*/
package jalview.gui;
-import jalview.analysis.AnnotationSorter.SortOrder;
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.analysis.NJTree;
import jalview.api.AlignViewportI;
import jalview.bin.Cache;
-import jalview.datamodel.AlignmentAnnotation;
+import jalview.commands.CommandI;
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;
- SortOrder sortAnnotationsBy = null;
+ SequenceAnnotationOrder sortAnnotationsBy = null;
int charHeight;
* Keys are the feature types which are currently visible. Note: Values are
* not used!
*/
- Hashtable featuresDisplayed = null;
+ private Hashtable featuresDisplayed = null;
boolean antiAlias = false;
boolean gatherViewsHere = false;
- Stack historyList = new Stack();
+ Stack<CommandI> historyList = new Stack<CommandI>();
- Stack redoList = new Stack();
+ Stack<CommandI> redoList = new Stack<CommandI>();
int thresholdTextColour = 0;
Color textColour2 = Color.white;
- boolean rightAlignIds = false;
+ private boolean rightAlignIds = false;
/**
* 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)
}
wrapAlignment = Cache.getDefault("WRAP_ALIGNMENT", false);
- showUnconserved = Cache.getDefault("SHOW_UNCONSERVED",
- false);
+ showUnconserved = Cache.getDefault("SHOW_UNCONSERVED", false);
sortByTree = Cache.getDefault("SORT_BY_TREE", false);
- followSelection = Cache.getDefault("FOLLOW_SELECTIONS",
- true);
- sortAnnotationsBy = SortOrder.valueOf(Cache.getDefault(
- "SORT_ANNOTATIONS", SortOrder.SEQUENCE_AND_TYPE.name()));
+ followSelection = Cache.getDefault("FOLLOW_SELECTIONS", true);
+ sortAnnotationsBy = SequenceAnnotationOrder.valueOf(Cache.getDefault(
+ Preferences.SORT_ANNOTATIONS,
+ SequenceAnnotationOrder.NONE.name()));
+ showAutocalculatedAbove = Cache.getDefault(
+ Preferences.SHOW_AUTOCALC_ABOVE, false);
}
/**
*/
public boolean getShowAnnotation()
{
- return showAnnotation;
+ return isShowAnnotation();
}
/**
private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<String, AutoCalcSetting>();
+ private boolean showAutocalculatedAbove;
+
public AutoCalcSetting getCalcIdSettingsFor(String calcId)
{
return calcIdParams.get(calcId);
}
}
- protected SortOrder getSortAnnotationsBy()
+
+ public Hashtable getFeaturesDisplayed()
+ {
+ return featuresDisplayed;
+ }
+
+ public void setFeaturesDisplayed(Hashtable featuresDisplayed)
+ {
+ this.featuresDisplayed = featuresDisplayed;
+ }
+ protected SequenceAnnotationOrder getSortAnnotationsBy()
{
return sortAnnotationsBy;
}
- protected void setSortAnnotationsBy(SortOrder sortAnnotationsBy)
+ protected void setSortAnnotationsBy(SequenceAnnotationOrder sortAnnotationsBy)
{
this.sortAnnotationsBy = sortAnnotationsBy;
}
+
+ protected boolean isShowAutocalculatedAbove()
+ {
+ return showAutocalculatedAbove;
+ }
+
+ protected void setShowAutocalculatedAbove(boolean showAutocalculatedAbove)
+ {
+ this.showAutocalculatedAbove = showAutocalculatedAbove;
+ }
+
+ public boolean isShowAnnotation()
+ {
+ return showAnnotation;
+ }
+
+ public boolean isRightAlignIds()
+ {
+ return rightAlignIds;
+ }
+
+ public void setRightAlignIds(boolean rightAlignIds)
+ {
+ this.rightAlignIds = rightAlignIds;
+ }
}