/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2006 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
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2007 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
import java.awt.*;\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
*/\r
public class ColourSchemeProperty\r
{\r
- /** DOCUMENT ME!! */\r
- public static final int CLUSTAL = 0;\r
+ /** DOCUMENT ME!! */\r
+ public static final int CLUSTAL = 0;\r
\r
- /** DOCUMENT ME!! */\r
- public static final int BLOSUM = 1;\r
+ /** DOCUMENT ME!! */\r
+ public static final int BLOSUM = 1;\r
\r
- /** DOCUMENT ME!! */\r
- public static final int PID = 2;\r
+ /** DOCUMENT ME!! */\r
+ public static final int PID = 2;\r
\r
- /** DOCUMENT ME!! */\r
- public static final int ZAPPO = 3;\r
+ /** DOCUMENT ME!! */\r
+ public static final int ZAPPO = 3;\r
\r
- /** DOCUMENT ME!! */\r
- public static final int TAYLOR = 4;\r
+ /** DOCUMENT ME!! */\r
+ public static final int TAYLOR = 4;\r
\r
- /** DOCUMENT ME!! */\r
- public static final int HYDROPHOBIC = 5;\r
+ /** DOCUMENT ME!! */\r
+ public static final int HYDROPHOBIC = 5;\r
\r
- /** DOCUMENT ME!! */\r
- public static final int HELIX = 6;\r
+ /** DOCUMENT ME!! */\r
+ public static final int HELIX = 6;\r
\r
- /** DOCUMENT ME!! */\r
- public static final int STRAND = 7;\r
+ /** DOCUMENT ME!! */\r
+ public static final int STRAND = 7;\r
\r
- /** DOCUMENT ME!! */\r
- public static final int TURN = 8;\r
+ /** DOCUMENT ME!! */\r
+ public static final int TURN = 8;\r
\r
- /** DOCUMENT ME!! */\r
- public static final int BURIED = 9;\r
+ /** DOCUMENT ME!! */\r
+ public static final int BURIED = 9;\r
\r
- /** DOCUMENT ME!! */\r
- public static final int NUCLEOTIDE = 10;\r
+ /** DOCUMENT ME!! */\r
+ public static final int NUCLEOTIDE = 10;\r
\r
- /** DOCUMENT ME!! */\r
- public static final int USER_DEFINED = 11;\r
+ /** DOCUMENT ME!! */\r
+ public static final int USER_DEFINED = 11;\r
\r
+ /** DOCUMENT ME!! */\r
+ public static final int NONE = 12;\r
\r
- /** DOCUMENT ME!! */\r
- public static final int NONE = 12;\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
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param name DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public static int getColourIndexFromName(String name)\r
+ if (name.equalsIgnoreCase("Clustal"))\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
+ ret = CLUSTAL;\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
+ 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
- int index = 12;\r
+ return ret;\r
+ }\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
+ * DOCUMENT ME!\r
+ *\r
+ * @param cs DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public static String getColourName(ColourSchemeI cs)\r
+ {\r
\r
- return getColourName(index);\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
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param index DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public static String getColourName(int index)\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
- String ret = null;\r
+ case CLUSTAL:\r
+ ret = "Clustal";\r
\r
- switch (index)\r
- {\r
- case CLUSTAL:\r
- ret = "Clustal";\r
+ break;\r
\r
- break;\r
+ case BLOSUM:\r
+ ret = "Blosum62";\r
\r
- case BLOSUM:\r
- ret = "Blosum62";\r
+ break;\r
\r
- break;\r
+ case PID:\r
