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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
39ded7f
..
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
@@
-92,12
+92,6
@@
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.
*
@@
-260,18
+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);
- AlignmentI al = getAlignment();
-
- if (Cache.getDefault("NORMALISE_GAPS", true))
- {
- al.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 (consensusProfiles == null && !isDataset)
+ if (hconsensus == null && !isDataset)
{
{
- if (!al.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);
@@
-295,7
+284,7
@@
public class AlignViewport extends AlignmentViewport
initAutoAnnotation();
// initInformation();
initAutoAnnotation();
// initInformation();
- String colourProperty = al.isNucleotide()
+ 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);
@@
-306,7
+295,7
@@
public class AlignViewport extends AlignmentViewport
ResidueColourScheme.NONE);
}
ColourSchemeI colourScheme = ColourSchemeProperty
ResidueColourScheme.NONE);
}
ColourSchemeI colourScheme = ColourSchemeProperty
- .getColourScheme(al, schemeName);
+ .getColourScheme(this, alignment, schemeName);
residueShading = new ResidueShader(colourScheme);
if (colourScheme instanceof UserColourScheme)
residueShading = new ResidueShader(colourScheme);
if (colourScheme instanceof UserColourScheme)
@@
-318,9
+307,12
@@
public class AlignViewport extends AlignmentViewport
if (residueShading != null)
{
if (residueShading != null)
{
- residueShading.setConsensus(consensusProfiles);
+ residueShading.setConsensus(hconsensus);
}
}
+ setColourAppliesToAllGroups(true);
}
}
+
+ boolean validCharWidth;
/**
* {@inheritDoc}
/**
* {@inheritDoc}
@@
-404,9
+396,9
@@
public class AlignViewport extends AlignmentViewport
/*
* replace mappings on our alignment
*/
/*
* replace mappings on our alignment
*/
- if (getAlignment() != null && align != null)
+ if (alignment != null && align != null)
{
{
- getAlignment().setCodonFrames(align.getCodonFrames());
+ alignment.setCodonFrames(align.getCodonFrames());
}
}
}
}
@@
-475,11
+467,11
@@
public class AlignViewport extends AlignmentViewport
}
else
{
}
else
{
- end = getAlignment().getWidth();
+ end = alignment.getWidth();
}
}
- return getAlignment().getHiddenColumns().getVisContigsIterator(start,
- end, false);
+ return (alignment.getHiddenColumns().getVisContigsIterator(start,
+ end, false));
}
/**
}
/**
@@
-528,6
+520,8
@@
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
@@
-592,6
+586,19
@@
public class AlignViewport extends AlignmentViewport
return StructureSelectionManager
.getStructureSelectionManager(Desktop.instance);
}
return StructureSelectionManager
.getStructureSelectionManager(Desktop.instance);
}
+
+ @Override
+ public boolean isNormaliseSequenceLogo()
+ {
+ return normaliseSequenceLogo;
+ }
+
+ @Override
+public void setNormaliseSequenceLogo(boolean state)
+ {
+ normaliseSequenceLogo = state;
+ }
+
/**
*
/**
*
@@
-602,6
+609,8
@@
public class AlignViewport extends AlignmentViewport
{
return validCharWidth;
}
{
return validCharWidth;
}
+
+ private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<>();
public AutoCalcSetting getCalcIdSettingsFor(String calcId)
{
public AutoCalcSetting getCalcIdSettingsFor(String calcId)
{
@@
-795,7
+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 }));
@@
-1033,4
+1042,13
@@
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;
+ }
}
}