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JAL-2423 refactored method to build panel title for tree either
[jalview.git]
/
src
/
jalview
/
viewmodel
/
AlignmentViewport.java
diff --git
a/src/jalview/viewmodel/AlignmentViewport.java
b/src/jalview/viewmodel/AlignmentViewport.java
index
1352cf2
..
0c470fe
100644
(file)
--- a/
src/jalview/viewmodel/AlignmentViewport.java
+++ b/
src/jalview/viewmodel/AlignmentViewport.java
@@
-44,9
+44,7
@@
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.renderer.ResidueShader;
import jalview.renderer.ResidueShaderI;
import jalview.datamodel.SequenceI;
import jalview.renderer.ResidueShader;
import jalview.renderer.ResidueShaderI;
-import jalview.schemes.Blosum62ColourScheme;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeI;
-import jalview.schemes.PIDColourScheme;
import jalview.structure.CommandListener;
import jalview.structure.StructureSelectionManager;
import jalview.structure.VamsasSource;
import jalview.structure.CommandListener;
import jalview.structure.StructureSelectionManager;
import jalview.structure.VamsasSource;
@@
-599,7
+597,7
@@
public abstract class AlignmentViewport implements AlignViewportI,
protected boolean ignoreGapsInConsensusCalculation = false;
protected boolean ignoreGapsInConsensusCalculation = false;
- protected ResidueShaderI globalColourScheme;
+ protected ResidueShaderI residueShading;
@Override
public void setGlobalColourScheme(ColourSchemeI cs)
@Override
public void setGlobalColourScheme(ColourSchemeI cs)
@@
-607,37
+605,32
@@
public abstract class AlignmentViewport implements AlignViewportI,
// TODO: logic refactored from AlignFrame changeColour -
// TODO: autorecalc stuff should be changed to rely on the worker system
// check to see if we should implement a changeColour(cs) method rather than
// TODO: logic refactored from AlignFrame changeColour -
// TODO: autorecalc stuff should be changed to rely on the worker system
// check to see if we should implement a changeColour(cs) method rather than
- // put th logic in here
+ // put the logic in here
// - means that caller decides if they want to just modify state and defer
// calculation till later or to do all calculations in thread.
// via changecolour
/*
// - means that caller decides if they want to just modify state and defer
// calculation till later or to do all calculations in thread.
// via changecolour
/*
- * only instantiate collection colour scheme once, thereafter update it
+ * only instantiate alignment colouring once, thereafter update it;
* this means that any conservation or PID threshold settings
* persist when the alignment colour scheme is changed
*/
* this means that any conservation or PID threshold settings
* persist when the alignment colour scheme is changed
*/
- if (globalColourScheme == null)
+ if (residueShading == null)
{
{
- globalColourScheme = new ResidueShader();
+ residueShading = new ResidueShader(viewStyle);
}
}
- globalColourScheme.setColourScheme(cs);
+ residueShading.setColourScheme(cs);
- // boolean recalc = false;
- // TODO: do threshold and increment belong in ViewStyle or colour scheme?
- // problem: groups need this but do not currently have a ViewStyle
+ // TODO: do threshold and increment belong in ViewStyle or ResidueShader?
+ // ...problem: groups need these, but do not currently have a ViewStyle
if (cs != null)
{
if (cs != null)
{
- if (getConservationSelected() || getAbovePIDThreshold()
- || cs instanceof PIDColourScheme
- || cs instanceof Blosum62ColourScheme)
+ if (getConservationSelected())
{
{
- globalColourScheme.setConservation(hconservation);
- globalColourScheme
- .setConservationApplied(getConservationSelected());
+ residueShading.setConservation(hconservation);
}
}
- globalColourScheme.alignmentChanged(alignment, hiddenRepSequences);
+ residueShading.alignmentChanged(alignment, hiddenRepSequences);
}
/*
}
/*
@@
-665,14
+658,14
@@
public abstract class AlignmentViewport implements AlignViewportI,
@Override
public ColourSchemeI getGlobalColourScheme()
{
@Override
public ColourSchemeI getGlobalColourScheme()
{
- return globalColourScheme == null ? null : globalColourScheme
+ return residueShading == null ? null : residueShading
.getColourScheme();
}
@Override
.getColourScheme();
}
@Override
- public ResidueShaderI getViewportColourScheme()
+ public ResidueShaderI getResidueShading()
{
{
- return globalColourScheme;
+ return residueShading;
}
protected AlignmentAnnotation consensus;
}
protected AlignmentAnnotation consensus;
@@
-932,7
+925,7
@@
public abstract class AlignmentViewport implements AlignViewportI,
hconsensus = null;
hcomplementConsensus = null;
// colour scheme may hold reference to consensus
hconsensus = null;
hcomplementConsensus = null;
// colour scheme may hold reference to consensus
- globalColourScheme = null;
+ residueShading = null;
// TODO remove listeners from changeSupport?