+ ret = "% Identity";\r
\r
- case PID:\r
- ret = "% Identity";\r
+ break;\r
\r
- break;\r
+ case ZAPPO:\r
+ ret = "Zappo";\r
\r
- case ZAPPO:\r
- ret = "Zappo";\r
+ break;\r
\r
- break;\r
+ case TAYLOR:\r
+ ret = "Taylor";\r
+ break;\r
\r
- case TAYLOR:\r
- ret = "Taylor";\r
- break;\r
+ case HYDROPHOBIC:\r
+ ret = "Hydrophobic";\r
\r
- case HYDROPHOBIC:\r
- ret = "Hydrophobic";\r
+ break;\r
\r
- break;\r
+ case HELIX:\r
+ ret = "Helix Propensity";\r
\r
- case HELIX:\r
- ret = "Helix Propensity";\r
+ break;\r
\r
- break;\r
+ case STRAND:\r
+ ret = "Strand Propensity";\r
\r
- case STRAND:\r
- ret = "Strand Propensity";\r
+ break;\r
\r
- break;\r
+ case TURN:\r
+ ret = "Turn Propensity";\r
\r
- case TURN:\r
- ret = "Turn Propensity";\r
+ break;\r
\r
- break;\r
+ case BURIED:\r
+ ret = "Buried Index";\r
\r
- case BURIED:\r
- ret = "Buried Index";\r
+ break;\r
\r
- break;\r
+ case NUCLEOTIDE:\r
+ ret = "Nucleotide";\r
\r
- case NUCLEOTIDE:\r
- ret = "Nucleotide";\r
+ break;\r
\r
- break;\r
+ case USER_DEFINED:\r
+ ret = "User Defined";\r
\r
- case USER_DEFINED:\r
- ret = "User Defined";\r
+ break;\r
\r
- break;\r
+ default:\r
+ ret = "None";\r
\r
- default:\r
- ret = "None";\r
+ break;\r
+ }\r
\r
- break;\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
+ {\r
+ return getColour(al.getSequences(), al.getWidth(), name);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param seqs DOCUMENT ME!\r
+ * @param width DOCUMENT ME!\r
+ * @param name DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public static ColourSchemeI getColour(java.util.Vector seqs, int width,\r
+ String name)\r
+ {\r
+ return getColour(seqs, width, getColourIndexFromName(name));\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param seqs DOCUMENT ME!\r
+ * @param width DOCUMENT ME!\r
+ * @param index DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public static ColourSchemeI getColour(java.util.Vector seqs, int width,\r
+ int index)\r
+ {\r
+ ColourSchemeI cs = null;\r
+\r
+ switch (index)\r
+ {\r
+ case CLUSTAL:\r
+ cs = new ClustalxColourScheme(seqs, width);\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
- {\r
- return getColour(al.getSequences(), al.getWidth(), name);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param seqs DOCUMENT ME!\r
- * @param width DOCUMENT ME!\r
- * @param name DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public static ColourSchemeI getColour(java.util.Vector seqs, int width,\r
- String name)\r
- {\r
- return getColour(seqs, width, getColourIndexFromName(name));\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param seqs DOCUMENT ME!\r
- * @param width DOCUMENT ME!\r
- * @param index DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public static ColourSchemeI getColour(java.util.Vector seqs, int width,\r
- int index)\r
- {\r
- ColourSchemeI cs = null;\r
-\r
- switch (index)\r
- {\r
- case CLUSTAL:\r
- cs = new ClustalxColourScheme(seqs, width);\r
+ break;\r
\r
- break;\r
+ case BLOSUM:\r
+ cs = new Blosum62ColourScheme();\r
\r
- case BLOSUM:\r
- cs = new Blosum62ColourScheme();\r
+ break;\r
\r
- break;\r
+ case PID:\r
+ cs = new PIDColourScheme();\r
\r
- case PID:\r
- cs = new PIDColourScheme();\r
+ break;\r
\r
- break;\r
+ case ZAPPO:\r
+ cs = new ZappoColourScheme();\r
\r
- case ZAPPO:\r
- cs = new ZappoColourScheme();\r
+ break;\r
\r
- break;\r
+ case TAYLOR:\r
