From 1e8006f71404e0afb34bcb2d754abce7f6d3fe25 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 25 Jul 2006 09:33:12 +0000
Subject: [PATCH] Extends AlignFile, dataset has PDBEntry added

---
 src/MCview/PDBfile.java |   89 +++++++++++++++++++----------------------------
 1 file changed, 36 insertions(+), 53 deletions(-)

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 63728ae..36eecb8 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -18,79 +18,44 @@
 */
 package MCview;
 
+import jalview.io.AppletFormatAdapter;
+import jalview.datamodel.*;
+
 import java.io.*;
 
 import java.net.*;
 
 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
     {
+        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)
         {
-
-           line = lineArray.elementAt(i).toString();
-
-
            if (line.indexOf("HEADER") == 0)
            {
              id = line.substring(62, 67).trim();
@@ -120,7 +85,6 @@ public class PDBfile extends jalview.io.FileParse {
               }
 
               Atom tmpatom = new Atom(line);
-
               tmpchain = findChain(tmpatom.chain);
               if (tmpchain != null)
               {
@@ -132,12 +96,31 @@ public class PDBfile extends jalview.io.FileParse {
                 chains.addElement(tmpchain);
                 tmpchain.atoms.addElement(tmpatom);
               }
-
           }
+          index ++;
         }
 
        makeResidueList();
        makeCaBondList();
+
+       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);
+         entry.setFile(inFile.getAbsolutePath());
+
+         seq.setDatasetSequence(dataset);
+         dataset.addPDBId(entry);
+
+         getSeqs().addElement(seq);
+       }
     }
 
     public void makeResidueList() {
-- 
1.7.10.2