- public static final int CLUSTAL = 0;\r
- public static final int BLOSUM = 1;\r
- public static final int PID = 2;\r
- public static final int ZAPPO = 3;\r
- public static final int HYDROPHOBIC=4;\r
- public static final int HELIX=5;\r
- public static final int STRAND=6;\r
- public static final int TURN = 7;\r
- public static final int BURIED = 8;\r
- public static final int NUCLEOTIDE = 9;\r
- public static final int USER_DEFINED = 10;\r
- public static final int NONE = 11;\r
-\r
- public static int getColourIndexFromName(String name)\r
- {\r
- int ret=11;\r
- if(name.equalsIgnoreCase("Clustal"))\r
- ret = CLUSTAL;\r
- else if(name.equalsIgnoreCase("Blosum62"))\r
- ret = BLOSUM;\r
- else if(name.equalsIgnoreCase("% Identity"))\r
- ret = PID;\r
- else if(name.equalsIgnoreCase("Zappo"))\r
- ret = ZAPPO;\r
- else if(name.equalsIgnoreCase("Hydrophobic"))\r
- ret = HYDROPHOBIC;\r
- else if(name.equalsIgnoreCase("Helix Propensity"))\r
- ret = HELIX;\r
- else if(name.equalsIgnoreCase("Strand Propensity"))\r
- ret = STRAND;\r
- else if(name.equalsIgnoreCase("Turn Propensity"))\r
- ret = TURN;\r
- else if(name.equalsIgnoreCase("Buried Index"))\r
- ret = BURIED;\r
- else if(name.equalsIgnoreCase("Nucleotide"))\r
- ret = NUCLEOTIDE;\r
- else if(name.equalsIgnoreCase("User Defined"))\r
- ret = USER_DEFINED;\r
-\r
- return ret;\r
- }\r
-\r
- public static String getColourName(ColourSchemeI cs)\r
- {\r
- if(cs instanceof ConservationColourScheme)\r
- cs = ((ConservationColourScheme)cs).cs;\r
-\r
-\r
- int index = 11;\r
- if(cs instanceof ClustalxColourScheme)\r
- index = CLUSTAL;\r
- else if(cs instanceof Blosum62ColourScheme)\r
- index = BLOSUM;\r
- else if(cs instanceof PIDColourScheme)\r
- index = PID;\r
- else if(cs instanceof ZappoColourScheme)\r
- index = ZAPPO;\r
- else if(cs instanceof HydrophobicColourScheme)\r
- index = HYDROPHOBIC;\r
- else if(cs instanceof HelixColourScheme)\r
- index = HELIX;\r
- else if(cs instanceof StrandColourScheme)\r
- index = STRAND;\r
- else if(cs instanceof TurnColourScheme)\r
- index = TURN;\r
- else if(cs instanceof BuriedColourScheme)\r
- index = BURIED;\r
- else if(cs instanceof NucleotideColourScheme)\r
- index = NUCLEOTIDE;\r
- else if(cs instanceof UserColourScheme)\r
- index = USER_DEFINED;\r
-\r
- return getColourName(index);\r
- }\r
-\r
- public static String getColourName(int index)\r
- {\r
- String ret=null;\r
- switch(index)\r
+ /** DOCUMENT ME!! */\r
+ public static final int CLUSTAL = 0;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public static final int BLOSUM = 1;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public static final int PID = 2;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public static final int ZAPPO = 3;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public static final int TAYLOR = 4;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public static final int HYDROPHOBIC = 5;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public static final int HELIX = 6;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public static final int STRAND = 7;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public static final int TURN = 8;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public static final int BURIED = 9;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public static final int NUCLEOTIDE = 10;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public static final int USER_DEFINED = 11;\r
+\r
+\r
+ /** DOCUMENT ME!! */\r
