X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=a99f172e0c5e6af954b117c44e71584ec9af09a8;hb=961eec1363ddc5f0f5a08b9063a7a2a9b1c9d2bd;hp=302f3b22e9bafc1fa3b9958c237dc4b757d64088;hpb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;p=jalview.git diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java index 302f3b2..a99f172 100755 --- a/src/MCview/PDBfile.java +++ b/src/MCview/PDBfile.java @@ -20,14 +20,20 @@ */ 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.Vector; public class PDBfile extends jalview.io.AlignFile { @@ -40,14 +46,33 @@ public class PDBfile extends jalview.io.AlignFile */ boolean VisibleChainAnnotation = false; - public PDBfile(String inFile, String inType) throws IOException + boolean processSecondaryStructure=true; + + + public PDBfile(boolean visibleChainAnnotation, + boolean processSecondaryStructure) + { + super(); + VisibleChainAnnotation = visibleChainAnnotation; + this.processSecondaryStructure = processSecondaryStructure; + } + + public PDBfile(boolean visibleChainAnnotation, + boolean processSecondaryStructure, String file, String protocol) throws IOException { - super(inFile, inType); + super(false, file, protocol); + VisibleChainAnnotation = visibleChainAnnotation; + this.processSecondaryStructure = processSecondaryStructure; + doParse(); } - public PDBfile(FileParse source) throws IOException + public PDBfile(boolean visibleChainAnnotation, + boolean processSecondaryStructure, FileParse source) throws IOException { - super(source); + super(false, source); + VisibleChainAnnotation = visibleChainAnnotation; + this.processSecondaryStructure = processSecondaryStructure; + doParse(); } public String print() @@ -195,13 +220,15 @@ public class PDBfile extends jalview.io.AlignFile { for (int ai = 0; ai < chainannot.length; ai++) { - chainannot[ai].visible = VisibleChainAnnotation; annotations.addElement(chainannot[ai]); } } } + if (processSecondaryStructure) + { if (rna.size() > 0) + { try { processPdbFileWithAnnotate3d(rna); @@ -212,35 +239,28 @@ public class PDBfile extends jalview.io.AlignFile 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(); - - } - ; - if (prot.size() > 0) - try - { - processPdbFileWithJmol(prot); - } catch (Exception x) - { - System.err - .println("Exceptions when dealing with RNA in pdb file"); + .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) @@ -249,8 +269,48 @@ 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 + && (calcId.startsWith(calcIdPrefix) && calcId.indexOf( + calcIdPrefix, + calcIdPrefix.length() + 1) > -1); + } + public static boolean isCalcIdForFile(String calcId, String pdbFile) + { + return (calcId != null && calcId.startsWith(calcIdPrefix + pdbFile + + ":" + calcIdPrefix)); + } + + 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) + { + for (AlignmentAnnotation aa : sq.getAnnotation()) + { + String oldId = aa.getCalcId(); + if (oldId == null) + { + oldId = ""; + } + aa.setCalcId("JalviewPDB:" + id + ":JalviewPDB:" + oldId); + } + } + } private void processPdbFileWithJmol(ArrayList prot) throws Exception { @@ -267,7 +327,18 @@ 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(); + } + } + AlignSeq.replaceMatchingSeqsWith(seqs, annotations, prot, al, AlignSeq.PEP, false); } } catch (ClassNotFoundException q) { @@ -295,78 +366,24 @@ 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 - { - ap++; - } + sq.getDatasetSequence().getPDBId().clear(); } - if (sq.getAnnotation() != null) + else { - annotations.addAll(inspos, Arrays.asList(sq.getAnnotation())); + sq.getPDBId().clear(); } } + AlignSeq.replaceMatchingSeqsWith(seqs, annotations, rna, al, AlignSeq.DNA, false); } + } catch (ClassNotFoundException x) + { + // ignore classnotfounds - occurs in applet } + ; } /** @@ -435,7 +452,7 @@ 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)); + 1.0f / i, .4f, 1.0f)); } }