+ cs = new TaylorColourScheme();\r
+ break;\r
\r
- case TAYLOR:\r
- cs = new TaylorColourScheme();\r
- break;\r
+ case HYDROPHOBIC:\r
+ cs = new HydrophobicColourScheme();\r
\r
- case HYDROPHOBIC:\r
- cs = new HydrophobicColourScheme();\r
+ break;\r
\r
- break;\r
+ case HELIX:\r
+ cs = new HelixColourScheme();\r
\r
- case HELIX:\r
- cs = new HelixColourScheme();\r
+ break;\r
\r
- break;\r
+ case STRAND:\r
+ cs = new StrandColourScheme();\r
\r
- case STRAND:\r
- cs = new StrandColourScheme();\r
+ break;\r
\r
- break;\r
+ case TURN:\r
+ cs = new TurnColourScheme();\r
\r
- case TURN:\r
- cs = new TurnColourScheme();\r
+ break;\r
\r
- break;\r
+ case BURIED:\r
+ cs = new BuriedColourScheme();\r
\r
- case BURIED:\r
- cs = new BuriedColourScheme();\r
+ break;\r
\r
- break;\r
+ case NUCLEOTIDE:\r
+ cs = new NucleotideColourScheme();\r
\r
- case NUCLEOTIDE:\r
- cs = new NucleotideColourScheme();\r
+ break;\r
\r
- break;\r
+ case USER_DEFINED:\r
+ Color[] col = new Color[24];\r
+ for (int i = 0; i < 24; i++)\r
+ {\r
+ col[i] = Color.white;\r
+ }\r
+ cs = new UserColourScheme(col);\r
+ break;\r
\r
- case USER_DEFINED:\r
- Color[] col = new Color[24];\r
- for (int i = 0; i < 24; i++)\r
- col[i] = Color.white;\r
- cs = new UserColourScheme(col);\r
- break;\r
+ default:\r
+ break;\r
+ }\r
\r
- default:\r
- break;\r
- }\r
+ return cs;\r
+ }\r
\r
- return cs;\r
- }\r
-\r
- public static Color getAWTColorFromName(String name)\r
- {\r
- Color col = null;\r
- name = name.toLowerCase();\r
- if(name.equals("black"))\r
- col = Color.black;\r
- else if(name.equals("blue"))\r
- col = Color.blue;\r
- else if(name.equals("cyan"))\r
- col = Color.cyan;\r
- else if(name.equals("darkGray"))\r
- col = Color.darkGray;\r
- else if(name.equals("gray"))\r
- col = Color.gray;\r
- else if(name.equals("green"))\r
- col = Color.green;\r
- else if(name.equals("lightGray"))\r
- col = Color.lightGray;\r
- else if(name.equals("magenta"))\r
- col = Color.magenta;\r
- else if(name.equals("orange"))\r
- col = Color.orange;\r
- else if(name.equals("pink"))\r
- col = Color.pink;\r
- else if(name.equals("red"))\r
- col = Color.red;\r
- else if(name.equals("white"))\r
- col = Color.white;\r
- else if(name.equals("yellow"))\r
- col = Color.yellow;\r
-\r
- return col;\r
+ public static Color getAWTColorFromName(String name)\r
+ {\r
+ Color col = null;\r
+ name = name.toLowerCase();\r
+ if (name.equals("black"))\r
+ {\r
+ col = Color.black;\r
+ }\r
+ else if (name.equals("blue"))\r
+ {\r
+ col = Color.blue;\r
+ }\r
+ else if (name.equals("cyan"))\r
+ {\r
+ col = Color.cyan;\r
+ }\r
+ else if (name.equals("darkGray"))\r
+ {\r
+ col = Color.darkGray;\r
+ }\r
+ else if (name.equals("gray"))\r
+ {\r
+ col = Color.gray;\r
}\r
+ else if (name.equals("green"))\r
+ {\r
+ col = Color.green;\r
+ }\r
+ else if (name.equals("lightGray"))\r
+ {\r
+ col = Color.lightGray;\r
+ }\r
+ else if (name.equals("magenta"))\r
+ {\r
+ col = Color.magenta;\r
+ }\r
+ else if (name.equals("orange"))\r
+ {\r
+ col = Color.orange;\r
+ }\r
+ else if (name.equals("pink"))\r
+ {\r
+ col = Color.pink;\r
+ }\r
+ else if (name.equals("red"))\r
+ {\r
+ col = Color.red;\r
+ }\r
+ else if (name.equals("white"))\r
+ {\r
+ col = Color.white;\r
+ }\r
+ else if (name.equals("yellow"))\r
+ {\r
+ col = Color.yellow;\r
+ }\r
+\r
+ return col;\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff