X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=58bba481587a6da743b068b0d49afa238ef56f03;hb=3325395b33ef3b52b4a62327621c5bddf12ee4e0;hp=880f72a419a63f803a515fd92faf4fd5e86b5166;hpb=a0a45f042ee77368a0ff6c82caccb1b93d9e0f72;p=jalview.git
diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 880f72a..58bba48 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -1,64 +1,108 @@
/*
- * 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 2.8.2)
+ * 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.
- *
+ * 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 .
+ * You should have received a copy of the GNU General Public License
+ * 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 MCview.*;
-import jalview.analysis.*;
-import jalview.api.AlignmentViewPanel;
+import jalview.analysis.AlignSeq;
import jalview.api.StructureSelectionManagerProvider;
-import jalview.datamodel.*;
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
+
+import java.io.PrintStream;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.IdentityHashMap;
+import java.util.Vector;
+
+import MCview.Atom;
+import MCview.PDBChain;
public class StructureSelectionManager
{
- static IdentityHashMap instances;
+ static IdentityHashMap instances;
StructureMapping[] mappings;
/**
* 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();
+ instances = new java.util.IdentityHashMap();
}
- StructureSelectionManager instance=instances.get(context);
- if (instance==null)
+ StructureSelectionManager instance = instances.get(context);
+ if (instance == null)
{
- instances.put(context, instance=new StructureSelectionManager());
+ if (nullProvider != null)
+ {
+ instance = nullProvider;
+ }
+ else
+ {
+ instance = new StructureSelectionManager();
+ }
+ instances.put(context, instance);
}
return instance;
}
@@ -96,6 +140,7 @@ public class StructureSelectionManager
/**
* register a listener for alignment sequence mouseover events
+ *
* @param svl
*/
public void addStructureViewerListener(Object svl)
@@ -144,15 +189,32 @@ public class StructureSelectionManager
* the tried and tested MCview pdb mapping
*/
MCview.PDBfile pdb = null;
+ boolean parseSecStr=true;
+ 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
+ if (MCview.PDBfile.isCalcIdForFile(ala.getCalcId(), pdbFile))
+ {
+ parseSecStr = false;
+ }
+ }
+ }
+ }
try
{
- pdb = new MCview.PDBfile(pdbFile, protocol);
+ pdb = new MCview.PDBfile(true, parseSecStr, pdbFile, protocol);
+
} catch (Exception ex)
{
ex.printStackTrace();
return null;
}
-
+
String targetChain;
for (int s = 0; s < sequence.length; s++)
{
@@ -180,7 +242,9 @@ public class StructureSelectionManager
}
}
else
+ {
targetChain = "";
+ }
int max = -10;
AlignSeq maxAlignseq = null;
@@ -189,16 +253,17 @@ public class StructureSelectionManager
boolean first = true;
for (int i = 0; i < pdb.chains.size(); i++)
{
- PDBChain chain = ((PDBChain) pdb.chains.elementAt(i));
- if (targetChain.length() > 0 && !targetChain.equals(chain.id) && !infChain)
+ 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,
- ((PDBChain) pdb.chains.elementAt(i)).isNa ? AlignSeq.DNA
+ pdb.chains.elementAt(i).sequence,
+ pdb.chains.elementAt(i).isNa ? AlignSeq.DNA
: AlignSeq.PEP);
as.calcScoreMatrix();
as.traceAlignment();
@@ -249,7 +314,8 @@ public class StructureSelectionManager
// 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;
@@ -278,7 +344,9 @@ public class StructureSelectionManager
}
if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
+ {
pdbFile = "INLINE" + pdb.id;
+ }
mappings[mappings.length - 1] = new StructureMapping(sequence[s],
pdbFile, pdb.id, maxChainId, mapping,
@@ -295,15 +363,16 @@ public class StructureSelectionManager
listeners.removeElement(svl);
if (svl instanceof SequenceListener)
{
- for (int i=0;i 0)
{
for (int cf = 0; cf < codonFrames.length; cf++)
@@ -682,8 +765,10 @@ public class StructureSelectionManager
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;
}
@@ -739,19 +824,21 @@ public class StructureSelectionManager
}
}
}
-
- Vector view_listeners=new Vector();
- public synchronized void sendViewPosition(jalview.api.AlignmentViewPanel source, int startRes,
- int endRes, int startSeq, int endSeq)
+
+ 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();
+ Enumeration 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);
@@ -760,45 +847,58 @@ public class StructureSelectionManager
}
}
}
-
- 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)
+ {
+ }
+ ;
+ }
}
}