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JAL-3285 add unmerged features to AlignViewport
[jalview.git]
/
src
/
jalview
/
gui
/
AlignViewport.java
diff --git
a/src/jalview/gui/AlignViewport.java
b/src/jalview/gui/AlignViewport.java
index
e0abfd9
..
0b40abd
100644
(file)
--- a/
src/jalview/gui/AlignViewport.java
+++ b/
src/jalview/gui/AlignViewport.java
@@
-254,14
+254,13
@@
public class AlignViewport extends AlignmentViewport
setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true);
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
// 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);
{
showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
showQuality = Cache.getDefault("SHOW_QUALITY", true);
@@
-273,13
+272,19
@@
public class AlignViewport extends AlignmentViewport
showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false);
normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO",
false);
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();
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);
? Preferences.DEFAULT_COLOUR_NUC
: Preferences.DEFAULT_COLOUR_PROT;
String schemeName = Cache.getProperty(colourProperty);
@@
-290,7
+295,7
@@
public class AlignViewport extends AlignmentViewport
ResidueColourScheme.NONE);
}
ColourSchemeI colourScheme = ColourSchemeProperty
ResidueColourScheme.NONE);
}
ColourSchemeI colourScheme = ColourSchemeProperty
- .getColourScheme(alignment, schemeName);
+ .getColourScheme(this, alignment, schemeName);
residueShading = new ResidueShader(colourScheme);
if (colourScheme instanceof UserColourScheme)
residueShading = new ResidueShader(colourScheme);
if (colourScheme instanceof UserColourScheme)
@@
-302,11
+307,11
@@
public class AlignViewport extends AlignmentViewport
if (residueShading != null)
{
if (residueShading != null)
{
- residueShading.setConsensus(hconsensus);
+ residueShading.setConsensus(hconsensus);
}
setColourAppliesToAllGroups(true);
}
}
setColourAppliesToAllGroups(true);
}
-
+
boolean validCharWidth;
/**
boolean validCharWidth;
/**
@@
-391,7
+396,7
@@
public class AlignViewport extends AlignmentViewport
/*
* replace mappings on our alignment
*/
/*
* replace mappings on our alignment
*/
- if (alignment != null && align != null)
+ if (alignment != null && align != null)
{
alignment.setCodonFrames(align.getCodonFrames());
}
{
alignment.setCodonFrames(align.getCodonFrames());
}
@@
-444,7
+449,7
@@
public class AlignViewport extends AlignmentViewport
}
/**
}
/**
- * 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
*
* @param selectedRegionOnly
* true to just return the contigs intersecting with the selected
@@
-464,8
+469,9
@@
public class AlignViewport extends AlignmentViewport
{
end = alignment.getWidth();
}
{
end = alignment.getWidth();
}
- return (alignment.getHiddenColumns().getVisContigsIterator(start, end,
- false));
+
+ return (alignment.getHiddenColumns().getVisContigsIterator(start,
+ end, false));
}
/**
}
/**
@@
-515,7
+521,7
@@
public class AlignViewport extends AlignmentViewport
}
public boolean followSelection = true;
}
public boolean followSelection = true;
-
+
/**
* @return true if view selection should always follow the selections
* broadcast by other selection sources
/**
* @return true if view selection should always follow the selections
* broadcast by other selection sources
@@
-580,18
+586,20
@@
public class AlignViewport extends AlignmentViewport
return StructureSelectionManager
.getStructureSelectionManager(Desktop.instance);
}
return StructureSelectionManager
.getStructureSelectionManager(Desktop.instance);
}
-
+
@Override
public boolean isNormaliseSequenceLogo()
{
return normaliseSequenceLogo;
}
@Override
public boolean isNormaliseSequenceLogo()
{
return normaliseSequenceLogo;
}
- public void setNormaliseSequenceLogo(boolean state)
+ @Override
+public void setNormaliseSequenceLogo(boolean state)
{
normaliseSequenceLogo = state;
}
{
normaliseSequenceLogo = state;
}
+
/**
*
* @return true if alignment characters should be displayed
/**
*
* @return true if alignment characters should be displayed
@@
-601,7
+609,7
@@
public class AlignViewport extends AlignmentViewport
{
return validCharWidth;
}
{
return validCharWidth;
}
-
+
private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<>();
public AutoCalcSetting getCalcIdSettingsFor(String calcId)
private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<>();
public AutoCalcSetting getCalcIdSettingsFor(String calcId)