1 Clazz.declarePackage ("jalview.appletgui");
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2 Clazz.load (["awt2swing.Canvas", "jalview.api.AlignViewControllerGuiI", "jalview.appletgui.EmbmenuFrame", "java.awt.event.ActionListener", "$.ItemListener", "$.KeyListener", "awt2swing.CheckboxMenuItem", "$.Label", "$.Menu", "$.MenuBar", "$.MenuItem", "jalview.util.MessageManager", "java.awt.BorderLayout"], "jalview.appletgui.AlignFrame", ["awt2swing.Frame", "jalview.analysis.AlignmentSorter", "$.AnnotationSorter", "jalview.appletgui.AlignViewport", "$.AlignmentPanel", "$.AnnotationColourChooser", "$.AnnotationColumnChooser", "$.AppletJmol", "$.CutAndPasteTransfer", "$.FeatureSettings", "$.Finder", "$.FontChooser", "$.OverviewPanel", "$.PCAPanel", "$.PaintRefresher", "$.PairwiseAlignPanel", "$.RedundancyPanel", "$.SliderPanel", "$.TreePanel", "$.UserDefinedColours", "jalview.bin.JalviewLite", "jalview.commands.EditCommand", "$.OrderCommand", "$.RemoveGapColCommand", "$.RemoveGapsCommand", "$.SlideSequencesCommand", "$.TrimRegionCommand", "jalview.controller.AlignViewController", "jalview.datamodel.Alignment", "$.PDBEntry", "$.Sequence", "$.SequenceGroup", "jalview.io.AlignmentProperties", "$.AnnotationFile", "$.AppletFormatAdapter", "$.FeaturesFile", "jalview.jsdev.GenericFileAdapter", "jalview.schemes.Blosum62ColourScheme", "$.BuriedColourScheme", "$.ClustalxColourScheme", "$.HelixColourScheme", "$.HydrophobicColourScheme", "$.NucleotideColourScheme", "$.PIDColourScheme", "$.PurinePyrimidineColourScheme", "$.RNAHelicesColourChooser", "$.RNAInteractionColourScheme", "$.StrandColourScheme", "$.TCoffeeColourScheme", "$.TaylorColourScheme", "$.TurnColourScheme", "$.ZappoColourScheme", "jalview.structure.StructureSelectionManager", "jalview.util.Comparison", "$.MappingUtils", "java.awt.Color", "$.Font", "java.awt.event.FocusListener", "$.WindowAdapter", "java.lang.Character", "$.StringBuffer", "java.net.URL", "$.URLEncoder", "java.util.Arrays", "$.HashMap", "$.Hashtable", "$.StringTokenizer", "$.Vector"], function () {
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3 c$ = Clazz.decorateAsClass (function () {
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5 this.alignPanel = null;
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6 this.viewport = null;
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7 this.frameWidth = 700;
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8 this.frameHeight = 500;
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9 this.jalviewServletURL = null;
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10 this.showAutoCalculatedAbove = false;
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11 this.annotationSortOrder = null;
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12 this.alignFrameMenuBar = null;
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13 this.fileMenu = null;
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14 this.loadApplication = null;
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15 this.$loadTree = null;
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16 this.$loadAnnotations = null;
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17 this.$outputFeatures = null;
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18 this.$outputAnnotations = null;
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19 this.closeMenuItem = null;
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20 this.selectAllSequenceMenuItem = null;
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21 this.deselectAllSequenceMenuItem = null;
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22 this.invertSequenceMenuItem = null;
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23 this.remove2LeftMenuItem = null;
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24 this.remove2RightMenuItem = null;
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25 this.removeGappedColumnMenuItem = null;
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26 this.removeAllGapsMenuItem = null;
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27 this.viewBoxesMenuItem = null;
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28 this.viewTextMenuItem = null;
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29 this.sortPairwiseMenuItem = null;
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30 this.sortIDMenuItem = null;
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31 this.sortLengthMenuItem = null;
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32 this.sortGroupMenuItem = null;
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33 this.removeRedundancyMenuItem = null;
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34 this.pairwiseAlignmentMenuItem = null;
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35 this.PCAMenuItem = null;
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36 this.averageDistanceTreeMenuItem = null;
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37 this.neighbourTreeMenuItem = null;
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38 this.borderLayout1 = null;
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39 this.statusBar = null;
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40 this.clustalColour = null;
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41 this.zappoColour = null;
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42 this.taylorColour = null;
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43 this.hydrophobicityColour = null;
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44 this.helixColour = null;
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45 this.strandColour = null;
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46 this.turnColour = null;
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47 this.buriedColour = null;
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48 this.purinePyrimidineColour = null;
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49 this.RNAInteractionColour = null;
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50 this.RNAHelixColour = null;
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51 this.userDefinedColour = null;
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52 this.PIDColour = null;
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53 this.BLOSUM62Colour = null;
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54 this.tcoffeeColour = null;
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55 this.njTreeBlosumMenuItem = null;
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56 this.avDistanceTreeBlosumMenuItem = null;
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57 this.annotationPanelMenuItem = null;
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58 this.colourTextMenuItem = null;
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59 this.displayNonconservedMenuItem = null;
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60 this.alProperties = null;
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61 this.overviewMenuItem = null;
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62 this.undoMenuItem = null;
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63 this.redoMenuItem = null;
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64 this.conservationMenuItem = null;
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65 this.noColourmenuItem = null;
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66 this.wrapMenuItem = null;
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67 this.renderGapsMenuItem = null;
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68 this.findMenuItem = null;
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69 this.abovePIDThreshold = null;
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70 this.nucleotideColour = null;
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71 this.deleteGroups = null;
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72 this.grpsFromSelection = null;
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73 this.createGroup = null;
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74 this.unGroup = null;
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75 this.$delete = null;
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78 this.pasteMenu = null;
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79 this.pasteNew = null;
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80 this.pasteThis = null;
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81 this.applyToAllGroups = null;
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83 this.scaleAbove = null;
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84 this.scaleLeft = null;
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85 this.scaleRight = null;
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86 this.modifyPID = null;
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87 this.modifyConservation = null;
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88 this.autoCalculate = null;
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89 this.$sortByTree = null;
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90 this.sortByTreeMenu = null;
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91 this.inputText = null;
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92 this.documentation = null;
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94 this.seqLimits = null;
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95 this.centreColumnLabelFlag = null;
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96 this.followMouseOverFlag = null;
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97 this.showSequenceLogo = null;
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98 this.applyAutoAnnotationSettings = null;
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99 this.showConsensusHistogram = null;
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100 this.showGroupConsensus = null;
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101 this.showGroupConservation = null;
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102 this.normSequenceLogo = null;
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103 this.featureSettings = null;
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104 this.sequenceFeatures = null;
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105 this.annotationColour = null;
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106 this.annotationColumnSelection = null;
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107 this.invertColSel = null;
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108 this.showColumns = null;
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109 this.showSeqs = null;
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110 this.hideColumns = null;
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111 this.hideSequences = null;
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112 this.hideAllButSelection = null;
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113 this.hideAllSelection = null;
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114 this.showAllHidden = null;
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115 this.$newView = null;
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116 this.showAlignmentAnnotations = null;
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117 this.showSequenceAnnotations = null;
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118 this.sortAnnBySequence = null;
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119 this.sortAnnByLabel = null;
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120 this.showAutoFirst = null;
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121 this.showAutoLast = null;
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122 this.splitFrame = null;
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123 Clazz.instantialize (this, arguments);
