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JAL-2360 structure viewers now using ColourMenuHelper, obsolete methods
[jalview.git]
/
src
/
jalview
/
schemes
/
ResidueColourScheme.java
diff --git
a/src/jalview/schemes/ResidueColourScheme.java
b/src/jalview/schemes/ResidueColourScheme.java
index
9cc4bd1
..
57f7d57
100755
(executable)
--- a/
src/jalview/schemes/ResidueColourScheme.java
+++ b/
src/jalview/schemes/ResidueColourScheme.java
@@
-40,6
+40,8
@@
public abstract class ResidueColourScheme implements ColourSchemeI
{
public static final String NONE = "None";
{
public static final String NONE = "None";
+ public static final String USER_DEFINED = "User Defined";
+
/*
* lookup up by character value e.g. 'G' to the colors array index
* e.g. if symbolIndex['K'] = 11 then colors[11] is the colour for K
/*
* lookup up by character value e.g. 'G' to the colors array index
* e.g. if symbolIndex['K'] = 11 then colors[11] is the colour for K
@@
-360,12
+362,16
@@
public abstract class ResidueColourScheme implements ColourSchemeI
}
/*
}
/*
- * inspect the data context (alignment dataset) for residue type
+ * inspect the data context (alignment) for residue type
*/
boolean nucleotide = false;
*/
boolean nucleotide = false;
- AnnotatedCollectionI context = ac.getContext();
- if (context != null)
+ if (ac instanceof AlignmentI)
+ {
+ nucleotide = ((AlignmentI) ac).isNucleotide();
+ }
+ else
{
{
+ AnnotatedCollectionI context = ac.getContext();
if (context instanceof AlignmentI)
{
nucleotide = ((AlignmentI) context).isNucleotide();
if (context instanceof AlignmentI)
{
nucleotide = ((AlignmentI) context).isNucleotide();
@@
-376,14
+382,6
@@
public abstract class ResidueColourScheme implements ColourSchemeI
return true;
}
}
return true;
}
}
- else if (ac instanceof AlignmentI)
- {
- nucleotide = ((AlignmentI) ac).isNucleotide();
- }
- else
- {
- return true;
- }
/*
* does data type match colour scheme type?
/*
* does data type match colour scheme type?
@@
-411,4
+409,14
@@
public abstract class ResidueColourScheme implements ColourSchemeI
{
return false;
}
{
return false;
}
+
+ /**
+ * Default method returns true. Override this to return false in colour
+ * schemes that are not determined solely by the sequence symbol.
+ */
+ @Override
+ public boolean isSimple()
+ {
+ return true;
+ }
}
}