1 Clazz.declarePackage ("jalview.viewmodel.seqfeatures");
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2 Clazz.load (["jalview.api.FeatureRenderer", "java.beans.PropertyChangeSupport", "java.lang.Boolean", "java.util.Hashtable", "java.util.concurrent.ConcurrentHashMap"], "jalview.viewmodel.seqfeatures.FeatureRendererModel", ["jalview.schemes.GraduatedColor", "$.UserColourScheme", "jalview.util.QuickSort", "jalview.viewmodel.seqfeatures.FeatureRendererSettings", "$.FeaturesDisplayed", "java.awt.Color", "java.lang.Error", "$.Float", "java.util.ArrayList", "$.Arrays"], function () {
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3 c$ = Clazz.decorateAsClass (function () {
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4 this.transparency = 1.0;
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5 this.featureColours = null;
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6 this.featureGroups = null;
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7 this.currentColour = null;
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8 this.renderOrder = null;
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9 this.changeSupport = null;
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12 this.newFeatureAdded = false;
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13 this.findingFeatures = false;
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15 this.featureOrder = null;
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16 Clazz.instantialize (this, arguments);
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17 }, jalview.viewmodel.seqfeatures, "FeatureRendererModel", null, jalview.api.FeatureRenderer);
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18 Clazz.prepareFields (c$, function () {
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19 this.featureColours = new java.util.concurrent.ConcurrentHashMap ();
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20 this.featureGroups = new java.util.concurrent.ConcurrentHashMap ();
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21 this.changeSupport = new java.beans.PropertyChangeSupport (this);
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22 this.minmax = new java.util.Hashtable ();
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23 this.firing = Boolean.FALSE;
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25 Clazz.overrideMethod (c$, "getViewport",
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29 Clazz.defineMethod (c$, "getSettings",
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31 return new jalview.viewmodel.seqfeatures.FeatureRendererSettings (this);
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33 Clazz.defineMethod (c$, "transferSettings",
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35 this.renderOrder = fr.renderOrder;
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36 this.featureGroups = fr.featureGroups;
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37 this.featureColours = fr.featureColours;
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38 this.transparency = fr.transparency;
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39 this.featureOrder = fr.featureOrder;
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40 }, "jalview.viewmodel.seqfeatures.FeatureRendererSettings");
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41 Clazz.defineMethod (c$, "transferSettings",
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44 var frs = new jalview.viewmodel.seqfeatures.FeatureRendererSettings (fr);
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45 this.renderOrder = frs.renderOrder;
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46 this.featureGroups = frs.featureGroups;
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47 this.featureColours = frs.featureColours;
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48 this.transparency = frs.transparency;
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49 this.featureOrder = frs.featureOrder;
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50 if (this.av != null && this.av !== fr.getViewport ()) {
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51 if (_fr.getFeaturesDisplayed () != null) {
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52 var fd = this.getFeaturesDisplayed ();
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54 this.setFeaturesDisplayedFrom (_fr.getFeaturesDisplayed ());
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58 var fdisp = _fr.getFeaturesDisplayed ().getVisibleFeatures ();
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59 while (fdisp.hasNext ()) {
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60 fd.setVisible (fdisp.next ());
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62 }}}}}, "jalview.api.FeatureRenderer");
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63 Clazz.defineMethod (c$, "setFeaturesDisplayedFrom",
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64 function (featuresDisplayed) {
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65 this.av.setFeaturesDisplayed ( new jalview.viewmodel.seqfeatures.FeaturesDisplayed (featuresDisplayed));
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66 }, "jalview.api.FeaturesDisplayedI");
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67 Clazz.overrideMethod (c$, "setVisible",
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68 function (featureType) {
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69 var fdi = this.av.getFeaturesDisplayed ();
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71 this.av.setFeaturesDisplayed (fdi = new jalview.viewmodel.seqfeatures.FeaturesDisplayed ());
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72 }if (!fdi.isRegistered (featureType)) {
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73 this.pushFeatureType (java.util.Arrays.asList ( Clazz.newArray (-1, [featureType])));
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74 }fdi.setVisible (featureType);
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76 Clazz.overrideMethod (c$, "setAllVisible",
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77 function (featureTypes) {
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78 var fdi = this.av.getFeaturesDisplayed ();
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80 this.av.setFeaturesDisplayed (fdi = new jalview.viewmodel.seqfeatures.FeaturesDisplayed ());
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81 }var nft = new java.util.ArrayList ();
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82 for (var featureType, $featureType = featureTypes.iterator (); $featureType.hasNext () && ((featureType = $featureType.next ()) || true);) {
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83 if (!fdi.isRegistered (featureType)) {
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84 nft.add (featureType);
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86 if (nft.size () > 0) {
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87 this.pushFeatureType (nft);
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88 }fdi.setAllVisible (featureTypes);
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89 }, "java.util.List");
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90 Clazz.defineMethod (c$, "pushFeatureType",
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92 var ts = types.size ();
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93 var neworder = new Array ((this.renderOrder == null ? 0 : this.renderOrder.length) + ts);
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94 types.toArray (neworder);
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95 if (this.renderOrder != null) {
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96 System.arraycopy (neworder, 0, neworder, this.renderOrder.length, ts);
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97 System.arraycopy (this.renderOrder, 0, neworder, 0, this.renderOrder.length);
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98 }this.renderOrder = neworder;
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99 }, "java.util.List");
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100 Clazz.defineMethod (c$, "getMinMax",
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102 return this.minmax;
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104 Clazz.defineMethod (c$, "normaliseScore",
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105 function (sequenceFeature) {
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106 var mm = (this.minmax.get (sequenceFeature.type))[0];
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107 var r = Clazz.newByteArray (-1, [0, 255]);
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109 if (r[0] != 0 || mm[0] < 0.0) {
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111 r[1] = Clazz.doubleToByte (Clazz.doubleToInt (128.0) + 127.0 * (sequenceFeature.score / mm[1]));
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113 r[1] = Clazz.floatToByte (Clazz.doubleToInt (255.0) * (sequenceFeature.score / mm[1]));
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115 }, "jalview.datamodel.SequenceFeature");
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116 Clazz.defineMethod (c$, "updateFeatures",
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118 if (this.av.getFeaturesDisplayed () == null || this.renderOrder == null || this.newFeatureAdded) {
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119 this.findAllFeatures ();
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120 if (this.av.getFeaturesDisplayed ().getVisibleFeatureCount () < 1) {
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124 Clazz.defineMethod (c$, "findAllFeatures",
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127 if (this.firing.equals (Boolean.FALSE)) {
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128 this.firing = Boolean.TRUE;
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129 this.findAllFeatures (true);
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130 this.changeSupport.firePropertyChange ("changeSupport", null, null);
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131 this.firing = Boolean.FALSE;
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133 Clazz.overrideMethod (c$, "findFeaturesAtRes",
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134 function (sequence, res) {
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135 var tmp = new java.util.ArrayList ();
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136 var features = sequence.getSequenceFeatures ();
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137 if (features != null) {
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138 for (var i = 0; i < features.length; i++) {
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139 if (!this.av.areFeaturesDisplayed () || !this.av.getFeaturesDisplayed ().isVisible (features[i].getType ())) {
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141 }if (features[i].featureGroup != null && this.featureGroups != null && this.featureGroups.containsKey (features[i].featureGroup) && !this.featureGroups.get (features[i].featureGroup).booleanValue ()) {
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143 }if ((features[i].getBegin () <= res) && (features[i].getEnd () >= res)) {
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144 tmp.add (features[i]);
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147 }, "jalview.datamodel.SequenceI,~N");
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148 Clazz.defineMethod (c$, "findAllFeatures",
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149 function (newMadeVisible) {
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150 this.newFeatureAdded = false;
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151 if (this.findingFeatures) {
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152 this.newFeatureAdded = true;
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154 }this.findingFeatures = true;
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155 if (this.av.getFeaturesDisplayed () == null) {
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156 this.av.setFeaturesDisplayed ( new jalview.viewmodel.seqfeatures.FeaturesDisplayed ());
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157 }var featuresDisplayed = this.av.getFeaturesDisplayed ();
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158 var allfeatures = new java.util.ArrayList ();
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159 var oldfeatures = new java.util.ArrayList ();
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160 if (this.renderOrder != null) {
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161 for (var i = 0; i < this.renderOrder.length; i++) {
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162 if (this.renderOrder[i] != null) {
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163 oldfeatures.add (this.renderOrder[i]);
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165 }if (this.minmax == null) {
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166 this.minmax = new java.util.Hashtable ();
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167 }var alignment = this.av.getAlignment ();
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168 for (var i = 0; i < alignment.getHeight (); i++) {
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169 var asq = alignment.getSequenceAt (i);
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170 var features = asq.getSequenceFeatures ();
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171 if (features == null) {
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174 while (index < features.length) {
