import jalview.analysis.AAFrequency;
import jalview.analysis.Conservation;
+import jalview.renderer.ResidueShader;
+import jalview.renderer.ResidueShaderI;
import jalview.schemes.ColourSchemeI;
import java.awt.Color;
/**
* Colourscheme applied to group if any
*/
- public ColourSchemeI cs;
+ public ResidueShaderI cs;
// start column (base 0)
int startRes = 0;
public SequenceGroup()
{
groupName = "JGroup:" + this.hashCode();
+ cs = new ResidueShader();
}
/**
ColourSchemeI scheme, boolean displayBoxes, boolean displayText,
boolean colourText, int start, int end)
{
+ this();
this.sequences = sequences;
this.groupName = groupName;
this.displayBoxes = displayBoxes;
this.displayText = displayText;
this.colourText = colourText;
- this.cs = scheme;
+ this.cs = new ResidueShader(scheme);
startRes = start;
endRes = end;
recalcConservation();
*/
public SequenceGroup(SequenceGroup seqsel)
{
+ this();
if (seqsel != null)
{
sequences = new ArrayList<SequenceI>();
private AnnotatedCollectionI context;
/**
- * set the alignment or group context for this group
+ * Sets the alignment or group context for this group
*
- * @param context
+ * @param ctx
+ * @throws IllegalArgumentException
+ * if setting the context would result in a circular reference chain
*/
- public void setContext(AnnotatedCollectionI context)
+ public void setContext(AnnotatedCollectionI ctx)
{
- this.context = context;
+ AnnotatedCollectionI ref = ctx;
+ while (ref != null)
+ {
+ if (ref == this)
+ {
+ throw new IllegalArgumentException(
+ "Circular reference in SequenceGroup.context");
+ }
+ ref = ref.getContext();
+ }
+ this.context = ctx;
}
/*
{
return context;
}
+
+ public void setColourScheme(ColourSchemeI scheme)
+ {
+ if (cs == null)
+ {
+ cs = new ResidueShader();
+ }
+ cs.setColourScheme(scheme);
+ }
+
+ public void setGroupColourScheme(ResidueShaderI scheme)
+ {
+ cs = scheme;
+ }
+
+ public ColourSchemeI getColourScheme()
+ {
+ return cs == null ? null : cs.getColourScheme();
+ }
+
+ public ResidueShaderI getGroupColourScheme()
+ {
+ return cs;
+ }
+
+ @Override
+ public boolean isNucleotide()
+ {
+ if (context != null) {
+ return context.isNucleotide();
+ }
+ return false;
+ }
}