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124 }, jalview.appletgui, "AlignFrame", jalview.appletgui.EmbmenuFrame, [java.awt.event.ActionListener, java.awt.event.ItemListener, java.awt.event.KeyListener, jalview.api.AlignViewControllerGuiI]);
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125 Clazz.prepareFields (c$, function () {
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126 this.alignFrameMenuBar = new awt2swing.MenuBar ();
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127 this.fileMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.file"));
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128 this.loadApplication = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.view_full_application"));
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129 this.$loadTree = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.load_associated_tree"));
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130 this.$loadAnnotations = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.load_features_annotations"));
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131 this.$outputFeatures = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.export_features").concat ("..."));
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132 this.$outputAnnotations = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.export_annotations").concat ("..."));
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133 this.closeMenuItem = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("action.close"));
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134 this.selectAllSequenceMenuItem = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("action.select_all"));
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135 this.deselectAllSequenceMenuItem = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("action.deselect_all"));
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136 this.invertSequenceMenuItem = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("action.invert_selection"));
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137 this.remove2LeftMenuItem = new awt2swing.MenuItem ();
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138 this.remove2RightMenuItem = new awt2swing.MenuItem ();
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139 this.removeGappedColumnMenuItem = new awt2swing.MenuItem ();
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140 this.removeAllGapsMenuItem = new awt2swing.MenuItem ();
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141 this.viewBoxesMenuItem = new awt2swing.CheckboxMenuItem ();
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142 this.viewTextMenuItem = new awt2swing.CheckboxMenuItem ();
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143 this.sortPairwiseMenuItem = new awt2swing.MenuItem ();
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144 this.sortIDMenuItem = new awt2swing.MenuItem ();
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145 this.sortLengthMenuItem = new awt2swing.MenuItem ();
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146 this.sortGroupMenuItem = new awt2swing.MenuItem ();
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147 this.removeRedundancyMenuItem = new awt2swing.MenuItem ();
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148 this.pairwiseAlignmentMenuItem = new awt2swing.MenuItem ();
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149 this.PCAMenuItem = new awt2swing.MenuItem ();
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150 this.averageDistanceTreeMenuItem = new awt2swing.MenuItem ();
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151 this.neighbourTreeMenuItem = new awt2swing.MenuItem ();
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152 this.borderLayout1 = new java.awt.BorderLayout ();
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153 this.statusBar = new awt2swing.Label ();
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154 this.clustalColour = new awt2swing.MenuItem ();
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155 this.zappoColour = new awt2swing.MenuItem ();
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156 this.taylorColour = new awt2swing.MenuItem ();
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157 this.hydrophobicityColour = new awt2swing.MenuItem ();
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158 this.helixColour = new awt2swing.MenuItem ();
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159 this.strandColour = new awt2swing.MenuItem ();
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160 this.turnColour = new awt2swing.MenuItem ();
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161 this.buriedColour = new awt2swing.MenuItem ();
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162 this.purinePyrimidineColour = new awt2swing.MenuItem ();
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163 this.RNAInteractionColour = new awt2swing.MenuItem ();
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164 this.RNAHelixColour = new awt2swing.MenuItem ();
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165 this.userDefinedColour = new awt2swing.MenuItem ();
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166 this.PIDColour = new awt2swing.MenuItem ();
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167 this.BLOSUM62Colour = new awt2swing.MenuItem ();
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168 this.tcoffeeColour = new awt2swing.MenuItem ();
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169 this.njTreeBlosumMenuItem = new awt2swing.MenuItem ();
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170 this.avDistanceTreeBlosumMenuItem = new awt2swing.MenuItem ();
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171 this.annotationPanelMenuItem = new awt2swing.CheckboxMenuItem ();
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172 this.colourTextMenuItem = new awt2swing.CheckboxMenuItem ();
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173 this.displayNonconservedMenuItem = new awt2swing.CheckboxMenuItem ();
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174 this.alProperties = new awt2swing.MenuItem (jalview.util.MessageManager.getString ("label.alignment_props"));
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175 this.overviewMenuItem = new awt2swing.MenuItem ();
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176 this.undoMenuItem = new awt2swing.MenuItem ();
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177 this.redoMenuItem = new awt2swing.MenuItem ();
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178 this.conservationMenuItem = new awt2swing.CheckboxMenuItem ();
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179 this.noColourmenuItem = new awt2swing.MenuItem ();
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180 this.wrapMenuItem = new awt2swing.CheckboxMenuItem ();
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181 this.renderGapsMenuItem = new awt2swing.CheckboxMenuItem ();
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182 this.findMenuItem = new awt2swing.MenuItem ();
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183 this.abovePIDThreshold = new awt2swing.CheckboxMenuItem ();
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184 this.nucleotideColour = new awt2swing.MenuItem ();
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185 this.deleteGroups = new awt2swing.MenuItem ();
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186 this.grpsFromSelection = new awt2swing.MenuItem ();
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187 this.createGroup = new awt2swing.MenuItem ();
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188 this.unGroup = new awt2swing.MenuItem ();
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189 this.$delete = new awt2swing.MenuItem ();
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190 this.copy = new awt2swing.MenuItem ();
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191 this.cut = new awt2swing.MenuItem ();
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192 this.pasteMenu = new awt2swing.Menu ();
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193 this.pasteNew = new awt2swing.MenuItem ();
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194 this.pasteThis = new awt2swing.MenuItem ();
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195 this.applyToAllGroups = new awt2swing.CheckboxMenuItem ();
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196 this.$font = new awt2swing.MenuItem ();
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197 this.scaleAbove = new awt2swing.CheckboxMenuItem ();
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198 this.scaleLeft = new awt2swing.CheckboxMenuItem ();
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199 this.scaleRight = new awt2swing.CheckboxMenuItem ();
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200 this.modifyPID = new awt2swing.MenuItem ();
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201 this.modifyConservation = new awt2swing.MenuItem ();
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202 this.$sortByTree = new awt2swing.CheckboxMenuItem ("Sort Alignment With New Tree", true);
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203 this.sortByTreeMenu = new awt2swing.Menu ();
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204 this.inputText = new awt2swing.MenuItem ();
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205 this.documentation = new awt2swing.MenuItem ();
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206 this.about = new awt2swing.MenuItem ();
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207 this.seqLimits = new awt2swing.CheckboxMenuItem ();
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208 this.centreColumnLabelFlag = new awt2swing.CheckboxMenuItem ();
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209 this.followMouseOverFlag = new awt2swing.CheckboxMenuItem ();
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210 this.showSequenceLogo = new awt2swing.CheckboxMenuItem ();
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211 this.applyAutoAnnotationSettings = new awt2swing.CheckboxMenuItem ();
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212 this.showConsensusHistogram = new awt2swing.CheckboxMenuItem ();
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213 this.showGroupConsensus = new awt2swing.CheckboxMenuItem ();
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214 this.showGroupConservation = new awt2swing.CheckboxMenuItem ();
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215 this.normSequenceLogo = new awt2swing.CheckboxMenuItem ();
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216 this.featureSettings = new awt2swing.MenuItem ();
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217 this.sequenceFeatures = new awt2swing.CheckboxMenuItem ();
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218 this.annotationColour = new awt2swing.MenuItem ();
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219 this.annotationColumnSelection = new awt2swing.MenuItem ();
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220 this.invertColSel = new awt2swing.MenuItem ();
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221 this.showColumns = new awt2swing.MenuItem ();
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222 this.showSeqs = new awt2swing.MenuItem ();
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223 this.hideColumns = new awt2swing.MenuItem ();
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224 this.hideSequences = new awt2swing.MenuItem ();
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225 this.hideAllButSelection = new awt2swing.MenuItem ();
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226 this.hideAllSelection = new awt2swing.MenuItem ();
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227 this.showAllHidden = new awt2swing.MenuItem ();
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228 this.$newView = new awt2swing.MenuItem ();
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230 Clazz.makeConstructor (c$,
