X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=f5a0255094f23ab858ddb3bb5b9df9a7e232aad6;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=19e13e758ef6289f0af637fb7c7991241086b176;hpb=97e37bce240ce2430ca838bfb3060bd06dfe1711;p=jalview.git diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java index 19e13e7..f5a0255 100755 --- a/src/MCview/PDBfile.java +++ b/src/MCview/PDBfile.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,75 +20,71 @@ */ 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.AlignmentAnnotation; +import jalview.datamodel.DBRefSource; +import jalview.datamodel.SequenceI; import jalview.io.FileParse; +import jalview.io.StructureFile; import jalview.util.MessageManager; -public class PDBfile extends jalview.io.AlignFile -{ - public Vector chains; - - public String id; - - /** - * set to true to add chain alignment annotation as visible annotation. - */ - boolean VisibleChainAnnotation = false; +import java.io.IOException; +import java.util.ArrayList; +import java.util.Hashtable; +import java.util.List; +import java.util.Vector; - boolean processSecondaryStructure=true; - +public class PDBfile extends StructureFile +{ + private static String CALC_ID_PREFIX = "JalviewPDB"; - public PDBfile(boolean visibleChainAnnotation, - boolean processSecondaryStructure) + public PDBfile(boolean addAlignmentAnnotations, + boolean predictSecondaryStructure, boolean externalSecStr) { super(); - VisibleChainAnnotation = visibleChainAnnotation; - this.processSecondaryStructure = processSecondaryStructure; + addSettings(addAlignmentAnnotations, predictSecondaryStructure, + externalSecStr); } - public PDBfile(boolean visibleChainAnnotation, - boolean processSecondaryStructure, String file, String protocol) throws IOException + public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr, + boolean externalSecStr, String dataObject, String protocol) + throws IOException { - super(false, file, protocol); - VisibleChainAnnotation = visibleChainAnnotation; - this.processSecondaryStructure = processSecondaryStructure; + super(false, dataObject, protocol); + addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr); doParse(); } - public PDBfile(boolean visibleChainAnnotation, - boolean processSecondaryStructure, FileParse source) throws IOException + public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr, + boolean externalSecStr, FileParse source) throws IOException { super(false, source); - VisibleChainAnnotation = visibleChainAnnotation; - this.processSecondaryStructure = processSecondaryStructure; + addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr); doParse(); } + @Override public String print() { return null; } + @Override public void parse() throws IOException { + setDbRefType(DBRefSource.PDB); // TODO set the filename sensibly - try using data source name. - id = safeName(getDataName()); + setId(safeName(getDataName())); - chains = new Vector(); - ArrayList rna = new ArrayList(), prot = new ArrayList(); + setChains(new Vector()); + List rna = new ArrayList(); + List prot = new ArrayList(); PDBChain tmpchain; String line = null; boolean modelFlag = false; boolean terFlag = false; String lastID = ""; - int index = 0; + int indexx = 0; String atomnam = null; try { @@ -109,7 +105,7 @@ public class PDBfile extends jalview.io.AlignFile } if (tid.length() > 0) { - id = tid; + setId(tid); } continue; } @@ -146,20 +142,19 @@ public class PDBfile extends jalview.io.AlignFile } Atom tmpatom = new Atom(line); - tmpchain = findChain(tmpatom.chain); - if (tmpchain != null) + try { + tmpchain = findChain(tmpatom.chain); if (tmpatom.resNumIns.trim().equals(lastID)) { // phosphorylated protein - seen both CA and P.. continue; } tmpchain.atoms.addElement(tmpatom); - } - else + } catch (Exception e) { - tmpchain = new PDBChain(id, tmpatom.chain); - chains.addElement(tmpchain); + tmpchain = new PDBChain(getId(), tmpatom.chain); + getChains().add(tmpchain); tmpchain.atoms.addElement(tmpatom); } lastID = tmpatom.resNumIns.trim(); @@ -170,37 +165,14 @@ public class PDBfile extends jalview.io.AlignFile makeResidueList(); makeCaBondList(); - if (id == null) + if (getId() == null) { - id = inFile.getName(); + setId(inFile.getName()); } - for (int i = 0; i < chains.size(); i++) + for (PDBChain chain : getChains()) { - SequenceI dataset = ((PDBChain) 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) - { - entry.getProperty().put("CHAIN", - ((PDBChain) chains.elementAt(i)).id); - } - if (inFile != null) - { - entry.setFile(inFile.getAbsolutePath()); - } - else - { - // TODO: decide if we should dump the datasource to disk - entry.setFile(getDataName()); - } - dataset.addPDBId(entry); - SequenceI chainseq = dataset.deriveSequence(); // PDBChain objects - // maintain reference to - // dataset - seqs.addElement(chainseq); - if (isRNA(chainseq) == true) + SequenceI chainseq = postProcessChain(chain); + if (isRNA(chainseq)) { rna.add(chainseq); } @@ -208,44 +180,10 @@ public class PDBfile extends jalview.io.AlignFile { prot.add(chainseq); } - - AlignmentAnnotation[] chainannot = chainseq.getAnnotation(); - - if (chainannot != null) - { - for (int ai = 0; ai < chainannot.length; ai++) - { - - chainannot[ai].visible = VisibleChainAnnotation; - annotations.addElement(chainannot[ai]); - } - } } - if (processSecondaryStructure) + if (predictSecondaryStructure) { - 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 from Jmol when processing data in pdb file"); - x.printStackTrace(); - - } + addSecondaryStructure(rna, prot); } } catch (OutOfMemoryError er) { @@ -261,143 +199,59 @@ public class PDBfile extends jalview.io.AlignFile System.err.println(line); } } - } - - private void processPdbFileWithJmol(ArrayList prot) - throws Exception - { - try - { - Class cl = Class.forName("jalview.ext.jmol.PDBFileWithJmol"); - if (cl != null) - { - Object jmf = cl.getConstructor(new Class[] - { FileParse.class }).newInstance(new Object[] - { new FileParse(getDataName(), type) }); - Alignment al = new Alignment((SequenceI[]) cl.getMethod( - "getSeqsAsArray", new Class[] - {}).invoke(jmf)); - cl.getMethod("addAnnotations", new Class[] - { Alignment.class }).invoke(jmf, al); - AlignSeq.replaceMatchingSeqsWith(seqs, annotations, prot, al, AlignSeq.PEP, false); - } - } catch (ClassNotFoundException q) - { - } - } - - private void processPdbFileWithAnnotate3d(ArrayList rna) - throws Exception - { - // System.out.println("this is a PDB format and RNA sequence"); - // note: we use reflection here so that the applet can compile and run - // without the HTTPClient bits and pieces needed for accessing Annotate3D - // web service - try - { - Class cl = Class.forName("jalview.ws.jws1.Annotate3D"); - if (cl != null) - { - // TODO: use the PDB ID of the structure if one is available, to save - // bandwidth and avoid uploading the whole structure to the service - Object annotate3d = cl.getConstructor(new Class[] - {}).newInstance(new Object[] - {}); - AlignmentI al = ((AlignmentI) cl.getMethod("getRNAMLFor", - new Class[] - { FileParse.class }).invoke(annotate3d, new Object[] - { new FileParse(getDataName(), type) })); - AlignSeq.replaceMatchingSeqsWith(seqs, annotations, rna, al, AlignSeq.DNA, false); - } - } catch (ClassNotFoundException x) - { - // ignore classnotfounds - occurs in applet - } - ; + markCalcIds(); } /** - * make a friendly ID string. + * Process a parsed chain to construct and return a Sequence, and add it to + * the list of sequences parsed. * - * @param dataName - * @return truncated dataName to after last '/' + * @param chain + * @return */ - private String safeName(String dataName) - { - int p = 0; - while ((p = dataName.indexOf("/")) > -1 && p < dataName.length()) - { - dataName = dataName.substring(p + 1); - } - return dataName; - } - public void makeResidueList() + public static boolean isCalcIdHandled(String calcId) { - for (int i = 0; i < chains.size(); i++) - { - ((PDBChain) chains.elementAt(i)).makeResidueList(); - } + return calcId != null && (CALC_ID_PREFIX.equals(calcId)); } - public void makeCaBondList() + public static boolean isCalcIdForFile(AlignmentAnnotation alan, + String pdbFile) { - for (int i = 0; i < chains.size(); i++) - { - ((PDBChain) chains.elementAt(i)).makeCaBondList(); - } + return alan.getCalcId() != null + && CALC_ID_PREFIX.equals(alan.getCalcId()) + && pdbFile.equals(alan.getProperty("PDBID")); } - public PDBChain findChain(String id) + public static String relocateCalcId(String calcId, + Hashtable alreadyLoadedPDB) throws Exception { - for (int i = 0; i < chains.size(); i++) - { - if (((PDBChain) chains.elementAt(i)).id.equals(id)) - { - return (PDBChain) chains.elementAt(i); - } - } - - return null; + int s = CALC_ID_PREFIX.length(), end = calcId + .indexOf(CALC_ID_PREFIX, s); + String between = calcId.substring(s, end - 1); + return CALC_ID_PREFIX + alreadyLoadedPDB.get(between) + ":" + + calcId.substring(end); } - public void setChargeColours() + private void markCalcIds() { - for (int i = 0; i < chains.size(); i++) + for (SequenceI sq : seqs) { - ((PDBChain) chains.elementAt(i)).setChargeColours(); - } - } - - public void setColours(jalview.schemes.ColourSchemeI cs) - { - for (int i = 0; i < chains.size(); i++) - { - ((PDBChain) chains.elementAt(i)).setChainColours(cs); - } - } - - public void setChainColours() - { - for (int i = 0; i < chains.size(); i++) - { - ((PDBChain) chains.elementAt(i)).setChainColours(Color.getHSBColor( - 1.0f / (float) i, .4f, 1.0f)); - } - } - - public boolean isRNA(SequenceI seqs) - { - for (int i = 0; i < seqs.getLength(); i++) - { - if ((seqs.getCharAt(i) != 'A') && (seqs.getCharAt(i) != 'C') - && (seqs.getCharAt(i) != 'G') && (seqs.getCharAt(i) != 'U')) + if (sq.getAnnotation() != null) { - return false; + for (AlignmentAnnotation aa : sq.getAnnotation()) + { + String oldId = aa.getCalcId(); + if (oldId == null) + { + oldId = ""; + } + aa.setCalcId(CALC_ID_PREFIX); + aa.setProperty("PDBID", getId()); + aa.setProperty("oldCalcId", oldId); + } } } - - return true; - } + }