*/
package jalview.schemes;
-import java.awt.*;
+import jalview.datamodel.AnnotatedCollectionI;
+
+import java.awt.Color;
/**
* ColourSchemeProperty Binds names to hardwired colourschemes and tries to deal
public static final int PURINEPYRIMIDINE = 13;
public static final int COVARIATION = 14;
+
+ public static final int TCOFFEE = 15;
+
/**
* index of first colourscheme (includes 'None')
{
ret = NUCLEOTIDE;
}
+ else if (name.equalsIgnoreCase("T-Coffee scores"))
+ {
+ ret = TCOFFEE;
+ }
+
else if (name.equalsIgnoreCase("User Defined"))
{
ret = USER_DEFINED;
return ret;
}
-
- /**
- * DOCUMENT ME!
- *
- * @param al
- * DOCUMENT ME!
- * @param name
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al,
- String name)
- {
- return getColour(al.getSequences(), al.getWidth(), name);
- }
-
/**
* retrieve or create colourscheme associated with name
- *
+ *
* @param seqs
* sequences to colour
* @param width
* string to parse as colour for new coloursheme
* @return Valid Colourscheme
*/
- public static ColourSchemeI getColour(java.util.Vector seqs, int width,
+ public static ColourSchemeI getColour(AnnotatedCollectionI alignment,
String name)
{
int colindex = getColourIndexFromName(name);
}
}
}
- return getColour(seqs, width, getColourIndexFromName(name));
+ return getColour(alignment, getColourIndexFromName(name));
}
/**
- * DOCUMENT ME!
+ * Construct an instance of ColourSchemeI corresponding to the given colourscheme index
*
* @param seqs
- * DOCUMENT ME!
+ * sequences to be coloured by colourscheme
* @param width
- * DOCUMENT ME!
+ * geometry of alignment
* @param index
- * DOCUMENT ME!
+ * colourscheme number
*
- * @return DOCUMENT ME!
+ * @return null or an instance of the colourscheme configured to colour given sequence set
*/
- public static ColourSchemeI getColour(java.util.Vector seqs, int width,
- int index)
+ public static ColourSchemeI getColour(jalview.datamodel.AnnotatedCollectionI coll, int index)
{
+ // TODO 3.0 2.8 refactor signature to take an alignmentI like container so colourschemes based on annotation can be initialised
ColourSchemeI cs = null;
switch (index)
{
case CLUSTAL:
- cs = new ClustalxColourScheme(seqs, width);
+ cs = new ClustalxColourScheme(coll, null);
break;