private Rectangle explodedGeometry;
- String viewName;
+ private String viewName;
/*
* Flag set true on the view that should 'gather' multiple views of the same
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.instance);
}
-
+
@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)
AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
newAlignFrame.setTitle(title);
- newAlignFrame.statusBar.setText(MessageManager
+ newAlignFrame.setStatus(MessageManager
.formatMessage("label.successfully_loaded_file", new Object[]
{ title }));
}
fr.setTransparency(featureSettings.getTransparency());
}
+
+ public String getViewName()
+ {
+ return viewName;
+ }
+
+ public void setViewName(String viewName)
+ {
+ this.viewName = viewName;
+ }
}