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231 function (al, applet, title, embedded) {
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232 this.construct (al, applet, title, embedded, true);
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233 }, "jalview.datamodel.AlignmentI,jalview.bin.JalviewLite,~S,~B");
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234 Clazz.makeConstructor (c$,
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235 function (al, applet, title, embedded, addToDisplay) {
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236 this.construct (al, null, null, applet, title, embedded, addToDisplay);
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237 }, "jalview.datamodel.AlignmentI,jalview.bin.JalviewLite,~S,~B,~B");
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238 Clazz.makeConstructor (c$,
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239 function (al, hiddenSeqs, columnSelection, applet, title, embedded) {
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240 this.construct (al, hiddenSeqs, columnSelection, applet, title, embedded, true);
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241 }, "jalview.datamodel.AlignmentI,~A,jalview.datamodel.ColumnSelection,jalview.bin.JalviewLite,~S,~B");
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242 Clazz.makeConstructor (c$,
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243 function (al, hiddenSeqs, columnSelection, applet, title, embedded, addToDisplay) {
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244 Clazz.superConstructor (this, jalview.appletgui.AlignFrame, []);
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245 if (applet != null) {
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246 this.jalviewServletURL = applet.jalviewServletURL;
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250 if (Clazz.exceptionOf (ex, Exception)) {
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251 ex.printStackTrace ();
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256 if (applet != null) {
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259 param = applet.windowWidth;
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260 if (param != null) {
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261 var width = Integer.parseInt (param);
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262 this.frameWidth = width;
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263 }param = applet.windowHeight;
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264 if (param != null) {
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265 var height = Integer.parseInt (param);
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266 this.frameHeight = height;
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268 if (Clazz.exceptionOf (ex, Exception)) {
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273 }this.viewport = new jalview.appletgui.AlignViewport (al, applet);
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274 if (hiddenSeqs != null && hiddenSeqs.length > 0) {
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275 this.viewport.hideSequence (hiddenSeqs);
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276 }if (columnSelection != null) {
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277 this.viewport.setColumnSelection (columnSelection);
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278 }this.alignPanel = new jalview.appletgui.AlignmentPanel (this, this.viewport);
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279 this.avc = new jalview.controller.AlignViewController (this, this.viewport, this.alignPanel);
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280 this.viewport.updateConservation (this.alignPanel);
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281 this.viewport.updateConsensus (this.alignPanel);
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282 this.displayNonconservedMenuItem.setState (this.viewport.getShowUnconserved ());
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283 this.followMouseOverFlag.setState (this.viewport.isFollowHighlight ());
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284 this.showGroupConsensus.setState (this.viewport.isShowGroupConsensus ());
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285 this.showGroupConservation.setState (this.viewport.isShowGroupConservation ());
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286 this.showConsensusHistogram.setState (this.viewport.isShowConsensusHistogram ());
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287 this.showSequenceLogo.setState (this.viewport.isShowSequenceLogo ());
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288 this.normSequenceLogo.setState (this.viewport.isNormaliseSequenceLogo ());
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289 this.applyToAllGroups.setState (this.viewport.getColourAppliesToAllGroups ());
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290 this.annotationPanelMenuItem.setState (this.viewport.isShowAnnotation ());
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291 this.showAlignmentAnnotations.setState (this.viewport.isShowAnnotation ());
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292 this.showSequenceAnnotations.setState (this.viewport.isShowAnnotation ());
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293 this.seqLimits.setState (this.viewport.getShowJVSuffix ());
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294 if (applet != null) {
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295 var param = applet.sortBy;
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296 if (param != null) {
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297 if (param.equalsIgnoreCase ("Id")) {
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298 this.sortIDMenuItem_actionPerformed ();
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299 } else if (param.equalsIgnoreCase ("Pairwise Identity")) {
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300 this.sortPairwiseMenuItem_actionPerformed ();
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301 } else if (param.equalsIgnoreCase ("Length")) {
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302 this.sortLengthMenuItem_actionPerformed ();
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303 }}param = applet.wrap;
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304 if (param != null) {
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305 if (param.equalsIgnoreCase ("true")) {
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306 this.wrapMenuItem.setState (true);
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307 this.wrapMenuItem_actionPerformed ();
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308 }}param = applet.centrecolumnlabels;
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309 if (param != null) {
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310 this.centreColumnLabelFlag.setState (true);
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311 this.centreColumnLabelFlag_stateChanged ();
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312 }}if (this.viewport.getAlignment ().isNucleotide ()) {
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313 this.viewport.updateStrucConsensus (this.alignPanel);
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314 if (this.viewport.getAlignment ().hasRNAStructure ()) {
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315 this.RNAHelixColour.setEnabled (true);
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317 this.RNAHelixColour.setEnabled (false);
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319 this.RNAHelixColour.setEnabled (false);
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320 this.purinePyrimidineColour.setEnabled (false);
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321 }this.addKeyListener (this);
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322 this.alignPanel.seqPanel.seqCanvas.addKeyListener (this);
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323 this.alignPanel.idPanel.idCanvas.addKeyListener (this);
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324 this.alignPanel.scalePanel.addKeyListener (this);
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325 this.alignPanel.annotationPanel.addKeyListener (this);
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326 this.alignPanel.annotationPanelHolder.addKeyListener (this);
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327 this.alignPanel.annotationSpaceFillerHolder.addKeyListener (this);
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328 this.alignPanel.alabels.addKeyListener (this);
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329 if (addToDisplay) {
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330 this.addToDisplay (embedded);
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331 }}, "jalview.datamodel.AlignmentI,~A,jalview.datamodel.ColumnSelection,jalview.bin.JalviewLite,~S,~B,~B");
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332 Clazz.defineMethod (c$, "addToDisplay",
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333 function (embedded) {
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334 this.createAlignFrameWindow (embedded);
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336 this.alignPanel.adjustAnnotationHeight ();
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337 this.alignPanel.paintAlignment (true);
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339 Clazz.defineMethod (c$, "getAlignViewport",
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341 return this.viewport;
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343 Clazz.defineMethod (c$, "getSeqcanvas",
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345 return this.alignPanel.seqPanel.seqCanvas;
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347 Clazz.defineMethod (c$, "parseFeaturesFile",
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348 function (file, type) {
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349 return this.parseFeaturesFile (file, type, true);
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351 Clazz.defineMethod (c$, "parseFeaturesFile",
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352 function (file, type, autoenabledisplay) {
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353 var featureLinks = new java.util.Hashtable ();
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354 var featuresFile = false;
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356 featuresFile = new jalview.io.FeaturesFile (file, type).parse (this.viewport.getAlignment (), this.alignPanel.seqPanel.seqCanvas.getFeatureRenderer ().getFeatureColours (), featureLinks, true, this.viewport.applet.getDefaultParameter ("relaxedidmatch", false));
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358 if (Clazz.exceptionOf (ex, Exception)) {
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359 ex.printStackTrace ();
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364 if (featuresFile) {
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365 if (featureLinks.size () > 0) {
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366 this.alignPanel.seqPanel.seqCanvas.getFeatureRenderer ().featureLinks = featureLinks;
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367 }if (autoenabledisplay) {
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368 this.viewport.setShowSequenceFeatures (true);
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369 this.sequenceFeatures.setState (true);
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370 }if (this.alignPanel.seqPanel.seqCanvas.fr != null) {
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371 this.alignPanel.seqPanel.seqCanvas.fr.findAllFeatures (true);
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372 }if (this.viewport.featureSettings != null) {
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373 this.viewport.featureSettings.refreshTable ();
