X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=cb3698995c4c2d708463237e56e7300118db6852;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=302f3b22e9bafc1fa3b9958c237dc4b757d64088;hpb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;p=jalview.git diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java index 302f3b2..cb36989 100755 --- a/src/MCview/PDBfile.java +++ b/src/MCview/PDBfile.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1) * Copyright (C) 2014 The Jalview Authors * * This file is part of Jalview. @@ -20,18 +20,25 @@ */ package MCview; -import java.io.*; -import java.util.*; - -import java.awt.*; - import jalview.analysis.AlignSeq; -import jalview.datamodel.*; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceI; import jalview.io.FileParse; +import jalview.util.MessageManager; + +import java.awt.Color; +import java.io.IOException; +import java.util.ArrayList; +import java.util.Hashtable; +import java.util.List; +import java.util.Vector; public class PDBfile extends jalview.io.AlignFile { - public Vector chains; + public Vector chains; public String id; @@ -40,14 +47,39 @@ public class PDBfile extends jalview.io.AlignFile */ boolean VisibleChainAnnotation = false; - public PDBfile(String inFile, String inType) throws IOException + boolean processSecondaryStructure = true; + + boolean externalSecondaryStructure = false; + + public PDBfile(boolean visibleChainAnnotation, + boolean processSecondaryStructure, boolean externalSecStr) + { + super(); + VisibleChainAnnotation = visibleChainAnnotation; + this.processSecondaryStructure = processSecondaryStructure; + this.externalSecondaryStructure = externalSecStr; + } + + public PDBfile(boolean visibleChainAnnotation, + boolean processSecondaryStructure, boolean externalSecStr, + String file, String protocol) throws IOException { - super(inFile, inType); + super(false, file, protocol); + VisibleChainAnnotation = visibleChainAnnotation; + this.processSecondaryStructure = processSecondaryStructure; + this.externalSecondaryStructure = externalSecStr; + doParse(); } - public PDBfile(FileParse source) throws IOException + public PDBfile(boolean visibleChainAnnotation, + boolean processSecondaryStructure, boolean externalSecStr, + FileParse source) throws IOException { - super(source); + super(false, source); + VisibleChainAnnotation = visibleChainAnnotation; + this.processSecondaryStructure = processSecondaryStructure; + this.externalSecondaryStructure = externalSecStr; + doParse(); } public String print() @@ -156,15 +188,14 @@ public class PDBfile extends jalview.io.AlignFile } for (int i = 0; i < chains.size(); i++) { - SequenceI dataset = ((PDBChain) chains.elementAt(i)).sequence; + SequenceI dataset = chains.elementAt(i).sequence; dataset.setName(id + "|" + dataset.getName()); PDBEntry entry = new PDBEntry(); entry.setId(id); entry.setProperty(new Hashtable()); - if (((PDBChain) chains.elementAt(i)).id != null) + if (chains.elementAt(i).id != null) { - entry.getProperty().put("CHAIN", - ((PDBChain) chains.elementAt(i)).id); + entry.getProperty().put("CHAIN", chains.elementAt(i).id); } if (inFile != null) { @@ -191,56 +222,51 @@ public class PDBfile extends jalview.io.AlignFile AlignmentAnnotation[] chainannot = chainseq.getAnnotation(); - if (chainannot != null) + if (chainannot != null && VisibleChainAnnotation) { for (int ai = 0; ai < chainannot.length; ai++) { - chainannot[ai].visible = VisibleChainAnnotation; annotations.addElement(chainannot[ai]); } } } - 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) + if (processSecondaryStructure) + { + if (externalSecondaryStructure && rna.size() > 0) { - System.err - .println("Exceptions when dealing with RNA in pdb file"); - x.printStackTrace(); + try + { + processPdbFileWithAnnotate3d(rna); + } catch (Exception x) + { + System.err + .println("Exceptions when dealing with RNA in pdb file"); + x.printStackTrace(); + } } - ; - if (prot.size() > 0) - try + ; + if (prot.size() > 0) { - processPdbFileWithJmol(prot); - } catch (Exception x) - { - System.err - .println("Exceptions when dealing with RNA in pdb file"); - x.printStackTrace(); + try + { + processPdbFileWithJmol(prot); + } catch (Exception x) + { + System.err + .println("Exceptions from Jmol when processing data 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"); + throw new IOException( + MessageManager + .getString("exception.outofmemory_loading_pdb_file")); } catch (NumberFormatException ex) { if (line != null) @@ -249,6 +275,52 @@ public class PDBfile extends jalview.io.AlignFile System.err.println(line); } } + markCalcIds(); + } + + private static String calcIdPrefix = "JalviewPDB"; + + public static boolean isCalcIdHandled(String calcId) + { + return calcId != null && (calcIdPrefix.equals(calcId)); + } + + public static boolean isCalcIdForFile(AlignmentAnnotation alan, + String pdbFile) + { + return alan.getCalcId() != null + && calcIdPrefix.equals(alan.getCalcId()) + && pdbFile.equals(alan.getProperty("PDBID")); + } + + public static String relocateCalcId(String calcId, + Hashtable alreadyLoadedPDB) throws Exception + { + int s = calcIdPrefix.length(), end = calcId.indexOf(calcIdPrefix, s); + String between = calcId.substring(s, end - 1); + return calcIdPrefix + alreadyLoadedPDB.get(between) + ":" + + calcId.substring(end); + } + + private void markCalcIds() + { + for (SequenceI sq : seqs) + { + if (sq.getAnnotation() != null) + { + for (AlignmentAnnotation aa : sq.getAnnotation()) + { + String oldId = aa.getCalcId(); + if (oldId == null) + { + oldId = ""; + } + aa.setCalcId(calcIdPrefix); + aa.setProperty("PDBID", id); + aa.setProperty("oldCalcId", oldId); + } + } + } } private void processPdbFileWithJmol(ArrayList prot) @@ -267,13 +339,53 @@ public class PDBfile extends jalview.io.AlignFile {}).invoke(jmf)); cl.getMethod("addAnnotations", new Class[] { Alignment.class }).invoke(jmf, al); - replaceMatchingSeqsWith(prot, al, AlignSeq.PEP); + for (SequenceI sq : al.getSequences()) + { + if (sq.getDatasetSequence() != null) + { + sq.getDatasetSequence().getPDBId().clear(); + } + else + { + sq.getPDBId().clear(); + } + } + replaceAndUpdateChains(prot, al, AlignSeq.PEP, false); } } catch (ClassNotFoundException q) { } } + private void replaceAndUpdateChains(ArrayList prot, + AlignmentI al, String pep, boolean b) + { + List> replaced = AlignSeq + .replaceMatchingSeqsWith(seqs, annotations, prot, al, pep, + false); + for (PDBChain ch : chains) + { + int p = 0; + for (SequenceI sq : (List) replaced.get(0)) + { + p++; + if (sq == ch.sequence || sq.getDatasetSequence() == ch.sequence) + { + p = -p; + break; + } + } + if (p < 0) + { + p = -p - 1; + // set shadow entry for chains + ch.shadow = (SequenceI) replaced.get(1).get(p); + ch.shadowMap = ((AlignSeq) replaced.get(2).get(p)) + .getMappingFromS1(false); + } + } + } + private void processPdbFileWithAnnotate3d(ArrayList rna) throws Exception { @@ -295,78 +407,30 @@ public class PDBfile extends jalview.io.AlignFile 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) + for (SequenceI sq : al.getSequences()) { - 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 (sq.getDatasetSequence() != null) { - if (((AlignmentAnnotation) annotations.get(ap)).sequenceRef == sp) - { - if (inspos == -1) - { - inspos = ap; - } - annotations.remove(ap); - } - else + if (sq.getDatasetSequence().getPDBId() != null) { - ap++; + sq.getDatasetSequence().getPDBId().clear(); } } - if (sq.getAnnotation() != null) + else { - annotations.addAll(inspos, Arrays.asList(sq.getAnnotation())); + if (sq.getPDBId() != null) + { + sq.getPDBId().clear(); + } } } + replaceAndUpdateChains(rna, al, AlignSeq.DNA, false); } + } catch (ClassNotFoundException x) + { + // ignore classnotfounds - occurs in applet } + ; } /** @@ -389,7 +453,7 @@ public class PDBfile extends jalview.io.AlignFile { for (int i = 0; i < chains.size(); i++) { - ((PDBChain) chains.elementAt(i)).makeResidueList(); + chains.elementAt(i).makeResidueList(VisibleChainAnnotation); } } @@ -397,7 +461,7 @@ public class PDBfile extends jalview.io.AlignFile { for (int i = 0; i < chains.size(); i++) { - ((PDBChain) chains.elementAt(i)).makeCaBondList(); + chains.elementAt(i).makeCaBondList(); } } @@ -405,9 +469,9 @@ public class PDBfile extends jalview.io.AlignFile { for (int i = 0; i < chains.size(); i++) { - if (((PDBChain) chains.elementAt(i)).id.equals(id)) + if (chains.elementAt(i).id.equals(id)) { - return (PDBChain) chains.elementAt(i); + return chains.elementAt(i); } } @@ -418,7 +482,7 @@ public class PDBfile extends jalview.io.AlignFile { for (int i = 0; i < chains.size(); i++) { - ((PDBChain) chains.elementAt(i)).setChargeColours(); + chains.elementAt(i).setChargeColours(); } } @@ -426,7 +490,7 @@ public class PDBfile extends jalview.io.AlignFile { for (int i = 0; i < chains.size(); i++) { - ((PDBChain) chains.elementAt(i)).setChainColours(cs); + chains.elementAt(i).setChainColours(cs); } } @@ -434,8 +498,8 @@ public class PDBfile extends jalview.io.AlignFile { for (int i = 0; i < chains.size(); i++) { - ((PDBChain) chains.elementAt(i)).setChainColours(Color.getHSBColor( - 1.0f / (float) i, .4f, 1.0f)); + chains.elementAt(i).setChainColours( + Color.getHSBColor(1.0f / i, .4f, 1.0f)); } }