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add partial button fix to annotation and statistics output
[jalview.git]
/
src
/
jalview
/
gui
/
AnnotationColumnChooser.java
diff --git
a/src/jalview/gui/AnnotationColumnChooser.java
b/src/jalview/gui/AnnotationColumnChooser.java
index
a23ca68
..
96299e7
100644
(file)
--- a/
src/jalview/gui/AnnotationColumnChooser.java
+++ b/
src/jalview/gui/AnnotationColumnChooser.java
@@
-21,8
+21,7
@@
package jalview.gui;
package jalview.gui;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.schemes.AnnotationColourGradient;
import jalview.util.MessageManager;
import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
import jalview.schemes.AnnotationColourGradient;
import jalview.util.MessageManager;
import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
@@
-87,7
+86,7
@@
public class AnnotationColumnChooser extends AnnotationRowFilter implements
private int actionOption = ACTION_OPTION_SELECT;
private int actionOption = ACTION_OPTION_SELECT;
- private ColumnSelection oldColumnSelection;
+ private HiddenColumns oldHiddenColumns;
protected int MIN_WIDTH = 420;
protected int MIN_WIDTH = 420;
@@
-111,7
+110,7
@@
public class AnnotationColumnChooser extends AnnotationRowFilter implements
{
return;
}
{
return;
}
- setOldColumnSelection(av.getColumnSelection());
+ setOldHiddenColumns(av.getAlignment().getHiddenColumns());
adjusting = true;
setAnnotations(new JComboBox<String>(getAnnotationItems(false)));
adjusting = true;
setAnnotations(new JComboBox<String>(getAnnotationItems(false)));
@@
-237,26
+236,26
@@
public class AnnotationColumnChooser extends AnnotationRowFilter implements
@Override
protected void reset()
{
@Override
protected void reset()
{
- if (this.getOldColumnSelection() != null)
+ if (this.getOldHiddenColumns() != null)
{
av.getColumnSelection().clear();
if (av.getAnnotationColumnSelectionState() != null)
{
{
av.getColumnSelection().clear();
if (av.getAnnotationColumnSelectionState() != null)
{
- ColumnSelection oldSelection = av
+ HiddenColumns oldHidden = av
.getAnnotationColumnSelectionState()
.getAnnotationColumnSelectionState()
- .getOldColumnSelection();
- if (oldSelection != null && oldSelection.getHiddenColumns() != null
- && !oldSelection.getHiddenColumns().isEmpty())
+ .getOldHiddenColumns();
+ if (oldHidden != null && oldHidden.getHiddenRegions() != null
+ && !oldHidden.getHiddenRegions().isEmpty())
{
{
- for (Iterator<int[]> itr = oldSelection.getHiddenColumns()
+ for (Iterator<int[]> itr = oldHidden.getHiddenRegions()
.iterator(); itr.hasNext();)
{
int positions[] = itr.next();
av.hideColumns(positions[0], positions[1]);
}
}
.iterator(); itr.hasNext();)
{
int positions[] = itr.next();
av.hideColumns(positions[0], positions[1]);
}
}
- av.setColumnSelection(oldSelection);
+ av.getAlignment().setHiddenColumns(oldHidden);
}
ap.paintAlignment(true);
}
}
ap.paintAlignment(true);
}
@@
-334,7
+333,7
@@
public class AnnotationColumnChooser extends AnnotationRowFilter implements
// build filter params
filterParams
.setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
// build filter params
filterParams
.setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
- if (getCurrentAnnotation().graph != AlignmentAnnotation.NO_GRAPH)
+ if (getCurrentAnnotation().isQuantitative())
{
filterParams
.setThresholdValue(getCurrentAnnotation().threshold.value);
{
filterParams
.setThresholdValue(getCurrentAnnotation().threshold.value);
@@
-409,17
+408,16
@@
public class AnnotationColumnChooser extends AnnotationRowFilter implements
ap.paintAlignment(true);
}
ap.paintAlignment(true);
}
-
- public ColumnSelection getOldColumnSelection()
+ public HiddenColumns getOldHiddenColumns()
{
{
- return oldColumnSelection;
+ return oldHiddenColumns;
}
}
- public void setOldColumnSelection(ColumnSelection currentColumnSelection)
+ public void setOldHiddenColumns(HiddenColumns currentHiddenColumns)
{
{
- if (currentColumnSelection != null)
+ if (currentHiddenColumns != null)
{
{
- this.oldColumnSelection = new ColumnSelection(currentColumnSelection);
+ this.oldHiddenColumns = new HiddenColumns(currentHiddenColumns);
}
}
}
}
@@
-495,8
+493,9
@@
public class AnnotationColumnChooser extends AnnotationRowFilter implements
public void selectedAnnotationChanged()
{
String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
public void selectedAnnotationChanged()
{
String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
- if (av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
- .getSelectedIndex()]].graph != AlignmentAnnotation.NO_GRAPH)
+ if (av.getAlignment()
+ .getAlignmentAnnotation()[annmap[getAnnotations()
+ .getSelectedIndex()]].isQuantitative())
{
currentView = AnnotationColumnChooser.GRAPH_VIEW;
}
{
currentView = AnnotationColumnChooser.GRAPH_VIEW;
}