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Merge branch 'develop' into developtomchmmer
[jalview.git]
/
src
/
jalview
/
gui
/
AlignViewport.java
diff --git
a/src/jalview/gui/AlignViewport.java
b/src/jalview/gui/AlignViewport.java
index
bc668fd
..
847084d
100644
(file)
--- a/
src/jalview/gui/AlignViewport.java
+++ b/
src/jalview/gui/AlignViewport.java
@@
-92,6
+92,12
@@
public class AlignViewport extends AlignmentViewport
private AnnotationColumnChooser annotationColumnSelectionState;
private AnnotationColumnChooser annotationColumnSelectionState;
+ boolean validCharWidth;
+
+ public boolean followSelection = true;
+
+ private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<>();
+
/**
* Creates a new AlignViewport object.
*
/**
* Creates a new AlignViewport object.
*
@@
-254,14
+260,18
@@
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));
+ AlignmentI al = getAlignment();
+
+ if (Cache.getDefault("NORMALISE_GAPS", true))
+ {
+ al.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 (consensusProfiles == null && !isDataset)
{
{
- if (!alignment.isNucleotide())
+ if (!al.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
+283,19
@@
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 = al.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);
@@
-302,13
+318,11
@@
public class AlignViewport extends AlignmentViewport
if (residueShading != null)
{
if (residueShading != null)
{
- residueShading.setConsensus(hconsensus);
+ residueShading.setConsensus(consensusProfiles);
}
setColourAppliesToAllGroups(true);
}
}
setColourAppliesToAllGroups(true);
}
- boolean validCharWidth;
-
/**
* {@inheritDoc}
*/
/**
* {@inheritDoc}
*/
@@
-391,9
+405,9
@@
public class AlignViewport extends AlignmentViewport
/*
* replace mappings on our alignment
*/
/*
* replace mappings on our alignment
*/
- if (alignment != null && align != null)
+ if (getAlignment() != null && align != null)
{
{
- alignment.setCodonFrames(align.getCodonFrames());
+ getAlignment().setCodonFrames(align.getCodonFrames());
}
}
}
}
@@
-444,7
+458,7
@@
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
@@
-462,10
+476,11
@@
public class AlignViewport extends AlignmentViewport
}
else
{
}
else
{
- end = alignment.getWidth();
+ end = getAlignment().getWidth();
}
}
- return (alignment.getHiddenColumns().getVisContigsIterator(start, end,
- false));
+
+ return getAlignment().getHiddenColumns().getVisContigsIterator(start,
+ end, false);
}
/**
}
/**
@@
-514,8
+529,6
@@
public class AlignViewport extends AlignmentViewport
return false;
}
return false;
}
- 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
@@
-581,17
+594,6
@@
public class AlignViewport extends AlignmentViewport
.getStructureSelectionManager(Desktop.instance);
}
.getStructureSelectionManager(Desktop.instance);
}
- @Override
- public boolean isNormaliseSequenceLogo()
- {
- return normaliseSequenceLogo;
- }
-
- public void setNormaliseSequenceLogo(boolean state)
- {
- normaliseSequenceLogo = state;
- }
-
/**
*
* @return true if alignment characters should be displayed
/**
*
* @return true if alignment characters should be displayed
@@
-602,8
+604,6
@@
public class AlignViewport extends AlignmentViewport
return validCharWidth;
}
return validCharWidth;
}
- private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<>();
-
public AutoCalcSetting getCalcIdSettingsFor(String calcId)
{
return calcIdParams.get(calcId);
public AutoCalcSetting getCalcIdSettingsFor(String calcId)
{
return calcIdParams.get(calcId);