X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=4d2a8d529d5c324737697c8d494a73f3f7d47439;hb=99bd0585b045d25fa719ee007e3310d27e53ac88;hp=63728ae816fe12b96a448fde9e38f7febb4aa25a;hpb=9a5435d4f6b25c70aa7c10c66f022ccd86eb4de1;p=jalview.git

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 63728ae..4d2a8d5 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -1,6 +1,6 @@
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+* 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
@@ -18,126 +18,116 @@
 */
 package MCview;
 
-import java.io.*;
+import jalview.datamodel.*;
 
-import java.net.*;
+import java.io.*;
 
 import java.util.*;
 import java.awt.Color;
-import jalview.io.AppletFormatAdapter;
 
 
-public class PDBfile extends jalview.io.FileParse {
-    public Vector chains = new Vector();
-    Vector lineArray = new Vector();
+public class PDBfile extends jalview.io.AlignFile {
+    public Vector chains;
     public String id;
 
-    public PDBfile(String[] lines) {
-        for (int i = 0; i < lines.length; i++)
-            lineArray.addElement(lines[i]);
-
-        parse();
-    }
-
-    public PDBfile(String inFile, String inType) throws IOException {
+    public PDBfile(String inFile, String inType) throws IOException
+    {
         super(inFile, inType);
+    }
 
-        String line;
-        this.lineArray = new Vector();
-
-        BufferedReader dataIn;
-
-
-        if (inType.equals(AppletFormatAdapter.FILE)) {
-            dataIn = new BufferedReader(new FileReader(inFile));
-        }
-        else if(inType.equals(AppletFormatAdapter.PASTE))
-        {
-            dataIn = new BufferedReader(new StringReader(inFile));
-        }
-        else if (inType.equalsIgnoreCase(AppletFormatAdapter.CLASSLOADER))
-        {
-          java.io.InputStream is = getClass().getResourceAsStream("/" +
-              inFile);
-
-          dataIn = new BufferedReader(new java.io.InputStreamReader(is));
-        }
-        else
-        {
-            URL url = new URL(inFile);
-            dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
-        }
-
-        while ((line = dataIn.readLine()) != null) {
-            lineArray.addElement(line);
-        }
-
-
-        parse();
-        lineArray = null;
+    public String print()
+    {
+      return null;
     }
 
-    public void parse()
+    public void parse() throws IOException
     {
+      try{
+        chains = new Vector();
+
         PDBChain tmpchain;
         String line;
         boolean modelFlag = false;
         boolean terFlag = false;
 
-
-        for (int i = 0; i < lineArray.size(); i++)
+        int index = 0;
+        while ( (line = nextLine()) != null)
         {
+          if (line.indexOf("HEADER") == 0)
+          {
+            id = line.substring(62, 67).trim();
+            continue;
+          }
 
-           line = lineArray.elementAt(i).toString();
-
-
-           if (line.indexOf("HEADER") == 0)
-           {
-             id = line.substring(62, 67).trim();
-             continue;
-           }
+          if (line.indexOf("MODEL") == 0)
+            modelFlag = true;
 
-           if(line.indexOf("MODEL")==0)
-             modelFlag = true;
+          if (line.indexOf("TER") == 0)
+            terFlag = true;
 
-           if(line.indexOf("TER")==0)
-             terFlag = true;
+          if (modelFlag && line.indexOf("ENDMDL") == 0)
+            break;
 
-           if(modelFlag && line.indexOf("ENDMDL")==0)
-             break;
+          if (line.indexOf("ATOM") == 0
+              || (line.indexOf("HETATM") == 0 && !terFlag)
+              )
+          {
+            terFlag = false;
 
-           if (    line.indexOf("ATOM")==0
-               || (line.indexOf("HETATM")==0 && !terFlag)
-             )
+            //Jalview is only interested in CA bonds????
+            if (!line.substring(12, 15).trim().equals("CA"))
             {
-              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);
-              }
+              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);
+            }
           }
+          index++;
         }
 
-       makeResidueList();
-       makeCaBondList();
+        makeResidueList();
+        makeCaBondList();
+
+        if (id == null)
+        {
+          id = inFile.getName();
+        }
+        for (int i = 0; i < chains.size(); i++)
+        {
+          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());
+
+          PDBEntry entry = new PDBEntry();
+          entry.setId(id);
+          if (inFile != null)
+            entry.setFile(inFile.getAbsolutePath());
+
+          seq.setDatasetSequence(dataset);
+          dataset.addPDBId(entry);
+
+          getSeqs().addElement(seq);
+        }
+      }catch(OutOfMemoryError er)
+      {
+        System.out.println("OUT OF MEMORY LOADING PDB FILE");
+        throw new IOException("Out of memory loading PDB File");
+      }
     }
 
     public void makeResidueList() {