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374 }this.alignPanel.paintAlignment (true);
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375 this.setStatus (jalview.util.MessageManager.getString ("label.successfully_added_features_alignment"));
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376 }return featuresFile;
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378 Clazz.overrideMethod (c$, "keyPressed",
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380 if (this.viewport.cursorMode && ((evt.getKeyCode () >= 48 && evt.getKeyCode () <= 57) || (evt.getKeyCode () >= 96 && evt.getKeyCode () <= 105)) && Character.isDigit (evt.getKeyChar ())) {
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381 this.alignPanel.seqPanel.numberPressed (evt.getKeyChar ());
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382 }switch (evt.getKeyCode ()) {
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384 this.deselectAllSequenceMenuItem_actionPerformed ();
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385 this.alignPanel.alabels.cancelDrag ();
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388 if (evt.isControlDown () || evt.isMetaDown ()) {
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389 this.cut_actionPerformed ();
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392 if (this.viewport.cursorMode && !evt.isControlDown ()) {
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393 this.alignPanel.seqPanel.setCursorColumn ();
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394 }if (evt.isControlDown () || evt.isMetaDown ()) {
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395 this.copy_actionPerformed ();
\r
398 if (evt.isControlDown ()) {
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399 this.paste (evt.isShiftDown ());
\r
402 if (evt.isControlDown () || evt.isMetaDown ()) {
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403 this.selectAllSequenceMenuItem_actionPerformed ();
\r
406 if (this.viewport.cursorMode) {
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407 this.alignPanel.seqPanel.moveCursor (0, 1);
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409 this.moveSelectedSequences (false);
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412 if (this.viewport.cursorMode) {
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413 this.alignPanel.seqPanel.moveCursor (0, -1);
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415 this.moveSelectedSequences (true);
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418 if (evt.isAltDown () || !this.viewport.cursorMode) {
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419 this.slideSequences (false, this.alignPanel.seqPanel.getKeyboardNo1 ());
\r
421 this.alignPanel.seqPanel.moveCursor (-1, 0);
\r
424 if (evt.isAltDown () || !this.viewport.cursorMode) {
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425 this.slideSequences (true, this.alignPanel.seqPanel.getKeyboardNo1 ());
\r
427 this.alignPanel.seqPanel.moveCursor (1, 0);
\r
430 if (this.viewport.cursorMode) {
\r
431 this.alignPanel.seqPanel.insertGapAtCursor (evt.isControlDown () || evt.isShiftDown () || evt.isAltDown ());
\r
435 if (this.viewport.cursorMode) {
\r
436 this.alignPanel.seqPanel.deleteGapAtCursor (evt.isControlDown () || evt.isShiftDown () || evt.isAltDown ());
\r
438 this.cut_actionPerformed ();
\r
439 this.alignPanel.seqPanel.seqCanvas.repaint ();
\r
442 if (this.viewport.cursorMode) {
\r
443 this.alignPanel.seqPanel.setCursorRow ();
\r
446 if (this.viewport.cursorMode) {
\r
447 this.alignPanel.seqPanel.setCursorPosition ();
\r
451 if (this.viewport.cursorMode) {
\r
452 this.alignPanel.seqPanel.setCursorRowAndColumn ();
\r
455 if (this.viewport.cursorMode) {
\r
456 this.alignPanel.seqPanel.setSelectionAreaAtCursor (true);
\r
459 if (this.viewport.cursorMode) {
\r
460 this.alignPanel.seqPanel.setSelectionAreaAtCursor (false);
\r
463 this.viewport.cursorMode = !this.viewport.cursorMode;
\r
464 this.setStatus (jalview.util.MessageManager.formatMessage ("label.keyboard_editing_mode", Clazz.newArray (-1, [(this.viewport.cursorMode ? "on" : "off")])));
\r
465 if (this.viewport.cursorMode) {
\r
466 this.alignPanel.seqPanel.seqCanvas.cursorX = this.viewport.startRes;
\r
467 this.alignPanel.seqPanel.seqCanvas.cursorY = this.viewport.startSeq;
\r
470 if (evt.isControlDown ()) {
\r
471 this.findMenuItem_actionPerformed ();
\r
475 var toggleSeqs = !evt.isControlDown ();
\r
476 var toggleCols = !evt.isShiftDown ();
\r
477 this.toggleHiddenRegions (toggleSeqs, toggleCols);
\r
480 if (this.viewport.getWrapAlignment ()) {
\r
481 this.alignPanel.scrollUp (true);
\r
483 this.alignPanel.setScrollValues (this.viewport.startRes, this.viewport.startSeq - this.viewport.endSeq + this.viewport.startSeq);
\r
486 if (this.viewport.getWrapAlignment ()) {
\r
487 this.alignPanel.scrollUp (false);
\r
489 this.alignPanel.setScrollValues (this.viewport.startRes, this.viewport.startSeq + this.viewport.endSeq - this.viewport.startSeq);
\r
492 if (evt.isControlDown ()) {
\r
493 this.undoMenuItem_actionPerformed ();
\r
496 if (evt.isControlDown ()) {
\r
497 this.redoMenuItem_actionPerformed ();
\r
500 if (evt.isControlDown ()) {
\r
501 this.trimAlignment (true);
\r
504 if (evt.isControlDown ()) {
\r
505 this.trimAlignment (false);
\r
508 if (evt.isControlDown ()) {
\r
509 if (evt.isShiftDown ()) {
\r
510 this.removeAllGapsMenuItem_actionPerformed ();
\r
512 this.removeGappedColumnMenuItem_actionPerformed ();
\r
515 if (evt.isControlDown ()) {
\r
516 if (evt.isAltDown ()) {
\r
517 this.invertColSel_actionPerformed ();
\r
519 this.invertSequenceMenuItem_actionPerformed ();
\r
522 if (evt.isControlDown ()) {
\r
523 if (evt.isShiftDown ()) {
\r
524 this.unGroup_actionPerformed ();
\r
526 this.createGroup_actionPerformed ();
\r
529 if (evt.isControlDown ()) {
\r
530 this.deleteGroups_actionPerformed ();
\r
533 if (evt.isControlDown ()) {
\r
534 this.newView (null);
\r
537 this.alignPanel.paintAlignment (true);
\r
538 }, "java.awt.event.KeyEvent");
\r
539 Clazz.defineMethod (c$, "toggleHiddenRegions",
\r
540 function (toggleSeqs, toggleCols) {
\r
542 var sg = this.viewport.getSelectionGroup ();
\r
543 if (!toggleSeqs && !toggleCols) {
\r
544 if ((this.viewport.getColumnSelection () != null && this.viewport.getColumnSelection ().getSelected () != null && this.viewport.getColumnSelection ().getSelected ().size () > 0) || (sg != null && sg.getSize () > 0 && sg.getStartRes () <= sg.getEndRes ())) {
\r
546 this.invertSequenceMenuItem_actionPerformed ();
\r
547 sg = this.viewport.getSelectionGroup ();
\r
549 }this.viewport.expandColSelection (sg, true);
\r
550 this.invertColSel_actionPerformed ();
\r
552 }}if (toggleSeqs) {
\r
553 if (sg != null && sg.getSize () != this.viewport.getAlignment ().getHeight ()) {
\r
555 this.viewport.hideAllSelectedSeqs ();
\r
556 } else if (!(toggleCols && this.viewport.getColumnSelection ().getSelected ().size () > 0)) {
\r
557 this.viewport.showAllHiddenSeqs ();
\r
558 }}if (toggleCols) {
\r
559 if (this.viewport.getColumnSelection ().getSelected ().size () > 0) {
\r
560 this.viewport.hideSelectedColumns ();
\r
562 this.viewport.setSelectionGroup (sg);
\r
563 }} else if (!hide) {
\r
564 this.viewport.showAllHiddenColumns ();
\r
566 Clazz.overrideMethod (c$, "keyReleased",
\r
568 }, "java.awt.event.KeyEvent");
\r
569 Clazz.overrideMethod (c$, "keyTyped",
\r
571 }, "java.awt.event.KeyEvent");
\r
572 Clazz.overrideMethod (c$, "itemStateChanged",
\r
574 var source = evt.getSource ();
\r
575 if (source === this.displayNonconservedMenuItem) {
\r
576 this.displayNonconservedMenuItem_actionPerformed ();
\r
577 } else if (source === this.colourTextMenuItem) {
\r
578 this.colourTextMenuItem_actionPerformed ();
\r
579 } else if (source === this.wrapMenuItem) {
\r
580 this.wrapMenuItem_actionPerformed ();
\r
581 } else if (source === this.scaleAbove) {
\r
582 this.viewport.setScaleAboveWrapped (this.scaleAbove.getState ());
\r
583 } else if (source === this.scaleLeft) {
\r
584 this.viewport.setScaleLeftWrapped (this.scaleLeft.getState ());
\r
585 } else if (source === this.scaleRight) {
\r
586 this.viewport.setScaleRightWrapped (this.scaleRight.getState ());
\r
587 } else if (source === this.seqLimits) {
\r
588 this.seqLimits_itemStateChanged ();
\r
589 } else if (source === this.viewBoxesMenuItem) {
\r
590 this.viewport.setShowBoxes (this.viewBoxesMenuItem.getState ());
\r
591 } else if (source === this.viewTextMenuItem) {
\r
592 this.viewport.setShowText (this.viewTextMenuItem.getState ());
\r
593 } else if (source === this.renderGapsMenuItem) {
\r
594 this.viewport.setRenderGaps (this.renderGapsMenuItem.getState ());
\r
595 } else if (source === this.annotationPanelMenuItem) {
\r
596 this.viewport.setShowAnnotation (this.annotationPanelMenuItem.getState ());
\r
597 this.alignPanel.setAnnotationVisible (this.annotationPanelMenuItem.getState ());
\r
598 } else if (source === this.sequenceFeatures) {
\r
599 this.viewport.setShowSequenceFeatures (this.sequenceFeatures.getState ());
\r
600 this.alignPanel.seqPanel.seqCanvas.repaint ();
\r
601 } else if (source === this.showAlignmentAnnotations) {
\r
602 this.setAnnotationsVisibility ();
\r
603 } else if (source === this.showSequenceAnnotations) {
\r
604 this.setAnnotationsVisibility ();
\r
605 } else if (source === this.sortAnnBySequence) {
\r
606 var newState = this.sortAnnBySequence.getState ();
\r
607 this.sortAnnByLabel.setState (false);
\r
608 this.setAnnotationSortOrder (newState ? jalview.analysis.AnnotationSorter.SequenceAnnotationOrder.SEQUENCE_AND_LABEL : jalview.analysis.AnnotationSorter.SequenceAnnotationOrder.NONE);
\r
609 this.setViewportAnnotationOrder ();
\r
610 } else if (source === this.sortAnnByLabel) {
\r
611 var newState = this.sortAnnByLabel.getState ();
\r
612 this.sortAnnBySequence.setState (false);
\r
613 this.setAnnotationSortOrder (newState ? jalview.analysis.AnnotationSorter.SequenceAnnotationOrder.LABEL_AND_SEQUENCE : jalview.analysis.AnnotationSorter.SequenceAnnotationOrder.NONE);
\r
614 this.setViewportAnnotationOrder ();
\r
615 } else if (source === this.showAutoFirst) {
\r
616 this.showAutoLast.setState (!this.showAutoFirst.getState ());
\r
617 this.setShowAutoCalculatedAbove (this.showAutoFirst.getState ());
\r
618 this.setViewportAnnotationOrder ();
\r
619 } else if (source === this.showAutoLast) {
\r
620 this.showAutoFirst.setState (!this.showAutoLast.getState ());
\r
621 this.setShowAutoCalculatedAbove (this.showAutoFirst.getState ());
\r
622 this.setViewportAnnotationOrder ();
\r
623 } else if (source === this.conservationMenuItem) {
\r
624 this.conservationMenuItem_actionPerformed ();
\r
625 } else if (source === this.abovePIDThreshold) {
\r
626 this.abovePIDThreshold_actionPerformed ();
\r
627 } else if (source === this.applyToAllGroups) {
\r
628 this.viewport.setColourAppliesToAllGroups (this.applyToAllGroups.getState ());
\r
629 } else if (source === this.autoCalculate) {
\r
630 this.viewport.autoCalculateConsensus = this.autoCalculate.getState ();
\r
631 } else if (source === this.$sortByTree) {
\r
632 this.viewport.sortByTree = this.$sortByTree.getState ();
\r
633 } else if (source === this.centreColumnLabelFlag) {
\r
634 this.centreColumnLabelFlag_stateChanged ();
\r
635 } else if (source === this.followMouseOverFlag) {
\r
636 this.mouseOverFlag_stateChanged ();
\r
637 } else if (source === this.showGroupConsensus) {
\r
638 this.showGroupConsensus_actionPerformed ();
\r
639 } else if (source === this.showGroupConservation) {
\r
640 this.showGroupConservation_actionPerformed ();
\r
641 } else if (source === this.showSequenceLogo) {
\r
642 this.showSequenceLogo_actionPerformed ();
\r
643 } else if (source === this.normSequenceLogo) {
\r
644 this.normSequenceLogo_actionPerformed ();
\r
645 } else if (source === this.showConsensusHistogram) {
\r
646 this.showConsensusHistogram_actionPerformed ();
\r
647 } else if (source === this.applyAutoAnnotationSettings) {
\r
648 this.applyAutoAnnotationSettings_actionPerformed ();
\r
649 }this.alignPanel.paintAlignment (true);
\r
