*/
package jalview.viewmodel;
+import java.awt.Color;
+import java.beans.PropertyChangeSupport;
+import java.util.ArrayDeque;
+import java.util.ArrayList;
+import java.util.BitSet;
+import java.util.Deque;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.analysis.Conservation;
import jalview.api.AlignCalcManagerI;
import jalview.workers.ConsensusThread;
import jalview.workers.StrucConsensusThread;
-import java.awt.Color;
-import java.beans.PropertyChangeSupport;
-import java.util.ArrayDeque;
-import java.util.ArrayList;
-import java.util.BitSet;
-import java.util.Deque;
-import java.util.HashMap;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Map;
-
/**
* base class holding visualization and analysis attributes and common logic for
* an active alignment view displayed in the GUI
protected AlignmentAnnotation complementConsensus;
+ protected AlignmentAnnotation gapcounts;
+
protected AlignmentAnnotation strucConsensus;
protected AlignmentAnnotation conservation;
}
@Override
+ public AlignmentAnnotation getAlignmentGapAnnotation()
+ {
+ return gapcounts;
+ }
+
+ @Override
public AlignmentAnnotation getComplementConsensusAnnotation()
{
return complementConsensus;
public void updateConsensus(final AlignmentViewPanel ap)
{
// see note in mantis : issue number 8585
- if (consensus == null || !autoCalculateConsensus)
+ if ((consensus == null || gapcounts == null) || !autoCalculateConsensus)
{
return;
}
consensus = new AlignmentAnnotation("Consensus", "PID",
new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
initConsensus(consensus);
+ gapcounts = new AlignmentAnnotation("Occupancy",
+ "Number of aligned positions",
+ new Annotation[1], 0f, alignment.getHeight(),
+ AlignmentAnnotation.BAR_GRAPH);
+ initGapCounts(gapcounts);
initComplementConsensus();
}
}
}
+ // these should be extracted from the view model - style and settings for
+ // derived annotation
+ private void initGapCounts(AlignmentAnnotation counts)
+ {
+ counts.hasText = false;
+ counts.autoCalculated = true;
+ counts.graph = AlignmentAnnotation.BAR_GRAPH;
+
+ if (showConsensus)
+ {
+ alignment.addAnnotation(counts);
+ }
+ }
+
private void initConservation()
{
if (showConservation)
*/
private boolean selectionIsDefinedGroup = false;
-
@Override
public boolean isSelectionDefinedGroup()
{