X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=0035914d2ccb762bf971631348ee46ad183561b9;hb=80c223c45fde0899c9794e887801dd82fffd3452;hp=ce98a0698a8e4c0fd7e9fad745f4c68a7001050c;hpb=9b22c11a0e12a9320e41eca2cbcbe30f81eb1cb4;p=jalview.git

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index ce98a06..0035914 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -1,137 +1,407 @@
-package MCview;
-
-import jalview.gui.*;
-import java.io.*;
-import java.net.*;
-import java.util.*;
-
-
-public class PDBfile extends jalview.io.FileParse {
-
-  public Vector chains = new Vector();
-
-  Vector lineArray = new Vector();
-
-  public PDBfile(String inFile, String inType) throws IOException {
-
-    super(inFile,inType);
-
-    String line;
-    this.lineArray = new Vector();
-    BufferedReader dataIn;
-
-    if (inType.equals("File"))
-      dataIn =  new BufferedReader(new FileReader( inFile ));
-
-    else
-    {
-      URL url = new URL(inFile);
-      this.fileSize = 0;
-      dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
-    }
-
-    while ((line = dataIn.readLine()) != null) {
-      lineArray.addElement(line);
-    }
-    noLines = lineArray.size();
-
-    parse();
-
-}
-
-
-  public void parse() {
-
-    System.out.println("Parsing");
-
-    for (int i = 0; i < lineArray.size(); i++) {
-      StringTokenizer str = new StringTokenizer(lineArray.elementAt(i).toString());
-      if (str.hasMoreTokens()) {
-        String inStr = str.nextToken();
-
-        if (inStr.indexOf("ATOM") != -1) {
-          try {
-            myAtom tmpatom = new myAtom(str);
-            if (findChain(tmpatom.chain) != null) {
-              System.out.println("Adding to chain " + tmpatom.chain);
-              findChain(tmpatom.chain).atoms.addElement(tmpatom);
-            } else {
-              System.out.println("Making chain " + tmpatom.chain);
-              PDBChain tmpchain = new PDBChain(tmpatom.chain);
-              chains.addElement(tmpchain);
-              tmpchain.atoms.addElement(tmpatom);
-            }
-          } catch(NumberFormatException e) {
-            System.out.println("Caught" +  e);
-            System.out.println("Atom not added");
-          }
-        }
-      }
-    }
-    makeResidueList();
-    makeCaBondList();
-    //    for (int i=0; i < chains.size() ; i++) {
-    //  String pog = ((PDBChain)chains.elementAt(i)).print();
-    //  System.out.println(pog);
-    // }
-  }
-
-  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++) {
-      // System.out.println("ID = " + id + " " +((PDBChain)chains.elementAt(i)).id);
-      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 setHydrophobicityColours() {
-    for (int i=0; i < chains.size(); i++) {
-      ((PDBChain)chains.elementAt(i)).setHydrophobicityColours();
-    }
-  }
-
-  public void colourBySequence(DrawableSequence seq) {
-//SMJS TODO
-//    int max = seq.maxchain;
-//    if (seq.maxchain != -1) {
-//      ((PDBChain)chains.elementAt(max)).colourBySequence(seq);
-//    }
-  }
-
-  public void setChainColours() {
-    for (int i=0; i < chains.size(); i++) {
-      ((PDBChain)chains.elementAt(i)).setChainColours();
-    }
-  }
-  public static void main(String[] args) {
-    try {
-      PDBfile pdb = new PDBfile("enkp1.pdb","File");
-    } catch(IOException e) {
-      System.out.println(e);
-      System.exit(0);
-    }
-  }
-}
-
-
-
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ */
+package MCview;
+
+import java.io.*;
+import java.util.*;
+
+import java.awt.*;
+
+import jalview.analysis.AlignSeq;
+import jalview.datamodel.*;
+import jalview.io.FileParse;
+
+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;
+
+  public PDBfile(String inFile, String inType) throws IOException
+  {
+    super(inFile, inType);
+  }
+
+  public PDBfile(FileParse source) throws IOException
+  {
+    super(source);
+  }
+
+  public String print()
+  {
+    return null;
+  }
+
+  public void parse() throws IOException
+  {
+    // TODO set the filename sensibly - try using data source name.
