/*
- * 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
- * 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.
- *
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * 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.
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.structure;
import MCview.*;
import jalview.analysis.*;
+import jalview.api.AlignmentViewPanel;
+import jalview.api.StructureSelectionManagerProvider;
import jalview.datamodel.*;
public class StructureSelectionManager
{
- static StructureSelectionManager instance;
+ static IdentityHashMap<StructureSelectionManagerProvider, StructureSelectionManager> instances;
StructureMapping[] mappings;
- Hashtable mappingData = new Hashtable();
+ /**
+ * debug function - write all mappings to stdout
+ */
+ public void reportMapping()
+ {
+ if (mappings == null)
+ {
+ System.err.println("reportMapping: No PDB/Sequence mappings.");
+ }
+ else
+ {
+ 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);
+ }
+ }
+ }
- public static StructureSelectionManager getStructureSelectionManager()
+ Hashtable mappingData = new Hashtable();
+ private static StructureSelectionManager nullProvider = null;
+ public static StructureSelectionManager getStructureSelectionManager(
+ StructureSelectionManagerProvider context)
{
+ if (context==null) {
+ if (nullProvider == null)
+ {
+ if (instances != null)
+ {
+ throw new Error(
+ "Implementation error. Structure selection manager's context is 'null'",
+ new NullPointerException("SSM context is null"));
+ }
+ else
+ {
+ nullProvider = new StructureSelectionManager();
+ }
+ return nullProvider;
+ }
+ }
+ if (instances == null)
+ {
+ instances = new java.util.IdentityHashMap<StructureSelectionManagerProvider, StructureSelectionManager>();
+ }
+ StructureSelectionManager instance = instances.get(context);
if (instance == null)
{
- instance = new StructureSelectionManager();
+ if (nullProvider!=null)
+ {
+ instance = nullProvider;
+ } else {
+ instance = new StructureSelectionManager();
+ }
+ instances.put(context, instance);
}
-
return instance;
}
Vector listeners = new Vector();
+ /**
+ * register a listener for alignment sequence mouseover events
+ *
+ * @param svl
+ */
public void addStructureViewerListener(Object svl)
{
if (!listeners.contains(svl))
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
+ /**
+ * 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
{
String targetChain;
for (int s = 0; s < sequence.length; s++)
{
+ 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);
+ if (targetChain.length() > 1)
+ {
+ if (targetChain.trim().length() == 0)
+ {
+ targetChain = " ";
+ }
+ else
+ {
+ // not a valid chain identifier
+ targetChain = "";
+ }
+ }
}
else
targetChain = "";
AlignSeq maxAlignseq = null;
String maxChainId = " ";
PDBChain maxChain = null;
-
+ boolean first = true;
for (int i = 0; i < pdb.chains.size(); i++)
{
- AlignSeq as = new AlignSeq(sequence[s], ((PDBChain) pdb.chains
- .elementAt(i)).sequence, AlignSeq.PEP);
+ PDBChain chain = ((PDBChain) 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,
+ ((PDBChain) pdb.chains.elementAt(i)).isNa ? AlignSeq.DNA
+ : AlignSeq.PEP);
as.calcScoreMatrix();
as.traceAlignment();
- PDBChain chain = ((PDBChain) pdb.chains.elementAt(i));
- if (as.maxscore > max
+ 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());
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;
pdbFile = "INLINE" + pdb.id;
mappings[mappings.length - 1] = new StructureMapping(sequence[s],
- pdbFile, pdb.id, maxChainId, mapping, mappingDetails
- .toString());
+ pdbFile, pdb.id, maxChainId, mapping,
+ mappingDetails.toString());
maxChain.transferResidueAnnotation(mappings[mappings.length - 1]);
}
// ///////
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);
+ }
+ }
+ }
+ 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);
- 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]);
}
public void mouseOverStructure(int pdbResNum, String chain, String pdbfile)
{
+ 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)
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))
{
- results.addResult(mappings[j].sequence, mappings[j]
- .getSeqPos(pdbResNum), mappings[j]
- .getSeqPos(pdbResNum));
+ 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.getSize() > 0)
- {
- ((SequenceListener) listeners.elementAt(i))
- .highlightSequence(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
- // pairs
-
- public void mouseOverSequence(SequenceI seq, int index)
+ /**
+ * 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);
else
{
if (relaySeqMappings && hasSequenceListeners
- && listeners.elementAt(i) instanceof SequenceListener)
+ && listener instanceof SequenceListener)
{
- // DEBUG
- //System.err.println("relay Seq " + seq.getDisplayId(false) + " " +
- // index);
+ // DEBUG
+ // System.err.println("relay Seq " + seq.getDisplayId(false) + " " +
+ // index);
if (results == null)
{
{
// construct highlighted sequence list
- if (seqmappings!=null)
+ if (seqmappings != null)
{
Enumeration e = seqmappings.elements();
while (e.hasMoreElements())
// 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);
+ ((SequenceListener) listener).highlightSequence(results);
}
}
- else if (listeners.elementAt(i) instanceof VamsasListener
- && !handlingVamsasMo)
+ else if (listener instanceof VamsasListener && !handlingVamsasMo)
{
- // DEBUG
- //System.err.println("Vamsas from Seq " + seq.getDisplayId(false) + " " +
+ // DEBUG
+ // System.err.println("Vamsas from Seq " + seq.getDisplayId(false) + "
+ // " +
// index);
- // pass the mouse over onto the VamsasListener(s)
- ((VamsasListener) listeners.elementAt(i)).mouseOver(seq, 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);
}
}
}
*/
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)
+ public void mouseOverVamsasSequence(SequenceI sequenceI, int position,
+ VamsasSource source)
{
handlingVamsasMo = true;
- mouseOverSequence(sequenceI, position);
+ long msg = sequenceI.hashCode() * (1 + position);
+ if (lastmsg != msg)
+ {
+ lastmsg = msg;
+ mouseOverSequence(sequenceI, position, -1, source);
+ }
handlingVamsasMo = false;
}
*
* 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);
+ * 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;
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++)
{
{
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)
+ {
+ // synchronized (instances)
+ {
+ if (instances == null)
+ {
+ return;
+ }
+ StructureSelectionManager mnger = (instances.get(jalviewLite));
+ if (mnger != null)
+ {
+ instances.remove(jalviewLite);
+ try
+ {
+ mnger.finalize();
+ } catch (Throwable x)
+ {
+ }
+ ;
+ }
+ }
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff