2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.schemes;
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21 public class ColourSchemeProperty {
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22 public static final int CLUSTAL = 0;
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23 public static final int BLOSUM = 1;
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24 public static final int PID = 2;
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25 public static final int ZAPPO = 3;
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26 public static final int HYDROPHOBIC = 4;
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27 public static final int HELIX = 5;
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28 public static final int STRAND = 6;
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29 public static final int TURN = 7;
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30 public static final int BURIED = 8;
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31 public static final int NUCLEOTIDE = 9;
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32 public static final int USER_DEFINED = 10;
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33 public static final int NONE = 11;
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35 public static int getColourIndexFromName(String name) {
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38 if (name.equalsIgnoreCase("Clustal")) {
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40 } else if (name.equalsIgnoreCase("Blosum62")) {
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42 } else if (name.equalsIgnoreCase("% Identity")) {
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44 } else if (name.equalsIgnoreCase("Zappo")) {
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46 } else if (name.equalsIgnoreCase("Hydrophobic")) {
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48 } else if (name.equalsIgnoreCase("Helix Propensity")) {
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50 } else if (name.equalsIgnoreCase("Strand Propensity")) {
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52 } else if (name.equalsIgnoreCase("Turn Propensity")) {
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54 } else if (name.equalsIgnoreCase("Buried Index")) {
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56 } else if (name.equalsIgnoreCase("Nucleotide")) {
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58 } else if (name.equalsIgnoreCase("User Defined")) {
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65 public static String getColourName(ColourSchemeI cs) {
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66 if (cs instanceof ConservationColourScheme) {
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67 cs = ((ConservationColourScheme) cs).cs;
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72 if (cs instanceof ClustalxColourScheme) {
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74 } else if (cs instanceof Blosum62ColourScheme) {
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76 } else if (cs instanceof PIDColourScheme) {
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78 } else if (cs instanceof ZappoColourScheme) {
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80 } else if (cs instanceof HydrophobicColourScheme) {
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81 index = HYDROPHOBIC;
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82 } else if (cs instanceof HelixColourScheme) {
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84 } else if (cs instanceof StrandColourScheme) {
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86 } else if (cs instanceof TurnColourScheme) {
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88 } else if (cs instanceof BuriedColourScheme) {
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90 } else if (cs instanceof NucleotideColourScheme) {
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92 } else if (cs instanceof UserColourScheme) {
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93 index = USER_DEFINED;
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96 return getColourName(index);
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99 public static String getColourName(int index) {
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114 ret = "% Identity";
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124 ret = "Hydrophobic";
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129 ret = "Helix Propensity";
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134 ret = "Strand Propensity";
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139 ret = "Turn Propensity";
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144 ret = "Buried Index";
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149 ret = "Nucleotide";
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154 ret = "User Defined";
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167 public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al, String name)
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169 return getColour(al.getSequences(), al.getWidth(), name);
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172 public static ColourSchemeI getColour(java.util.Vector seqs, int width,
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174 return getColour(seqs, width, getColourIndexFromName(name));
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177 public static ColourSchemeI getColour(java.util.Vector seqs, int width,
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179 ColourSchemeI cs = null;
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183 cs = new ClustalxColourScheme(seqs, width);
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188 cs = new Blosum62ColourScheme();
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193 cs = new PIDColourScheme();
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198 cs = new ZappoColourScheme();
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203 cs = new HydrophobicColourScheme();
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208 cs = new HelixColourScheme();
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213 cs = new StrandColourScheme();
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218 cs = new TurnColourScheme();
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223 cs = new BuriedColourScheme();
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228 cs = new NucleotideColourScheme();
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233 cs = new UserColourScheme(null);
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