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JAL-2490 tidy code and tests for feature export in Jalview format
[jalview.git]
/
src
/
jalview
/
gui
/
AnnotationPanel.java
diff --git
a/src/jalview/gui/AnnotationPanel.java
b/src/jalview/gui/AnnotationPanel.java
index
84f3e6c
..
919356f
100755
(executable)
--- a/
src/jalview/gui/AnnotationPanel.java
+++ b/
src/jalview/gui/AnnotationPanel.java
@@
-23,6
+23,7
@@
package jalview.gui;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SequenceI;
import jalview.renderer.AnnotationRenderer;
import jalview.renderer.AwtRenderPanelI;
import jalview.datamodel.SequenceI;
import jalview.renderer.AnnotationRenderer;
import jalview.renderer.AwtRenderPanelI;
@@
-290,7
+291,7
@@
public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
{
for (int index : av.getColumnSelection().getSelected())
{
{
for (int index : av.getColumnSelection().getSelected())
{
- if (av.getColumnSelection().isVisible(index))
+ if (av.getAlignment().getHiddenColumns().isVisible(index))
{
anot[index] = null;
}
{
anot[index] = null;
}
@@
-314,7
+315,7
@@
public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
for (int index : av.getColumnSelection().getSelected())
{
for (int index : av.getColumnSelection().getSelected())
{
- if (!av.getColumnSelection().isVisible(index))
+ if (!av.getAlignment().getHiddenColumns().isVisible(index))
{
continue;
}
{
continue;
}
@@
-337,7
+338,7
@@
public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
for (int index : av.getColumnSelection().getSelected())
{
for (int index : av.getColumnSelection().getSelected())
{
- if (!av.getColumnSelection().isVisible(index))
+ if (!av.getAlignment().getHiddenColumns().isVisible(index))
{
continue;
}
{
continue;
}
@@
-397,7
+398,7
@@
public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
}
for (int index : av.getColumnSelection().getSelected())
{
}
for (int index : av.getColumnSelection().getSelected())
{
- if (!av.getColumnSelection().isVisible(index))
+ if (!av.getAlignment().getHiddenColumns().isVisible(index))
{
continue;
}
{
continue;
}
@@
-440,6
+441,7
@@
public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
StringBuilder collatedInput = new StringBuilder(64);
String last = "";
ColumnSelection viscols = av.getColumnSelection();
StringBuilder collatedInput = new StringBuilder(64);
String last = "";
ColumnSelection viscols = av.getColumnSelection();
+ HiddenColumns hidden = av.getAlignment().getHiddenColumns();
/*
* the selection list (read-only view) is in selection order, not
/*
* the selection list (read-only view) is in selection order, not
@@
-450,7
+452,7
@@
public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
for (int index : selected)
{
// always check for current display state - just in case
for (int index : selected)
{
// always check for current display state - just in case
- if (!viscols.isVisible(index))
+ if (!hidden.isVisible(index))
{
continue;
}
{
continue;
}
@@
-712,7
+714,8
@@
public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
if (av.hasHiddenColumns())
{
if (av.hasHiddenColumns())
{
- column = av.getColumnSelection().adjustForHiddenColumns(column);
+ column = av.getAlignment().getHiddenColumns()
+ .adjustForHiddenColumns(column);
}
AlignmentAnnotation ann = aa[row];
}
AlignmentAnnotation ann = aa[row];