From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 20 Mar 2019 15:19:48 +0000 (+0000)
Subject: Merge branch 'develop' into Jalview-JS/develop
X-Git-Tag: Release_2_11_4_0~45^2~18^2~214
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=0b79ea556e792594cab9bd2b4f6cba3b01abaf24;p=jalview.git

Merge branch 'develop' into Jalview-JS/develop

Conflicts:
	src/jalview/gui/AlignFrame.java
	src/jalview/gui/ScalePanel.java
---

0b79ea556e792594cab9bd2b4f6cba3b01abaf24
diff --cc src/jalview/gui/AlignFrame.java
index 4bf424b,4ff1b4f..e2c3ac3
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@@ -851,7 -821,7 +851,7 @@@ public class AlignFrame extends GAlignF
          Desktop.instance.removeJalviewPropertyChangeListener("services",
                  thisListener);
          closeMenuItem_actionPerformed(true);
--      };
++      }
      });
      // Finally, build the menu once to get current service state
      new Thread(new Runnable()
@@@ -3374,7 -3282,7 +3369,7 @@@
                {
                  overview.dispose();
                  alignPanel.setOverviewPanel(null);
--              };
++              }
              });
      if (getKeyListeners().length > 0)
      {
@@@ -5009,7 -4903,7 +5004,7 @@@
          trimrs.setSelected(trimrs.isSelected());
          Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
                  Boolean.valueOf(trimrs.isSelected()).toString());
--      };
++      }
      });
      rfetch.add(trimrs);
      JMenuItem fetchr = new JMenuItem(
@@@ -5728,22 -5631,18 +5723,22 @@@
      chooser.setFileView(new JalviewFileView());
      chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
      chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
 -
 -    int value = chooser.showOpenDialog(null);
 -
 -    if (value == JalviewFileChooser.APPROVE_OPTION)
 +    final AlignFrame us = this;
 +    chooser.setResponseHandler(0, new Runnable()
      {
 -      String choice = chooser.getSelectedFile().getPath();
 -      Cache.setProperty("LAST_DIRECTORY", choice);
 -      SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
 -      new VCFLoader(choice).loadVCF(seqs, this);
 -    }
 +      @Override
 +      public void run()
 +      {
 +        String choice = chooser.getSelectedFile().getPath();
 +        Cache.setProperty("LAST_DIRECTORY", choice);
 +        SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
 +        new VCFLoader(choice).loadVCF(seqs, us);
-       };
++      }
 +    });
 +    chooser.showOpenDialog(null);
  
    }
 +
  }
  
  class PrintThread extends Thread
diff --cc src/jalview/gui/ScalePanel.java
index 9c2b42f,b392c8f..bb15bd2
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@@ -48,7 -48,7 +48,6 @@@ import java.util.List
  import javax.swing.JMenuItem;
  import javax.swing.JPanel;
  import javax.swing.JPopupMenu;
--import javax.swing.SwingUtilities;
  import javax.swing.ToolTipManager;
  
  /**
@@@ -276,11 -278,11 +275,12 @@@ public class ScalePanel extends JPane
      mouseDragging = false;
      ap.getSeqPanel().stopScrolling();
  
 +    // todo res calculation should be a method on AlignViewport
      int xCords = Math.max(0, evt.getX()); // prevent negative X coordinates
+     ViewportRanges ranges = av.getRanges();
      int res = (xCords / av.getCharWidth())
-             + av.getRanges().getStartRes();
- 
+             + ranges.getStartRes();
+     res = Math.min(res, ranges.getEndRes());
      if (av.hasHiddenColumns())
      {
        res = av.getAlignment().getHiddenColumns()