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(JAL-969) refactored alignmentViewport base class to own package and pulled up most...
[jalview.git]
/
src
/
jalview
/
gui
/
TreeCanvas.java
diff --git
a/src/jalview/gui/TreeCanvas.java
b/src/jalview/gui/TreeCanvas.java
index
b62a1c7
..
b23fbc2
100755
(executable)
--- a/
src/jalview/gui/TreeCanvas.java
+++ b/
src/jalview/gui/TreeCanvas.java
@@
-125,7
+125,7
@@
public class TreeCanvas extends JPanel implements MouseListener, Runnable,
aps[a].av.setSelectionGroup(selected);
}
aps[a].av.setSelectionGroup(selected);
}
- selected.setEndRes(aps[a].av.alignment.getWidth() - 1);
+ selected.setEndRes(aps[a].av.getAlignment().getWidth() - 1);
selected.addOrRemove(sequence, true);
}
}
selected.addOrRemove(sequence, true);
}
}
@@
-851,7
+851,7
@@
public class TreeCanvas extends JPanel implements MouseListener, Runnable,
for (int a = 0; a < aps.length; a++)
{
aps[a].av.setSelectionGroup(null);
for (int a = 0; a < aps.length; a++)
{
aps[a].av.setSelectionGroup(null);
- aps[a].av.alignment.deleteAllGroups();
+ aps[a].av.getAlignment().deleteAllGroups();
aps[a].av.sequenceColours = null;
}
colourGroups();
aps[a].av.sequenceColours = null;
}
colourGroups();
@@
-901,7
+901,7
@@
public class TreeCanvas extends JPanel implements MouseListener, Runnable,
}
else
{
}
else
{
- cs = ColourSchemeProperty.getColour(sequences, av.alignment
+ cs = ColourSchemeProperty.getColour(sequences, av.getAlignment()
.getWidth(), ColourSchemeProperty.getColourName(av
.getGlobalColourScheme()));
}
.getWidth(), ColourSchemeProperty.getColourName(av
.getGlobalColourScheme()));
}
@@
-914,7
+914,7
@@
public class TreeCanvas extends JPanel implements MouseListener, Runnable,
}
SequenceGroup sg = new SequenceGroup(sequences, null, cs, true, true,
}
SequenceGroup sg = new SequenceGroup(sequences, null, cs, true, true,
- false, 0, av.alignment.getWidth() - 1);
+ false, 0, av.getAlignment().getWidth() - 1);
sg.setName("JTreeGroup:" + sg.hashCode());
sg.setIdColour(col);
sg.setName("JTreeGroup:" + sg.hashCode());
sg.setIdColour(col);
@@
-932,7
+932,7
@@
public class TreeCanvas extends JPanel implements MouseListener, Runnable,
sg.cs.setConservation(c);
}
sg.cs.setConservation(c);
}
- aps[a].av.alignment.addGroup(sg);
+ aps[a].av.getAlignment().addGroup(sg);
}
}
// notify the panel to redo any group specific stuff.
}
}
// notify the panel to redo any group specific stuff.