From 8299aae37669227dfa5468a51d922d38595ae7bf Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Thu, 17 Apr 2008 15:04:16 +0000
Subject: [PATCH] todos

---
 src/jalview/ws/MsaWSThread.java |    7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/src/jalview/ws/MsaWSThread.java b/src/jalview/ws/MsaWSThread.java
index 3be0c56..8d373ac 100644
--- a/src/jalview/ws/MsaWSThread.java
+++ b/src/jalview/ws/MsaWSThread.java
@@ -522,6 +522,7 @@ class MsaWSThread
   private jalview.datamodel.Sequence[] getVamsasAlignment(
       vamsas.objects.simple.Alignment valign)
   {
+    // TODO: refactor to helper class for vamsas.objects.simple objects
     vamsas.objects.simple.Sequence[] seqs = valign.getSeqs().getSeqs();
     jalview.datamodel.Sequence[] msa = new jalview.datamodel.Sequence[seqs.
         length];
@@ -606,7 +607,6 @@ class MsaWSThread
     Vector alorders = new Vector();
     SequenceI[][] results = new SequenceI[jobs.length][];
     AlignmentOrder[] orders = new AlignmentOrder[jobs.length];
-
     for (int j = 0; j < jobs.length; j++)
     {
       if (jobs[j].hasResults())
@@ -615,6 +615,7 @@ class MsaWSThread
         alorders.add(res[1]);
         results[j] = (SequenceI[]) res[0];
         orders[j] = (AlignmentOrder) res[1];
+         
 //    SequenceI[] alignment = input.getUpdated
       }
       else
@@ -632,7 +633,7 @@ class MsaWSThread
     SequenceI[] alignment = (SequenceI[]) newview[0];
     ColumnSelection columnselection = (ColumnSelection) newview[1];
     Alignment al = new Alignment(alignment);
-
+    // TODO: add 'provenance' property to alignment from the method notes accompanying each subjob
     if (dataset != null)
     {
       al.setDataset(dataset);
@@ -709,7 +710,7 @@ class MsaWSThread
     else
     {
       System.out.println("MERGE WITH OLD FRAME");
-
+      // TODO: modify alignment in original frame, replacing old for new alignment using the commands.EditCommand model to ensure the update can be undone
     }
   }
 
-- 
1.7.10.2