
+ 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)
+ {
+ if (results == null)
+ {
+ results = new SearchResults();
+ }
+ if (mappings != null)
+ {
+ for (int j = 0; j < mappings.length; j++)
+ {
+ 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);
+ }
+ }
+ }
+
+ }
+ }
+ }
+ }
+ }
+ if (results!=null)
+ {
+ for (int i = 0; i < listeners.size(); i++)
+ {
+ Object li = listeners.elementAt(i);
+ if (li instanceof SequenceListener)
+ ((SequenceListener) li).highlightSequence(results);
+ }
+ }
+ }
+
+ 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)
+ {
+ sl = (StructureListener) listeners.elementAt(i);
+ if (mappings == null)
+ {
+ continue;
+ }
+ for (int j = 0; j < mappings.length; j++)
+ {
+ 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);
+ }
+ }
+ }
+ }
+ else
+ {
+ if (relaySeqMappings && hasSequenceListeners
+ && listeners.elementAt(i) instanceof SequenceListener)
+ {
+ // DEBUG
+ // System.err.println("relay Seq " + seq.getDisplayId(false) + " " +
+ // index);
+
+ if (results == null)
+ {
+ results = new SearchResults();
+ if (index >= seq.getStart() && index <= seq.getEnd())
+ {
+ // construct highlighted sequence list
+
+ if (seqmappings != null)
+ {
+ Enumeration e = seqmappings.elements();
+ while (e.hasMoreElements())
+
+ {
+ ((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);
+ }
+ }
+ }
+ if (hasSequenceListeners)
+ {
+ ((SequenceListener) listeners.elementAt(i))
+ .highlightSequence(results);
+ }
+ }
+ else if (listeners.elementAt(i) 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) listeners.elementAt(i)).mouseOver(seq,
+ indexpos, source);
+ }
+ }
+ }
+ }
+
+ /**
+ * true if a mouse over event from an external (ie Vamsas) source is being
+ * handled
+ */
+ boolean handlingVamsasMo = false;
+
+ 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)
+ {
+ handlingVamsasMo = true;
+ long msg = sequenceI.hashCode() * (1 + position);
+ if (lastmsg != msg)
+ {
+ 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<seq.getLength(); index++) {
+ * if(jalview.util.Comparison.isGap(seq.getCharAt(index))) continue;
+ *
+ * atomNo = mappings[j].getAtomNum(seq.findPosition(index)); col =
+ * java.awt.Color.white; if (atomNo > 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()
+ {
+ }
+
+ public void sequenceColoursChanged(Object source)
+ {
+ StructureListener sl;
+ for (int i = 0; i < listeners.size(); i++)
+ {
+ if (listeners.elementAt(i) instanceof StructureListener)
+ {
+ sl = (StructureListener) listeners.elementAt(i);
+ sl.updateColours(source);
+ }
+ }
+ }
+
+ public StructureMapping[] getMapping(String pdbfile)
+ {
+ Vector tmp = new Vector();
+ if (mappings != null)
+ {
+ for (int i = 0; i < mappings.length; 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++)
+ {
+ ret[i] = (StructureMapping) tmp.elementAt(i);
+ }
+
+ return ret;
+ }
+
+ public String printMapping(String pdbfile)
+ {
+ StringBuffer sb = new StringBuffer();
+ for (int i = 0; i < mappings.length; i++)
+ {
+ if (mappings[i].pdbfile.equals(pdbfile))
+ {
+ sb.append(mappings[i].mappingDetails);
+ }
+ }
+
+ 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<SelectionListener> sel_listeners = new Vector<SelectionListener>();
+
+ 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<AlignmentViewPanelListener> view_listeners=new Vector<AlignmentViewPanelListener>();
+ 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<AlignmentViewPanelListener> 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 (mappingData!=null)
+ {
+ mappingData.clear();
+ mappingData=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)
+ {
+ StructureSelectionManager mnger=(instances.get(jalviewLite));
+ if (mnger!=null)
+ {
+ instances.remove(jalviewLite);
+ try {
+ mnger.finalize();
+ } catch (Throwable x){};
+ }
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff