X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=0434aac9b8ca38fae132e7133286f8e3af6c967a;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=f9e8fdba4db2f673da6c0c458a6c8a912d758d55;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git
diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index f9e8fdb..0434aac 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -1,64 +1,203 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.PDBEntry;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
+import jalview.util.MessageManager;
+
+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 IdentityHashMap instances;
+ static IdentityHashMap instances;
StructureMapping[] mappings;
+ private boolean processSecondaryStructure = false,
+ secStructServices = false, addTempFacAnnot = false;
+
+ /**
+ * @return true if will try to use external services for processing secondary
+ * structure
+ */
+ public boolean isSecStructServices()
+ {
+ 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{
- System.err.println("reportMapping: There are "+mappings.length+" mappings.");
- for (int m=0;m 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();
+ 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 +235,7 @@ public class StructureSelectionManager
/**
* register a listener for alignment sequence mouseover events
+ *
* @param svl
*/
public void addStructureViewerListener(Object svl)
@@ -122,9 +262,33 @@ public class StructureSelectionManager
}
/**
+ * 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[] 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
@@ -136,7 +300,8 @@ public class StructureSelectionManager
* - how to resolve data from resource
* @return null or the structure data parsed as a pdb file
*/
- synchronized public MCview.PDBfile setMapping(SequenceI[] sequence,
+ synchronized public MCview.PDBfile setMapping(boolean forStructureView,
+ SequenceI[] sequence,
String[] targetChains, String pdbFile, String protocol)
{
/*
@@ -144,15 +309,48 @@ public class StructureSelectionManager
* the tried and tested MCview pdb mapping
*/
MCview.PDBfile pdb = null;
+ boolean parseSecStr = processSecondaryStructure;
+ if (isPDBFileRegistered(pdbFile))
+ {
+ 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;
+ }
+ }
+ }
+ }
+ }
try
{
- pdb = new MCview.PDBfile(pdbFile, protocol);
+ 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++)
{
@@ -180,7 +378,9 @@ public class StructureSelectionManager
}
}
else
+ {
targetChain = "";
+ }
int max = -10;
AlignSeq maxAlignseq = null;
@@ -189,16 +389,17 @@ 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();
@@ -224,11 +425,13 @@ public class StructureSelectionManager
+ 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");
@@ -244,12 +447,16 @@ public class StructureSelectionManager
+ (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);
// 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;
@@ -266,24 +473,30 @@ public class StructureSelectionManager
index++;
} 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());
- maxChain.transferResidueAnnotation(mappings[mappings.length - 1]);
+ mappings[mappings.length - 1] = newMapping;
+ }
+ maxChain.transferResidueAnnotation(newMapping, sqmpping);
}
// ///////
@@ -295,24 +508,26 @@ public class StructureSelectionManager
listeners.removeElement(svl);
if (svl instanceof SequenceListener)
{
- for (int i=0;i 0)
{
for (int cf = 0; cf < codonFrames.length; cf++)
@@ -679,8 +909,10 @@ 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;
}
@@ -736,19 +968,21 @@ 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);
@@ -757,39 +991,41 @@ 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 (pdbIdFileName != null)
{
- mappingData.clear();
- mappingData=null;
+ pdbIdFileName.clear();
+ pdbIdFileName = 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)
{
-// synchronized (instances)
+ // synchronized (instances)
{
if (instances == null)
{
@@ -810,4 +1046,13 @@ public class StructureSelectionManager
}
}
+ public void registerPDBEntry(PDBEntry pdbentry)
+ {
+ if (pdbentry.getFile() != null
+ && pdbentry.getFile().trim().length() > 0)
+ {
+ registerPDBFile(pdbentry.getId(), pdbentry.getFile());
+ }
+ }
+
}