-package jalview.schemes;
-
-public class ColourSchemeProperty
-{
- public static final int CLUSTAL = 0;
- public static final int BLOSUM = 1;
- public static final int PID = 2;
- public static final int ZAPPO = 3;
- public static final int HYDROPHOBIC=4;
- public static final int HELIX=5;
- public static final int STRAND=6;
- public static final int TURN = 7;
- public static final int BURIED = 8;
- public static final int NUCLEOTIDE = 9;
- public static final int USER_DEFINED = 10;
- public static final int NONE = 11;
-
-
- public static String getColourName(int index)
- {
- 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 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 USER_DEFINED:ret="User Defined";break;
- default: ret = "None"; break;
- }
- return ret;
- }
-
- public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al, String name)
- {
- for(int i=0; i<12; i++)
- {
- if(getColourName(i).equals(name))
- return getColour(al, i);
- }
- return null;
- }
-
- public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al, int index)
- {
- 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)
- {
- cs = jalview.gui.UserDefinedColours.loadDefaultColours(jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR"));
- }
- break;
-
- default: break;
- }
-
- return cs;
- }
-}
+package jalview.schemes;\r
+\r
+public class ColourSchemeProperty\r
+{\r
+ 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(int index)\r
+ {\r
+ String ret=null;\r
+ switch(index)\r
+ {\r
+ case CLUSTAL: ret = "Clustal"; break;\r
+ case BLOSUM: ret = "Blosum62"; break;\r
+ case PID: ret = "% Identity"; break;\r
+ case ZAPPO: ret = "Zappo"; break;\r
+ case HYDROPHOBIC: ret="Hydrophobic";break;\r
+ case HELIX: ret="Helix Propensity";break;\r
+ case STRAND: ret="Strand Propensity";break;\r
+ case TURN: ret="Turn Propensity";break;\r
+ case BURIED: ret="Buried Index";break;\r
+ case NUCLEOTIDE:ret="Nucleotide"; break;\r
+ case USER_DEFINED:ret="User Defined";break;\r
+ default: ret = "None"; break;\r
+ }\r
+ return ret;\r
+ }\r
+\r
+ public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al, String name)\r
+ {\r
+ return getColour(al, getColourIndexFromName(name));\r
+ }\r
+\r
+ public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al, int index)\r
+ {\r
+ ColourSchemeI cs = null;\r
+ switch(index)\r
+ {\r
+ case CLUSTAL: cs = new ClustalxColourScheme(al.getSequences(), al.getWidth()); break;\r
+ case BLOSUM: cs = new Blosum62ColourScheme(); break;\r
+ case PID: cs = new PIDColourScheme(); break;\r
+ case ZAPPO: cs = new ZappoColourScheme(); break;\r
+ case HYDROPHOBIC: cs = new HydrophobicColourScheme(); break;\r
+ case HELIX: cs = new HelixColourScheme(); break;\r
+ case STRAND: cs = new StrandColourScheme(); break;\r
+ case TURN: cs = new TurnColourScheme(); break;\r
+ case BURIED: cs = new BuriedColourScheme(); break;\r
+ case NUCLEOTIDE: cs = new NucleotideColourScheme(); break;\r
+ case USER_DEFINED:\r
+ // if(jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR")!=null)\r
+ {\r
+ // cs = jalview.gui.UserDefinedColours.loadDefaultColours(jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR"));\r
+ }\r
+ break;\r
+\r
+ default: break;\r
+ }\r
+\r
+ return cs;\r
+ }\r
+}\r
git://source.jalview.org / jalview.git / blobdiff