X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=6fdd9787028e0f3d55742872e0f3f81b6753f0d0;hb=b390a772cdffb7edc500b0c4952a997853cdf0bb;hp=26f1701d1cc2d654ab63b7594ddd4eec800760e9;hpb=c44b1974aea543db46790f6cb88f5ac0aae10a94;p=jalview.git

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 26f1701..6fdd978 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -1,179 +1,195 @@
-/*
-* 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 java.io.*;
-
-import java.net.*;
-
-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 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 void parse()
-    {
-        PDBChain tmpchain;
-        String line;
-        boolean modelFlag = false;
-        boolean terFlag = false;
-
-
-        for (int i = 0; i < lineArray.size(); i++)
-        {
-
-           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("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);
-              }
-
-          }
-        }
-
-       makeResidueList();
-       makeCaBondList();
-    }
-
-    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 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);
-            }
-        }
-
-        return null;
-    }
-
-    public void setChargeColours() {
-        for (int i = 0; i < chains.size(); i++) {
-            ((PDBChain) chains.elementAt(i)).setChargeColours();
-        }
-    }
-
-    public void setColours(jalview.schemes.ColourSchemeI cs) {
-        for (int i = 0; i < chains.size(); i++) {
-            ((PDBChain) chains.elementAt(i)).setChainColours(cs);
-        }
-    }
-
-    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)
-                );
-        }
-    }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 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 java.io.*;
+import java.util.*;
+
+import java.awt.*;
+
+import jalview.datamodel.*;
+
+public class PDBfile
+    extends jalview.io.AlignFile
+{
+  public Vector chains;
+  public String id;
+
+  public PDBfile(String inFile, String inType)
+      throws IOException
+  {
+    super(inFile, inType);
+  }
+
+  public String print()
+  {
+    return null;
+  }
+
+  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;
+        }
+        // Were we to do anything with SEQRES - we start it here
+        if (line.indexOf("SEQRES") == 0)
+        {
+        }
+
+        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(id, tmpatom.chain);
+            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 dataset = ( (PDBChain) chains.elementAt(i)).
+            sequence;
+        dataset.setName(id + "|" + dataset.getName());
+        PDBEntry entry = new PDBEntry();
+        entry.setId(id);
+        if (inFile != null)
+        {
+          entry.setFile(inFile.getAbsolutePath());
+        }
+        dataset.addPDBId(entry);
+        getSeqs().addElement(dataset.deriveSequence()); // PDBChain objects maintain reference to dataset
+      }
+    }
+    catch (OutOfMemoryError er)
+    {
+      System.out.println("OUT OF MEMORY LOADING PDB FILE");
+      throw new IOException("Out of memory loading PDB File");
+    }
+  }
+
+  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 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);
+      }
+    }
+
+    return null;
+  }
+
+  public void setChargeColours()
+  {
+    for (int i = 0; i < chains.size(); i++)
+    {
+      ( (PDBChain) chains.elementAt(i)).setChargeColours();
+    }
+  }
+
+  public void setColours(jalview.schemes.ColourSchemeI cs)
+  {
+    for (int i = 0; i < chains.size(); i++)
+    {
+      ( (PDBChain) chains.elementAt(i)).setChainColours(cs);
+    }
+  }
+
+  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)
+          );
+    }
+  }
+}