From: jprocter <Jim Procter>
Date: Thu, 18 Jan 2007 18:21:42 +0000 (+0000)
Subject: transfer and update of sequenceFeatures for associated alignment sequence
X-Git-Tag: Release_2_3~473
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=b68dc1d95eeed4ab36914797f7d97c72ad54c11d;hp=0c198a7cc68d8c9989e82dc785112b6efaa74e87;p=jalview.git

transfer and update of sequenceFeatures for associated alignment sequence
---

diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java
index 4cba94d..609126c 100755
--- a/src/MCview/AppletPDBCanvas.java
+++ b/src/MCview/AppletPDBCanvas.java
@@ -155,7 +155,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener, MouseMotion
         mainchain.seqend = seqend;
         mainchain.isVisible = true;
         mainchain.makeExactMapping(maxAlignseq, sequence);
-
+        mainchain.transferRESNUMFeatures(sequence, null);
         this.pdb = pdb;
         this.prefsize = new Dimension(getSize().width, getSize().height);
 
diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 4d2a8d5..f4a213f 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -1,176 +1,178 @@
-/*
-* 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
-    {
-      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;
-
-          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);
-        }
-      }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)
-                );
-        }
-    }
-}
+/*
+* 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
+    {
+      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(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());
+          dataset.setSequenceFeatures(seq.getSequenceFeatures());
+          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");
+      }
+    }
+
+    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)
+                );
+        }
+    }
+}