X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=2c7bd9dbd49205afa07ec946bed02cedea67cd94;hb=12ce4678159da9497740a02b4790d962c7625cbd;hp=f4a213f0137f9740d380717f6d4b1cdec110f572;hpb=b68dc1d95eeed4ab36914797f7d97c72ad54c11d;p=jalview.git

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index f4a213f..2c7bd9d 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -1,178 +1,211 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 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
-* 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.
-*
-* 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
-*/
+ * 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
+ * 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.
+ *
+ * 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
+ */
 package MCview;
 
-import jalview.datamodel.*;
-
 import java.io.*;
-
 import java.util.*;
-import java.awt.Color;
 
+import java.awt.*;
 
-public class PDBfile extends jalview.io.AlignFile {
-    public Vector chains;
-    public String id;
+import jalview.datamodel.*;
 
-    public PDBfile(String inFile, String inType) throws IOException
+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 String print()
+  {
+    return null;
+  }
+
+  public void parse()
+      throws IOException
+  {
+    // TODO set the filename sensibly 
+    id = (inFile==null) ? "PDBFILE" : inFile.getName();
+    try
     {
-        super(inFile, inType);
-    }
+      chains = new Vector();
 
-    public String print()
-    {
-      return null;
-    }
+      PDBChain tmpchain;
+      String line;
+      boolean modelFlag = false;
+      boolean terFlag = false;
 
-    public void parse() throws IOException
-    {
-      try{
-        chains = new Vector();
+      int index = 0;
+      while ( (line = nextLine()) != null)
+      {
+        if (line.indexOf("HEADER") == 0)
+        {
+          id = line.substring(62, 67).trim();
+          continue;
+        }
+        // Were we to do anything with SEQRES - we start it here
+        if (line.indexOf("SEQRES") == 0)
+        {
+        }
+
+        if (line.indexOf("MODEL") == 0)
+        {
+          modelFlag = true;
+        }
 
-        PDBChain tmpchain;
-        String line;
-        boolean modelFlag = false;
-        boolean terFlag = false;
+        if (line.indexOf("TER") == 0)
+        {
+          terFlag = true;
+        }
 
-        int index = 0;
-        while ( (line = nextLine()) != null)
+        if (modelFlag && line.indexOf("ENDMDL") == 0)
         {
-          if (line.indexOf("HEADER") == 0)
+          break;
+        }
+        if (line.indexOf("ATOM") == 0
+            || (line.indexOf("HETATM") == 0 && !terFlag)
+            )
+        {
+          terFlag = false;
+
+          //Jalview is only interested in CA bonds????
+          if (!line.substring(12, 15).trim().equals("CA"))
           {
-            id = line.substring(62, 67).trim();
             continue;
           }
-          // Were we to do anything with SEQRES - we start it here
-          if (line.indexOf("SEQRES") == 0) {              
+
+          Atom tmpatom = new Atom(line);
+          tmpchain = findChain(tmpatom.chain);
+          if (tmpchain != null)
+          {
+            tmpchain.atoms.addElement(tmpatom);
           }
-          
-          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)
-              )
+          else
           {
-            terFlag = false;
-
-            //Jalview is only interested in CA bonds????
-            if (!line.substring(12, 15).trim().equals("CA"))
-            {
-              continue;
-            }
-
-            Atom tmpatom = new Atom(line);
-            tmpchain = findChain(tmpatom.chain);
-            if (tmpchain != null)
-            {
-              tmpchain.atoms.addElement(tmpatom);
-            }
-            else
-            {
-              tmpchain = new PDBChain(tmpatom.chain);
-              chains.addElement(tmpchain);
-              tmpchain.atoms.addElement(tmpatom);
-            }
+            tmpchain = new PDBChain(id, tmpatom.chain);
+            chains.addElement(tmpchain);
+            tmpchain.atoms.addElement(tmpatom);
           }
-          index++;
         }
+        index++;
+      }
 
-        makeResidueList();
-        makeCaBondList();
+      makeResidueList();
+      makeCaBondList();
 
-        if (id == null)
+      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);
+        if (inFile != null)
         {
-          id = inFile.getName();
+          entry.setFile(inFile.getAbsolutePath());
         }
-        for (int i = 0; i < chains.size(); i++)
+        dataset.addPDBId(entry);
+        SequenceI chainseq = dataset.deriveSequence(); // PDBChain objects maintain reference to dataset
+        seqs.addElement(chainseq);
+        AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
+        if (chainannot!=null)
         {
-          SequenceI seq = ( (PDBChain) chains.elementAt(i)).
-              sequence;
-          seq.setName(id + "|" + seq.getName());
-          Sequence dataset = new Sequence(seq.
-                                          getName(),
-                                          seq.getSequence().toString(),
-                                          seq.getStart(), seq.getEnd());
-          dataset.setSequenceFeatures(seq.getSequenceFeatures());
-          PDBEntry entry = new PDBEntry();
-          entry.setId(id);
-          if (inFile != null)
-            entry.setFile(inFile.getAbsolutePath());
-
-          seq.setDatasetSequence(dataset);
-          dataset.addPDBId(entry);
-
-          getSeqs().addElement(seq);
+          for (int ai=0; ai<chainannot.length; ai++)
+          {
+            chainannot[ai].visible=VisibleChainAnnotation;
+            annotations.addElement(chainannot[ai]);
+          }
         }
-      }catch(OutOfMemoryError er)
-      {
-        System.out.println("OUT OF MEMORY LOADING PDB FILE");
-        throw new IOException("Out of memory loading PDB File");
       }
     }
-
-    public void makeResidueList() {
-        for (int i = 0; i < chains.size(); i++) {
-            ((PDBChain) chains.elementAt(i)).makeResidueList();
-        }
+    catch (OutOfMemoryError er)
+    {
+      System.out.println("OUT OF MEMORY LOADING PDB FILE");
+      throw new IOException("Out of memory loading PDB File");
     }
+  }
 
-    public void makeCaBondList() {
-        for (int i = 0; i < chains.size(); i++) {
-            ((PDBChain) chains.elementAt(i)).makeCaBondList();
-        }
+  public void makeResidueList()
+  {
+    for (int i = 0; i < chains.size(); i++)
+    {
+      ( (PDBChain) chains.elementAt(i)).makeResidueList();
     }
+  }
 
-    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);
-            }
-        }
+  public void makeCaBondList()
+  {
+    for (int i = 0; i < chains.size(); i++)
+    {
+      ( (PDBChain) chains.elementAt(i)).makeCaBondList();
+    }
+  }
 
-        return null;
+  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);
+      }
     }
 
-    public void setChargeColours() {
-        for (int i = 0; i < chains.size(); i++) {
-            ((PDBChain) chains.elementAt(i)).setChargeColours();
-        }
+    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 setColours(jalview.schemes.ColourSchemeI cs)
+  {
+    for (int i = 0; i < chains.size(); i++)
+    {
+      ( (PDBChain) chains.elementAt(i)).setChainColours(cs);
     }
+  }
 
-    public void setChainColours()
+  public void setChainColours()
+  {
+    for (int i = 0; i < chains.size(); i++)
     {
-       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)
+          );
     }
+  }
 }