- ColourSchemeI cs = null;
- switch(index)
- {
- case CLUSTAL: cs = new ClustalxColourScheme(al.getSequences(), al.getWidth()); break;
- case BLOSUM: cs = new Blosum62ColourScheme(); break;
- case PID: cs = new PIDColourScheme(); break;
- case ZAPPO: cs = new ZappoColourScheme(); break;
- case HYDROPHOBIC: cs = new HydrophobicColourScheme(); break;
- case HELIX: cs = new HelixColourScheme(); break;
- case STRAND: cs = new StrandColourScheme(); break;
- case TURN: cs = new TurnColourScheme(); break;
- case BURIED: cs = new BuriedColourScheme(); break;
- case NUCLEOTIDE: cs = new NucleotideColourScheme(); break;
- case USER_DEFINED:
- if(jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR")!=null)
+ String ret = null;
+
+ switch (index)
+ {
+ case CLUSTAL:
+ ret = "Clustal";
+
+ break;
+
+ case BLOSUM:
+ ret = "Blosum62";
+
+ break;
+
+ case PID:
+ ret = "% Identity";
+
+ break;
+
+ case ZAPPO:
+ ret = "Zappo";
+
+ break;
+
+ case TAYLOR:
+ ret = "Taylor";
+ break;
+
+ case HYDROPHOBIC:
+ ret = "Hydrophobic";
+
+ break;
+
+ case HELIX:
+ ret = "Helix Propensity";
+
+ break;
+
+ case STRAND:
+ ret = "Strand Propensity";
+
+ break;
+
+ case TURN:
+ ret = "Turn Propensity";
+
+ break;
+
+ case BURIED:
+ ret = "Buried Index";
+
+ break;
+
+ case NUCLEOTIDE:
+ ret = "Nucleotide";
+
+ break;
+
+ case PURINEPYRIMIDINE:
+ ret = "Purine/Pyrimidine";
+
+ break;
+
+ /*
+ * case COVARIATION: ret = "Covariation";
+ *
+ * break;
+ */
+ case USER_DEFINED:
+ ret = "User Defined";
+
+ break;
+
+ default:
+ ret = "None";
+
+ break;
+ }
+
+ 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
+ * range of sequences to colour
+ * @param name
+ * colourscheme name, applet colour parameter specification, or
+ * string to parse as colour for new coloursheme
+ * @return Valid Colourscheme
+ */
+ public static ColourSchemeI getColour(java.util.Vector seqs, int width,
+ String name)
+ {
+ int colindex = getColourIndexFromName(name);
+ if (colindex == UNDEFINED)
+ {
+ if (name.indexOf('=') == -1)
+ {
+ // try to build a colour from the string directly
+ try