+    id = safeName(getDataName());
+
+    chains = new Vector();
+    ArrayList<SequenceI> rna=new ArrayList<SequenceI>(), prot=new ArrayList<SequenceI>();
+    PDBChain tmpchain;
+    String line = null;
+    boolean modelFlag = false;
+    boolean terFlag = false;
+    String lastID = "";
+
+    int index = 0;
+    String atomnam = null;
+    try
+    {
+      while ((line = nextLine()) != null)
+      {
+        if (line.indexOf("HEADER") == 0)
+        {
+          if (line.length() > 62)
+          {
+            String tid;
+            if (line.length() > 67)
+            {
+              tid = line.substring(62, 67).trim();
+            }
+            else
+            {
+              tid = line.substring(62).trim();
+            }
+            if (tid.length() > 0)
+            {
+              id = tid;
+            }
+            continue;
+          }
+        }
+        // Were we to do anything with SEQRES - we start it here
+        if (line.indexOf("SEQRES") == 0)
+        {
+        }
+
+        if (line.indexOf("MODEL") == 0)
+        {
+          modelFlag = true;
+        }
+
+        if (line.indexOf("TER") == 0)
+        {
+          terFlag = true;
+        }
+
+        if (modelFlag && line.indexOf("ENDMDL") == 0)
+        {
+          break;
+        }
+        if (line.indexOf("ATOM") == 0
+                || (line.indexOf("HETATM") == 0 && !terFlag))
+        {
+          terFlag = false;
+
+          // Jalview is only interested in CA bonds????
+          atomnam = line.substring(12, 15).trim();
+          if (!atomnam.equals("CA") && !atomnam.equals("P"))
+          {
+            continue;
+          }
+
+          Atom tmpatom = new Atom(line);
+          tmpchain = findChain(tmpatom.chain);
+          if (tmpchain != null)
+          {
+            if (tmpatom.resNumIns.trim().equals(lastID))
+            {
+              // phosphorylated protein - seen both CA and P..
+              continue;
+            }
+            tmpchain.atoms.addElement(tmpatom);
+          }
+          else
+          {
+            tmpchain = new PDBChain(id, tmpatom.chain);
+            chains.addElement(tmpchain);
+            tmpchain.atoms.addElement(tmpatom);
+          }
+          lastID = tmpatom.resNumIns.trim();
+        }
+        index++;
+      }
+
+      makeResidueList();
+      makeCaBondList();
+
+      if (id == null)
+      {
+        id = inFile.getName();
+      }
+      for (int i = 0; i < chains.size(); i++)
+      {
+        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)
+       {
+         rna.add(chainseq);
+       } else {
+         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 (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 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");
+        x.printStackTrace();
+        
+      };
+    } catch (OutOfMemoryError er)
+    {
+      System.out.println("OUT OF MEMORY LOADING PDB FILE");
+      throw new IOException("Out of memory loading PDB File");
+    } catch (NumberFormatException ex)
+    {
+      if (line != null)
+      {
+        System.err.println("Couldn't read number from line:");
+        System.err.println(line);
+      }
+    }
+  }
+  private void processPdbFileWithJmol(ArrayList<SequenceI> 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);
+        replaceMatchingSeqsWith(prot, al, AlignSeq.PEP);
+      }
+    } catch (ClassNotFoundException q)
+    {}
+  }
+  private void processPdbFileWithAnnotate3d(ArrayList<SequenceI> 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)}));
+      replaceMatchingSeqsWith(rna, al, AlignSeq.DNA);
+    }
+    } catch (ClassNotFoundException x)
+    {
+      //ignore classnotfounds - occurs in applet
+    };
+  }
+  private void replaceMatchingSeqsWith(ArrayList<SequenceI> ochains, AlignmentI al, String dnaOrProtein)
+  {
+    if (al!=null && al.getHeight()>0)
+    {
+      ArrayList<SequenceI> matches=new ArrayList<SequenceI>();
+      ArrayList<AlignSeq> aligns=new ArrayList<AlignSeq>();
+      
+      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)
+        {
+          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 (((AlignmentAnnotation)annotations.get(ap)).sequenceRef==sp) {
+              if (inspos==-1)
+              {
+                inspos=ap;
+              }
+              annotations.remove(ap);
+            } else {
+              ap++;
+            }
+          }
+          if (sq.getAnnotation()!=null) {
+            annotations.addAll(inspos, Arrays.asList(sq.getAnnotation()));
+          }
+        }
+      }
+    }
+  }
+  /**
+   * 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 / (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'))
+		  {
+			  return false;
+		  }
+	  }
+	 
+		  return true;
+	  
+	  
+  }
+}