1 Clazz.declarePackage ("jalview.schemes");
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2 Clazz.load (["jalview.schemes.ResidueColourScheme"], "jalview.schemes.PIDColourScheme", ["jalview.schemes.ResidueProperties", "jalview.util.Comparison", "java.awt.Color"], function () {
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3 c$ = Clazz.decorateAsClass (function () {
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4 this.pidColours = null;
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5 this.thresholds = null;
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7 Clazz.instantialize (this, arguments);
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8 }, jalview.schemes, "PIDColourScheme", jalview.schemes.ResidueColourScheme);
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9 Clazz.makeConstructor (c$,
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11 Clazz.superConstructor (this, jalview.schemes.PIDColourScheme, []);
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12 this.pidColours = jalview.schemes.ResidueProperties.pidColours;
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13 this.thresholds = jalview.schemes.ResidueProperties.pidThresholds;
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15 Clazz.defineMethod (c$, "findColour",
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16 function (c, j, seq) {
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17 if ('a' <= c && c <= 'z') {
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18 c = String.fromCharCode (c.charCodeAt (0) - (32));
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19 }if (this.consensus == null || j >= this.consensus.length || this.consensus[j] == null) {
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20 return java.awt.Color.white;
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21 }if ((this.threshold != 0) && !this.aboveThreshold (c, j)) {
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22 return java.awt.Color.white;
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23 }var currentColour = java.awt.Color.white;
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25 if (this.consensus.length <= j) {
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26 return java.awt.Color.white;
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27 }if ((Integer.parseInt (this.consensus[j].get ("C").toString ()) != -1) && this.consensus[j].contains (String.valueOf (c))) {
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28 sc = (this.consensus[j].get (this.ignoreGaps)).floatValue ();
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29 if (!jalview.util.Comparison.isGap (c)) {
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30 for (var i = 0; i < this.thresholds.length; i++) {
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31 if (sc > this.thresholds[i]) {
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32 currentColour = this.pidColours[i];
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35 }}if (this.conservationColouring) {
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36 currentColour = this.applyConservation (currentColour, j);
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37 }return currentColour;
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38 }, "~S,~N,jalview.datamodel.SequenceI");
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