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Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
[jalview.git]
/
src
/
jalview
/
gui
/
AlignViewport.java
diff --git
a/src/jalview/gui/AlignViewport.java
b/src/jalview/gui/AlignViewport.java
index
f1bb8de
..
f22a911
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;
@@
-51,7
+51,7
@@
import jalview.structure.StructureSelectionManager;
import jalview.structure.VamsasSource;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
import jalview.structure.VamsasSource;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
-import jalview.viewmodel.ViewportPositionProps;
+import jalview.viewmodel.ViewportRanges;
import jalview.ws.params.AutoCalcSetting;
import java.awt.Container;
import jalview.ws.params.AutoCalcSetting;
import java.awt.Container;
@@
-76,7
+76,7
@@
public class AlignViewport extends AlignmentViewport implements
{
Font font;
{
Font font;
- NJTree currentTree = null;
+ TreeModel currentTree = null;
boolean cursorMode = false;
boolean cursorMode = false;
@@
-150,11
+150,10
@@
public class AlignViewport extends AlignmentViewport implements
public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns)
{
setAlignment(al);
public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns)
{
setAlignment(al);
- posProps.setHiddenColumns(hiddenColumns);
- /*if (hiddenColumns != null)
+ if (hiddenColumns != null)
{
colSel = hiddenColumns;
{
colSel = hiddenColumns;
- }*/
+ }
init();
}
init();
}
@@
-198,11
+197,10
@@
public class AlignViewport extends AlignmentViewport implements
Cache.log.debug("Setting viewport's view id : " + viewId);
}
setAlignment(al);
Cache.log.debug("Setting viewport's view id : " + viewId);
}
setAlignment(al);
- posProps.setHiddenColumns(hiddenColumns);
- /*if (hiddenColumns != null)
+ if (hiddenColumns != null)
{
colSel = hiddenColumns;
{
colSel = hiddenColumns;
- }*/
+ }
init();
}
init();
}
@@
-240,11
+238,7
@@
public class AlignViewport extends AlignmentViewport implements
void init()
{
void init()
{
-
- /*setStartRes(0);
- setEndRes(alignment.getWidth() - 1);
- setStartSeq(0);
- setEndSeq(alignment.getHeight() - 1);*/
+ ranges = new ViewportRanges(this.alignment);
applyViewProperties();
String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
applyViewProperties();
String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
@@
-285,6
+279,8
@@
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
@@
-311,8
+307,6
@@
public class AlignViewport extends AlignmentViewport implements
{
residueShading.setConsensus(hconsensus);
}
{
residueShading.setConsensus(hconsensus);
}
-
- posProps = new ViewportPositionProps(this.alignment, this.viewStyle);
}
/**
}
/**
@@
-499,7
+493,7
@@
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;
}
@@
-509,7
+503,7
@@
public class AlignViewport extends AlignmentViewport implements
*
* @return DOCUMENT ME!
*/
*
* @return DOCUMENT ME!
*/
- public NJTree getCurrentTree()
+ public TreeModel getCurrentTree()
{
return currentTree;
}
{
return currentTree;
}
@@
-535,9
+529,7
@@
public class AlignViewport extends AlignmentViewport implements
{
end = alignment.getWidth();
}
{
end = alignment.getWidth();
}
- viscontigs = posProps.getColumnSelection()
- .getVisibleContigs(start, end);
- // viscontigs = colSel.getVisibleContigs(start, end);
+ viscontigs = colSel.getVisibleContigs(start, end);
return viscontigs;
}
return viscontigs;
}
@@
-862,7
+854,7
@@
public class AlignViewport extends AlignmentViewport implements
}
}
}
}
- setEndSeq(getAlignment().getHeight());
+ ranges.setEndSeq(getAlignment().getHeight());
firePropertyChange("alignment", null, getAlignment().getSequences());
}
firePropertyChange("alignment", null, getAlignment().getSequences());
}