650 }, "java.awt.event.ItemEvent");
\r
651 Clazz.defineMethod (c$, "setAnnotationsVisibility",
\r
653 var showForAlignment = this.showAlignmentAnnotations.getState ();
\r
654 var showForSequences = this.showSequenceAnnotations.getState ();
\r
655 for (var aa, $aa = 0, $$aa = this.alignPanel.getAlignment ().getAlignmentAnnotation (); $aa < $$aa.length && ((aa = $$aa[$aa]) || true); $aa++) {
\r
656 var visible = (aa.sequenceRef == null ? showForAlignment : showForSequences);
\r
657 aa.visible = visible;
\r
659 this.alignPanel.validateAnnotationDimensions (true);
\r
663 Clazz.defineMethod (c$, "setAnnotationSortOrder",
\r
665 this.annotationSortOrder = order;
\r
666 }, "jalview.analysis.AnnotationSorter.SequenceAnnotationOrder");
\r
667 Clazz.defineMethod (c$, "setViewportAnnotationOrder",
\r
669 this.alignPanel.av.setSortAnnotationsBy (this.annotationSortOrder);
\r
670 this.alignPanel.av.setShowAutocalculatedAbove (this.showAutoCalculatedAbove);
\r
672 Clazz.defineMethod (c$, "setShowAutoCalculatedAbove",
\r
673 function (showAbove) {
\r
674 this.showAutoCalculatedAbove = showAbove;
\r
676 Clazz.defineMethod (c$, "mouseOverFlag_stateChanged",
\r
678 this.viewport.setFollowHighlight (this.followMouseOverFlag.getState ());
\r
680 Clazz.defineMethod (c$, "centreColumnLabelFlag_stateChanged",
\r
682 this.viewport.centreColumnLabels = this.centreColumnLabelFlag.getState ();
\r
683 this.alignPanel.annotationPanel.repaint ();
\r
685 Clazz.overrideMethod (c$, "actionPerformed",
\r
687 var source = evt.getSource ();
\r
688 if (source === this.inputText) {
\r
689 this.inputText_actionPerformed ();
\r
690 } else if (source === this.$loadTree) {
\r
691 this.loadTree_actionPerformed ();
\r
692 } else if (source === this.loadApplication) {
\r
693 this.launchFullApplication ();
\r
694 } else if (source === this.$loadAnnotations) {
\r
695 this.loadAnnotations ();
\r
696 } else if (source === this.$outputAnnotations) {
\r
697 this.outputAnnotations (true);
\r
698 } else if (source === this.$outputFeatures) {
\r
699 this.outputFeatures (true, "Jalview");
\r
700 } else if (source === this.closeMenuItem) {
\r
701 this.closeMenuItem_actionPerformed ();
\r
702 } else if (source === this.copy) {
\r
703 this.copy_actionPerformed ();
\r
704 } else if (source === this.undoMenuItem) {
\r
705 this.undoMenuItem_actionPerformed ();
\r
706 } else if (source === this.redoMenuItem) {
\r
707 this.redoMenuItem_actionPerformed ();
\r
708 } else if (source === this.inputText) {
\r
709 this.inputText_actionPerformed ();
\r
710 } else if (source === this.closeMenuItem) {
\r
711 this.closeMenuItem_actionPerformed ();
\r
712 } else if (source === this.undoMenuItem) {
\r
713 this.undoMenuItem_actionPerformed ();
\r
714 } else if (source === this.redoMenuItem) {
\r
715 this.redoMenuItem_actionPerformed ();
\r
716 } else if (source === this.copy) {
\r
717 this.copy_actionPerformed ();
\r
718 } else if (source === this.pasteNew) {
\r
719 this.pasteNew_actionPerformed ();
\r
720 } else if (source === this.pasteThis) {
\r
721 this.pasteThis_actionPerformed ();
\r
722 } else if (source === this.cut) {
\r
723 this.cut_actionPerformed ();
\r
724 } else if (source === this.$delete) {
\r
725 this.delete_actionPerformed ();
\r
726 } else if (source === this.grpsFromSelection) {
\r
727 this.makeGrpsFromSelection_actionPerformed ();
\r
728 } else if (source === this.deleteGroups) {
\r
729 this.deleteGroups_actionPerformed ();
\r
730 } else if (source === this.selectAllSequenceMenuItem) {
\r
731 this.selectAllSequenceMenuItem_actionPerformed ();
\r
732 } else if (source === this.deselectAllSequenceMenuItem) {
\r
733 this.deselectAllSequenceMenuItem_actionPerformed ();
\r
734 } else if (source === this.invertSequenceMenuItem) {
\r
735 this.invertSequenceMenuItem_actionPerformed ();
\r
736 } else if (source === this.invertColSel) {
\r
737 this.viewport.invertColumnSelection ();
\r
738 this.alignPanel.paintAlignment (true);
\r
739 } else if (source === this.remove2LeftMenuItem) {
\r
740 this.trimAlignment (true);
\r
741 } else if (source === this.remove2RightMenuItem) {
\r
742 this.trimAlignment (false);
\r
743 } else if (source === this.removeGappedColumnMenuItem) {
\r
744 this.removeGappedColumnMenuItem_actionPerformed ();
\r
745 } else if (source === this.removeAllGapsMenuItem) {
\r
746 this.removeAllGapsMenuItem_actionPerformed ();
\r
747 } else if (source === this.findMenuItem) {
\r
748 this.findMenuItem_actionPerformed ();
\r
749 } else if (source === this.$font) {
\r
750 new jalview.appletgui.FontChooser (this.alignPanel);
\r
751 } else if (source === this.$newView) {
\r
752 this.newView (null);
\r
753 } else if (source === this.showColumns) {
\r
754 this.viewport.showAllHiddenColumns ();
\r
755 this.alignPanel.paintAlignment (true);
\r
756 } else if (source === this.showSeqs) {
\r
757 this.viewport.showAllHiddenSeqs ();
\r
758 this.alignPanel.paintAlignment (true);
\r
759 } else if (source === this.hideColumns) {
\r
760 this.viewport.hideSelectedColumns ();
\r
761 this.alignPanel.paintAlignment (true);
\r
762 } else if (source === this.hideSequences && this.viewport.getSelectionGroup () != null) {
\r
763 this.viewport.hideAllSelectedSeqs ();
\r
764 this.alignPanel.paintAlignment (true);
\r
765 } else if (source === this.hideAllButSelection) {
\r
766 this.toggleHiddenRegions (false, false);
\r
767 this.alignPanel.paintAlignment (true);
\r
768 } else if (source === this.hideAllSelection) {
\r
769 var sg = this.viewport.getSelectionGroup ();
\r
770 this.viewport.expandColSelection (sg, false);
\r
771 this.viewport.hideAllSelectedSeqs ();
\r
772 this.viewport.hideSelectedColumns ();
\r
773 this.alignPanel.paintAlignment (true);
\r
774 } else if (source === this.showAllHidden) {
\r
775 this.viewport.showAllHiddenColumns ();
\r
776 this.viewport.showAllHiddenSeqs ();
\r
777 this.alignPanel.paintAlignment (true);
\r
778 } else if (source === this.showGroupConsensus) {
\r
779 this.showGroupConsensus_actionPerformed ();
\r
780 } else if (source === this.showGroupConservation) {
\r
781 this.showGroupConservation_actionPerformed ();
\r
782 } else if (source === this.showSequenceLogo) {
\r
783 this.showSequenceLogo_actionPerformed ();
\r
784 } else if (source === this.normSequenceLogo) {
\r
785 this.normSequenceLogo_actionPerformed ();
\r
786 } else if (source === this.showConsensusHistogram) {
\r
787 this.showConsensusHistogram_actionPerformed ();
\r
788 } else if (source === this.applyAutoAnnotationSettings) {
\r
789 this.applyAutoAnnotationSettings_actionPerformed ();
\r
790 } else if (source === this.featureSettings) {
\r
791 new jalview.appletgui.FeatureSettings (this.alignPanel);
\r
792 } else if (source === this.alProperties) {
\r
793 var contents = new jalview.io.AlignmentProperties (this.viewport.getAlignment ()).formatAsString ();
\r
794 var cap = new jalview.appletgui.CutAndPasteTransfer (false, this);
\r
795 cap.setText (contents.toString ());
\r
796 var frame = new awt2swing.Frame ();
\r
798 jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.formatMessage ("label.alignment_properties", Clazz.newArray (-1, [this.getTitle ()])), 400, 250);
\r
799 } else if (source === this.overviewMenuItem) {
\r
800 this.overviewMenuItem_actionPerformed ();
\r
801 } else if (source === this.noColourmenuItem) {
\r
802 this.changeColour (null);
\r
803 } else if (source === this.clustalColour) {
\r
804 this.abovePIDThreshold.setState (false);
\r
805 this.changeColour ( new jalview.schemes.ClustalxColourScheme (this.viewport.getAlignment (), null));
\r
806 } else if (source === this.zappoColour) {
\r
807 this.changeColour ( new jalview.schemes.ZappoColourScheme ());
\r
808 } else if (source === this.taylorColour) {
\r
809 this.changeColour ( new jalview.schemes.TaylorColourScheme ());
\r
810 } else if (source === this.hydrophobicityColour) {
\r
811 this.changeColour ( new jalview.schemes.HydrophobicColourScheme ());
\r
812 } else if (source === this.helixColour) {
\r
813 this.changeColour ( new jalview.schemes.HelixColourScheme ());
\r
814 } else if (source === this.strandColour) {
\r
815 this.changeColour ( new jalview.schemes.StrandColourScheme ());
\r
816 } else if (source === this.turnColour) {
\r
817 this.changeColour ( new jalview.schemes.TurnColourScheme ());
\r
818 } else if (source === this.buriedColour) {
\r
819 this.changeColour ( new jalview.schemes.BuriedColourScheme ());
\r
820 } else if (source === this.nucleotideColour) {
\r
821 this.changeColour ( new jalview.schemes.NucleotideColourScheme ());
\r
822 } else if (source === this.purinePyrimidineColour) {
\r
823 this.changeColour ( new jalview.schemes.PurinePyrimidineColourScheme ());
\r
824 } else if (source === this.RNAInteractionColour) {
\r
825 this.changeColour ( new jalview.schemes.RNAInteractionColourScheme ());
\r
826 } else if (source === this.RNAHelixColour) {
\r
827 new jalview.schemes.RNAHelicesColourChooser (this.viewport, this.alignPanel);
\r
828 } else if (source === this.modifyPID) {
\r
829 this.modifyPID_actionPerformed ();
\r
830 } else if (source === this.modifyConservation) {
\r
831 this.modifyConservation_actionPerformed ();
\r
832 } else if (source === this.userDefinedColour) {
\r
833 new jalview.appletgui.UserDefinedColours (this.alignPanel, null);
\r
834 } else if (source === this.PIDColour) {
\r
835 this.changeColour ( new jalview.schemes.PIDColourScheme ());
\r
836 } else if (source === this.BLOSUM62Colour) {
\r
837 this.changeColour ( new jalview.schemes.Blosum62ColourScheme ());
\r
838 } else if (source === this.tcoffeeColour) {
\r
839 this.changeColour ( new jalview.schemes.TCoffeeColourScheme (this.alignPanel.getAlignment ()));
\r
840 } else if (source === this.annotationColour) {
\r
841 new jalview.appletgui.AnnotationColourChooser (this.viewport, this.alignPanel);
\r
842 } else if (source === this.annotationColumnSelection) {
\r
843 new jalview.appletgui.AnnotationColumnChooser (this.viewport, this.alignPanel);
\r
844 } else if (source === this.sortPairwiseMenuItem) {
\r
845 this.sortPairwiseMenuItem_actionPerformed ();
\r
846 } else if (source === this.sortIDMenuItem) {
\r
847 this.sortIDMenuItem_actionPerformed ();
\r
848 } else if (source === this.sortLengthMenuItem) {
\r
849 this.sortLengthMenuItem_actionPerformed ();
\r
850 } else if (source === this.sortGroupMenuItem) {
\r
851 this.sortGroupMenuItem_actionPerformed ();
\r
852 } else if (source === this.removeRedundancyMenuItem) {
\r
853 this.removeRedundancyMenuItem_actionPerformed ();
\r
854 } else if (source === this.pairwiseAlignmentMenuItem) {
\r
855 this.pairwiseAlignmentMenuItem_actionPerformed ();
\r
856 } else if (source === this.PCAMenuItem) {
\r
857 this.PCAMenuItem_actionPerformed ();
\r
858 } else if (source === this.averageDistanceTreeMenuItem) {
\r
859 this.averageDistanceTreeMenuItem_actionPerformed ();
\r
860 } else if (source === this.neighbourTreeMenuItem) {
\r
861 this.neighbourTreeMenuItem_actionPerformed ();
\r
862 } else if (source === this.njTreeBlosumMenuItem) {
\r
863 this.njTreeBlosumMenuItem_actionPerformed ();
\r
864 } else if (source === this.avDistanceTreeBlosumMenuItem) {
\r
865 this.avTreeBlosumMenuItem_actionPerformed ();
\r
866 } else if (source === this.documentation) {
\r
867 this.documentation_actionPerformed ();
\r
868 } else if (source === this.about) {
\r
869 this.about_actionPerformed ();
\r
870 }}, "java.awt.event.ActionEvent");
\r
871 Clazz.defineMethod (c$, "inputText_actionPerformed",
\r
873 var cap = new jalview.appletgui.CutAndPasteTransfer (true, this);
\r
874 var frame = new awt2swing.Frame ();
\r
876 jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.getString ("label.input_cut_paste"), 500, 500);
\r
878 Clazz.defineMethod (c$, "outputText_actionPerformed",
\r
880 var cap = new jalview.appletgui.CutAndPasteTransfer (true, this);
\r
881 var frame = new awt2swing.Frame ();
\r
883 jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.formatMessage ("label.alignment_output_command", Clazz.newArray (-1, [e.getActionCommand ()])), 600, 500);
\r
884 var fr = this.alignPanel.cloneFeatureRenderer ();
\r
