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JAL-2629 can now choose number of jackhmmer iterations
[jalview.git]
/
src
/
jalview
/
gui
/
AlignViewport.java
diff --git
a/src/jalview/gui/AlignViewport.java
b/src/jalview/gui/AlignViewport.java
index
15c0971
..
0b40abd
100644
(file)
--- a/
src/jalview/gui/AlignViewport.java
+++ b/
src/jalview/gui/AlignViewport.java
@@
-79,7
+79,7
@@
public class AlignViewport extends AlignmentViewport
private Rectangle explodedGeometry;
private Rectangle explodedGeometry;
- String viewName;
+ private String viewName;
/*
* Flag set true on the view that should 'gather' multiple views of the same
/*
* Flag set true on the view that should 'gather' multiple views of the same
@@
-254,16
+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);
- if (Cache.getDefault("NORMALISE_GAPS", 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);
@@
-275,13
+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);
@@
-292,7
+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)
@@
-304,10
+307,11
@@
public class AlignViewport extends AlignmentViewport
if (residueShading != null)
{
if (residueShading != null)
{
- residueShading.setConsensus(hconsensus);
+ residueShading.setConsensus(hconsensus);
}
}
+ setColourAppliesToAllGroups(true);
}
}
-
+
boolean validCharWidth;
/**
boolean validCharWidth;
/**
@@
-392,7
+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());
}
@@
-445,7
+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
@@
-465,8
+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));
}
/**
}
/**
@@
-516,7
+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
@@
-581,18
+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
@@
-602,7
+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)
@@
-797,7
+804,7
@@
public class AlignViewport extends AlignmentViewport
AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
newAlignFrame.setTitle(title);
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 }));
.formatMessage("label.successfully_loaded_file", new Object[]
{ title }));
@@
-1034,4
+1041,14
@@
public class AlignViewport extends AlignmentViewport
}
fr.setTransparency(featureSettings.getTransparency());
}
}
fr.setTransparency(featureSettings.getTransparency());
}
+
+ public String getViewName()
+ {
+ return viewName;
+ }
+
+ public void setViewName(String viewName)
+ {
+ this.viewName = viewName;
+ }
}
}