import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.FeatureMatcherSetI;
import jalview.renderer.ResidueShader;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true);
- alignment
- .setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
+ alignment.setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
// We must set conservation and consensus before setting colour,
// as Blosum and Clustal require this to be done
- if (hconsensus == null && !isDataset)
+ if (hconsensus == null && !isDataset)
{
- if (!alignment.isNucleotide())
+ if (!alignment.isNucleotide())
{
showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
showQuality = Cache.getDefault("SHOW_QUALITY", true);
showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false);
normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO",
false);
+ // for now, use consensus options for Information till it gets its own
+ setShowHMMSequenceLogo(showSequenceLogo);
+ setNormaliseHMMSequenceLogo(normaliseSequenceLogo);
+ setShowInformationHistogram(showConsensusHistogram);
showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true);
}
initAutoAnnotation();
- String colourProperty = alignment.isNucleotide()
+ // initInformation();
+
+ String colourProperty = alignment.isNucleotide()
? Preferences.DEFAULT_COLOUR_NUC
: Preferences.DEFAULT_COLOUR_PROT;
String schemeName = Cache.getProperty(colourProperty);
if (residueShading != null)
{
- residueShading.setConsensus(hconsensus);
+ residueShading.setConsensus(hconsensus);
}
setColourAppliesToAllGroups(true);
}
-
+
boolean validCharWidth;
/**
/*
* replace mappings on our alignment
*/
- if (alignment != null && align != null)
+ if (alignment != null && align != null)
{
alignment.setCodonFrames(align.getCodonFrames());
}
}
/**
- * returns the visible column regions of the alignment
+ * Returns an iterator over the visible column regions of the alignment
*
* @param selectedRegionOnly
* true to just return the contigs intersecting with the selected
{
end = alignment.getWidth();
}
- return (alignment.getHiddenColumns().getVisContigsIterator(start, end,
- false));
+
+ return (alignment.getHiddenColumns().getVisContigsIterator(start,
+ end, false));
}
/**
}
public boolean followSelection = true;
-
+
/**
* @return true if view selection should always follow the selections
* broadcast by other selection sources
return StructureSelectionManager
.getStructureSelectionManager(Desktop.getInstance());
}
-
+
@Override
public boolean isNormaliseSequenceLogo()
{
return normaliseSequenceLogo;
}
- public void setNormaliseSequenceLogo(boolean state)
+ @Override
+public void setNormaliseSequenceLogo(boolean state)
{
normaliseSequenceLogo = state;
}
+
/**
*
* @return true if alignment characters should be displayed
{
return validCharWidth;
}
-
+
private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<>();
public AutoCalcSetting getCalcIdSettingsFor(String calcId)
{
FeatureColourI preferredColour = featureSettings
.getFeatureColour(type);
+ FeatureMatcherSetI preferredFilters = featureSettings
+ .getFeatureFilters(type);
+
FeatureColourI origColour = fr.getFeatureStyle(type);
if (!mergeOnly || (!origRenderOrder.contains(type)
|| origColour == null
{
fr.setColour(type, preferredColour);
}
+ if (preferredFilters != null
+ && (!mergeOnly || fr.getFeatureFilter(type) != null))
+ {
+ fr.setFeatureFilter(type, preferredFilters);
+ }
if (featureSettings.isFeatureDisplayed(type))
{
displayed.setVisible(type);