X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=99a0a2b6b05400dd460674f53b30fbf9e138540e;hb=5655997c202bfcb4ab2778999d785490d3a7dbae;hp=d7b7c9778115281b9c58e853149c780d1fb867e2;hpb=8893c2ac9824d4c566ae69c73d34889c5316b058;p=jalview.git

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index d7b7c97..99a0a2b 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
@@ -18,72 +18,41 @@
 */
 package MCview;
 
-import java.io.*;
+import jalview.datamodel.*;
 
-import java.net.*;
+import java.io.*;
 
 import java.util.*;
 import java.awt.Color;
 
 
-public class PDBfile extends jalview.io.FileParse {
-    public Vector chains = new Vector();
-    Vector lineArray = new Vector();
-    String id;
-
-    public PDBfile(String[] lines) {
-        for (int i = 0; i < lines.length; i++)
-            lineArray.addElement(lines[i]);
-
-        noLines = lineArray.size();
-        parse();
-    }
+public class PDBfile extends jalview.io.AlignFile {
+    public Vector chains;
+    public String id;
 
-    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("File")) {
-            dataIn = new BufferedReader(new FileReader(inFile));
-        }
-        else if(inType.equals("Paste"))
-        {
-            dataIn = new BufferedReader(new StringReader(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();
-        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();
@@ -113,7 +82,6 @@ public class PDBfile extends jalview.io.FileParse {
               }
 
               Atom tmpatom = new Atom(line);
-
               tmpchain = findChain(tmpatom.chain);
               if (tmpchain != null)
               {
@@ -125,12 +93,36 @@ public class PDBfile extends jalview.io.FileParse {
                 chains.addElement(tmpchain);
                 tmpchain.atoms.addElement(tmpatom);
               }
-
           }
+          index ++;
         }
 
        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);
+       }
     }
 
     public void makeResidueList() {
@@ -161,9 +153,9 @@ public class PDBfile extends jalview.io.FileParse {
         }
     }
 
-    public void setHydrophobicityColours() {
+    public void setColours(jalview.schemes.ColourSchemeI cs) {
         for (int i = 0; i < chains.size(); i++) {
-            ((PDBChain) chains.elementAt(i)).setHydrophobicityColours();
+            ((PDBChain) chains.elementAt(i)).setChainColours(cs);
         }
     }