X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=302f3b22e9bafc1fa3b9958c237dc4b757d64088;hb=29cb169e896b943eaa832791c5bf754fb2cb7eee;hp=0ab28f6662ffcb854a73e554c43ecb08c8baf3e5;hpb=ef115e318fc0d0b963a5f9a2a209478d052f2389;p=jalview.git
diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 0ab28f6..302f3b2 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -1,19 +1,22 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 MCview;
@@ -22,21 +25,9 @@ import java.util.*;
import java.awt.*;
-import javax.xml.parsers.ParserConfigurationException;
-
-import org.xml.sax.SAXException;
-
-import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
-import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
-import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
-import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
-
import jalview.analysis.AlignSeq;
import jalview.datamodel.*;
-import jalview.io.AppletFormatAdapter;
import jalview.io.FileParse;
-import jalview.io.RnamlFile;
-import jalview.ws.jws1.Annotate3D;
public class PDBfile extends jalview.io.AlignFile
{
@@ -49,12 +40,12 @@ public class PDBfile extends jalview.io.AlignFile
*/
boolean VisibleChainAnnotation = false;
- public PDBfile(String inFile, String inType) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+ public PDBfile(String inFile, String inType) throws IOException
{
super(inFile, inType);
}
- public PDBfile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
+ public PDBfile(FileParse source) throws IOException
{
super(source);
}
@@ -64,13 +55,13 @@ public class PDBfile extends jalview.io.AlignFile
return null;
}
- public void parse() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+ public void parse() throws IOException
{
// TODO set the filename sensibly - try using data source name.
id = safeName(getDataName());
chains = new Vector();
- ArrayList rna=new ArrayList();
+ ArrayList rna = new ArrayList(), prot = new ArrayList();
PDBChain tmpchain;
String line = null;
boolean modelFlag = false;
@@ -170,7 +161,11 @@ public class PDBfile extends jalview.io.AlignFile
PDBEntry entry = new PDBEntry();
entry.setId(id);
entry.setProperty(new Hashtable());
- entry.getProperty().put("CHAIN", ((PDBChain)chains.elementAt(i)).id);
+ if (((PDBChain) chains.elementAt(i)).id != null)
+ {
+ entry.getProperty().put("CHAIN",
+ ((PDBChain) chains.elementAt(i)).id);
+ }
if (inFile != null)
{
entry.setFile(inFile.getAbsolutePath());
@@ -185,87 +180,63 @@ public class PDBfile extends jalview.io.AlignFile
// maintain reference to
// dataset
seqs.addElement(chainseq);
- if(isRNA(chainseq)==true)
- {
- rna.add(chainseq);
- }
-
+ if (isRNA(chainseq) == true)
+ {
+ rna.add(chainseq);
+ }
+ else
+ {
+ prot.add(chainseq);
+ }
+
AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
-
+
if (chainannot != null)
{
for (int ai = 0; ai < chainannot.length; ai++)
{
-
+
chainannot[ai].visible = VisibleChainAnnotation;
annotations.addElement(chainannot[ai]);
}
}
}
- if (rna.size()>0)
- try {
- String path =inFile.getPath();
- System.out.println("this is a PDB format and RNA sequence");
- Annotate3D an3d = new Annotate3D();
- AlignmentI al = an3d.getRNAMLFor(new FileParse(getDataName(),type));
- if (al!=null && al.getHeight()>0)
+ if (rna.size() > 0)
+ try
{
- ArrayList matches=new ArrayList();
- ArrayList aligns=new ArrayList();
- for (SequenceI sq:rna)
- {
- SequenceI bestm=null;
- AlignSeq bestaseq=null;
- int bestscore=0;
- for (SequenceI msq:al.getSequences())
- {
- AlignSeq aseq = AlignSeq.doGlobalNWAlignment(msq, sq, AlignSeq.DNA);
- if (bestm==null || aseq.getMaxScore()>bestscore)
- {
- bestscore=aseq.getMaxScore();
- bestaseq= aseq;
- bestm=msq;
- }
- }
- System.out.println("Best Score for "+(matches.size()+1)+" :"+bestscore);
- matches.add(bestm);
- aligns.add(bestaseq);
- al.deleteSequence(bestm);
- }
- for (int p=0,pSize=seqs.size();p-1)
- {
- seqs.set(p, sq=matches.get(q));
- sq.setName(sp.getName());
