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JAL-3633 Help documentation updated
[jalview.git]
/
src
/
jalview
/
appletgui
/
AnnotationColourChooser.java
diff --git
a/src/jalview/appletgui/AnnotationColourChooser.java
b/src/jalview/appletgui/AnnotationColourChooser.java
index
8de751a
..
9456986
100644
(file)
--- a/
src/jalview/appletgui/AnnotationColourChooser.java
+++ b/
src/jalview/appletgui/AnnotationColourChooser.java
@@
-85,7
+85,7
@@
public class AnnotationColourChooser extends Panel implements
oldcs = av.getGlobalColourScheme();
if (av.getAlignment().getGroups() != null)
{
oldcs = av.getGlobalColourScheme();
if (av.getAlignment().getGroups() != null)
{
- oldgroupColours = new HashMap<SequenceGroup, ColourSchemeI>();
+ oldgroupColours = new HashMap<>();
for (SequenceGroup sg : ap.av.getAlignment().getGroups())
{
oldgroupColours.put(sg, sg.getColourScheme());
for (SequenceGroup sg : ap.av.getAlignment().getGroups())
{
oldgroupColours.put(sg, sg.getColourScheme());
@@
-180,8
+180,8
@@
public class AnnotationColourChooser extends Panel implements
// TODO remove duplication with gui.AnnotationRowFilter
// TODO add 'per sequence only' option / parameter
// TODO remove duplication with gui.AnnotationRowFilter
// TODO add 'per sequence only' option / parameter
- annotationLabels = new HashMap<AlignmentAnnotation, String>();
- Vector<String> list = new Vector<String>();
+ annotationLabels = new HashMap<>();
+ Vector<String> list = new Vector<>();
AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
if (anns == null)
{
AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
if (anns == null)
{
@@
-350,7
+350,7
@@
public class AnnotationColourChooser extends Panel implements
{
try
{
{
try
{
- float f = new Float(thresholdValue.getText()).floatValue();
+ float f = Float.valueOf(thresholdValue.getText()).floatValue();
slider.setValue((int) (f * 1000));
adjustmentValueChanged(null);
} catch (NumberFormatException ex)
slider.setValue((int) (f * 1000));
adjustmentValueChanged(null);
} catch (NumberFormatException ex)
@@
-376,7
+376,7
@@
public class AnnotationColourChooser extends Panel implements
else if (evt.getSource() == cancel)
{
reset();
else if (evt.getSource() == cancel)
{
reset();
- ap.paintAlignment(true);
+ ap.paintAlignment(true, true);
frame.setVisible(false);
}
frame.setVisible(false);
}
@@
-417,7
+417,7
@@
public class AnnotationColourChooser extends Panel implements
}
currentAnnotation.threshold.value = slider.getValue() / 1000f;
}
currentAnnotation.threshold.value = slider.getValue() / 1000f;
- ap.paintAlignment(false);
+ ap.paintAlignment(false, false);
}
}
}
}
@@
-559,7
+559,7
@@
public class AnnotationColourChooser extends Panel implements
// update colours in linked windows
ap.alignmentChanged();
// update colours in linked windows
ap.alignmentChanged();
- ap.paintAlignment(true);
+ ap.paintAlignment(true, true);
}
void reset()
}
void reset()
@@
-572,7
+572,7
@@
public class AnnotationColourChooser extends Panel implements
sg.setColourScheme(oldgroupColours.get(sg));
}
}
sg.setColourScheme(oldgroupColours.get(sg));
}
}
- ap.paintAlignment(true);
+ ap.paintAlignment(true, true);
}
@Override
}
@Override
@@
-588,7
+588,7
@@
public class AnnotationColourChooser extends Panel implements
@Override
public void mouseReleased(MouseEvent evt)
{
@Override
public void mouseReleased(MouseEvent evt)
{
- ap.paintAlignment(true);
+ ap.paintAlignment(true, true);
}
@Override
}
@Override