/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * 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;
public class StructureSelectionManager
{
- static IdentityHashMap<StructureSelectionManagerProvider,StructureSelectionManager> instances;
+ static IdentityHashMap<StructureSelectionManagerProvider, StructureSelectionManager> instances;
StructureMapping[] mappings;
/**
* debug function - write all mappings to stdout
*/
- public void reportMapping() {\r
- if (mappings==null)\r
- {\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
- System.err.println("mapping "+m+" : "+mappings[m].pdbfile);\r
- }\r
- }\r
- }\r
+ 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);
+ }
+ }
+ }
+
Hashtable mappingData = new Hashtable();
- public static StructureSelectionManager getStructureSelectionManager(StructureSelectionManagerProvider context)
+ public static StructureSelectionManager getStructureSelectionManager(
+ StructureSelectionManagerProvider context)
{
+ if (context==null)
+ {
+ throw new Error("Implementation error. Structure selection manager's context is 'null'", new NullPointerException("SSM context is null"));
+ }
if (instances == null)
{
- instances = new java.util.IdentityHashMap<StructureSelectionManagerProvider,StructureSelectionManager>();
+ instances = new java.util.IdentityHashMap<StructureSelectionManagerProvider, StructureSelectionManager>();
}
- StructureSelectionManager instance=instances.get(context);
- if (instance==null)
+ StructureSelectionManager instance = instances.get(context);
+ if (instance == null)
{
- instances.put(context, instance=new StructureSelectionManager());
+ instances.put(context, instance = new StructureSelectionManager());
}
return instance;
}
/**
* register a listener for alignment sequence mouseover events
+ *
* @param svl
*/
public void addStructureViewerListener(Object svl)
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 = "";
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))
+ if (targetChain.length() > 0 && !targetChain.equals(chain.id)
+ && !infChain)
{
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],
// 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[][] mapping = new int[sequence[s].findPosition(sequence[s]
+ .getLength()) + 2][2];
int resNum = -10000;
int index = 0;
listeners.removeElement(svl);
if (svl instanceof SequenceListener)
{
- for (int i=0;i<listeners.size();i++)
+ for (int i = 0; i < listeners.size(); i++)
{
if (listeners.elementAt(i) instanceof StructureListener)
{
- ((StructureListener)listeners.elementAt(i)).releaseReferences(svl);
+ ((StructureListener) listeners.elementAt(i))
+ .releaseReferences(svl);
}
}
}
-
+
if (pdbfiles == null)
{
return;
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;
}
}
}
- if (results!=null)
+ if (results != null)
{
for (int i = 0; i < listeners.size(); i++)
{
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;
else
{
if (relaySeqMappings && hasSequenceListeners
- && listeners.elementAt(i) instanceof SequenceListener)
+ && listener instanceof SequenceListener)
{
// DEBUG
// System.err.println("relay Seq " + seq.getDisplayId(false) + " " +
}
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) + "
// index);
// pass the mouse over and absolute position onto the
// VamsasListener(s)
- ((VamsasListener) listeners.elementAt(i)).mouseOver(seq,
- indexpos, source);
+ ((VamsasListener) listener).mouseOver(seq, indexpos, source);
+ }
+ else if (listener instanceof SecondaryStructureListener)
+ {
+ ((SecondaryStructureListener) listener).mouseOverSequence(seq,
+ indexpos);
}
}
}
}
}
}
-
- Vector<AlignmentViewPanelListener> view_listeners=new Vector<AlignmentViewPanelListener>();
- public synchronized void sendViewPosition(jalview.api.AlignmentViewPanel source, int startRes,
- int endRes, int startSeq, int endSeq)
+
+ 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();
+ Enumeration<AlignmentViewPanelListener> listeners = view_listeners
+ .elements();
while (listeners.hasMoreElements())
{
- AlignmentViewPanelListener slis = listeners
- .nextElement();
+ AlignmentViewPanelListener slis = listeners.nextElement();
if (slis != source)
{
slis.viewPosition(startRes, endRes, startSeq, endSeq, source);
}
}
}
-
- public void finalize() throws Throwable {
- if (listeners!=null) {
+ public void finalize() throws Throwable
+ {
+ if (listeners != null)
+ {
listeners.clear();
- listeners=null;
+ listeners = null;
}
- if (mappingData!=null)
+ if (mappingData != null)
{
mappingData.clear();
- mappingData=null;
+ mappingData = null;
}
- if (sel_listeners!=null)
+ if (sel_listeners != null)
{
sel_listeners.clear();
- sel_listeners=null;
+ sel_listeners = null;
}
- if (view_listeners!=null)
+ if (view_listeners != null)
{
view_listeners.clear();
- view_listeners=null;
+ view_listeners = null;
}
- mappings=null;
- seqmappingrefs=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)
+ // synchronized (instances)
{
- instances.remove(jalviewLite);
- try {
- mnger.finalize();
- } catch (Throwable x){};
+ 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