git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
JAL-2668 add tests for HMMER commands, annotation and io
[jalview.git]
/
src
/
jalview
/
gui
/
AnnotationPanel.java
diff --git
a/src/jalview/gui/AnnotationPanel.java
b/src/jalview/gui/AnnotationPanel.java
index
6997517
..
452f002
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;
@@
-294,7
+295,7
@@
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;
}
@@
-318,7
+319,7
@@
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;
}
@@
-341,7
+342,7
@@
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;
}
@@
-401,7
+402,7
@@
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;
}
@@
-444,6
+445,7
@@
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
@@
-454,7
+456,7
@@
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;
}
@@
-716,7
+718,8
@@
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];