From 4ec235370b49c38ae7e7b3a46f92f926fc430bf1 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Wed, 24 Jun 2009 08:28:23 +0000
Subject: [PATCH] all alignment sequences associated with a dataset sequence
 must have start-end updated (and any mappings adjusted -
 see TODO)

---
 src/jalview/ws/DBRefFetcher.java |   26 ++++++++++++++++++++++++--
 1 file changed, 24 insertions(+), 2 deletions(-)

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index 1fd9f1c..73d106a 100644
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -74,6 +74,8 @@ public class DBRefFetcher implements Runnable
 
   SequenceFetcher sfetcher;
 
+  private SequenceI[] alseqs;
+
   public DBRefFetcher()
   {
   }
@@ -106,9 +108,11 @@ public class DBRefFetcher implements Runnable
   public DBRefFetcher(SequenceI[] seqs, AlignFrame af, String[] sources)
   {
     this.af = af;
+    alseqs = new SequenceI[seqs.length];
     SequenceI[] ds = new SequenceI[seqs.length];
     for (int i = 0; i < seqs.length; i++)
     {
+      alseqs[i] = seqs[i];
       if (seqs[i].getDatasetSequence() != null)
         ds[i] = seqs[i].getDatasetSequence();
       else
@@ -608,8 +612,9 @@ public class DBRefFetcher implements Runnable
           // absStart+sequence.getStart()+entrySeq.length()-1},
           // new int[] { entry.getStart(), entry.getEnd() }, 1, 1);
           // relocate local features for updated start
-          if (updateRefFrame && sequence.getSequenceFeatures() != null)
-          {
+          if (updateRefFrame) {
+            if (sequence.getSequenceFeatures() != null)
+            {
             SequenceFeature[] sf = sequence.getSequenceFeatures();
             int start = sequence.getStart();
             int end = sequence.getEnd();
@@ -624,6 +629,7 @@ public class DBRefFetcher implements Runnable
                 sf[sfi].setEnd(sf[sfi].getEnd() + startShift);
               }
             }
+            }
           }
         }
 
@@ -638,6 +644,22 @@ public class DBRefFetcher implements Runnable
           // finally, update local sequence reference frame if we're allowed
           sequence.setStart(absStart);
           sequence.setEnd(absEnd);
+          // search for alignment sequences to update coordinate frame for
+          for (int alsq = 0; alsq<alseqs.length; alsq++)
+          {
+            if (alseqs[alsq].getDatasetSequence()==sequence)
+            {
+              String ngAlsq = AlignSeq.extractGaps("-. ",
+                      alseqs[alsq].getSequenceAsString()).toUpperCase();
+              int oldstrt = alseqs[alsq].getStart();
+              alseqs[alsq].setStart(sequence.getSequenceAsString().toUpperCase().indexOf(ngAlsq)+sequence.getStart());
+              if (oldstrt != alseqs[alsq].getStart()) {
+                alseqs[alsq].setEnd(ngAlsq.length()+alseqs[alsq].getStart()-1);
+              }
+            }
+          }
+          // TODO:  search for all other references to this dataset sequence, and update start/end
+          // TODO: update all AlCodonMappings which involve this alignment sequence (e.g. Q30167 cdna translation from exon2 product (vamsas demo)
         }
         // and remove it from the rest
         // TODO: decide if we should remove annotated sequence from set
-- 
1.7.10.2