*/
package jalview.gui;
+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;
+ SequenceAnnotationOrder sortAnnotationsBy = null;
+
int charHeight;
int charWidth;
* 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;
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 = jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false);
- showUnconserved = jalview.bin.Cache.getDefault("SHOW_UNCONSERVED",
- false);
- sortByTree = jalview.bin.Cache.getDefault("SORT_BY_TREE", false);
- followSelection = jalview.bin.Cache.getDefault("FOLLOW_SELECTIONS",
- true);
+ wrapAlignment = Cache.getDefault("WRAP_ALIGNMENT", false);
+ showUnconserved = Cache.getDefault("SHOW_UNCONSERVED", false);
+ sortByTree = Cache.getDefault("SORT_BY_TREE", false);
+ 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);
}
/**
{
// TODO: JAL-1126
if (historyList == null || redoList == null)
+ {
return new long[]
{ -1, -1 };
+ }
return new long[]
{ historyList.hashCode(), this.redoList.hashCode() };
}
centreColumnLabels = centrecolumnlabels;
}
-
/**
* enable or disable the display of Database Cross References in the sequence
* ID tooltip
Vector pdbs = alignment.getSequenceAt(i).getDatasetSequence()
.getPDBId();
if (pdbs == null)
+ {
continue;
+ }
SequenceI sq;
for (int p = 0; p < pdbs.size(); p++)
{
if (p1.getId().equals(pdb.getId()))
{
if (!seqs.contains(sq = alignment.getSequenceAt(i)))
+ {
seqs.add(sq);
+ }
continue;
}
private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<String, AutoCalcSetting>();
+ private boolean showAutocalculatedAbove;
+
public AutoCalcSetting getCalcIdSettingsFor(String calcId)
{
return calcIdParams.get(calcId);
Cache.log.debug("trigger update for " + calcId);
}
}
+
+
+ public Hashtable getFeaturesDisplayed()
+ {
+ return featuresDisplayed;
+ }
+
+ public void setFeaturesDisplayed(Hashtable featuresDisplayed)
+ {
+ this.featuresDisplayed = featuresDisplayed;
+ }
+ protected SequenceAnnotationOrder getSortAnnotationsBy()
+ {
+ return sortAnnotationsBy;
+ }
+
+ protected void setSortAnnotationsBy(SequenceAnnotationOrder sortAnnotationsBy)
+ {
+ this.sortAnnotationsBy = sortAnnotationsBy;
+ }
+
+ protected boolean isShowAutocalculatedAbove()
+ {
+ return showAutocalculatedAbove;
+ }
+
+ protected void setShowAutocalculatedAbove(boolean showAutocalculatedAbove)
+ {
+ this.showAutocalculatedAbove = showAutocalculatedAbove;
+ }
}