+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+*\r
+* This program is free software; you can redistribute it and/or\r
+* modify it under the terms of the GNU General Public License\r
+* as published by the Free Software Foundation; either version 2\r
+* of the License, or (at your option) any later version.\r
+*\r
+* This program is distributed in the hope that it will be useful,\r
+* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+* GNU General Public License for more details.\r
+*\r
+* You should have received a copy of the GNU General Public License\r
+* 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
package jalview.schemes;\r
\r
public class ColourSchemeProperty {\r
- String description;\r
- String className;\r
- String menuString = null;\r
-\r
- public ColourSchemeProperty(String description, String className, String menuString) {\r
- this.description = new String(description);\r
- this.className = new String(className);\r
- if (menuString != null) {\r
- this.menuString = new String(menuString);\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
+\r
+ public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al, String name)\r
+ {\r
+ return getColour(al.getSequences(), al.getWidth(), name);\r
+ }\r
+\r
+ public static ColourSchemeI getColour(java.util.Vector seqs, int width,\r
+ String name) {\r
+ return getColour(seqs, width, getColourIndexFromName(name));\r
+ }\r
+\r
+ public static ColourSchemeI getColour(java.util.Vector seqs, int width,\r
+ int index) {\r
+ ColourSchemeI cs = null;\r
+\r
+ switch (index) {\r
+ case CLUSTAL:\r
+ cs = new ClustalxColourScheme(seqs, width);\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
-\r
- public String getClassName() {\r
- return className;\r
- }\r
- public String getDescription() {\r
- return description;\r
- }\r
- public String getMenuString() {\r
- return menuString;\r
- }\r
- public boolean isMenuItem() {\r
- return (menuString != null);\r
- }\r
}\r
git://source.jalview.org / jalview.git / blobdiff