1 Clazz.declarePackage ("jalview.schemes");
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2 Clazz.load (["jalview.schemes.ResidueColourScheme", "java.util.Hashtable"], "jalview.schemes.CovariationColourScheme", ["jalview.schemes.ResidueProperties", "jalview.util.ColorUtils", "java.awt.Color"], function () {
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3 c$ = Clazz.decorateAsClass (function () {
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4 this.helixcolorhash = null;
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5 this.positionsToHelix = null;
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7 this.annotation = null;
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8 Clazz.instantialize (this, arguments);
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9 }, jalview.schemes, "CovariationColourScheme", jalview.schemes.ResidueColourScheme);
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10 Clazz.prepareFields (c$, function () {
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11 this.helixcolorhash = new java.util.Hashtable ();
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12 this.positionsToHelix = new java.util.Hashtable ();
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14 Clazz.makeConstructor (c$,
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15 function (annotation) {
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16 Clazz.superConstructor (this, jalview.schemes.CovariationColourScheme, []);
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17 this.annotation = annotation;
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18 for (var x = 0; x < this.annotation._rnasecstr.length; x++) {
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19 this.positionsToHelix.put (new Integer (this.annotation._rnasecstr[x].getBegin ()), this.annotation._rnasecstr[x].getFeatureGroup ());
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20 this.positionsToHelix.put (new Integer (this.annotation._rnasecstr[x].getEnd ()), this.annotation._rnasecstr[x].getFeatureGroup ());
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21 if (Integer.parseInt (this.annotation._rnasecstr[x].getFeatureGroup ()) > this.numHelix) {
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22 this.numHelix = Integer.parseInt (this.annotation._rnasecstr[x].getFeatureGroup ());
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24 for (var j = 0; j <= this.numHelix; j++) {
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25 this.helixcolorhash.put (Integer.toString (j), jalview.util.ColorUtils.generateRandomColor (java.awt.Color.white));
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27 }, "jalview.datamodel.AlignmentAnnotation");
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28 Clazz.defineMethod (c$, "findColour",
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30 return jalview.schemes.ResidueProperties.purinepyrimidine[jalview.schemes.ResidueProperties.purinepyrimidineIndex[c.charCodeAt (0)]];
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32 Clazz.defineMethod (c$, "findColour",
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34 var currentColour = java.awt.Color.white;
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35 var currentHelix = null;
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36 currentHelix = this.positionsToHelix.get (new Integer (j));
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37 if (currentHelix != null) {
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38 currentColour = this.helixcolorhash.get (currentHelix);
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39 }return currentColour;
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