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JAL-2543 identify as JSON before HTML
[jalview.git]
/
src
/
jalview
/
gui
/
AlignViewport.java
diff --git
a/src/jalview/gui/AlignViewport.java
b/src/jalview/gui/AlignViewport.java
index
670d830
..
6409b56
100644
(file)
--- a/
src/jalview/gui/AlignViewport.java
+++ b/
src/jalview/gui/AlignViewport.java
@@
-22,7
+22,7
@@
package jalview.gui;
import jalview.analysis.AlignmentUtils;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.analysis.AlignmentUtils;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
-import jalview.analysis.NJTree;
+import jalview.analysis.TreeModel;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureColourI;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureColourI;
@@
-57,6
+57,7
@@
import jalview.ws.params.AutoCalcSetting;
import java.awt.Container;
import java.awt.Dimension;
import java.awt.Font;
import java.awt.Container;
import java.awt.Dimension;
import java.awt.Font;
+import java.awt.FontMetrics;
import java.awt.Rectangle;
import java.util.ArrayList;
import java.util.Hashtable;
import java.awt.Rectangle;
import java.util.ArrayList;
import java.util.Hashtable;
@@
-76,7
+77,7
@@
public class AlignViewport extends AlignmentViewport implements
{
Font font;
{
Font font;
- NJTree currentTree = null;
+ TreeModel currentTree = null;
boolean cursorMode = false;
boolean cursorMode = false;
@@
-280,6
+281,8
@@
public class AlignViewport extends AlignmentViewport implements
false);
showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
false);
showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
+
+ showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true);
}
initAutoAnnotation();
String colourProperty = alignment.isNucleotide() ? Preferences.DEFAULT_COLOUR_NUC
}
initAutoAnnotation();
String colourProperty = alignment.isNucleotide() ? Preferences.DEFAULT_COLOUR_NUC
@@
-349,23
+352,19
@@
public class AlignViewport extends AlignmentViewport implements
boolean validCharWidth;
/**
boolean validCharWidth;
/**
- * update view settings with the given font. You may need to call
- * alignPanel.fontChanged to update the layout geometry
- *
- * @param setGrid
- * when true, charWidth/height is set according to font mentrics
+ * {@inheritDoc}
*/
*/
+ @Override
public void setFont(Font f, boolean setGrid)
{
font = f;
Container c = new Container();
public void setFont(Font f, boolean setGrid)
{
font = f;
Container c = new Container();
- java.awt.FontMetrics fm = c.getFontMetrics(font);
- int w = viewStyle.getCharWidth(), ww = fm.charWidth('M'), h = viewStyle
- .getCharHeight();
if (setGrid)
{
if (setGrid)
{
+ FontMetrics fm = c.getFontMetrics(font);
+ int ww = fm.charWidth('M');
setCharHeight(fm.getHeight());
setCharWidth(ww);
}
setCharHeight(fm.getHeight());
setCharWidth(ww);
}
@@
-492,7
+491,7
@@
public class AlignViewport extends AlignmentViewport implements
* @param tree
* DOCUMENT ME!
*/
* @param tree
* DOCUMENT ME!
*/
- public void setCurrentTree(NJTree tree)
+ public void setCurrentTree(TreeModel tree)
{
currentTree = tree;
}
{
currentTree = tree;
}
@@
-502,7
+501,7
@@
public class AlignViewport extends AlignmentViewport implements
*
* @return DOCUMENT ME!
*/
*
* @return DOCUMENT ME!
*/
- public NJTree getCurrentTree()
+ public TreeModel getCurrentTree()
{
return currentTree;
}
{
return currentTree;
}