import jalview.api.AlignViewportI;
import jalview.bin.Cache;
import jalview.commands.CommandI;
-import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
boolean showSequenceFeatures = false;
- boolean showAnnotation = true;
+ private boolean showAnnotation = true;
SequenceAnnotationOrder sortAnnotationsBy = null;
* Keys are the feature types which are currently visible. Note: Values are
* not used!
*/
- Hashtable featuresDisplayed = null;
+ private Hashtable featuresDisplayed = null;
boolean antiAlias = false;
Color textColour2 = Color.white;
- boolean rightAlignIds = false;
+ private boolean rightAlignIds = false;
+ private AnnotationColumnSelection currentAnnotationColumnSelectionState;
/**
* Creates a new AlignViewport object.
*
antiAlias = Cache.getDefault("ANTI_ALIAS", false);
showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
- showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
+ setShowAnnotation(Cache.getDefault("SHOW_ANNOTATIONS", true));
- rightAlignIds = Cache.getDefault("RIGHT_ALIGN_IDS", false);
+ setRightAlignIds(Cache.getDefault("RIGHT_ALIGN_IDS", false));
centreColumnLabels = Cache.getDefault("CENTRE_COLUMN_LABELS", false);
autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
false);
showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
- consensus = new AlignmentAnnotation("Consensus", "PID",
- new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
- consensus.hasText = true;
- consensus.autoCalculated = true;
}
initAutoAnnotation();
if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
*/
public boolean getShowAnnotation()
{
- return showAnnotation;
+ return isShowAnnotation();
}
/**
}
}
+
+ public Hashtable getFeaturesDisplayed()
+ {
+ return featuresDisplayed;
+ }
+
+ public void setFeaturesDisplayed(Hashtable featuresDisplayed)
+ {
+ this.featuresDisplayed = featuresDisplayed;
+ }
protected SequenceAnnotationOrder getSortAnnotationsBy()
{
return sortAnnotationsBy;
{
this.showAutocalculatedAbove = showAutocalculatedAbove;
}
+
+ public boolean isShowAnnotation()
+ {
+ return showAnnotation;
+ }
+
+ public boolean isRightAlignIds()
+ {
+ return rightAlignIds;
+ }
+
+ public void setRightAlignIds(boolean rightAlignIds)
+ {
+ this.rightAlignIds = rightAlignIds;
+ }
+
+ public AnnotationColumnSelection getCurrentAnnotationColumnSelectionState()
+ {
+ return currentAnnotationColumnSelectionState;
+ }
+
+ public void setCurrentAnnotationColumnSelectionState(
+ AnnotationColumnSelection currentAnnotationColumnSelectionState)
+ {
+ this.currentAnnotationColumnSelectionState = currentAnnotationColumnSelectionState;
+ }
}