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175 if (!featuresDisplayed.isRegistered (features[index].getType ())) {
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176 var fgrp = features[index].getFeatureGroup ();
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177 if (fgrp != null) {
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178 var groupDisplayed = this.featureGroups.get (fgrp);
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179 if (groupDisplayed == null) {
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180 groupDisplayed = Boolean.$valueOf (newMadeVisible);
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181 this.featureGroups.put (fgrp, groupDisplayed);
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182 }if (!groupDisplayed.booleanValue ()) {
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185 }}if (!(features[index].begin == 0 && features[index].end == 0)) {
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186 if (newMadeVisible && !oldfeatures.contains (features[index].getType ())) {
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187 featuresDisplayed.setVisible (features[index].getType ());
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188 this.setOrder (features[index].getType (), 0);
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189 }}}if (!allfeatures.contains (features[index].getType ())) {
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190 allfeatures.add (features[index].getType ());
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191 }if (!Float.isNaN (features[index].score)) {
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192 var nonpos = features[index].getBegin () >= 1 ? 0 : 1;
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193 var mm = this.minmax.get (features[index].getType ());
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195 mm = Clazz.newArray (-1, [null, null]);
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196 this.minmax.put (features[index].getType (), mm);
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197 }if (mm[nonpos] == null) {
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198 mm[nonpos] = Clazz.newFloatArray (-1, [features[index].score, features[index].score]);
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200 if (mm[nonpos][0] > features[index].score) {
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201 mm[nonpos][0] = features[index].score;
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202 }if (mm[nonpos][1] < features[index].score) {
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203 mm[nonpos][1] = features[index].score;
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207 this.updateRenderOrder (allfeatures);
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208 this.findingFeatures = false;
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210 Clazz.defineMethod (c$, "updateRenderOrder",
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211 function (allFeatures) {
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212 var allfeatures = new java.util.ArrayList (allFeatures);
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213 var oldRender = this.renderOrder;
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214 this.renderOrder = new Array (allfeatures.size ());
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217 var initOrders = (this.featureOrder == null);
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219 if (oldRender != null && oldRender.length > 0) {
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220 for (var j = 0; j < oldRender.length; j++) {
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221 if (oldRender[j] != null) {
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223 this.setOrder (oldRender[j], (1 - (1 + j) / oldRender.length));
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224 }if (allfeatures.contains (oldRender[j])) {
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225 this.renderOrder[opos++] = oldRender[j];
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226 allfeatures.remove (oldRender[j]);
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227 if (this.minmax != null) {
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228 mmrange = this.minmax.get (oldRender[j]);
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229 if (mmrange != null) {
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230 fc = this.featureColours.get (oldRender[j]);
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231 if (fc != null && Clazz.instanceOf (fc, jalview.schemes.GraduatedColor) && (fc).isAutoScale ()) {
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232 (fc).updateBounds ((mmrange)[0][0], (mmrange)[0][1]);
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234 }if (allfeatures.size () == 0) {
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236 }var i = allfeatures.size () - 1;
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239 var newf = new Array (allfeatures.size ());
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240 var sortOrder = Clazz.newFloatArray (allfeatures.size (), 0);
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241 for (var newfeat, $newfeat = allfeatures.iterator (); $newfeat.hasNext () && ((newfeat = $newfeat.next ()) || true);) {
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243 if (this.minmax != null) {
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244 mmrange = this.minmax.get (newf[i]);
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245 if (mmrange != null) {
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246 fc = this.featureColours.get (newf[i]);
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247 if (fc != null && Clazz.instanceOf (fc, jalview.schemes.GraduatedColor) && (fc).isAutoScale ()) {
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248 (fc).updateBounds ((mmrange)[0][0], (mmrange)[0][1]);
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249 }}}if (initOrders || !this.featureOrder.containsKey (newf[i])) {
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250 var denom = initOrders ? allfeatures.size () : this.featureOrder.size ();
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251 this.setOrder (newf[i], i / denom);
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252 }sortOrder[i] = 2 - (this.featureOrder.get (newf[i])).floatValue ();
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254 sort = sort || sortOrder[i] > sortOrder[i + 1];
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257 if (iSize > 1 && sort) {
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258 jalview.util.QuickSort.sortFloatObject (sortOrder, newf);
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260 System.arraycopy (newf, 0, this.renderOrder, opos, newf.length);
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261 }, "java.util.List");
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262 Clazz.overrideMethod (c$, "getFeatureStyle",
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263 function (featureType) {
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264 var fc = this.featureColours.get (featureType);
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266 var ucs = new jalview.schemes.UserColourScheme ();
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267 var col = ucs.createColourFromName (featureType);
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268 this.featureColours.put (featureType, fc = col);
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271 Clazz.defineMethod (c$, "getColour",
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272 function (featureType) {
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273 var fc = this.getFeatureStyle (featureType);
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274 if (Clazz.instanceOf (fc, java.awt.Color)) {
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277 if (Clazz.instanceOf (fc, jalview.schemes.GraduatedColor)) {
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278 return (fc).getMaxColor ();
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279 }}throw new Error ("Implementation Error: Unrecognised render object " + fc.getClass () + " for features of type " + featureType);
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281 Clazz.defineMethod (c$, "getColour",
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282 function (feature) {
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283 var fc = this.getFeatureStyle (feature.getType ());
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284 if (Clazz.instanceOf (fc, java.awt.Color)) {
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287 if (Clazz.instanceOf (fc, jalview.schemes.GraduatedColor)) {
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288 return (fc).findColor (feature);
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289 }}throw new Error ("Implementation Error: Unrecognised render object " + fc.getClass () + " for features of type " + feature.getType ());
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290 }, "jalview.datamodel.SequenceFeature");
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291 Clazz.defineMethod (c$, "showFeature",
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292 function (sequenceFeature) {
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293 var fc = this.getFeatureStyle (sequenceFeature.type);
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294 if (Clazz.instanceOf (fc, jalview.schemes.GraduatedColor)) {
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295 return (fc).isColored (sequenceFeature);
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298 }}, "jalview.datamodel.SequenceFeature");
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299 Clazz.defineMethod (c$, "showFeatureOfType",
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301 return this.av.getFeaturesDisplayed ().isVisible (type);
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303 Clazz.overrideMethod (c$, "setColour",
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304 function (featureType, col) {
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306 this.featureColours.put (featureType, col);
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308 Clazz.defineMethod (c$, "setTransparency",
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310 this.transparency = value;
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312 Clazz.defineMethod (c$, "getTransparency",
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314 return this.transparency;
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316 Clazz.defineMethod (c$, "setOrder",
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317 function (type, position) {
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318 if (this.featureOrder == null) {
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319 this.featureOrder = new java.util.Hashtable ();
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320 }this.featureOrder.put (type, new Float (position));
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323 Clazz.defineMethod (c$, "getOrder",
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325 if (this.featureOrder != null) {
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326 if (this.featureOrder.containsKey (type)) {
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327 return (this.featureOrder.get (type)).floatValue ();
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330 Clazz.overrideMethod (c$, "getFeatureColours",
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332 return new java.util.concurrent.ConcurrentHashMap (this.featureColours);
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334 Clazz.defineMethod (c$, "setFeaturePriority",
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336 this.setFeaturePriority (data, true);
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338 Clazz.defineMethod (c$, "setFeaturePriority",
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339 function (data, visibleNew) {
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340 var av_featuresdisplayed = null;
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342 if ((av_featuresdisplayed = this.av.getFeaturesDisplayed ()) != null) {
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343 this.av.getFeaturesDisplayed ().clear ();
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345 this.av.setFeaturesDisplayed (av_featuresdisplayed = new jalview.viewmodel.seqfeatures.FeaturesDisplayed ());
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347 av_featuresdisplayed = this.av.getFeaturesDisplayed ();
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348 }if (data == null) {
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350 }this.renderOrder = new Array (data.length);
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351 if (data.length > 0) {
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352 for (var i = 0; i < data.length; i++) {
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353 var type = data[i][0].toString ();
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354 this.setColour (type, data[i][1]);
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355 if ((data[i][2]).booleanValue ()) {
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356 av_featuresdisplayed.setVisible (type);
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357 }this.renderOrder[data.length - i - 1] = type;
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360 Clazz.defineMethod (c$, "addPropertyChangeListener",
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361 function (listener) {
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362 this.changeSupport.addPropertyChangeListener (listener);
