*/
Hashtable featuresDisplayed = null;
-
- boolean isDataset = false;
-
boolean antiAlias = false;
Rectangle explodedPosition;
{
if (!alignment.isNucleotide())
{
- conservation = new AlignmentAnnotation("Conservation",
- "Conservation of total alignment less than " + getConsPercGaps()
- + "% gaps", new Annotation[1], 0f, 11f,
- AlignmentAnnotation.BAR_GRAPH);
- conservation.hasText = true;
- conservation.autoCalculated = true;
-
- if (Cache.getDefault("SHOW_CONSERVATION", true))
- {
- alignment.addAnnotation(conservation);
- }
-
- if (Cache.getDefault("SHOW_QUALITY", true))
- {
- quality = new AlignmentAnnotation("Quality",
- "Alignment Quality based on Blosum62 scores",
- new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
- quality.hasText = true;
- quality.autoCalculated = true;
-
- alignment.addAnnotation(quality);
- }
+ showConservation=Cache.getDefault("SHOW_CONSERVATION", true);
+ showQuality=Cache.getDefault("SHOW_QUALITY", true);
showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION",
false);
-
- {
-
- }
- }
+ }
showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM",
true);
showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false);
normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO", false);
showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
- // TODO: add menu option action that nulls or creates consensus object
- // depending on if the user wants to see the annotation or not in a
- // specific alignment
+ 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;
-
- if (alignment.isNucleotide() && alignment.hasRNAStructure())
- {
- strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID",
- new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
- strucConsensus.hasText = true;
- strucConsensus.autoCalculated = true;
- }
-
- if (Cache.getDefault("SHOW_IDENTITY", true))
- {
- alignment.addAnnotation(consensus);
- // TODO: Make own if for structure
- if (alignment.isNucleotide() && alignment.hasRNAStructure())
- {
- alignment.addAnnotation(strucConsensus);
- }
- }
-
}
-
+ initAutoAnnotation();
if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
{
globalColourScheme = ColourSchemeProperty.getColour(alignment,