X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=99d55b02b7e7db63d499ad2fff1c6dd065aa4c6c;hb=7d00e99455868f5895682506e495d4e12e8c2fc2;hp=fe2851a6510036e1f7a8426fdaae39308b191f8a;hpb=d7c00f48b00e3ede57c46ae4daf6a9203b9b6059;p=jalview.git diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java index fe2851a..99d55b0 100755 --- a/src/MCview/PDBfile.java +++ b/src/MCview/PDBfile.java @@ -1,13 +1,13 @@ /* - * 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 @@ -22,18 +22,10 @@ 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.FileParse; -import jalview.io.RnamlFile; import jalview.ws.jws1.Annotate3D; public class PDBfile extends jalview.io.AlignFile @@ -47,12 +39,12 @@ 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 Exception { super(inFile, inType); } - public PDBfile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses + public PDBfile(FileParse source) throws Exception { super(source); } @@ -62,23 +54,23 @@ public class PDBfile extends jalview.io.AlignFile return null; } - public void parse() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException + public void parse() throws Exception { // 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 rna=new ArrayList(), prot=new ArrayList(); + 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) @@ -167,6 +159,8 @@ public class PDBfile extends jalview.io.AlignFile 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()); @@ -183,28 +177,11 @@ public class PDBfile extends jalview.io.AlignFile 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); + } else { + prot.add(chainseq); } - + AlignmentAnnotation[] chainannot = chainseq.getAnnotation(); if (chainannot != null) @@ -217,20 +194,105 @@ public class PDBfile extends jalview.io.AlignFile } } } + if (rna.size()>0) + try { + processPdbFileWithAnnotate3d(rna); + } 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"); 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); } } } - + private void processPdbFileWithJmol(ArrayList prot) throws Exception + { +// System.out.println("this is a PDB format and RNA sequence"); + Annotate3D an3d = new Annotate3D(); + AlignmentI al = an3d.getRNAMLFor(new FileParse(getDataName(),type)); + replaceMatchingSeqsWith(prot, al, AlignSeq.PEP); + } + private void processPdbFileWithAnnotate3d(ArrayList rna) throws Exception { +// System.out.println("this is a PDB format and RNA sequence"); + Annotate3D an3d = new Annotate3D(); + AlignmentI al = an3d.getRNAMLFor(new FileParse(getDataName(),type)); + replaceMatchingSeqsWith(rna, al, AlignSeq.DNA); + } + 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-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