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Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges
[jalview.git]
/
src
/
jalview
/
appletgui
/
AlignViewport.java
diff --git
a/src/jalview/appletgui/AlignViewport.java
b/src/jalview/appletgui/AlignViewport.java
index
d64cd75
..
7369c3c
100644
(file)
--- a/
src/jalview/appletgui/AlignViewport.java
+++ b/
src/jalview/appletgui/AlignViewport.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
* Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-54,10
+54,16
@@
public class AlignViewport extends AlignmentViewport
private AnnotationColumnChooser annotationColumnSelectionState;
private AnnotationColumnChooser annotationColumnSelectionState;
+ java.awt.Frame nullFrame;
+
+ protected FeatureSettings featureSettings = null;
+
+ private float heightScale = 1, widthScale = 1;
+
public AlignViewport(AlignmentI al, JalviewLite applet)
{
super(al);
public AlignViewport(AlignmentI al, JalviewLite applet)
{
super(al);
- calculator = new jalview.workers.AlignCalcManager();
+ calculator = new jalview.workers.AlignCalcManager2();
this.applet = applet;
// we always pad gaps
this.applet = applet;
// we always pad gaps
@@
-196,7
+202,7
@@
public class AlignViewport extends AlignmentViewport
.getColourScheme(this, alignment, colour));
if (residueShading != null)
{
.getColourScheme(this, alignment, colour));
if (residueShading != null)
{
- residueShading.setConsensus(hconsensus);
+ residueShading.setConsensus(consensusProfiles);
}
}
}
}
@@
-207,15
+213,8
@@
public class AlignViewport extends AlignmentViewport
}
}
initAutoAnnotation();
}
}
initAutoAnnotation();
-
}
}
- java.awt.Frame nullFrame;
-
- protected FeatureSettings featureSettings = null;
-
- private float heightScale = 1, widthScale = 1;
-
/**
* {@inheritDoc}
*/
/**
* {@inheritDoc}
*/
@@
-295,17
+294,6
@@
public class AlignViewport extends AlignmentViewport
.getStructureSelectionManager(applet);
}
.getStructureSelectionManager(applet);
}
- @Override
- public boolean isNormaliseSequenceLogo()
- {
- return normaliseSequenceLogo;
- }
-
- public void setNormaliseSequenceLogo(boolean state)
- {
- normaliseSequenceLogo = state;
- }
-
/**
*
* @return true if alignment characters should be displayed
/**
*
* @return true if alignment characters should be displayed
@@
-351,7
+339,7
@@
public class AlignViewport extends AlignmentViewport
if (mappedCommand != null)
{
mappedCommand.doCommand(null);
if (mappedCommand != null)
{
mappedCommand.doCommand(null);
- firePropertyChange("alignment", null, getAlignment().getSequences());
+ notifyAlignment();
// ap.scalePanelHolder.repaint();
// ap.repaint();
// ap.scalePanelHolder.repaint();
// ap.repaint();