885 cap.setText ( new jalview.io.AppletFormatAdapter (this.alignPanel).formatSequences (e.getActionCommand (), this.viewport.getAlignment (), this.viewport.getShowJVSuffix ()));
\r
886 }, "java.awt.event.ActionEvent");
\r
887 Clazz.defineMethod (c$, "loadAnnotations",
\r
889 var cap = new jalview.appletgui.CutAndPasteTransfer (true, this);
\r
890 cap.setText (jalview.util.MessageManager.getString ("label.paste_features_annotations_Tcoffee_here"));
\r
891 cap.setAnnotationImport ();
\r
892 var frame = new awt2swing.Frame ();
\r
894 jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.getString ("action.paste_annotations"), 400, 300);
\r
896 Clazz.defineMethod (c$, "outputAnnotations",
\r
897 function (displayTextbox) {
\r
898 var annotation = new jalview.io.AnnotationFile ().printAnnotationsForView (this.viewport);
\r
899 if (displayTextbox) {
\r
900 var cap = new jalview.appletgui.CutAndPasteTransfer (false, this);
\r
901 var frame = new awt2swing.Frame ();
\r
903 jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.getString ("label.annotations"), 600, 500);
\r
904 cap.setText (annotation);
\r
905 }return annotation;
\r
907 Clazz.defineMethod (c$, "getDisplayedFeatureCols",
\r
909 if (this.alignPanel.getFeatureRenderer () != null && this.viewport.getFeaturesDisplayed () != null) {
\r
910 return this.alignPanel.getFeatureRenderer ().getDisplayedFeatureCols ();
\r
913 Clazz.defineMethod (c$, "outputFeatures",
\r
914 function (displayTextbox, format) {
\r
916 if (format.equalsIgnoreCase ("Jalview")) {
\r
917 features = new jalview.io.FeaturesFile ().printJalviewFormat (this.viewport.getAlignment ().getSequencesArray (), this.getDisplayedFeatureCols ());
\r
919 features = new jalview.io.FeaturesFile ().printGFFFormat (this.viewport.getAlignment ().getSequencesArray (), this.getDisplayedFeatureCols ());
\r
920 }if (displayTextbox) {
\r
921 var frimport = false;
\r
922 if (features == null || features.equals ("No Features Visible")) {
\r
923 features = "# No features visible - paste some and import them here.";
\r
925 }var cap = new jalview.appletgui.CutAndPasteTransfer (frimport, this);
\r
927 cap.setAnnotationImport ();
\r
928 }var frame = new awt2swing.Frame ();
\r
930 jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.getString ("label.features"), 600, 500);
\r
931 cap.setText (features);
\r
933 if (features == null) {
\r
937 Clazz.defineMethod (c$, "launchFullApplication",
\r
939 var url = new StringBuffer (this.jalviewServletURL);
\r
940 var firstSep = url.lastIndexOf ("?") > url.lastIndexOf ("/") ? "&" : "?";
\r
941 url.append (firstSep);
\r
942 var applet = this.viewport.applet;
\r
943 var s = applet.startupFile;
\r
944 url.append ("open=" + this.appendProtocol (s));
\r
945 if (this.viewport.applet.features != null) {
\r
946 url.append ("&features=");
\r
947 url.append (this.appendProtocol (applet.features));
\r
948 }if (applet.annotations != null) {
\r
949 url.append ("&annotations=");
\r
950 url.append (this.appendProtocol (applet.annotations));
\r
951 }if (applet.jnetFile != null) {
\r
952 url.append ("&annotations=");
\r
953 url.append (this.appendProtocol (applet.jnetFile));
\r
954 }if (applet.defaultColour != null) {
\r
955 url.append ("&colour=" + this.removeWhiteSpace (applet.defaultColour));
\r
956 }if (applet.userDefinedColour != null) {
\r
957 url.append ("&colour=" + this.removeWhiteSpace (applet.userDefinedColour));
\r
958 }if (applet.treeFile != null) {
\r
959 url.append ("&tree=" + this.appendProtocol (applet.treeFile));
\r
960 }this.showURL (url.toString (), "FULL_APP");
\r
962 Clazz.defineMethod (c$, "removeWhiteSpace",
\r
963 function (colour) {
\r
964 var sb = new StringBuffer ();
\r
965 for (var i = 0; i < colour.length; i++) {
\r
966 if (Character.isWhitespace (colour.charAt (i))) {
\r
969 sb.append (colour.charAt (i));
\r
971 return sb.toString ();
\r
973 Clazz.defineMethod (c$, "appendProtocol",
\r
976 new java.net.URL (url);
\r
977 url = java.net.URLEncoder.encode (url);
\r
979 if (Clazz.exceptionOf (ex, java.net.MalformedURLException)) {
\r
980 url = this.viewport.applet.getCodeBase () + url;
\r
987 Clazz.defineMethod (c$, "closeMenuItem_actionPerformed",
\r
989 jalview.appletgui.PaintRefresher.RemoveComponent (this.alignPanel);
\r
990 if (this.alignPanel.seqPanel != null && this.alignPanel.seqPanel.seqCanvas != null) {
\r
991 jalview.appletgui.PaintRefresher.RemoveComponent (this.alignPanel.seqPanel.seqCanvas);
\r
992 }if (this.alignPanel.idPanel != null && this.alignPanel.idPanel.idCanvas != null) {
\r
993 jalview.appletgui.PaintRefresher.RemoveComponent (this.alignPanel.idPanel.idCanvas);
\r
994 }if (jalview.appletgui.PaintRefresher.components.size () == 0 && this.viewport.applet == null) {
\r
997 }this.viewport = null;
\r
998 this.alignPanel = null;
\r
1001 Clazz.defineMethod (c$, "updateEditMenuBar",
\r
1003 if (this.viewport.getHistoryList ().size () > 0) {
\r
1004 this.undoMenuItem.setEnabled (true);
\r
1005 var command = this.viewport.getHistoryList ().peek ();
\r
1006 this.undoMenuItem.setLabel (jalview.util.MessageManager.formatMessage ("label.undo_command", Clazz.newArray (-1, [command.getDescription ()])));
\r
1008 this.undoMenuItem.setEnabled (false);
\r
1009 this.undoMenuItem.setLabel (jalview.util.MessageManager.getString ("action.undo"));
\r
1010 }if (this.viewport.getRedoList ().size () > 0) {
\r
1011 this.redoMenuItem.setEnabled (true);
\r
1012 var command = this.viewport.getRedoList ().peek ();
\r
1013 this.redoMenuItem.setLabel (jalview.util.MessageManager.formatMessage ("label.redo_command", Clazz.newArray (-1, [command.getDescription ()])));
\r
1015 this.redoMenuItem.setEnabled (false);
\r
1016 this.redoMenuItem.setLabel (jalview.util.MessageManager.getString ("action.redo"));
\r
1018 Clazz.overrideMethod (c$, "addHistoryItem",
\r
1019 function (command) {
\r
1020 if (command.getSize () > 0) {
\r
1021 this.viewport.addToHistoryList (command);
\r
1022 this.viewport.clearRedoList ();
\r
1023 this.updateEditMenuBar ();
\r
1024 this.viewport.updateHiddenColumns ();
\r
1025 }}, "jalview.commands.CommandI");
\r
1026 Clazz.defineMethod (c$, "undoMenuItem_actionPerformed",
\r
1028 if (this.viewport.getHistoryList ().isEmpty ()) {
\r
1030 }var command = this.viewport.getHistoryList ().pop ();
\r
1031 this.viewport.addToRedoList (command);
\r
1032 command.undoCommand (null);
\r
1033 var originalSource = this.getOriginatingSource (command);
\r
1034 if (originalSource !== this.viewport) {
\r
1035 System.err.println ("Warning: Viewport object mismatch whilst undoing");
\r
1036 }originalSource.updateHiddenColumns ();
\r
1037 this.updateEditMenuBar ();
\r
1038 originalSource.firePropertyChange ("alignment", null, originalSource.getAlignment ().getSequences ());
\r
1040 Clazz.defineMethod (c$, "redoMenuItem_actionPerformed",
\r
1042 if (this.viewport.getRedoList ().isEmpty ()) {
\r
1044 }var command = this.viewport.getRedoList ().pop ();
\r
1045 this.viewport.addToHistoryList (command);
\r
1046 command.doCommand (null);
\r
1047 var originalSource = this.getOriginatingSource (command);
\r
1048 if (originalSource !== this.viewport) {
\r
1049 System.err.println ("Warning: Viewport object mismatch whilst re-doing");
\r
1050 }originalSource.updateHiddenColumns ();
\r
1051 this.updateEditMenuBar ();
\r
1052 originalSource.firePropertyChange ("alignment", null, originalSource.getAlignment ().getSequences ());
\r
1054 Clazz.defineMethod (c$, "getOriginatingSource",
\r
1055 function (command) {
\r
1056 var originalSource = null;
\r
1058 if (Clazz.instanceOf (command, jalview.commands.EditCommand)) {
\r
1059 var editCommand = command;
\r
1060 al = editCommand.getAlignment ();
\r
1061 var comps = jalview.appletgui.PaintRefresher.components.get (this.viewport.getSequenceSetId ());
\r
1062 for (var i = 0; i < comps.size (); i++) {
\r
1063 if (Clazz.instanceOf (comps.elementAt (i), jalview.appletgui.AlignmentPanel)) {
\r
1064 if (al === (comps.elementAt (i)).av.getAlignment ()) {
\r
1065 originalSource = (comps.elementAt (i)).av;
\r
1068 }if (originalSource == null) {
\r
1070 jalview.appletgui.PaintRefresher.validateSequences (al, this.viewport.getAlignment ());
\r
1071 }originalSource = this.viewport;
\r
1072 }return originalSource;
\r
1073 }, "jalview.commands.CommandI");
\r
1074 Clazz.defineMethod (c$, "moveSelectedSequences",
\r
1076 var sg = this.viewport.getSelectionGroup ();
\r
1079 }this.viewport.getAlignment ().moveSelectedSequencesByOne (sg, up ? null : this.viewport.getHiddenRepSequences (), up);
\r
1080 this.alignPanel.paintAlignment (true);
\r
1081 var complement = this.viewport.getCodingComplement ();
\r
1082 if (complement != null) {
\r
1083 var mappedSelection = jalview.util.MappingUtils.mapSequenceGroup (sg, this.viewport, complement);
\r
1084 complement.getAlignment ().moveSelectedSequencesByOne (mappedSelection, up ? null : complement.getHiddenRepSequences (), up);
\r
1086 Clazz.defineMethod (c$, "slideSequences",
\r
1087 function (right, size) {
\r
1088 var sg = new java.util.Vector ();
\r
1089 if (this.viewport.cursorMode) {
\r
1090 sg.add (this.viewport.getAlignment ().getSequenceAt (this.alignPanel.seqPanel.seqCanvas.cursorY));
\r
1091 } else if (this.viewport.getSelectionGroup () != null && this.viewport.getSelectionGroup ().getSize () != this.viewport.getAlignment ().getHeight ()) {
\r
1092 sg = this.viewport.getSelectionGroup ().getSequences (this.viewport.getHiddenRepSequences ());
\r
1093 }if (sg.size () < 1) {
\r
1095 }var invertGroup = new java.util.Vector ();
\r
1096 for (var i = 0; i < this.viewport.getAlignment ().getHeight (); i++) {
\r
1097 if (!sg.contains (this.viewport.getAlignment ().getSequenceAt (i))) {
\r
1098 invertGroup.addElement (this.viewport.getAlignment ().getSequenceAt (i));
\r
1100 var seqs1 = sg.toArray ( new Array (sg.size ()));
\r
1101 var seqs2 = invertGroup.toArray ( new Array (invertGroup.size ()));
\r
1102 for (var i = 0; i < invertGroup.size (); i++) {
\r
1103 seqs2[i] = invertGroup.elementAt (i);
\r
1107 ssc = new jalview.commands.SlideSequencesCommand ("Slide Sequences", seqs2, seqs1, size, this.viewport.getGapCharacter ());
\r
1109 ssc = new jalview.commands.SlideSequencesCommand ("Slide Sequences", seqs1, seqs2, size, this.viewport.getGapCharacter ());
\r
1110 }var groupAdjustment = 0;
\r
1111 if (ssc.getGapsInsertedBegin () && right) {
\r
1112 if (this.viewport.cursorMode) {
\r
1113 this.alignPanel.seqPanel.moveCursor (size, 0);
\r
1115 groupAdjustment = size;
\r
1116 }} else if (!ssc.getGapsInsertedBegin () && !right) {
\r
1117 if (this.viewport.cursorMode) {
\r
1118 this.alignPanel.seqPanel.moveCursor (-size, 0);
\r
1120 groupAdjustment = -size;
\r
1121 }}if (groupAdjustment != 0) {
\r
1122 this.viewport.getSelectionGroup ().setStartRes (this.viewport.getSelectionGroup ().getStartRes () + groupAdjustment);
\r
1123 this.viewport.getSelectionGroup ().setEndRes (this.viewport.getSelectionGroup ().getEndRes () + groupAdjustment);
\r
1124 }var appendHistoryItem = false;
\r
1125 var historyList = this.viewport.getHistoryList ();
\r
1126 if (historyList != null && historyList.size () > 0 && Clazz.instanceOf (historyList.peek (), jalview.commands.SlideSequencesCommand)) {
\r
1127 appendHistoryItem = ssc.appendSlideCommand (historyList.peek ());
\r
1128 }if (!appendHistoryItem) {
\r
1129 this.addHistoryItem (ssc);
\r
1132 Clazz.defineMethod (c$, "copy_actionPerformed",
\r
1134 if (this.viewport.getSelectionGroup () == null) {
\r
1136 }var sg = this.viewport.getSelectionGroup ();
\r
1137 jalview.appletgui.AlignFrame.copiedSequences = new StringBuffer ();
\r
1138 var orderedSeqs = new java.util.HashMap ();
\r
1139 for (var i = 0; i < sg.getSize (); i++) {
\r
1140 var seq = sg.getSequenceAt (i);
\r
1141 var index = this.viewport.getAlignment ().findIndex (seq);
\r
1142 orderedSeqs.put (new Integer (index), seq);
\r
1148 if (this.viewport.hasHiddenColumns () && this.viewport.getSelectionGroup () != null) {
\r
1149 jalview.appletgui.AlignFrame.copiedHiddenColumns = new java.util.Vector ();
\r
1150 var hiddenOffset = this.viewport.getSelectionGroup ().getStartRes ();
\r
1151 for (var region, $region = this.viewport.getColumnSelection ().getHiddenColumns ().iterator (); $region.hasNext () && ((region = $region.next ()) || true);) {
