From f8ccad28f3a8fc90f4f0a13ec0c8d230dec6b230 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 19 Jan 2007 16:01:33 +0000
Subject: [PATCH] PDBChain maintains reference to dataset of sequences created
 by PDBfile reader.

---
 src/MCview/PDBChain.java |   45 ++++++++++++++++++++++++++-------------------
 src/MCview/PDBfile.java  |   16 ++++------------
 2 files changed, 30 insertions(+), 31 deletions(-)

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index a9d2d3a..12e7978 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -33,6 +33,7 @@ public class PDBChain {
      * SequenceFeature group for PDB File features added to sequences
      */
     private static final String PDBFILEFEATURE = "PDBFile";
+    private static final String IEASTATUS = "IEA:jalview";
     public String id;
     public Vector bonds = new Vector();
     public Vector atoms = new Vector();
@@ -44,8 +45,9 @@ public class PDBChain {
     public int pdbend = 0;
     public int seqstart = 0;
     public int seqend = 0;
-
-    public PDBChain(String id) {
+    public String pdbid="";
+    public PDBChain(String pdbid, String id) {
+        this.pdbid=pdbid.toLowerCase();
         this.id = id;
     }
 
@@ -93,28 +95,33 @@ public class PDBChain {
     /**
      * copy over the RESNUM seqfeatures from the internal chain sequence to the mapped sequence
      * @param seq
+     * @param status The Status of the transferred annotation
      */
     public void transferRESNUMFeatures(SequenceI seq, String status) {
-        if (seq != sequence) {
-            /** SequenceFeature[] seqsfeatures=seq.getSequenceFeatures();
+        SequenceI sq = seq;
+        while (sq!=null) {
+            if (sq==sequence)
+                return;
+            sq = sq.getDatasetSequence();
+        }
+        /** 
+         * Remove any existing features for this chain if they exist ?
+         * SequenceFeature[] seqsfeatures=seq.getSequenceFeatures();
             int totfeat=seqsfeatures.length;
             // Remove any features for this exact chain ?
             for (int i=0; i<seqsfeatures.length; i++) {
-                
             } */
-            if (status==null)
-                status = "IEA:jalview";
-            SequenceFeature[] features = sequence.getSequenceFeatures();
-            for (int i=0; i<features.length; i++) {
-                if (features[i].getFeatureGroup().equals(PDBChain.PDBFILEFEATURE)) {
-                    SequenceFeature tx = new SequenceFeature(features[i]);
-                    tx.setBegin(1+((Atom)((Residue)residues.elementAt(tx.getBegin()-offset)).atoms.elementAt(0)).alignmentMapping);
-                    tx.setEnd(1+((Atom)((Residue)residues.elementAt(tx.getEnd()-offset)).atoms.elementAt(0)).alignmentMapping);
-                    tx.setStatus(status+((tx.getStatus()==null || tx.getStatus().length()==0) ? "" : ":"+tx.getStatus()));
-                    seq.getDatasetSequence().addSequenceFeature(tx);
-                }
+        if (status==null)
+            status = PDBChain.IEASTATUS;
+        SequenceFeature[] features = sequence.getSequenceFeatures();
+        for (int i=0; i<features.length; i++) {
+            if (features[i].getFeatureGroup().equals(PDBChain.PDBFILEFEATURE)) {
+                SequenceFeature tx = new SequenceFeature(features[i]);
+                tx.setBegin(1+((Atom)((Residue)residues.elementAt(tx.getBegin()-offset)).atoms.elementAt(0)).alignmentMapping);
+                tx.setEnd(1+((Atom)((Residue)residues.elementAt(tx.getEnd()-offset)).atoms.elementAt(0)).alignmentMapping);
+                tx.setStatus(status+((tx.getStatus()==null || tx.getStatus().length()==0) ? "" : ":"+tx.getStatus()));
+                seq.addSequenceFeature(tx);
             }
-            
         }
     }
 
@@ -194,7 +201,7 @@ public class PDBChain {
             Atom tmpat = (Atom) tmpres.atoms.elementAt(0);
             // Make A new SequenceFeature for the current residue numbering
             SequenceFeature sf = 
-                new SequenceFeature("RESNUM",tmpat.resName+":"+tmpat.resNumIns,
+                new SequenceFeature("RESNUM",tmpat.resName+":"+tmpat.resNumIns+" "+pdbid+id,
                         "",offset+count,offset+count,MCview.PDBChain.PDBFILEFEATURE);
             resFeatures.addElement(sf);
             // Keep totting up the sequence
@@ -214,7 +221,7 @@ public class PDBChain {
         if(id.length()<1 || id.equals(" "))
            id = "_";
         
-        sequence = new Sequence(id, seq.toString(), offset, resNumber); // resNumber-offset ~= seq.size() 
+        sequence = new Sequence(id, seq.toString(), offset, resNumber-1); // Note: resNumber-offset ~= seq.size() 
       //  System.out.println("PDB Sequence is :\nSequence = " + seq);
      //   System.out.println("No of residues = " + residues.size());
         for (i=0,iSize=resFeatures.size(); i<iSize; i++) {
diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index f4a213f..26d44b1 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -90,7 +90,7 @@ public class PDBfile extends jalview.io.AlignFile {
             }
             else
             {
-              tmpchain = new PDBChain(tmpatom.chain);
+              tmpchain = new PDBChain(id,tmpatom.chain);
               chains.addElement(tmpchain);
               tmpchain.atoms.addElement(tmpatom);
             }
@@ -107,23 +107,15 @@ public class PDBfile extends jalview.io.AlignFile {
         }
         for (int i = 0; i < chains.size(); i++)
         {
-          SequenceI seq = ( (PDBChain) chains.elementAt(i)).
+          SequenceI dataset = ( (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());
+          dataset.setName(id + "|" + dataset.getName());
           PDBEntry entry = new PDBEntry();
           entry.setId(id);
           if (inFile != null)
             entry.setFile(inFile.getAbsolutePath());
-
-          seq.setDatasetSequence(dataset);
           dataset.addPDBId(entry);
-
-          getSeqs().addElement(seq);
+          getSeqs().addElement(dataset.deriveSequence()); // PDBChain objects maintain reference to dataset
         }
       }catch(OutOfMemoryError er)
       {
-- 
1.7.10.2