X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemeProperty.java;h=98e90bdf769f07363b4b8bb598d97a5edf6d3db2;hb=d4271d32477e99e9fbbfa5db3e11f1b79324e60d;hp=0d5ecc7b1478aff8a9a6bd1f56edcef8efa938d6;hpb=6bd69f196a5bdb8bdbc329166485d5da60b27389;p=jalview.git
diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index 0d5ecc7..98e90bd 100755
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -1,243 +1,156 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-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 int getColourIndexFromName(String name) {
- int ret = 11;
-
- if (name.equalsIgnoreCase("Clustal")) {
- ret = CLUSTAL;
- } else if (name.equalsIgnoreCase("Blosum62")) {
- ret = BLOSUM;
- } else if (name.equalsIgnoreCase("% Identity")) {
- ret = PID;
- } else if (name.equalsIgnoreCase("Zappo")) {
- ret = ZAPPO;
- } else if (name.equalsIgnoreCase("Hydrophobic")) {
- ret = HYDROPHOBIC;
- } else if (name.equalsIgnoreCase("Helix Propensity")) {
- ret = HELIX;
- } else if (name.equalsIgnoreCase("Strand Propensity")) {
- ret = STRAND;
- } else if (name.equalsIgnoreCase("Turn Propensity")) {
- ret = TURN;
- } else if (name.equalsIgnoreCase("Buried Index")) {
- ret = BURIED;
- } else if (name.equalsIgnoreCase("Nucleotide")) {
- ret = NUCLEOTIDE;
- } else if (name.equalsIgnoreCase("User Defined")) {
- ret = USER_DEFINED;
- }
-
- return ret;
- }
-
- public static String getColourName(ColourSchemeI cs) {
- if (cs instanceof ConservationColourScheme) {
- cs = ((ConservationColourScheme) cs).cs;
- }
-
- int index = 11;
-
- if (cs instanceof ClustalxColourScheme) {
- index = CLUSTAL;
- } else if (cs instanceof Blosum62ColourScheme) {
- index = BLOSUM;
- } else if (cs instanceof PIDColourScheme) {
- index = PID;
- } else if (cs instanceof ZappoColourScheme) {
- index = ZAPPO;
- } else if (cs instanceof HydrophobicColourScheme) {
- index = HYDROPHOBIC;
- } else if (cs instanceof HelixColourScheme) {
- index = HELIX;
- } else if (cs instanceof StrandColourScheme) {
- index = STRAND;
- } else if (cs instanceof TurnColourScheme) {
- index = TURN;
- } else if (cs instanceof BuriedColourScheme) {
- index = BURIED;
- } else if (cs instanceof NucleotideColourScheme) {
- index = NUCLEOTIDE;
- } else if (cs instanceof UserColourScheme) {
- index = USER_DEFINED;
- }
-
- return getColourName(index);
- }
-
- 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)
- {
- return getColour(al.getSequences(), al.getWidth(), name);
- }
-
- public static ColourSchemeI getColour(java.util.Vector seqs, int width,
- String name) {
- return getColour(seqs, width, getColourIndexFromName(name));
- }
-
- public static ColourSchemeI getColour(java.util.Vector seqs, int width,
- int index) {
- ColourSchemeI cs = null;
-
- switch (index) {
- case CLUSTAL:
- cs = new ClustalxColourScheme(seqs, width);
-
- 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:
- cs = new UserColourScheme(null);
-
- break;
-
- default:
- break;
- }
-
- return cs;
- }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see