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JAL-1397 getters for originalColours flag
author
Jim Procter
<jprocter@compbio.dundee.ac.uk>
Thu, 17 Oct 2013 10:06:50 +0000
(11:06 +0100)
committer
Jim Procter
<jprocter@compbio.dundee.ac.uk>
Thu, 17 Oct 2013 10:07:48 +0000
(11:07 +0100)
src/jalview/appletgui/AnnotationColourChooser.java
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src/jalview/gui/AnnotationColourChooser.java
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src/jalview/gui/PopupMenu.java
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src/jalview/schemes/AnnotationColourGradient.java
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diff --git
a/src/jalview/appletgui/AnnotationColourChooser.java
b/src/jalview/appletgui/AnnotationColourChooser.java
index
5f61ead
..
c9e9ee4
100644
(file)
--- a/
src/jalview/appletgui/AnnotationColourChooser.java
+++ b/
src/jalview/appletgui/AnnotationColourChooser.java
@@
-84,8
+84,8
@@
public class AnnotationColourChooser extends Panel implements
if (oldcs instanceof AnnotationColourGradient)
{
AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
if (oldcs instanceof AnnotationColourGradient)
{
AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
- currentColours.setState(acg.predefinedColours);
- if (!acg.predefinedColours)
+ currentColours.setState(acg.isPredefinedColours());
+ if (!acg.isPredefinedColours())
{
minColour.setBackground(acg.getMinColour());
maxColour.setBackground(acg.getMaxColour());
{
minColour.setBackground(acg.getMinColour());
maxColour.setBackground(acg.getMaxColour());
@@
-458,7
+458,7
@@
public class AnnotationColourChooser extends Panel implements
if (currentAnnotation.graphMin == 0f
&& currentAnnotation.graphMax == 0f)
{
if (currentAnnotation.graphMin == 0f
&& currentAnnotation.graphMax == 0f)
{
- acg.predefinedColours = true;
+ acg.setPredefinedColours(true);
}
acg.thresholdIsMinMax = thresholdIsMin.getState();
}
acg.thresholdIsMinMax = thresholdIsMin.getState();
diff --git
a/src/jalview/gui/AnnotationColourChooser.java
b/src/jalview/gui/AnnotationColourChooser.java
index
61ef75f
..
3278a76
100644
(file)
--- a/
src/jalview/gui/AnnotationColourChooser.java
+++ b/
src/jalview/gui/AnnotationColourChooser.java
@@
-123,8
+123,8
@@
public class AnnotationColourChooser extends JPanel
if (oldcs instanceof AnnotationColourGradient)
{
AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
if (oldcs instanceof AnnotationColourGradient)
{
AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
- currentColours.setSelected(acg.predefinedColours);
- if (!acg.predefinedColours)
+ currentColours.setSelected(acg.isPredefinedColours());
+ if (!acg.isPredefinedColours())
{
minColour.setBackground(acg.getMinColour());
maxColour.setBackground(acg.getMaxColour());
{
minColour.setBackground(acg.getMinColour());
maxColour.setBackground(acg.getMaxColour());
@@
-550,7
+550,7
@@
public class AnnotationColourChooser extends JPanel
if (currentAnnotation.graphMin == 0f
&& currentAnnotation.graphMax == 0f)
{
if (currentAnnotation.graphMin == 0f
&& currentAnnotation.graphMax == 0f)
{
- acg.predefinedColours = true;
+ acg.setPredefinedColours(true);
}
acg.thresholdIsMinMax = thresholdIsMin.isSelected();
}
acg.thresholdIsMinMax = thresholdIsMin.isSelected();
diff --git
a/src/jalview/gui/PopupMenu.java
b/src/jalview/gui/PopupMenu.java
index
29370ac
..
3bc7c5c
100644
(file)
--- a/
src/jalview/gui/PopupMenu.java
+++ b/
src/jalview/gui/PopupMenu.java
@@
-1642,7
+1642,7
@@
public class PopupMenu extends JPopupMenu
sequence.getAnnotation()[0], null,
AnnotationColourGradient.NO_THRESHOLD);
sequence.getAnnotation()[0], null,
AnnotationColourGradient.NO_THRESHOLD);
- acg.predefinedColours = true;
+ acg.setPredefinedColours(true);
sg.cs = acg;
refresh();
sg.cs = acg;
refresh();
diff --git
a/src/jalview/schemes/AnnotationColourGradient.java
b/src/jalview/schemes/AnnotationColourGradient.java
index
729065c
..
17af427
100755
(executable)
--- a/
src/jalview/schemes/AnnotationColourGradient.java
+++ b/
src/jalview/schemes/AnnotationColourGradient.java
@@
-47,9
+47,9
@@
public class AnnotationColourGradient extends ResidueColourScheme
ColourSchemeI colourScheme;
ColourSchemeI colourScheme;
- public boolean predefinedColours = false;
+ private boolean predefinedColours = false;
- public boolean seqAssociated = false;
+ private boolean seqAssociated = false;
IdentityHashMap<SequenceI, AlignmentAnnotation> seqannot = null;
IdentityHashMap<SequenceI, AlignmentAnnotation> seqannot = null;
@@
-270,6
+270,16
@@
public class AnnotationColourGradient extends ResidueColourScheme
return currentColour;
}
return currentColour;
}
+ public boolean isPredefinedColours()
+ {
+ return predefinedColours;
+ }
+
+ public void setPredefinedColours(boolean predefinedColours)
+ {
+ this.predefinedColours = predefinedColours;
+ }
+
public boolean isSeqAssociated()
{
return seqAssociated;
public boolean isSeqAssociated()
{
return seqAssociated;