X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=3dd567e62b099b3d722863507aa88afaaab1562f;hb=10b903bf6b22d53e8920091efb2145d6b6a677ba;hp=227bcf7da2f992929adbc3b219873674c838434c;hpb=c11ccf600bdcfa62302eeeb4898ff431eea6de14;p=jalview.git

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 227bcf7..3dd567e 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -1,20 +1,22 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ * 
+ * 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.
- *
- * This program 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.
- *
+ *  
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package MCview;
 
@@ -23,48 +25,75 @@ import java.util.*;
 
 import java.awt.*;
 
+import jalview.analysis.AlignSeq;
 import jalview.datamodel.*;
+import jalview.io.FileParse;
+import jalview.util.MessageManager;
 
-public class PDBfile
-    extends jalview.io.AlignFile
+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
+  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
+  public void parse() throws IOException
   {
-    try
-    {
-      chains = new Vector();
+    // TODO set the filename sensibly - try using data source name.
+    id = safeName(getDataName());
 
-      PDBChain tmpchain;
-      String line;
-      boolean modelFlag = false;
-      boolean terFlag = false;
+    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;
-      while ( (line = nextLine()) != null)
+    int index = 0;
+    String atomnam = null;
+    try
+    {
+      while ((line = nextLine()) != null)
       {
         if (line.indexOf("HEADER") == 0)
         {
-          id = line.substring(62, 67).trim();
-          continue;
+          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)
@@ -86,13 +115,13 @@ public class PDBfile
           break;
         }
         if (line.indexOf("ATOM") == 0
-            || (line.indexOf("HETATM") == 0 && !terFlag)
-            )
+                || (line.indexOf("HETATM") == 0 && !terFlag))
         {
           terFlag = false;
 
-          //Jalview is only interested in CA bonds????
-          if (!line.substring(12, 15).trim().equals("CA"))
+          // Jalview is only interested in CA bonds????
+          atomnam = line.substring(12, 15).trim();
+          if (!atomnam.equals("CA") && !atomnam.equals("P"))
           {
             continue;
           }
@@ -101,6 +130,11 @@ public class PDBfile
           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
@@ -109,6 +143,7 @@ public class PDBfile
             chains.addElement(tmpchain);
             tmpchain.atoms.addElement(tmpatom);
           }
+          lastID = tmpatom.resNumIns.trim();
         }
         index++;
       }
@@ -122,41 +157,240 @@ public class PDBfile
       }
       for (int i = 0; i < chains.size(); i++)
       {
-        SequenceI dataset = ( (PDBChain) chains.elementAt(i)).
-            sequence;
+        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
+        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)
+
+        if (chainannot != null)
         {
-          for (int ai=0; ai<chainannot.length; ai++)
+          for (int ai = 0; ai < chainannot.length; ai++)
           {
-            chainannot[ai].visible=VisibleChainAnnotation;
+
+            chainannot[ai].visible = VisibleChainAnnotation;
             annotations.addElement(chainannot[ai]);
           }
         }
       }
-    }
-    catch (OutOfMemoryError er)
+      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");
+      throw new IOException(MessageManager.getString("exception.outofmemory_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();
+      ((PDBChain) chains.elementAt(i)).makeResidueList();
     }
   }
 
@@ -164,7 +398,7 @@ public class PDBfile
   {
     for (int i = 0; i < chains.size(); i++)
     {
-      ( (PDBChain) chains.elementAt(i)).makeCaBondList();
+      ((PDBChain) chains.elementAt(i)).makeCaBondList();
     }
   }
 
@@ -172,7 +406,7 @@ public class PDBfile
   {
     for (int i = 0; i < chains.size(); i++)
     {
-      if ( ( (PDBChain) chains.elementAt(i)).id.equals(id))
+      if (((PDBChain) chains.elementAt(i)).id.equals(id))
       {
         return (PDBChain) chains.elementAt(i);
       }
@@ -185,7 +419,7 @@ public class PDBfile
   {
     for (int i = 0; i < chains.size(); i++)
     {
-      ( (PDBChain) chains.elementAt(i)).setChargeColours();
+      ((PDBChain) chains.elementAt(i)).setChargeColours();
     }
   }
 
@@ -193,7 +427,7 @@ public class PDBfile
   {
     for (int i = 0; i < chains.size(); i++)
     {
-      ( (PDBChain) chains.elementAt(i)).setChainColours(cs);
+      ((PDBChain) chains.elementAt(i)).setChainColours(cs);
     }
   }
 
@@ -201,9 +435,23 @@ public class PDBfile
   {
     for (int i = 0; i < chains.size(); i++)
     {
-      ( (PDBChain) chains.elementAt(i)).setChainColours(
-          Color.getHSBColor(1.0f / (float) i, .4f, 1.0f)
-          );
+      ((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;
+
+  }
 }