X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=5824575b2301610a5c30e48a9d7c190b31802bd7;hb=e894eb87d40be6e8452d19032ddffe80dad5f804;hp=63728ae816fe12b96a448fde9e38f7febb4aa25a;hpb=0f71bfca98457c30f1051f142c31b6aaa3e23ead;p=jalview.git

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 63728ae..5824575 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -1,186 +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 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 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 {
-        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 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) 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
+* 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.util.*;
+import java.awt.Color;
+
+
+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
+    {
+        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();
+
+       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() {
+        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)
+                );
+        }
+    }
+}