From: Jim Procter <jprocter@dundee.ac.uk>
Date: Tue, 10 Feb 2015 15:35:48 +0000 (+0000)
Subject: JAL-845 @mungoc TODO comments - addAlignment needs a bit more thought
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=4065be0b102659a046a75ac1c8902d9a8086d63b;p=jalview.git

JAL-845 @mungoc TODO comments - addAlignment needs a bit more thought
---

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 6ea8df1..638d3e5 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1000,6 +1000,10 @@ public class AlignViewport extends AlignmentViewport implements
   {
     // TODO: promote to AlignViewportI? applet CutAndPasteTransfer is different
 
+    // JBPComment: title is a largely redundant parameter at the moment
+    // JBPComment: this really should be an 'insert/pre/append' controller
+    // JBPComment: but the DNA/Protein check makes it a bit more complex
+
     // refactored from FileLoader / CutAndPasteTransfer / SequenceFetcher with
     // this comment:
     // TODO: create undo object for this JAL-1101
@@ -1010,6 +1014,7 @@ public class AlignViewport extends AlignmentViewport implements
      */
     if (getAlignment().isNucleotide() != al.isNucleotide())
     {
+      // TODO: JAL-845 try a bit harder to link up imported sequences
       final Set<String> sequenceNames = getAlignment().getSequenceNames();
       sequenceNames.retainAll(al.getSequenceNames());
       if (!sequenceNames.isEmpty()) // at least one sequence name in both
@@ -1020,6 +1025,8 @@ public class AlignViewport extends AlignmentViewport implements
         }
       }
     }
+    // TODO: JAL-407 regardless of above - identical sequences (based on ID and
+    // provenance) should share the same dataset sequence
 
     for (int i = 0; i < al.getHeight(); i++)
     {
@@ -1027,6 +1034,8 @@ public class AlignViewport extends AlignmentViewport implements
     }
     // TODO this call was done by SequenceFetcher but not FileLoader or
     // CutAndPasteTransfer. Is it needed?
+    // JBPComment: this repositions the view to show the new sequences
+    // JBPComment: so it is needed for UX
     setEndSeq(getAlignment().getHeight());
     firePropertyChange("alignment", null, getAlignment().getSequences());
   }