\r
1152 jalview.appletgui.AlignFrame.copiedHiddenColumns.addElement ( Clazz.newIntArray (-1, [region[0] - hiddenOffset, region[1] - hiddenOffset]));
\r
1155 jalview.appletgui.AlignFrame.copiedHiddenColumns = null;
\r
1156 }for (var i = 0; i < sg.getSize (); i++) {
\r
1158 while (seq == null) {
\r
1159 if (orderedSeqs.containsKey (new Integer (index))) {
\r
1160 seq = orderedSeqs.get (new Integer (index));
\r
1166 startRes = seq.findPosition (sg.getStartRes ());
\r
1168 for (var j = 0; j < sg.getEndRes () + 1 && j < seq.getLength (); j++) {
\r
1169 ch = seq.getCharAt (j);
\r
1170 if (!jalview.util.Comparison.isGap ((ch))) {
\r
1174 endRes += seq.getStart () - 1;
\r
1175 }jalview.appletgui.AlignFrame.copiedSequences.append (seq.getName () + "\t" + startRes + "\t" + endRes + "\t" + seq.getSequenceAsString (sg.getStartRes (), sg.getEndRes () + 1) + "\n");
\r
1178 Clazz.defineMethod (c$, "pasteNew_actionPerformed",
\r
1180 this.paste (true);
\r
1182 Clazz.defineMethod (c$, "pasteThis_actionPerformed",
\r
1184 this.paste (false);
\r
1186 Clazz.defineMethod (c$, "paste",
\r
1187 function (newAlignment) {
\r
1189 if (jalview.appletgui.AlignFrame.copiedSequences == null) {
\r
1191 }var st = new java.util.StringTokenizer (jalview.appletgui.AlignFrame.copiedSequences.toString ());
\r
1192 var seqs = new java.util.Vector ();
\r
1193 while (st.hasMoreElements ()) {
\r
1194 var name = st.nextToken ();
\r
1195 var start = Integer.parseInt (st.nextToken ());
\r
1196 var end = Integer.parseInt (st.nextToken ());
\r
1197 seqs.addElement ( new jalview.datamodel.Sequence (name, st.nextToken (), start, end));
\r
1199 var newSeqs = new Array (seqs.size ());
\r
1200 for (var i = 0; i < seqs.size (); i++) {
\r
1201 newSeqs[i] = seqs.elementAt (i);
\r
1203 if (newAlignment) {
\r
1204 var newtitle = jalview.util.MessageManager.getString ("label.copied_sequences");
\r
1205 if (this.getTitle ().startsWith (jalview.util.MessageManager.getString ("label.copied_sequences"))) {
\r
1206 newtitle = this.getTitle ();
\r
1208 newtitle = newtitle.concat (jalview.util.MessageManager.formatMessage ("label.from_msname", Clazz.newArray (-1, [this.getTitle ()])));
\r
1209 }var af = new jalview.appletgui.AlignFrame ( new jalview.datamodel.Alignment (newSeqs), this.viewport.applet, newtitle, false);
\r
1210 if (jalview.appletgui.AlignFrame.copiedHiddenColumns != null) {
\r
1211 for (var i = 0; i < jalview.appletgui.AlignFrame.copiedHiddenColumns.size (); i++) {
\r
1212 var region = jalview.appletgui.AlignFrame.copiedHiddenColumns.elementAt (i);
\r
1213 af.viewport.hideColumns (region[0], region[1]);
\r
1215 }jalview.bin.JalviewLite.addFrame (af, newtitle, this.frameWidth, this.frameHeight);
\r
1217 this.addSequences (newSeqs);
\r
1219 if (Clazz.exceptionOf (ex, Exception)) {
\r
1225 Clazz.defineMethod (c$, "addSequences",
\r
1227 for (var i = 0; i < seqs.length; i++) {
\r
1228 this.viewport.getAlignment ().addSequence (seqs[i]);
\r
1230 this.addHistoryItem ( new jalview.commands.EditCommand (jalview.util.MessageManager.getString ("label.add_sequences"), jalview.commands.EditCommand.Action.PASTE, seqs, 0, this.viewport.getAlignment ().getWidth (), this.viewport.getAlignment ()));
\r
1231 this.viewport.setEndSeq (this.viewport.getAlignment ().getHeight ());
\r
1232 this.viewport.getAlignment ().getWidth ();
\r
1233 this.viewport.firePropertyChange ("alignment", null, this.viewport.getAlignment ().getSequences ());
\r
1235 Clazz.defineMethod (c$, "cut_actionPerformed",
\r
1237 this.copy_actionPerformed ();
\r
1238 this.delete_actionPerformed ();
\r
1240 Clazz.defineMethod (c$, "delete_actionPerformed",
\r
1242 var sg = this.viewport.getSelectionGroup ();
\r
1245 }var seqs = new java.util.Vector ();
\r
1247 for (var i = 0; i < sg.getSize (); i++) {
\r
1248 seq = sg.getSequenceAt (i);
\r
1249 seqs.addElement (seq);
\r
1251 if (sg.getSize () == this.viewport.getAlignment ().getHeight ()) {
\r
1252 this.viewport.getColumnSelection ().removeElements (sg.getStartRes (), sg.getEndRes () + 1);
\r
1253 }var cut = new Array (seqs.size ());
\r
1254 for (var i = 0; i < seqs.size (); i++) {
\r
1255 cut[i] = seqs.elementAt (i);
\r
1257 this.addHistoryItem ( new jalview.commands.EditCommand (jalview.util.MessageManager.getString ("label.cut_sequences"), jalview.commands.EditCommand.Action.CUT, cut, sg.getStartRes (), sg.getEndRes () - sg.getStartRes () + 1, this.viewport.getAlignment ()));
\r
1258 this.viewport.setSelectionGroup (null);
\r
1259 this.viewport.getAlignment ().deleteGroup (sg);
\r
1260 this.viewport.firePropertyChange ("alignment", null, this.viewport.getAlignment ().getSequences ());
\r
1261 if (this.viewport.getAlignment ().getHeight () < 1) {
\r
1262 this.setVisible (false);
\r
1263 }this.viewport.sendSelection ();
\r
1265 Clazz.defineMethod (c$, "showGroupConsensus_actionPerformed",
\r
1267 this.viewport.setShowGroupConsensus (this.showGroupConsensus.getState ());
\r
1268 this.alignPanel.updateAnnotation (this.applyAutoAnnotationSettings.getState ());
\r
1270 Clazz.defineMethod (c$, "showGroupConservation_actionPerformed",
\r
1272 this.viewport.setShowGroupConservation (this.showGroupConservation.getState ());
\r
1273 this.alignPanel.updateAnnotation (this.applyAutoAnnotationSettings.getState ());
\r
1275 Clazz.defineMethod (c$, "showConsensusHistogram_actionPerformed",
\r
1277 this.viewport.setShowConsensusHistogram (this.showConsensusHistogram.getState ());
\r
1278 this.alignPanel.updateAnnotation (this.applyAutoAnnotationSettings.getState ());
\r
1280 Clazz.defineMethod (c$, "showSequenceLogo_actionPerformed",
\r
1282 this.viewport.setShowSequenceLogo (this.showSequenceLogo.getState ());
\r
1283 this.alignPanel.updateAnnotation (this.applyAutoAnnotationSettings.getState ());
\r
1285 Clazz.defineMethod (c$, "normSequenceLogo_actionPerformed",
\r
1287 this.showSequenceLogo.setState (true);
\r
1288 this.viewport.setShowSequenceLogo (true);
\r
1289 this.viewport.setNormaliseSequenceLogo (this.normSequenceLogo.getState ());
\r
1290 this.alignPanel.updateAnnotation (this.applyAutoAnnotationSettings.getState ());
\r
1292 Clazz.defineMethod (c$, "applyAutoAnnotationSettings_actionPerformed",
\r
1294 this.alignPanel.updateAnnotation (this.applyAutoAnnotationSettings.getState ());
\r
1296 Clazz.defineMethod (c$, "makeGrpsFromSelection_actionPerformed",
\r
1298 if (this.avc.makeGroupsFromSelection ()) {
\r
1299 jalview.appletgui.PaintRefresher.Refresh (this, this.viewport.getSequenceSetId ());
\r
1300 this.alignPanel.updateAnnotation ();
\r
1301 this.alignPanel.paintAlignment (true);
\r
1303 Clazz.defineMethod (c$, "createGroup_actionPerformed",
\r
1305 this.avc.createGroup ();
\r
1307 Clazz.defineMethod (c$, "unGroup_actionPerformed",
\r
1309 if (this.avc.unGroup ()) {
\r
1310 this.alignPanel.alignmentChanged ();
\r
1312 Clazz.defineMethod (c$, "deleteGroups_actionPerformed",
\r
1314 if (this.avc.deleteGroups ()) {
\r
1315 this.alignPanel.alignmentChanged ();
\r
1317 Clazz.defineMethod (c$, "selectAllSequenceMenuItem_actionPerformed",
\r
1319 var sg = new jalview.datamodel.SequenceGroup ();
\r
1320 for (var i = 0; i < this.viewport.getAlignment ().getSequences ().size (); i++) {
\r
1321 sg.addSequence (this.viewport.getAlignment ().getSequenceAt (i), false);
\r
1323 sg.setEndRes (this.viewport.getAlignment ().getWidth () - 1);
\r
1324 this.viewport.setSelectionGroup (sg);
\r
1325 this.alignPanel.paintAlignment (true);
\r
1326 jalview.appletgui.PaintRefresher.Refresh (this.alignPanel, this.viewport.getSequenceSetId ());
\r
1327 this.viewport.sendSelection ();
\r
1329 Clazz.defineMethod (c$, "deselectAllSequenceMenuItem_actionPerformed",
\r
1331 if (this.viewport.cursorMode) {
\r
1332 this.alignPanel.seqPanel.keyboardNo1 = null;
\r
1333 this.alignPanel.seqPanel.keyboardNo2 = null;
\r
1334 }this.viewport.setSelectionGroup (null);
\r
1335 this.viewport.getColumnSelection ().clear ();
\r
1336 this.viewport.setSelectionGroup (null);
\r
1337 this.alignPanel.idPanel.idCanvas.searchResults = null;
\r
1338 this.alignPanel.seqPanel.seqCanvas.highlightSearchResults (null);
\r
1339 this.alignPanel.paintAlignment (true);
\r
1340 jalview.appletgui.PaintRefresher.Refresh (this.alignPanel, this.viewport.getSequenceSetId ());
\r
1341 this.viewport.sendSelection ();
\r
1343 Clazz.defineMethod (c$, "invertSequenceMenuItem_actionPerformed",
\r
1345 var sg = this.viewport.getSelectionGroup ();
\r
1346 for (var i = 0; i < this.viewport.getAlignment ().getSequences ().size (); i++) {
\r
1347 sg.addOrRemove (this.viewport.getAlignment ().getSequenceAt (i), false);
\r
1349 jalview.appletgui.PaintRefresher.Refresh (this.alignPanel, this.viewport.getSequenceSetId ());
\r
1350 this.viewport.sendSelection ();
\r
1352 Clazz.defineMethod (c$, "invertColSel_actionPerformed",
\r
1354 this.viewport.invertColumnSelection ();
\r
1355 this.alignPanel.paintAlignment (true);
\r
1356 jalview.appletgui.PaintRefresher.Refresh (this.alignPanel, this.viewport.getSequenceSetId ());
\r
1357 this.viewport.sendSelection ();
\r
1359 Clazz.defineMethod (c$, "trimAlignment",
\r
1360 function (trimLeft) {
\r
1361 var colSel = this.viewport.getColumnSelection ();
\r
1363 if (colSel.size () > 0) {
\r
1365 column = colSel.getMin ();
\r
1367 column = colSel.getMax ();
\r
1369 if (this.viewport.getSelectionGroup () != null) {
\r
1370 seqs = this.viewport.getSelectionGroup ().getSequencesAsArray (this.viewport.getHiddenRepSequences ());
\r
1372 seqs = this.viewport.getAlignment ().getSequencesArray ();
\r
1375 trimRegion = new jalview.commands.TrimRegionCommand ("Remove Left", jalview.commands.TrimRegionCommand.TRIM_LEFT, seqs, column, this.viewport.getAlignment (), this.viewport.getColumnSelection (), this.viewport.getSelectionGroup ());
\r
1376 this.viewport.setStartRes (0);
\r
1378 trimRegion = new jalview.commands.TrimRegionCommand ("Remove Right", jalview.commands.TrimRegionCommand.TRIM_RIGHT, seqs, column, this.viewport.getAlignment (), this.viewport.getColumnSelection (), this.viewport.getSelectionGroup ());
\r
1379 }this.setStatus (jalview.util.MessageManager.formatMessage ("label.removed_columns", Clazz.newArray (-1, [Integer.$valueOf (trimRegion.getSize ()).toString ()])));
\r
1380 this.addHistoryItem (trimRegion);
\r
1381 for (var sg, $sg = this.viewport.getAlignment ().getGroups ().iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) {
\r
1382 if ((trimLeft && !sg.adjustForRemoveLeft (column)) || (!trimLeft && !sg.adjustForRemoveRight (column))) {
\r
1383 this.viewport.getAlignment ().deleteGroup (sg);
\r
1385 this.viewport.firePropertyChange ("alignment", null, this.viewport.getAlignment ().getSequences ());
\r
1387 Clazz.defineMethod (c$, "removeGappedColumnMenuItem_actionPerformed",
\r
1390 var end = this.viewport.getAlignment ().getWidth () - 1;
\r
1392 if (this.viewport.getSelectionGroup () != null) {
\r
1393 seqs = this.viewport.getSelectionGroup ().getSequencesAsArray (this.viewport.getHiddenRepSequences ());
\r
1394 start = this.viewport.getSelectionGroup ().getStartRes ();
\r
1395 end = this.viewport.getSelectionGroup ().getEndRes ();
\r
1397 seqs = this.viewport.getAlignment ().getSequencesArray ();
\r
1398 }var removeGapCols = new jalview.commands.RemoveGapColCommand ("Remove Gapped Columns", seqs, start, end, this.viewport.getAlignment ());
\r
1399 this.addHistoryItem (removeGapCols);
\r
1400 this.setStatus (jalview.util.MessageManager.formatMessage ("label.removed_empty_columns", Clazz.newArray (-1, [Integer.$valueOf (removeGapCols.getSize ()).toString ()])));
\r
1401 var seq = this.viewport.getAlignment ().getSequenceAt (0);
\r
1402 var startRes = seq.findPosition (this.viewport.startRes);
\r
1403 this.viewport.setStartRes (seq.findIndex (startRes) - 1);
\r
1404 this.viewport.firePropertyChange ("alignment", null, this.viewport.getAlignment ().getSequences ());
\r
1406 Clazz.defineMethod (c$, "removeAllGapsMenuItem_actionPerformed",
\r
1409 var end = this.viewport.getAlignment ().getWidth () - 1;
\r
1411 if (this.viewport.getSelectionGroup () != null) {
\r
1412 seqs = this.viewport.getSelectionGroup ().getSequencesAsArray (this.viewport.getHiddenRepSequences ());
