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JAL-2349 JAL-4027 JAL-3855 quick hack to add contact matrices accompanying alignment...
author
Jim Procter
<j.procter@dundee.ac.uk>
Fri, 10 Jun 2022 11:57:43 +0000
(12:57 +0100)
committer
Jim Procter
<j.procter@dundee.ac.uk>
Fri, 10 Jun 2022 11:57:43 +0000
(12:57 +0100)
src/jalview/gui/AlignViewport.java
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diff --git
a/src/jalview/gui/AlignViewport.java
b/src/jalview/gui/AlignViewport.java
index
30ccdbe
..
c61fe34
100644
(file)
--- a/
src/jalview/gui/AlignViewport.java
+++ b/
src/jalview/gui/AlignViewport.java
@@
-20,6
+20,17
@@
*/
package jalview.gui;
*/
package jalview.gui;
+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.util.List;
+
+import javax.swing.JInternalFrame;
+
import jalview.analysis.AlignmentUtils;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.api.AlignViewportI;
import jalview.analysis.AlignmentUtils;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.api.AlignViewportI;
@@
-35,6
+46,7
@@
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.ContactMatrixI;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResultsI;
@@
-53,17
+65,6
@@
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
import jalview.ws.params.AutoCalcSetting;
import jalview.viewmodel.AlignmentViewport;
import jalview.ws.params.AutoCalcSetting;
-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.util.List;
-
-import javax.swing.JInternalFrame;
-
/**
* DOCUMENT ME!
*
/**
* DOCUMENT ME!
*
@@
-719,7
+720,10
@@
public class AlignViewport extends AlignmentViewport
al.addSequence(seq);
}
}
al.addSequence(seq);
}
}
-
+ for (ContactMatrixI cm : toAdd.getContactMaps())
+ {
+ al.addContactList(cm);
+ }
ranges.setEndSeq(getAlignment().getHeight() - 1); // BH 2019.04.18
firePropertyChange("alignment", null, getAlignment().getSequences());
}
ranges.setEndSeq(getAlignment().getHeight() - 1); // BH 2019.04.18
firePropertyChange("alignment", null, getAlignment().getSequences());
}