X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=3153e3c87101cf4e34817c59037110dcd9b1c622;hb=9816dd282fa1ec6731dd8afe6c4f255f6d0a2dd4;hp=b06e98fc9ebea825b959b383d32371edb3837046;hpb=9279a3f8e4145e3bc3884f305ec00431f1a3e1a6;p=jalview.git

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index b06e98f..3153e3c 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -1,144 +1,171 @@
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 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.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() {
-
-    for (int i = 0; i < lineArray.size(); i++) {
-      StringTokenizer str = new StringTokenizer(lineArray.elementAt(i).toString());
-      if (str.hasMoreTokens()) {
-        String inStr = str.nextToken();
-
-        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);
-              chains.addElement(tmpchain);
-              tmpchain.atoms.addElement(tmpatom);
-            }
-          } catch(NumberFormatException e) {
-            System.out.println("Caught" +  e);
-            System.out.println("Atom not added");
+    public void parse() throws IOException
+    {
+        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;
+
+           if(modelFlag && line.indexOf("ENDMDL")==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"))
+              {
+                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();
-    //    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();
+
+       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 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);
-      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)
+                );
+        }
     }
-  }
 }
-
-
-