X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=4d2a8d529d5c324737697c8d494a73f3f7d47439;hb=99bd0585b045d25fa719ee007e3310d27e53ac88;hp=1937a8f0aaba0f3eed94408ab8678ad78fe190a8;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 1937a8f..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
@@ -16,149 +16,161 @@
 * 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.net.*;
-import java.util.*;
-
-
-public class PDBfile extends jalview.io.FileParse {
 
-  public Vector chains = new Vector();
-
-  Vector lineArray = new Vector();
-
-  public PDBfile(String [] lines)
-  {
-    for(int i=0; i<lines.length; i++)
-      lineArray.addElement(lines[i]);
-
-    noLines = lineArray.size();
-    parse();
-  }
-
-  public PDBfile(String inFile, String inType) throws IOException {
+import java.io.*;
 
-    super(inFile,inType);
+import java.util.*;
+import java.awt.Color;
 
-    String line;
-    this.lineArray = new Vector();
-    BufferedReader dataIn;
 
-    if (inType.equals("File"))
-      dataIn =  new BufferedReader(new FileReader( inFile ));
+public class PDBfile extends jalview.io.AlignFile {
+    public Vector chains;
+    public String id;
 
-    else
+    public PDBfile(String inFile, String inType) throws IOException
     {
-      URL url = new URL(inFile);
-      this.fileSize = 0;
-      dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
+        super(inFile, inType);
     }
 
-    while ((line = dataIn.readLine()) != null) {
-      lineArray.addElement(line);
+    public String print()
+    {
+      return null;
     }
-    noLines = lineArray.size();
 
-    parse();
+    public void parse() throws IOException
+    {
+      try{
+        chains = new Vector();
+
+        PDBChain tmpchain;
+        String line;
+        boolean modelFlag = false;
+        boolean terFlag = false;
+
+        int index = 0;
+        while ( (line = nextLine()) != null)
+        {
+          if (line.indexOf("HEADER") == 0)
+          {
+            id = line.substring(62, 67).trim();
+            continue;
+          }
 
-}
+          if (line.indexOf("MODEL") == 0)
+            modelFlag = true;
 
+          if (line.indexOf("TER") == 0)
+            terFlag = true;
 
-  public void parse() {
+          if (modelFlag && line.indexOf("ENDMDL") == 0)
+            break;
 
-    for (int i = 0; i < lineArray.size(); i++) {
-      StringTokenizer str = new StringTokenizer(lineArray.elementAt(i).toString());
-      if (str.hasMoreTokens()) {
-        String inStr = str.nextToken();
+          if (line.indexOf("ATOM") == 0
+              || (line.indexOf("HETATM") == 0 && !terFlag)
+              )
+          {
+            terFlag = false;
 
-        if (inStr.indexOf("ATOM") != -1) {
-          try {
-            myAtom tmpatom = new myAtom(str);
-            if (findChain(tmpatom.chain) != null) {
-           //   System.out.println("Adding to chain " + tmpatom.chain);
-              findChain(tmpatom.chain).atoms.addElement(tmpatom);
-            } else {
-            //  System.out.println("Making chain " + tmpatom.chain);
-              PDBChain tmpchain = new PDBChain(tmpatom.chain);
+            //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);
             }
-          } catch(NumberFormatException e) {
-            System.err.println("Caught" +  e);
-            System.err.println("Record not added to PDB model:"+lineArray.elementAt(i).toString());
           }
+          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);
+        }
+      }catch(OutOfMemoryError er)
+      {
+        System.out.println("OUT OF MEMORY LOADING PDB FILE");
+        throw new IOException("Out of memory loading PDB File");
       }
     }
-    makeResidueList();
-    makeCaBondList();
-    //    for (int i=0; i < chains.size() ; i++) {
-    //  String pog = ((PDBChain)chains.elementAt(i)).print();
-    //  System.out.println(pog);
-    // }
-  }
-
-  public void makeResidueList() {
-    for (int i=0; i < chains.size() ; i++) {
-      ((PDBChain)chains.elementAt(i)).makeResidueList();
-    }
-  }
-  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++) {
-      // System.out.println("ID = " + id + " " +((PDBChain)chains.elementAt(i)).id);
-      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 setHydrophobicityColours() {
-    for (int i=0; i < chains.size(); i++) {
-      ((PDBChain)chains.elementAt(i)).setHydrophobicityColours();
+    public void setChargeColours() {
+        for (int i = 0; i < chains.size(); i++) {
+            ((PDBChain) chains.elementAt(i)).setChargeColours();
+        }
     }
-  }
-
-  public void colourBySequence(Sequence seq) {
-//SMJS TODO
-//    int max = seq.maxchain;
-//    if (seq.maxchain != -1) {
-//      ((PDBChain)chains.elementAt(max)).colourBySequence(seq);
-//    }
-  }
-
-  public void setChainColours() {
-    for (int i=0; i < chains.size(); i++) {
-      ((PDBChain)chains.elementAt(i)).setChainColours();
+
+    public void setColours(jalview.schemes.ColourSchemeI cs) {
+        for (int i = 0; i < chains.size(); i++) {
+            ((PDBChain) chains.elementAt(i)).setChainColours(cs);
+        }
     }
-  }
-  public static void main(String[] args) {
-    try {
-      PDBfile pdb = new PDBfile("enkp1.pdb","File");
-    } catch(IOException e) {
-      System.out.println(e);
-      e.printStackTrace();
-      System.exit(0);
+
+    public void setChainColours()
+    {
+       for (int i = 0; i < chains.size(); i++)
+       {
+            ((PDBChain) chains.elementAt(i)).setChainColours(
+                     Color.getHSBColor(1.0f / (float)i, .4f, 1.0f)
+                );
+        }
     }
-  }
 }
-
-
-