X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=ebc52aaf0aa0643410590de2c330fd5611782160;hb=39b4859e1a1b011af5d06058461db4d075acb578;hp=019aba946980a7f6604c04233b259f5326f1b450;hpb=e05ad4f9199d673b327277d1266d97f3a51419ae;p=jalview.git diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java index 019aba9..ebc52aa 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. * @@ -20,80 +20,72 @@ */ package MCview; -import jalview.analysis.AlignSeq; -import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; -import jalview.datamodel.AlignmentI; -import jalview.datamodel.PDBEntry; +import jalview.datamodel.DBRefSource; import jalview.datamodel.SequenceI; +import jalview.io.DataSourceType; import jalview.io.FileParse; +import jalview.io.StructureFile; 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 class PDBfile extends StructureFile { - public Vector chains; + private static String CALC_ID_PREFIX = "JalviewPDB"; - public String id; - - /** - * set to true to add chain alignment annotation as visible annotation. - */ - boolean VisibleChainAnnotation = false; - - boolean processSecondaryStructure=true; - - - 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, + DataSourceType sourceType) throws IOException { - super(false, file, protocol); - VisibleChainAnnotation = visibleChainAnnotation; - this.processSecondaryStructure = processSecondaryStructure; + super(false, dataObject, sourceType); + 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(); } - public String print() + @Override + public String print(SequenceI[] seqs, boolean jvSuffix) { 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 { @@ -114,7 +106,7 @@ public class PDBfile extends jalview.io.AlignFile } if (tid.length() > 0) { - id = tid; + setId(tid); } continue; } @@ -151,20 +143,19 @@ 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(); @@ -175,37 +166,14 @@ 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); } @@ -213,54 +181,16 @@ 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 (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) + if (predictSecondaryStructure) { - 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) { System.out.println("OUT OF MEMORY LOADING PDB FILE"); - throw new IOException( - MessageManager - .getString("exception.outofmemory_loading_pdb_file")); + throw new IOException(MessageManager + .getString("exception.outofmemory_loading_pdb_file")); } catch (NumberFormatException ex) { if (line != null) @@ -272,27 +202,34 @@ public class PDBfile extends jalview.io.AlignFile markCalcIds(); } - private static String calcIdPrefix = "JalviewPDB:"; + /** + * Process a parsed chain to construct and return a Sequence, and add it to + * the list of sequences parsed. + * + * @param chain + * @return + */ public static boolean isCalcIdHandled(String calcId) { - return calcId != null - && (calcId.startsWith(calcIdPrefix) && calcId.indexOf( - calcIdPrefix, - calcIdPrefix.length() + 1) > -1); + return calcId != null && (CALC_ID_PREFIX.equals(calcId)); } - public static boolean isCalcIdForFile(String calcId, String pdbFile) + + public static boolean isCalcIdForFile(AlignmentAnnotation alan, + String pdbFile) { - return (calcId != null && calcId.startsWith(calcIdPrefix + pdbFile - + ":" + calcIdPrefix)); + return alan.getCalcId() != null + && CALC_ID_PREFIX.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); + int s = CALC_ID_PREFIX.length(), + end = calcId.indexOf(CALC_ID_PREFIX, s); String between = calcId.substring(s, end - 1); - return calcIdPrefix + alreadyLoadedPDB.get(between) + ":" + return CALC_ID_PREFIX + alreadyLoadedPDB.get(between) + ":" + calcId.substring(end); } @@ -300,152 +237,21 @@ public class PDBfile extends jalview.io.AlignFile { for (SequenceI sq : seqs) { - for (AlignmentAnnotation aa : sq.getAnnotation()) + if (sq.getAnnotation() != null) { - String oldId = aa.getCalcId(); - if (oldId == null) + for (AlignmentAnnotation aa : sq.getAnnotation()) { - oldId = ""; + String oldId = aa.getCalcId(); + if (oldId == null) + { + oldId = ""; + } + aa.setCalcId(CALC_ID_PREFIX); + aa.setProperty("PDBID", getId()); + aa.setProperty("oldCalcId", oldId); } - aa.setCalcId("JalviewPDB:" + id + ":JalviewPDB:" + oldId); - } - } - } - 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 - } - ; - } - - /** - * make a friendly ID string. - * - * @param dataName - * @return truncated dataName to after last '/' - */ - 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() - { - for (int i = 0; i < chains.size(); i++) - { - ((PDBChain) chains.elementAt(i)).makeResidueList(); - } - } - - public void makeCaBondList() - { - for (int i = 0; i < chains.size(); i++) - { - ((PDBChain) chains.elementAt(i)).makeCaBondList(); - } - } - - public PDBChain findChain(String id) - { - for (int i = 0; i < chains.size(); i++) - { - if (((PDBChain) chains.elementAt(i)).id.equals(id)) - { - return (PDBChain) chains.elementAt(i); } } - - return null; - } - - public void setChargeColours() - { - for (int i = 0; i < chains.size(); i++) - { - ((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 / 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')) - { - return false; - } - } - - return true; - - } }