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Merge branch 'develop' into features/JAL-2360colourSchemeApplicability
[jalview.git]
/
src
/
jalview
/
gui
/
Jalview2XML.java
diff --git
a/src/jalview/gui/Jalview2XML.java
b/src/jalview/gui/Jalview2XML.java
index
2629f0a
..
7057c2a
100644
(file)
--- a/
src/jalview/gui/Jalview2XML.java
+++ b/
src/jalview/gui/Jalview2XML.java
@@
-3344,7
+3344,7
@@
public class Jalview2XML
}
else
{
}
else
{
- cs = ColourSchemeProperty.getColour(al, jGroup.getColour());
+ cs = ColourSchemeProperty.getColourScheme(al, jGroup.getColour());
}
if (cs != null)
}
if (cs != null)
@@
-4420,10
+4420,12
@@
public class Jalview2XML
af.viewport.setShowAnnotation(view.getShowAnnotation());
af.viewport.setAbovePIDThreshold(view.getPidSelected());
af.viewport.setShowAnnotation(view.getShowAnnotation());
af.viewport.setAbovePIDThreshold(view.getPidSelected());
+ af.viewport.setThreshold(view.getPidThreshold());
af.viewport.setColourText(view.getShowColourText());
af.viewport.setConservationSelected(view.getConservationSelected());
af.viewport.setColourText(view.getShowColourText());
af.viewport.setConservationSelected(view.getConservationSelected());
+ af.viewport.setIncrement(view.getConsThreshold());
af.viewport.setShowJVSuffix(view.getShowFullId());
af.viewport.setRightAlignIds(view.getRightAlignIds());
af.viewport.setFont(
af.viewport.setShowJVSuffix(view.getShowFullId());
af.viewport.setRightAlignIds(view.getRightAlignIds());
af.viewport.setFont(
@@
-4468,12
+4470,11
@@
public class Jalview2XML
}
else
{
}
else
{
- cs = ColourSchemeProperty.getColour(al, view.getBgColour());
+ cs = ColourSchemeProperty.getColourScheme(al, view.getBgColour());
}
if (cs != null)
{
}
if (cs != null)
{
- cs.setThreshold(view.getPidThreshold(), true);
cs.setConsensus(af.viewport.getSequenceConsensusHash());
}
}
cs.setConsensus(af.viewport.getSequenceConsensusHash());
}
}
@@
-4749,7
+4750,7
@@
public class Jalview2XML
{
cs = new AnnotationColourGradient(
annAlignment.getAlignmentAnnotation()[i],
{
cs = new AnnotationColourGradient(
annAlignment.getAlignmentAnnotation()[i],
- ColourSchemeProperty.getColour(al,
+ ColourSchemeProperty.getColourScheme(al,
viewAnnColour.getColourScheme()),
viewAnnColour.getAboveThreshold());
}
viewAnnColour.getColourScheme()),
viewAnnColour.getAboveThreshold());
}