changeSupport = null;
setAlignment(null);
// TODO remove listeners from changeSupport?
changeSupport = null;
setAlignment(null);
@@
-1080,7
+1073,8
@@
public abstract class AlignmentViewport implements AlignViewportI,
}
/**
}
/**
- * Set the selection group for this window.
+ * Set the selection group for this window. Also sets the current alignment as
+ * the context for the group, if it does not already have one.
*
* @param sg
* - group holding references to sequences in this alignment view
*
* @param sg
* - group holding references to sequences in this alignment view
@@
-1090,6
+1084,10
@@
public abstract class AlignmentViewport implements AlignViewportI,
public void setSelectionGroup(SequenceGroup sg)
{
selectionGroup = sg;
public void setSelectionGroup(SequenceGroup sg)
{
selectionGroup = sg;
+ if (sg != null && sg.getContext() == null)
+ {
+ sg.setContext(alignment);
+ }
}
public void setHiddenColumns(ColumnSelection colsel)
}
public void setHiddenColumns(ColumnSelection colsel)
@@
-1202,9
+1200,9
@@
public abstract class AlignmentViewport implements AlignViewportI,
if (ap != null)
{
updateConsensus(ap);
if (ap != null)
{
updateConsensus(ap);
- if (globalColourScheme != null)
+ if (residueShading != null)
{
{
- globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
+ residueShading.setThreshold(residueShading.getThreshold(),
ignoreGapsInConsensusCalculation);
}
}
ignoreGapsInConsensusCalculation);
}
}
@@
-1840,7
+1838,7
@@
public abstract class AlignmentViewport implements AlignViewportI,
selectionGroup.setEndRes(alWidth - 1);
}
selectionGroup.setEndRes(alWidth - 1);
}
- resetAllColourSchemes();
+ updateAllColourSchemes();
calculator.restartWorkers();
// alignment.adjustSequenceAnnotations();
}
calculator.restartWorkers();
// alignment.adjustSequenceAnnotations();
}
@@
-1848,17
+1846,17
@@
public abstract class AlignmentViewport implements AlignViewportI,
/**
* reset scope and do calculations for all applied colourschemes on alignment
*/
/**
* reset scope and do calculations for all applied colourschemes on alignment
*/
- void resetAllColourSchemes()
+ void updateAllColourSchemes()
{
{
- ResidueShaderI cs = globalColourScheme;
- if (cs != null)
+ ResidueShaderI rs = residueShading;
+ if (rs != null)
{
{
- cs.alignmentChanged(alignment, hiddenRepSequences);
+ rs.alignmentChanged(alignment, hiddenRepSequences);
- cs.setConsensus(hconsensus);
- if (cs.conservationApplied())
+ rs.setConsensus(hconsensus);
+ if (rs.conservationApplied())
{
{
- cs.setConservation(Conservation.calculateConservation("All",
+ rs.setConservation(Conservation.calculateConservation("All",
alignment.getSequences(), 0, alignment.getWidth(), false,
getConsPercGaps(), false));
}
alignment.getSequences(), 0, alignment.getWidth(), false,
getConsPercGaps(), false));
}
@@
-2432,6
+2430,11
@@
public abstract class AlignmentViewport implements AlignViewportI,
public void setViewStyle(ViewStyleI settingsForView)
{
viewStyle = new ViewStyle(settingsForView);
public void setViewStyle(ViewStyleI settingsForView)
{
viewStyle = new ViewStyle(settingsForView);
+ if (residueShading != null)
+ {
+ residueShading.setConservationApplied(settingsForView
+ .isConservationColourSelected());
+ }
}
@Override
}
@Override