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363 }, "java.beans.PropertyChangeListener");
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364 Clazz.defineMethod (c$, "removePropertyChangeListener",
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365 function (listener) {
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366 this.changeSupport.removePropertyChangeListener (listener);
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367 }, "java.beans.PropertyChangeListener");
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368 Clazz.defineMethod (c$, "getAllFeatureColours",
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370 return this.featureColours.keySet ();
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372 Clazz.defineMethod (c$, "clearRenderOrder",
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374 this.renderOrder = null;
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376 Clazz.defineMethod (c$, "hasRenderOrder",
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378 return this.renderOrder != null;
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380 Clazz.defineMethod (c$, "getRenderOrder",
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382 if (this.renderOrder == null) {
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383 return java.util.Arrays.asList ( Clazz.newArray (-1, []));
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384 }return java.util.Arrays.asList (this.renderOrder);
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386 Clazz.defineMethod (c$, "getFeatureGroupsSize",
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388 return this.featureGroups != null ? 0 : this.featureGroups.size ();
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390 Clazz.overrideMethod (c$, "getFeatureGroups",
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392 return (this.featureGroups == null) ? java.util.Arrays.asList ( new Array (0)) : java.util.Arrays.asList (this.featureGroups.keySet ().toArray ( new Array (0)));
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394 Clazz.defineMethod (c$, "checkGroupVisibility",
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395 function (group, newGroupsVisible) {
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396 if (this.featureGroups == null) {
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397 }if (this.featureGroups.containsKey (group)) {
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398 return this.featureGroups.get (group).booleanValue ();
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399 }if (newGroupsVisible) {
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400 this.featureGroups.put (group, new Boolean (true));
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404 Clazz.overrideMethod (c$, "getGroups",
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405 function (visible) {
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406 if (this.featureGroups != null) {
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407 var gp = new java.util.ArrayList ();
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408 for (var grp, $grp = this.featureGroups.keySet ().iterator (); $grp.hasNext () && ((grp = $grp.next ()) || true);) {
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409 var state = this.featureGroups.get (grp);
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410 if (state.booleanValue () == visible) {
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416 Clazz.defineMethod (c$, "setGroupVisibility",
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417 function (group, visible) {
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418 this.featureGroups.put (group, new Boolean (visible));
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420 Clazz.defineMethod (c$, "setGroupVisibility",
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421 function (toset, visible) {
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422 if (toset != null && toset.size () > 0 && this.featureGroups != null) {
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424 for (var gst, $gst = toset.iterator (); $gst.hasNext () && ((gst = $gst.next ()) || true);) {
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425 var st = this.featureGroups.get (gst);
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426 this.featureGroups.put (gst, new Boolean (visible));
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428 rdrw = rdrw || (visible != st.booleanValue ());
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431 }}}, "java.util.List,~B");
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432 Clazz.overrideMethod (c$, "getDisplayedFeatureCols",
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434 var fcols = new java.util.Hashtable ();
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435 if (this.getViewport ().getFeaturesDisplayed () == null) {
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437 }var en = this.getViewport ().getFeaturesDisplayed ().getVisibleFeatures ();
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438 while (en.hasNext ()) {
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439 var col = en.next ();
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440 fcols.put (col, this.getColour (col));
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444 Clazz.defineMethod (c$, "getFeaturesDisplayed",
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446 return this.av.getFeaturesDisplayed ();
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448 Clazz.overrideMethod (c$, "getDisplayedFeatureTypes",
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451 typ = this.getRenderOrder ().toArray ( new Array (0));
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452 var feature_disp = this.av.getFeaturesDisplayed ();
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453 if (feature_disp != null) {
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455 for (var i = 0; i < typ.length; i++) {
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456 if (!feature_disp.isVisible (typ[i])) {
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461 Clazz.overrideMethod (c$, "getDisplayedFeatureGroups",
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464 var _gps = new java.util.ArrayList ();
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465 var en = this.getFeatureGroups ().iterator ();
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468 while (en.hasNext ()) {
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469 var gp = en.next ();
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470 if (this.checkGroupVisibility (gp, false)) {
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476 gps = new Array (_gps.size ());
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477 _gps.toArray (gps);
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