+ public static final int NONE = 12;\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param name DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public static int getColourIndexFromName(String name)\r
+ {\r
+ int ret = 12;\r
+\r
+ if (name.equalsIgnoreCase("Clustal"))\r
+ {\r
+ ret = CLUSTAL;\r
+ }\r
+ else if (name.equalsIgnoreCase("Blosum62"))\r
+ {\r
+ ret = BLOSUM;\r
+ }\r
+ else if (name.equalsIgnoreCase("% Identity"))\r
+ {\r
+ ret = PID;\r
+ }\r
+ else if (name.equalsIgnoreCase("Zappo"))\r
+ {\r
+ ret = ZAPPO;\r
+ }\r
+ else if (name.equalsIgnoreCase("Taylor"))\r
+ {\r
+ ret = TAYLOR;\r
+ }\r
+ else if (name.equalsIgnoreCase("Hydrophobic"))\r
+ {\r
+ ret = HYDROPHOBIC;\r
+ }\r
+ else if (name.equalsIgnoreCase("Helix Propensity"))\r
+ {\r
+ ret = HELIX;\r
+ }\r
+ else if (name.equalsIgnoreCase("Strand Propensity"))\r
+ {\r
+ ret = STRAND;\r
+ }\r
+ else if (name.equalsIgnoreCase("Turn Propensity"))\r
+ {\r
+ ret = TURN;\r
+ }\r
+ else if (name.equalsIgnoreCase("Buried Index"))\r
+ {\r
+ ret = BURIED;\r
+ }\r
+ else if (name.equalsIgnoreCase("Nucleotide"))\r
+ {\r
+ ret = NUCLEOTIDE;\r
+ }\r
+ else if (name.equalsIgnoreCase("User Defined"))\r
+ {\r
+ ret = USER_DEFINED;\r
+ }\r
+\r
+ return ret;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param cs DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public static String getColourName(ColourSchemeI cs)\r
+ {\r
+\r
+ int index = 12;\r
+\r
+ if (cs instanceof ClustalxColourScheme)\r
+ {\r
+ index = CLUSTAL;\r
+ }\r
+ else if (cs instanceof Blosum62ColourScheme)\r
+ {\r
+ index = BLOSUM;\r
+ }\r
+ else if (cs instanceof PIDColourScheme)\r
+ {\r
+ index = PID;\r
+ }\r
+ else if (cs instanceof ZappoColourScheme)\r
+ {\r
+ index = ZAPPO;\r
+ }\r
+ else if (cs instanceof TaylorColourScheme)\r
+ {\r
+ index = TAYLOR;\r
+ }\r
+ else if (cs instanceof HydrophobicColourScheme)\r
+ {\r
+ index = HYDROPHOBIC;\r
+ }\r
+ else if (cs instanceof HelixColourScheme)\r
+ {\r
+ index = HELIX;\r
+ }\r
+ else if (cs instanceof StrandColourScheme)\r
+ {\r
+ index = STRAND;\r
+ }\r
+ else if (cs instanceof TurnColourScheme)\r
+ {\r
+ index = TURN;\r
+ }\r
+ else if (cs instanceof BuriedColourScheme)\r
+ {\r
+ index = BURIED;\r
+ }\r
+ else if (cs instanceof NucleotideColourScheme)\r
+ {\r
+ index = NUCLEOTIDE;\r
+ }\r
+ else if (cs instanceof UserColourScheme)\r
+ {\r
+ index = USER_DEFINED;\r
+ }\r
+\r
+ return getColourName(index);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param index DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public static String getColourName(int index)\r
+ {\r
+ String ret = null;\r
+\r
+ switch (index)\r
+ {\r
+ case CLUSTAL:\r
+ ret = "Clustal";\r
+\r
+ break;\r
+\r
+ case BLOSUM:\r
+ ret = "Blosum62";\r
+\r
+ break;\r
+\r
+ case PID:\r
+ ret = "% Identity";\r
+\r
+ break;\r
+\r
+ case ZAPPO:\r
+ ret = "Zappo";\r
+\r
+ break;\r
+\r
+ case TAYLOR:\r
+ ret = "Taylor";\r
+ break;\r
+\r
+ case HYDROPHOBIC:\r
+ ret = "Hydrophobic";\r
+\r
+ break;\r
+\r
+ case HELIX:\r
+ ret = "Helix Propensity";\r
+\r
+ break;\r
+\r
+ case STRAND:\r
+ ret = "Strand Propensity";\r
+\r
+ break;\r
+\r
+ case TURN:\r
+ ret = "Turn Propensity";\r
+\r
+ break;\r
+\r
+ case BURIED:\r
+ ret = "Buried Index";\r
+\r
+ break;\r
+\r
+ case NUCLEOTIDE:\r
+ ret = "Nucleotide";\r
+\r
+ break;\r
+\r
+ case USER_DEFINED:\r
+ ret = "User Defined";\r
+\r
+ break;\r
+\r
+ default:\r
+ ret = "None";\r
+\r
+ break;\r
+ }\r
+\r
+ return ret;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param al DOCUMENT ME!\r
+ * @param name DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al,\r
+ String name)\r