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Merge branch 'releases/Release_2_10_4_Branch'
[jalview.git]
/
src
/
jalview
/
gui
/
AlignViewport.java
diff --git
a/src/jalview/gui/AlignViewport.java
b/src/jalview/gui/AlignViewport.java
index
14b7af0
..
7e77bec
100644
(file)
--- a/
src/jalview/gui/AlignViewport.java
+++ b/
src/jalview/gui/AlignViewport.java
@@
-22,7
+22,6
@@
package jalview.gui;
import jalview.analysis.AlignmentUtils;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.analysis.AlignmentUtils;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
-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;
@@
-36,7
+35,6
@@
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.PDBEntry;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceGroup;
@@
-58,10
+56,9
@@
import java.awt.Dimension;
import java.awt.Font;
import java.awt.FontMetrics;
import java.awt.Rectangle;
import java.awt.Font;
import java.awt.FontMetrics;
import java.awt.Rectangle;
-import java.util.ArrayList;
import java.util.Hashtable;
import java.util.Hashtable;
+import java.util.Iterator;
import java.util.List;
import java.util.List;
-import java.util.Vector;
import javax.swing.JInternalFrame;
import javax.swing.JInternalFrame;
@@
-76,8
+73,6
@@
public class AlignViewport extends AlignmentViewport
{
Font font;
{
Font font;
- TreeModel currentTree = null;
-
boolean cursorMode = false;
boolean antiAlias = false;
boolean cursorMode = false;
boolean antiAlias = false;
@@
-448,27
+443,6
@@
public class AlignViewport extends AlignmentViewport
}
/**
}
/**
- * DOCUMENT ME!
- *
- * @param tree
- * DOCUMENT ME!
- */
- public void setCurrentTree(TreeModel tree)
- {
- currentTree = tree;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public TreeModel getCurrentTree()
- {
- return currentTree;
- }
-
- /**
* returns the visible column regions of the alignment
*
* @param selectedRegionOnly
* returns the visible column regions of the alignment
*
* @param selectedRegionOnly
@@
-476,10
+450,10
@@
public class AlignViewport extends AlignmentViewport
* area
* @return
*/
* area
* @return
*/
- public int[] getViewAsVisibleContigs(boolean selectedRegionOnly)
+ public Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly)
{
{
- int[] viscontigs = null;
- int start = 0, end = 0;
+ int start = 0;
+ int end = 0;
if (selectedRegionOnly && selectionGroup != null)
{
start = selectionGroup.getStartRes();
if (selectedRegionOnly && selectionGroup != null)
{
start = selectionGroup.getStartRes();
@@
-489,8
+463,8
@@
public class AlignViewport extends AlignmentViewport
{
end = alignment.getWidth();
}
{
end = alignment.getWidth();
}
- viscontigs = alignment.getHiddenColumns().getVisibleContigs(start, end);
- return viscontigs;
+ return (alignment.getHiddenColumns().getVisContigsIterator(start, end,
+ false));
}
/**
}
/**
@@
-627,7
+601,7
@@
public class AlignViewport extends AlignmentViewport
return validCharWidth;
}
return validCharWidth;
}
- private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<String, AutoCalcSetting>();
+ private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<>();
public AutoCalcSetting getCalcIdSettingsFor(String calcId)
{
public AutoCalcSetting getCalcIdSettingsFor(String calcId)
{
@@
-1058,5
+1032,4
@@
public class AlignViewport extends AlignmentViewport
}
fr.setTransparency(featureSettings.getTransparency());
}
}
fr.setTransparency(featureSettings.getTransparency());
}
-
}
}