git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
JAL-3148 show/hide features on structure independent of alignment
[jalview.git]
/
src
/
jalview
/
structures
/
models
/
AAStructureBindingModel.java
diff --git
a/src/jalview/structures/models/AAStructureBindingModel.java
b/src/jalview/structures/models/AAStructureBindingModel.java
index
fc82827
..
0b19d51
100644
(file)
--- a/
src/jalview/structures/models/AAStructureBindingModel.java
+++ b/
src/jalview/structures/models/AAStructureBindingModel.java
@@
-46,6
+46,8
@@
import java.util.Arrays;
import java.util.BitSet;
import java.util.List;
import java.util.BitSet;
import java.util.List;
+import org.springframework.web.filter.ShallowEtagHeaderFilter;
+
/**
*
* A base class to hold common function for protein structure model binding.
/**
*
* A base class to hold common function for protein structure model binding.
@@
-74,6
+76,12
@@
public abstract class AAStructureBindingModel
*/
private ColourSchemeI colourScheme;
*/
private ColourSchemeI colourScheme;
+ /*
+ * flag for whether to include feature colouring, if using a Jalview colour
+ * scheme (independently of whether features are shown on alignment)
+ */
+ private boolean showFeatures;
+
private StructureSelectionManager ssm;
/*
private StructureSelectionManager ssm;
/*
@@
-350,7
+358,7
@@
public abstract class AAStructureBindingModel
public void setColourBy(ColourBy option)
{
public void setColourBy(ColourBy option)
{
- colourBy = option;
+ colourBy = option;
}
public boolean isColourBySequence()
}
public boolean isColourBySequence()
@@
-360,7
+368,7
@@
public abstract class AAStructureBindingModel
protected boolean isJalviewColourScheme()
{
protected boolean isJalviewColourScheme()
{
- return colourBy == ColourBy.Jalview;
+ return colourBy == ColourBy.Jalview;
}
protected void addSequenceAndChain(int pe, SequenceI[] seq,
}
protected void addSequenceAndChain(int pe, SequenceI[] seq,
@@
-773,19
+781,22
@@
public abstract class AAStructureBindingModel
*
* @param cs
* @param ap
*
* @param cs
* @param ap
+ * @param showFeats
*/
*/
- public void setJalviewColourScheme(ColourSchemeI cs, AlignmentViewPanel ap)
+ public void setJalviewColourScheme(ColourSchemeI cs, AlignmentViewPanel ap,
+ boolean showFeats)
{
colourBy = ColourBy.Jalview;
colourScheme = cs;
{
colourBy = ColourBy.Jalview;
colourScheme = cs;
+ showFeatures = showFeats;
- if (cs == null || cs.isSimple())
+ if (!showFeats && (cs == null || cs.isSimple()))
{
setSimpleColourScheme(cs);
}
else
{
{
setSimpleColourScheme(cs);
}
else
{
- colourBySequence(ap, new SequenceRenderer(ap.getAlignViewport(), cs));
+ colourBySequence(ap, new SequenceRenderer(ap.getAlignViewport(), cs), showFeatures);
}
}
}
}
@@
-819,7
+830,7
@@
public abstract class AAStructureBindingModel
public abstract void setBackgroundColour(Color col);
protected abstract StructureMappingcommandSet[] getColourBySequenceCommands(
public abstract void setBackgroundColour(Color col);
protected abstract StructureMappingcommandSet[] getColourBySequenceCommands(
- String[] files, SequenceRendererI sr, AlignmentViewPanel avp);
+ String[] files, SequenceRendererI sr, AlignmentViewPanel avp, boolean showFeatures);
protected abstract void colourBySequence(
StructureMappingcommandSet[] colourBySequenceCommands);
protected abstract void colourBySequence(
StructureMappingcommandSet[] colourBySequenceCommands);
@@
-831,20
+842,21
@@
public abstract class AAStructureBindingModel
public void colourByCharge()
{
public void colourByCharge()
{
- colourBy = ColourBy.ChargeAndCysteine;
+ colourBy = ColourBy.ChargeAndCysteine;
}
}
- public void colourBySequence(AlignmentViewPanel alignmentv)
+ public void colourBySequence(AlignmentViewPanel alignmentv, boolean showFeatures)
{
{
- colourBySequence(alignmentv, alignmentv.getSequenceRenderer());
+ colourBySequence(alignmentv, alignmentv.getSequenceRenderer(), showFeatures);
}
/**
* Colours any structures associated with sequences in the given alignment view
* using the getFeatureRenderer() and getSequenceRenderer() renderers
*/
}
/**
* Colours any structures associated with sequences in the given alignment view
* using the getFeatureRenderer() and getSequenceRenderer() renderers
*/
- public void colourBySequence(AlignmentViewPanel alignmentv, SequenceRendererI sr)
+ public void colourBySequence(AlignmentViewPanel alignmentv, SequenceRendererI sr, boolean showFeats)
{
{
+ showFeatures = showFeats;
if (!isLoadingFinished())
{
return;
if (!isLoadingFinished())
{
return;
@@
-856,7
+868,7
@@
public abstract class AAStructureBindingModel
String[] files = getStructureFiles();
StructureMappingcommandSet[] colourBySequenceCommands = getColourBySequenceCommands(
String[] files = getStructureFiles();
StructureMappingcommandSet[] colourBySequenceCommands = getColourBySequenceCommands(
- files, sr, alignmentv);
+ files, sr, alignmentv, showFeatures);
colourBySequence(colourBySequenceCommands);
}
colourBySequence(colourBySequenceCommands);
}
@@
-888,7
+900,7
@@
public void updateColours(Object source) {
{
return;
}
{
return;
}
- if (colourScheme == null || colourScheme.isSimple())
+ if (!showFeatures && (colourScheme == null || colourScheme.isSimple()))
{
return;
}
{
return;
}
@@
-897,11
+909,13
@@
public void updateColours(Object source) {
{
if (isColourBySequence())
{
{
if (isColourBySequence())
{
- colourBySequence(ap, new SequenceRenderer(ap.getAlignViewport()));
+ colourBySequence(ap, new SequenceRenderer(ap.getAlignViewport()),
+ showFeatures);
}
else
{
}
else
{
- colourBySequence(ap, new SequenceRenderer(ap.getAlignViewport(), colourScheme));
+ colourBySequence(ap, new SequenceRenderer(ap.getAlignViewport(),
+ colourScheme), showFeatures);
}
}
}
}
}
}