/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * 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
*
* 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
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;
*/
boolean VisibleChainAnnotation = false;
- public PDBfile(String inFile, String inType) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+ public PDBfile(String inFile, String inType) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
{
super(inFile, inType);
}
- public PDBfile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+ public PDBfile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
{
super(source);
}
{
// TODO set the filename sensibly - try using data source name.
id = safeName(getDataName());
-
- chains = new Vector();
- PDBChain tmpchain;
- String line=null;
- boolean modelFlag = false;
- boolean terFlag = false;
- String lastID = "";
+ chains = new Vector();
+ ArrayList<SequenceI> rna=new ArrayList<SequenceI>();
+ PDBChain tmpchain;
+ String line = null;
+ boolean modelFlag = false;
+ boolean terFlag = false;
+ String lastID = "";
- int index = 0;
- String atomnam = null;
- try
- {
+ int index = 0;
+ String atomnam = null;
+ try
+ {
while ((line = nextLine()) != null)
{
if (line.indexOf("HEADER") == 0)
dataset.setName(id + "|" + dataset.getName());
PDBEntry entry = new PDBEntry();
entry.setId(id);
+ entry.setProperty(new Hashtable());
+ entry.getProperty().put("CHAIN", ((PDBChain)chains.elementAt(i)).id);
if (inFile != null)
{
entry.setFile(inFile.getAbsolutePath());
seqs.addElement(chainseq);
if(isRNA(chainseq)==true)
{
- String path =inFile.getPath();
- System.out.println("this is a PDB format and RNA sequence");
- Annotate3D an3d = new Annotate3D(path);
- System.out.println(id);
- //BufferedWriter r = an3d.getReader();
-
- // BufferedReader in = new BufferedReader(new FileReader("temp.rnaml"));
-
- //String str;
- // while ((str = in.readLine()) != null) {
- // System.out.println(str);
- // System.out.println("toto");
-
- // }
- //String type = "File";
- //RnamlFile rnaml =new RnamlFile("temp.rnaml",type);
- System.out.println("Create rnamfile object");
- //rnaml.parse("temp");
- //this.annotations =rnaml.getAnnot();
-
+ rna.add(chainseq);
}
-
+
AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
if (chainannot != null)
}
}
}
+ 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)
+ {
+ ArrayList<SequenceI> matches=new ArrayList<SequenceI>();
+ ArrayList<AlignSeq> aligns=new ArrayList<AlignSeq>();
+ 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<pSize;p++)
+ {
+ SequenceI sq,sp=seqs.get(p);
+ int q;
+ if ((q=rna.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));
+ //sq.setSequenceFeatures(sp.getSequenceFeatures());
+ 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++;
+ }
+ }
+ annotations.addAll(inspos, Arrays.asList(sq.getAnnotation()));
+ }
+ }
+ }
+ } 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");
throw new IOException("Out of memory loading PDB File");
- }
- catch (NumberFormatException ex)
+ } catch (NumberFormatException ex)
{
- if (line!=null) {
+ if (line != null)
+ {
System.err.println("Couldn't read number from line:");
System.err.println(line);
}
git://source.jalview.org / jalview.git / blobdiff