git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
JAL-2295 tweak order and wording of Superpose menu items and tooltip
[jalview.git]
/
src
/
jalview
/
viewmodel
/
AlignmentViewport.java
diff --git
a/src/jalview/viewmodel/AlignmentViewport.java
b/src/jalview/viewmodel/AlignmentViewport.java
index
230864e
..
94d0dd1
100644
(file)
--- a/
src/jalview/viewmodel/AlignmentViewport.java
+++ b/
src/jalview/viewmodel/AlignmentViewport.java
@@
-20,6
+20,17
@@
*/
package jalview.viewmodel;
*/
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.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.analysis.Conservation;
import jalview.api.AlignCalcManagerI;
@@
-57,17
+68,6
@@
import jalview.workers.ComplementConsensusThread;
import jalview.workers.ConsensusThread;
import jalview.workers.StrucConsensusThread;
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
/**
* base class holding visualization and analysis attributes and common logic for
* an active alignment view displayed in the GUI
@@
-672,6
+672,8
@@
public abstract class AlignmentViewport implements AlignViewportI,
protected AlignmentAnnotation complementConsensus;
protected AlignmentAnnotation complementConsensus;
+ protected AlignmentAnnotation gapcounts;
+
protected AlignmentAnnotation strucConsensus;
protected AlignmentAnnotation conservation;
protected AlignmentAnnotation strucConsensus;
protected AlignmentAnnotation conservation;
@@
-774,6
+776,12
@@
public abstract class AlignmentViewport implements AlignViewportI,
}
@Override
}
@Override
+ public AlignmentAnnotation getAlignmentGapAnnotation()
+ {
+ return gapcounts;
+ }
+
+ @Override
public AlignmentAnnotation getComplementConsensusAnnotation()
{
return complementConsensus;
public AlignmentAnnotation getComplementConsensusAnnotation()
{
return complementConsensus;
@@
-813,7
+821,7
@@
public abstract class AlignmentViewport implements AlignViewportI,
public void updateConsensus(final AlignmentViewPanel ap)
{
// see note in mantis : issue number 8585
public void updateConsensus(final AlignmentViewPanel ap)
{
// see note in mantis : issue number 8585
- if (consensus == null || !autoCalculateConsensus)
+ if ((consensus == null || gapcounts == null) || !autoCalculateConsensus)
{
return;
}
{
return;
}
@@
-1073,7
+1081,8
@@
public abstract class AlignmentViewport implements AlignViewportI,
}
/**
}
/**
- * Set the selection group for this window.
+ * Set the selection group for this window. Also sets the current alignment as
+ * the context for the group, if it does not already have one.
*
* @param sg
* - group holding references to sequences in this alignment view
*
* @param sg
* - group holding references to sequences in this alignment view
@@
-1083,6
+1092,10
@@
public abstract class AlignmentViewport implements AlignViewportI,
public void setSelectionGroup(SequenceGroup sg)
{
selectionGroup = sg;
public void setSelectionGroup(SequenceGroup sg)
{
selectionGroup = sg;
+ if (sg != null && sg.getContext() == null)
+ {
+ sg.setContext(alignment);
+ }
}
public void setHiddenColumns(ColumnSelection colsel)
}
public void setHiddenColumns(ColumnSelection colsel)
@@
-1887,6
+1900,11
@@
public abstract class AlignmentViewport implements AlignViewportI,
consensus = new AlignmentAnnotation("Consensus", "PID",
new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
initConsensus(consensus);
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();
}
initComplementConsensus();
}
@@
-1939,6
+1957,20
@@
public abstract class AlignmentViewport implements AlignViewportI,
}
}
}
}
+ // 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 void initConservation()
{
if (showConservation)
@@
-2425,6
+2457,11
@@
public abstract class AlignmentViewport implements AlignViewportI,
public void setViewStyle(ViewStyleI settingsForView)
{
viewStyle = new ViewStyle(settingsForView);
public void setViewStyle(ViewStyleI settingsForView)
{
viewStyle = new ViewStyle(settingsForView);
+ if (residueShading != null)
+ {
+ residueShading.setConservationApplied(settingsForView
+ .isConservationColourSelected());
+ }
}
@Override
}
@Override
@@
-2809,7
+2846,6
@@
public abstract class AlignmentViewport implements AlignViewportI,
*/
private boolean selectionIsDefinedGroup = false;
*/
private boolean selectionIsDefinedGroup = false;
-
@Override
public boolean isSelectionDefinedGroup()
{
@Override
public boolean isSelectionDefinedGroup()
{