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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30 * @version $Revision$
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32 public class ResidueColourScheme implements ColourSchemeI
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37 /** DOCUMENT ME!! */
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38 public Vector consensus;
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41 * Creates a new ResidueColourScheme object.
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43 * @param colors DOCUMENT ME!
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44 * @param threshold DOCUMENT ME!
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46 public ResidueColourScheme(Color[] colors, int threshold)
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48 this.colors = colors;
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49 this.threshold = threshold;
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53 * Creates a new ResidueColourScheme object.
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55 public ResidueColourScheme()
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62 * @param consensus DOCUMENT ME!
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64 public void setConsensus(Vector consensus)
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66 this.consensus = consensus;
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72 * @param aa DOCUMENT ME!
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74 * @return DOCUMENT ME!
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76 public Color findColour(String aa)
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78 return colors[((Integer) (ResidueProperties.aaHash.get(aa))).intValue()];
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84 * @param s DOCUMENT ME!
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85 * @param j DOCUMENT ME!
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87 * @return DOCUMENT ME!
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89 public Color findColour(String s, int j)
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91 if ((threshold == 0) || aboveThreshold(s, j))
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93 return colors[((Integer) (ResidueProperties.aaHash.get(s))).intValue()];
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104 * @return DOCUMENT ME!
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106 public int getThreshold()
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114 * @param ct DOCUMENT ME!
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116 public void setThreshold(int ct)
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124 * @param s DOCUMENT ME!
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125 * @param j DOCUMENT ME!
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127 * @return DOCUMENT ME!
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129 public boolean aboveThreshold(String s, int j)
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131 Hashtable hash = (Hashtable) consensus.elementAt(j);
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133 if ((((Integer) hash.get("maxCount")).intValue() != -1) &&
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136 //// resCount//////////////////// ///////////////seq count////////////
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137 double sc = (((Integer) hash.get(s)).intValue() * 100.0) / ((Integer) hash.get(
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138 "size")).intValue();
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140 if (sc >= threshold)
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