From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Wed, 11 Nov 2015 13:04:11 +0000 (+0000)
Subject: merge
X-Git-Tag: Release_2_10_0~341^2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=0611a46a5652c852426da0d024bb43e0756501c7;hp=-c;p=jalview.git

merge
---

0611a46a5652c852426da0d024bb43e0756501c7
diff --combined src/jalview/gui/AlignFrame.java
index a41e519,d20d62e..5e15195
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@@ -2572,18 -2572,14 +2572,14 @@@ public class AlignFrame extends GAlignF
        TrimRegionCommand trimRegion;
        if (trimLeft)
        {
-         trimRegion = new TrimRegionCommand("Remove Left",
-                 TrimRegionCommand.TRIM_LEFT, seqs, column,
-                 viewport.getAlignment(), viewport.getColumnSelection(),
-                 viewport.getSelectionGroup());
+         trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
+                 column, viewport.getAlignment());
          viewport.setStartRes(0);
        }
        else
        {
-         trimRegion = new TrimRegionCommand("Remove Right",
-                 TrimRegionCommand.TRIM_RIGHT, seqs, column,
-                 viewport.getAlignment(), viewport.getColumnSelection(),
-                 viewport.getSelectionGroup());
+         trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
+                 column, viewport.getAlignment());
        }
  
        statusBar.setText(MessageManager.formatMessage(
@@@ -5535,14 -5531,8 +5531,14 @@@
            @Override
            public void run()
            {
 +            boolean isNuclueotide = alignPanel.alignFrame
 +                    .getViewport().getAlignment()
 +                    .isNucleotide();
              new jalview.ws.DBRefFetcher(alignPanel.av
 -                    .getSequenceSelection(), alignPanel.alignFrame)
 +                    .getSequenceSelection(),
 +                    alignPanel.alignFrame, null,
 +                    alignPanel.alignFrame.featureSettings,
 +                    isNuclueotide)
                      .fetchDBRefs(false);
            }
          }).start();
@@@ -5611,14 -5601,9 +5607,14 @@@
                        @Override
                        public void run()
                        {
 +                        boolean isNuclueotide = alignPanel.alignFrame
 +                                .getViewport().getAlignment()
 +                                .isNucleotide();
                          new jalview.ws.DBRefFetcher(alignPanel.av
                                  .getSequenceSelection(),
 -                                alignPanel.alignFrame, dassource)
 +                                alignPanel.alignFrame, dassource,
 +                                alignPanel.alignFrame.featureSettings,
 +                                isNuclueotide)
                                  .fetchDBRefs(false);
                        }
                      }).start();
@@@ -5652,14 -5637,9 +5648,14 @@@
                        @Override
                        public void run()
                        {
 +                        boolean isNuclueotide = alignPanel.alignFrame
 +                                .getViewport().getAlignment()
 +                                .isNucleotide();
                          new jalview.ws.DBRefFetcher(alignPanel.av
                                  .getSequenceSelection(),
 -                                alignPanel.alignFrame, dassource)
 +                                alignPanel.alignFrame, dassource,
 +                                alignPanel.alignFrame.featureSettings,
 +                                isNuclueotide)
                                  .fetchDBRefs(false);
                        }
                      }).start();
@@@ -5708,14 -5688,9 +5704,14 @@@
                          @Override
                          public void run()
                          {
 +                          boolean isNuclueotide = alignPanel.alignFrame
 +                                  .getViewport().getAlignment()
 +                                  .isNucleotide();
                            new jalview.ws.DBRefFetcher(alignPanel.av
                                    .getSequenceSelection(),
 -                                  alignPanel.alignFrame, dassrc)
 +                                  alignPanel.alignFrame, dassrc,
 +                                  alignPanel.alignFrame.featureSettings,
 +                                  isNuclueotide)
                                    .fetchDBRefs(false);
                          }
                        }).start();