* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
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(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
- {\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
+public class ColourSchemeProperty {\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
+ int ret = 11;\r
+\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
+\r
+ return ret;\r
+ }\r
+\r
+ public static String getColourName(ColourSchemeI cs) {\r
+ if (cs instanceof ConservationColourScheme) {\r
+ cs = ((ConservationColourScheme) cs).cs;\r
+ }\r
+\r
+ int index = 11;\r
+\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
+\r
+ return getColourName(index);\r
+ }\r
+\r
+ public static String getColourName(int index) {\r
+ String ret = null;\r
+\r
+ switch (index) {\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 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
- 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: cs = new UserColourScheme(null);\r
- break;\r
-\r
- default: break;\r
+\r
+ public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al,\r
+ String name) {\r
+ return getColour(al, getColourIndexFromName(name));\r
}\r
\r
- return cs;\r
- }\r
+ public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al,\r
+ int index) {\r
+ ColourSchemeI cs = null;\r
+\r
+ switch (index) {\r
+ case CLUSTAL:\r
+ cs = new ClustalxColourScheme(al.getSequences(), al.getWidth());\r
+\r
+ break;\r
+\r
+ case BLOSUM:\r
+ cs = new Blosum62ColourScheme();\r
+\r
+ break;\r
+\r
+ case PID:\r
+ cs = new PIDColourScheme();\r
+\r
+ break;\r
+\r
+ case ZAPPO:\r
+ cs = new ZappoColourScheme();\r
+\r
+ break;\r
+\r
+ case HYDROPHOBIC:\r
+ cs = new HydrophobicColourScheme();\r
+\r
+ break;\r
+\r
+ case HELIX:\r
+ cs = new HelixColourScheme();\r
+\r
+ break;\r
+\r
+ case STRAND:\r
+ cs = new StrandColourScheme();\r
+\r
+ break;\r
+\r
+ case TURN:\r
+ cs = new TurnColourScheme();\r
+\r
+ break;\r
+\r
+ case BURIED:\r
+ cs = new BuriedColourScheme();\r
+\r
+ break;\r
+\r
+ case NUCLEOTIDE:\r
+ cs = new NucleotideColourScheme();\r
+\r
+ break;\r
+\r
+ case USER_DEFINED:\r
+ cs = new UserColourScheme(null);\r
+\r
+ break;\r
+\r
+ default:\r
+ break;\r
+ }\r
+\r
+ return cs;\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff