X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=11e7188b87cf68b1f418375afdb686efa0a64d51;hb=0b7943691883db09c5dd85e525bfc95539f15566;hp=19e13e758ef6289f0af637fb7c7991241086b176;hpb=97e37bce240ce2430ca838bfb3060bd06dfe1711;p=jalview.git diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java index 19e13e7..11e7188 100755 --- a/src/MCview/PDBfile.java +++ b/src/MCview/PDBfile.java @@ -20,19 +20,25 @@ */ package MCview; -import java.io.*; -import java.util.*; -import java.util.List; -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; @@ -176,15 +182,15 @@ 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); + chains.elementAt(i).id); } if (inFile != null) { @@ -215,7 +221,6 @@ public class PDBfile extends jalview.io.AlignFile { for (int ai = 0; ai < chainannot.length; ai++) { - chainannot[ai].visible = VisibleChainAnnotation; annotations.addElement(chainannot[ai]); } @@ -224,6 +229,7 @@ public class PDBfile extends jalview.io.AlignFile if (processSecondaryStructure) { if (rna.size() > 0) + { try { processPdbFileWithAnnotate3d(rna); @@ -234,8 +240,10 @@ public class PDBfile extends jalview.io.AlignFile x.printStackTrace(); } + } ; if (prot.size() > 0) + { try { processPdbFileWithJmol(prot); @@ -247,6 +255,7 @@ public class PDBfile extends jalview.io.AlignFile } } + } } catch (OutOfMemoryError er) { System.out.println("OUT OF MEMORY LOADING PDB FILE"); @@ -261,8 +270,48 @@ 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 { @@ -279,13 +328,54 @@ public class PDBfile extends jalview.io.AlignFile {}).invoke(jmf)); cl.getMethod("addAnnotations", new Class[] { Alignment.class }).invoke(jmf, al); - AlignSeq.replaceMatchingSeqsWith(seqs, annotations, prot, al, AlignSeq.PEP, false); + 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, AlignSeq.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 { @@ -307,7 +397,24 @@ public class PDBfile extends jalview.io.AlignFile new Class[] { FileParse.class }).invoke(annotate3d, new Object[] { new FileParse(getDataName(), type) })); - AlignSeq.replaceMatchingSeqsWith(seqs, annotations, rna, al, AlignSeq.DNA, false); + for (SequenceI sq : al.getSequences()) + { + if (sq.getDatasetSequence() != null) + { + if (sq.getDatasetSequence().getPDBId() != null) + { + sq.getDatasetSequence().getPDBId().clear(); + } + } + else + { + if (sq.getPDBId() != null) + { + sq.getPDBId().clear(); + } + } + } + replaceAndUpdateChains(rna, al, AlignSeq.DNA, false); } } catch (ClassNotFoundException x) { @@ -336,7 +443,7 @@ public class PDBfile extends jalview.io.AlignFile { for (int i = 0; i < chains.size(); i++) { - ((PDBChain) chains.elementAt(i)).makeResidueList(); + chains.elementAt(i).makeResidueList(); } } @@ -344,7 +451,7 @@ public class PDBfile extends jalview.io.AlignFile { for (int i = 0; i < chains.size(); i++) { - ((PDBChain) chains.elementAt(i)).makeCaBondList(); + chains.elementAt(i).makeCaBondList(); } } @@ -352,9 +459,9 @@ 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); } } @@ -365,7 +472,7 @@ public class PDBfile extends jalview.io.AlignFile { for (int i = 0; i < chains.size(); i++) { - ((PDBChain) chains.elementAt(i)).setChargeColours(); + chains.elementAt(i).setChargeColours(); } } @@ -373,7 +480,7 @@ 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); } } @@ -381,8 +488,8 @@ 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)); } }