- sq.setDescription(sp.getDescription());
- sq.transferAnnotation(sp, aligns.get(q).getMappingFromS1(false));
- //sq.setSequenceFeatures(sp.getSequenceFeatures());
- int inspos=-1;
- for (int ap=0;p 0)
+ try
+ {
+ processPdbFileWithJmol(prot);
+ } catch (Exception x)
+ {
+ System.err
+ .println("Exceptions when dealing with RNA in pdb file");
+ x.printStackTrace();
+
+ }
+ ;
+ if (prot.size() > 0)
+ try
+ {
+ processPdbFileWithJmol(prot);
+ } catch (Exception x)
+ {
+ System.err
+ .println("Exceptions when dealing with RNA in pdb file");
+ x.printStackTrace();
+
+ }
+ ;
} catch (OutOfMemoryError er)
{
System.out.println("OUT OF MEMORY LOADING PDB FILE");
@@ -280,6 +251,124 @@ public class PDBfile extends jalview.io.AlignFile
}
}
+ private void processPdbFileWithJmol(ArrayList prot)
+ throws Exception
+ {
+ try
+ {
+ Class cl = Class.forName("jalview.ext.jmol.PDBFileWithJmol");
+ if (cl != null)
+ {
+ Object jmf = cl.getConstructor(new Class[]
+ { FileParse.class }).newInstance(new Object[]
+ { new FileParse(getDataName(), type) });
+ Alignment al = new Alignment((SequenceI[]) cl.getMethod(
+ "getSeqsAsArray", new Class[]
+ {}).invoke(jmf));
+ cl.getMethod("addAnnotations", new Class[]
+ { Alignment.class }).invoke(jmf, al);
+ replaceMatchingSeqsWith(prot, al, AlignSeq.PEP);
+ }
+ } catch (ClassNotFoundException q)
+ {
+ }
+ }
+
+ private void processPdbFileWithAnnotate3d(ArrayList rna)
+ throws Exception
+ {
+ // System.out.println("this is a PDB format and RNA sequence");
+ // note: we use reflection here so that the applet can compile and run
+ // without the HTTPClient bits and pieces needed for accessing Annotate3D
+ // web service
+ try
+ {
+ Class cl = Class.forName("jalview.ws.jws1.Annotate3D");
+ if (cl != null)
+ {
+ // TODO: use the PDB ID of the structure if one is available, to save
+ // bandwidth and avoid uploading the whole structure to the service
+ Object annotate3d = cl.getConstructor(new Class[]
+ {}).newInstance(new Object[]
+ {});
+ AlignmentI al = ((AlignmentI) cl.getMethod("getRNAMLFor",
+ new Class[]
+ { FileParse.class }).invoke(annotate3d, new Object[]
+ { new FileParse(getDataName(), type) }));
+ replaceMatchingSeqsWith(rna, al, AlignSeq.DNA);
+ }
+ } catch (ClassNotFoundException x)
+ {
+ // ignore classnotfounds - occurs in applet
+ }
+ ;
+ }
+
+ private void replaceMatchingSeqsWith(ArrayList ochains,
+ AlignmentI al, String dnaOrProtein)
+ {
+ if (al != null && al.getHeight() > 0)
+ {
+ ArrayList matches = new ArrayList();
+ ArrayList aligns = new ArrayList();
+
+ for (SequenceI sq : ochains)
+ {
+ SequenceI bestm = null;
+ AlignSeq bestaseq = null;
+ int bestscore = 0;
+ for (SequenceI msq : al.getSequences())
+ {
+ AlignSeq aseq = AlignSeq.doGlobalNWAlignment(msq, sq,
+ dnaOrProtein);
+ if (bestm == null || aseq.getMaxScore() > bestscore)
+ {
+ bestscore = aseq.getMaxScore();
+ bestaseq = aseq;
+ bestm = msq;
+ }
+ }
+ System.out.println("Best Score for " + (matches.size() + 1) + " :"
+ + bestscore);
+ matches.add(bestm);
+ aligns.add(bestaseq);
+ al.deleteSequence(bestm);
+ }
+ for (int p = 0, pSize = seqs.size(); p < pSize; p++)
+ {
+ SequenceI sq, sp = seqs.get(p);
+ int q;
+ if ((q = ochains.indexOf(sp)) > -1)
+ {
+ seqs.set(p, sq = matches.get(q));
+ sq.setName(sp.getName());
+ sq.setDescription(sp.getDescription());
+ sq.transferAnnotation(sp, aligns.get(q).getMappingFromS1(false));
+ int inspos = -1;
+ for (int ap = 0; ap < annotations.size();)
+ {
+ if (((AlignmentAnnotation) annotations.get(ap)).sequenceRef == sp)
+ {
+ if (inspos == -1)
+ {
+ inspos = ap;
+ }
+ annotations.remove(ap);
+ }
+ else
+ {
+ ap++;
+ }
+ }
+ if (sq.getAnnotation() != null)
+ {
+ annotations.addAll(inspos, Arrays.asList(sq.getAnnotation()));
+ }
+ }
+ }
+ }
+ }
+
/**
* make a friendly ID string.
*
@@ -349,17 +438,19 @@ public class PDBfile extends jalview.io.AlignFile
1.0f / (float) i, .4f, 1.0f));
}
}
+
public boolean isRNA(SequenceI seqs)
{
- for (int i=0;i