*/
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 showAnnotation = true;
- SortOrder sortAnnotationsBy = null;
+ SequenceAnnotationOrder sortAnnotationsBy = null;
int charHeight;
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;
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);
}
/**
private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<String, AutoCalcSetting>();
+ private boolean showAutocalculatedAbove;
+
public AutoCalcSetting getCalcIdSettingsFor(String calcId)
{
return calcIdParams.get(calcId);
}
}
- protected SortOrder getSortAnnotationsBy()
+ 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;
+ }
}