From 70103cf21e1f8f4e6d645a752b46ab8870bd65af Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 20 Nov 2006 17:58:03 +0000
Subject: [PATCH] Memory check on PDB file

---
 src/MCview/PDBfile.java |  131 ++++++++++++++++++++++++-----------------------
 1 file changed, 68 insertions(+), 63 deletions(-)

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 99a0a2b..4d2a8d5 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -42,6 +42,7 @@ public class PDBfile extends jalview.io.AlignFile {
 
     public void parse() throws IOException
     {
+      try{
         chains = new Vector();
 
         PDBChain tmpchain;
@@ -49,80 +50,84 @@ public class PDBfile extends jalview.io.AlignFile {
         boolean modelFlag = false;
         boolean terFlag = false;
 
-
         int index = 0;
-        while((line = nextLine())!=null)
+        while ( (line = nextLine()) != null)
         {
-           if (line.indexOf("HEADER") == 0)
-           {
-             id = line.substring(62, 67).trim();
-             continue;
-           }
+          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(line.indexOf("MODEL")==0)
-             modelFlag = true;
+          if (modelFlag && line.indexOf("ENDMDL") == 0)
+            break;
 
-           if(line.indexOf("TER")==0)
-             terFlag = true;
+          if (line.indexOf("ATOM") == 0
+              || (line.indexOf("HETATM") == 0 && !terFlag)
+              )
+          {
+            terFlag = false;
 
-           if(modelFlag && line.indexOf("ENDMDL")==0)
-             break;
+            //Jalview is only interested in CA bonds????
+            if (!line.substring(12, 15).trim().equals("CA"))
+            {
+              continue;
+            }
 
-           if (    line.indexOf("ATOM")==0
-               || (line.indexOf("HETATM")==0 && !terFlag)
-             )
+            Atom tmpatom = new Atom(line);
+            tmpchain = findChain(tmpatom.chain);
+            if (tmpchain != null)
+            {
+              tmpchain.atoms.addElement(tmpatom);
+            }
+            else
             {
-              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);
-              }
+              tmpchain = new PDBChain(tmpatom.chain);
+              chains.addElement(tmpchain);
+              tmpchain.atoms.addElement(tmpatom);
+            }
           }
-          index ++;
+          index++;
         }
 
-       makeResidueList();
-       makeCaBondList();
+        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);
-       }
+        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() {
-- 
1.7.10.2