\r
1413 start = this.viewport.getSelectionGroup ().getStartRes ();
\r
1414 end = this.viewport.getSelectionGroup ().getEndRes ();
\r
1416 seqs = this.viewport.getAlignment ().getSequencesArray ();
\r
1417 }var seq = this.viewport.getAlignment ().getSequenceAt (0);
\r
1418 var startRes = seq.findPosition (this.viewport.startRes);
\r
1419 this.addHistoryItem ( new jalview.commands.RemoveGapsCommand ("Remove Gaps", seqs, start, end, this.viewport.getAlignment ()));
\r
1420 this.viewport.setStartRes (seq.findIndex (startRes) - 1);
\r
1421 this.viewport.firePropertyChange ("alignment", null, this.viewport.getAlignment ().getSequences ());
\r
1423 Clazz.defineMethod (c$, "findMenuItem_actionPerformed",
\r
1425 new jalview.appletgui.Finder (this.alignPanel);
\r
1427 Clazz.defineMethod (c$, "newView",
\r
1428 function (viewtitle) {
\r
1430 if (this.viewport.hasHiddenRows ()) {
\r
1431 newal = new jalview.datamodel.Alignment (this.viewport.getAlignment ().getHiddenSequences ().getFullAlignment ().getSequencesArray ());
\r
1433 newal = new jalview.datamodel.Alignment (this.viewport.getAlignment ().getSequencesArray ());
\r
1434 }if (this.viewport.getAlignment ().getAlignmentAnnotation () != null) {
\r
1435 for (var i = 0; i < this.viewport.getAlignment ().getAlignmentAnnotation ().length; i++) {
\r
1436 if (!this.viewport.getAlignment ().getAlignmentAnnotation ()[i].autoCalculated) {
\r
1437 newal.addAnnotation (this.viewport.getAlignment ().getAlignmentAnnotation ()[i]);
\r
1439 }var newaf = new jalview.appletgui.AlignFrame (newal, this.viewport.applet, "", false);
\r
1440 newaf.viewport.setSequenceSetId (this.alignPanel.av.getSequenceSetId ());
\r
1441 jalview.appletgui.PaintRefresher.Register (this.alignPanel, this.alignPanel.av.getSequenceSetId ());
\r
1442 jalview.appletgui.PaintRefresher.Register (newaf.alignPanel, newaf.alignPanel.av.getSequenceSetId ());
\r
1443 jalview.appletgui.PaintRefresher.Register (newaf.alignPanel.idPanel.idCanvas, newaf.alignPanel.av.getSequenceSetId ());
\r
1444 jalview.appletgui.PaintRefresher.Register (newaf.alignPanel.seqPanel.seqCanvas, newaf.alignPanel.av.getSequenceSetId ());
\r
1445 var comps = jalview.appletgui.PaintRefresher.components.get (this.viewport.getSequenceSetId ());
\r
1446 var viewSize = -1;
\r
1447 for (var i = 0; i < comps.size (); i++) {
\r
1448 if (Clazz.instanceOf (comps.elementAt (i), jalview.appletgui.AlignmentPanel)) {
\r
1451 var title = String.instantialize (this.getTitle ());
\r
1452 if (viewtitle != null) {
\r
1453 title = viewtitle + " ( " + title + ")";
\r
1455 if (title.indexOf ("(View") > -1) {
\r
1456 title = title.substring (0, title.indexOf ("(View"));
\r
1457 }title += "(View " + viewSize + ")";
\r
1458 }newaf.setTitle (title.toString ());
\r
1459 newaf.viewport.setHistoryList (this.viewport.getHistoryList ());
\r
1460 newaf.viewport.setRedoList (this.viewport.getRedoList ());
\r
1463 Clazz.defineMethod (c$, "getFeatureGroups",
\r
1466 if (this.alignPanel != null && (fr = this.alignPanel.getFeatureRenderer ()) != null) {
\r
1467 var gps = fr.getFeatureGroups ();
\r
1468 var _gps = gps.toArray ( new Array (gps.size ()));
\r
1472 Clazz.defineMethod (c$, "getFeatureGroupsOfState",
\r
1473 function (visible) {
\r
1475 if (this.alignPanel != null && (fr = this.alignPanel.getFeatureRenderer ()) != null) {
\r
1476 var gps = fr.getGroups (visible);
\r
1477 var _gps = gps.toArray ( new Array (gps.size ()));
\r
1481 Clazz.defineMethod (c$, "setFeatureGroupState",
\r
1482 function (groups, state) {
\r
1484 this.sequenceFeatures.setState (true);
\r
1485 this.viewport.setShowSequenceFeatures (true);
\r
1486 if (this.alignPanel != null && (fr = this.alignPanel.getFeatureRenderer ()) != null) {
\r
1487 fr.setGroupVisibility (java.util.Arrays.asList (groups), state);
\r
1488 this.alignPanel.seqPanel.seqCanvas.repaint ();
\r
1489 if (this.alignPanel.overviewPanel != null) {
\r
1490 this.alignPanel.overviewPanel.updateOverviewImage ();
\r
1492 Clazz.defineMethod (c$, "seqLimits_itemStateChanged",
\r
1494 this.viewport.setShowJVSuffix (this.seqLimits.getState ());
\r
1495 this.alignPanel.fontChanged ();
\r
1496 this.alignPanel.paintAlignment (true);
\r
1498 Clazz.defineMethod (c$, "colourTextMenuItem_actionPerformed",
\r
1500 this.viewport.setColourText (this.colourTextMenuItem.getState ());
\r
1501 this.alignPanel.paintAlignment (true);
\r
1503 Clazz.defineMethod (c$, "displayNonconservedMenuItem_actionPerformed",
\r
1505 this.viewport.setShowUnconserved (this.displayNonconservedMenuItem.getState ());
\r
1506 this.alignPanel.paintAlignment (true);
\r
1508 Clazz.defineMethod (c$, "wrapMenuItem_actionPerformed",
\r
1510 this.viewport.setWrapAlignment (this.wrapMenuItem.getState ());
\r
1511 this.alignPanel.setWrapAlignment (this.wrapMenuItem.getState ());
\r
1512 this.scaleAbove.setEnabled (this.wrapMenuItem.getState ());
\r
1513 this.scaleLeft.setEnabled (this.wrapMenuItem.getState ());
\r
1514 this.scaleRight.setEnabled (this.wrapMenuItem.getState ());
\r
1515 this.alignPanel.paintAlignment (true);
\r
1517 Clazz.defineMethod (c$, "overviewMenuItem_actionPerformed",
\r
1519 if (this.alignPanel.overviewPanel != null) {
\r
1521 }var frame = new awt2swing.Frame ();
\r
1522 var overview = new jalview.appletgui.OverviewPanel (this.alignPanel);
\r
1523 frame.add (overview);
\r
1524 jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.formatMessage ("label.overview_params", Clazz.newArray (-1, [this.getTitle ()])), overview.getPreferredSize ().width, overview.getPreferredSize ().height + 50);
\r
1526 var ap = this.alignPanel;
\r
1527 frame.addWindowListener (((Clazz.isClassDefined ("jalview.appletgui.AlignFrame$1") ? 0 : jalview.appletgui.AlignFrame.$AlignFrame$1$ ()), Clazz.innerTypeInstance (jalview.appletgui.AlignFrame$1, this, Clazz.cloneFinals ("ap", ap))));
\r
1528 this.alignPanel.setOverviewPanel (overview);
\r
1530 Clazz.overrideMethod (c$, "changeColour",
\r
1532 var threshold = 0;
\r
1534 if (this.viewport.getAbovePIDThreshold ()) {
\r
1535 this.viewport.setThreshold (jalview.appletgui.SliderPanel.setPIDSliderSource (this.alignPanel, cs, "Background"));
\r
1536 }if (this.viewport.getConservationSelected ()) {
\r
1537 cs.setConservationApplied (true);
\r
1538 this.viewport.setIncrement (jalview.appletgui.SliderPanel.setConservationSlider (this.alignPanel, cs, "Background"));
\r
1540 cs.setConservationApplied (false);
\r
1541 }}this.viewport.setGlobalColourScheme (cs);
\r
1542 if (this.alignPanel.getOverviewPanel () != null) {
\r
1543 this.alignPanel.getOverviewPanel ().updateOverviewImage ();
\r
1544 }jalview.structure.StructureSelectionManager.getStructureSelectionManager (this.viewport.applet).sequenceColoursChanged (this.alignPanel);
\r
1545 this.alignPanel.paintAlignment (true);
\r
1546 }, "jalview.schemes.ColourSchemeI");
\r
1547 Clazz.defineMethod (c$, "modifyPID_actionPerformed",
\r
1549 if (this.viewport.getAbovePIDThreshold () && this.viewport.getGlobalColourScheme () != null) {
\r
1550 jalview.appletgui.SliderPanel.setPIDSliderSource (this.alignPanel, this.viewport.getGlobalColourScheme (), "Background");
\r
1551 jalview.appletgui.SliderPanel.showPIDSlider ();
\r
1553 Clazz.defineMethod (c$, "modifyConservation_actionPerformed",
\r
1555 if (this.viewport.getConservationSelected () && this.viewport.getGlobalColourScheme () != null) {
\r
1556 jalview.appletgui.SliderPanel.setConservationSlider (this.alignPanel, this.viewport.getGlobalColourScheme (), "Background");
\r
1557 jalview.appletgui.SliderPanel.showConservationSlider ();
\r
1559 Clazz.defineMethod (c$, "conservationMenuItem_actionPerformed",
\r
1561 this.viewport.setConservationSelected (this.conservationMenuItem.getState ());
\r
1562 this.viewport.setAbovePIDThreshold (false);
\r
1563 this.abovePIDThreshold.setState (false);
\r
1564 this.changeColour (this.viewport.getGlobalColourScheme ());
\r
1565 this.modifyConservation_actionPerformed ();
\r
1567 Clazz.defineMethod (c$, "abovePIDThreshold_actionPerformed",
\r
1569 this.viewport.setAbovePIDThreshold (this.abovePIDThreshold.getState ());
\r
1570 this.conservationMenuItem.setState (false);
\r
1571 this.viewport.setConservationSelected (false);
\r
1572 this.changeColour (this.viewport.getGlobalColourScheme ());
\r
1573 this.modifyPID_actionPerformed ();
\r
1575 Clazz.defineMethod (c$, "sortPairwiseMenuItem_actionPerformed",
\r
1577 var oldOrder = this.viewport.getAlignment ().getSequencesArray ();
\r
1578 jalview.analysis.AlignmentSorter.sortByPID (this.viewport.getAlignment (), this.viewport.getAlignment ().getSequenceAt (0), null);
\r
1579 this.addHistoryItem ( new jalview.commands.OrderCommand ("Pairwise Sort", oldOrder, this.viewport.getAlignment ()));
\r
1580 this.alignPanel.paintAlignment (true);
\r
1582 Clazz.defineMethod (c$, "sortIDMenuItem_actionPerformed",
\r
1584 var oldOrder = this.viewport.getAlignment ().getSequencesArray ();
\r
1585 jalview.analysis.AlignmentSorter.sortByID (this.viewport.getAlignment ());
\r
1586 this.addHistoryItem ( new jalview.commands.OrderCommand ("ID Sort", oldOrder, this.viewport.getAlignment ()));
\r
1587 this.alignPanel.paintAlignment (true);
\r
1589 Clazz.defineMethod (c$, "sortLengthMenuItem_actionPerformed",
\r
1591 var oldOrder = this.viewport.getAlignment ().getSequencesArray ();
\r
1592 jalview.analysis.AlignmentSorter.sortByLength (this.viewport.getAlignment ());
\r
1593 this.addHistoryItem ( new jalview.commands.OrderCommand ("Length Sort", oldOrder, this.viewport.getAlignment ()));
\r
1594 this.alignPanel.paintAlignment (true);
\r
1596 Clazz.defineMethod (c$, "sortGroupMenuItem_actionPerformed",
\r
1598 var oldOrder = this.viewport.getAlignment ().getSequencesArray ();
\r
1599 jalview.analysis.AlignmentSorter.sortByGroup (this.viewport.getAlignment ());
\r
1600 this.addHistoryItem ( new jalview.commands.OrderCommand ("Group Sort", oldOrder, this.viewport.getAlignment ()));
\r
1601 this.alignPanel.paintAlignment (true);
\r
1603 Clazz.defineMethod (c$, "removeRedundancyMenuItem_actionPerformed",
\r
1605 new jalview.appletgui.RedundancyPanel (this.alignPanel);
\r
1607 Clazz.defineMethod (c$, "pairwiseAlignmentMenuItem_actionPerformed",
\r
1609 if (this.viewport.getSelectionGroup () != null && this.viewport.getSelectionGroup ().getSize () > 1) {
\r
1610 var frame = new awt2swing.Frame ();
\r
1611 frame.add ( new jalview.appletgui.PairwiseAlignPanel (this.alignPanel));
\r
1612 jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.getString ("action.pairwise_alignment"), 600, 500);
\r
1614 Clazz.defineMethod (c$, "PCAMenuItem_actionPerformed",
\r
1616 if (!this.viewport.getAlignment ().isAligned (false)) {
\r
1618 var Width = this.viewport.getAlignment ().getWidth ();
\r
1619 for (var i = 0; i < this.viewport.getAlignment ().getSequences ().size (); i++) {
\r
1620 current = this.viewport.getAlignment ().getSequenceAt (i);
\r
1621 if (current.getLength () < Width) {
\r
1622 current.insertCharAt (Width - 1, this.viewport.getGapCharacter ());
\r
1624 this.alignPanel.paintAlignment (true);
\r
1625 }if ((this.viewport.getSelectionGroup () != null && this.viewport.getSelectionGroup ().getSize () < 4 && this.viewport.getSelectionGroup ().getSize () > 0) || this.viewport.getAlignment ().getHeight () < 4) {
\r
1628 new jalview.appletgui.PCAPanel (this.viewport);
\r
1630 if (Clazz.exceptionOf (ex, OutOfMemoryError)) {
\r
1636 Clazz.defineMethod (c$, "averageDistanceTreeMenuItem_actionPerformed",
\r
1638 this.NewTreePanel ("AV", "PID", "Average distance tree using PID");
\r
1640 Clazz.defineMethod (c$, "neighbourTreeMenuItem_actionPerformed",
\r
1642 this.NewTreePanel ("NJ", "PID", "Neighbour joining tree using PID");
\r
1644 Clazz.defineMethod (c$, "njTreeBlosumMenuItem_actionPerformed",
\r
1646 this.NewTreePanel ("NJ", "BL", "Neighbour joining tree using BLOSUM62");
\r
1648 Clazz.defineMethod (c$, "avTreeBlosumMenuItem_actionPerformed",
\r
1650 this.NewTreePanel ("AV", "BL", "Average distance tree using BLOSUM62");
\r
1652 Clazz.defineMethod (c$, "NewTreePanel",
\r
1653 function (type, pwType, title) {
\r
1654 if (!this.viewport.getAlignment ().isAligned (false)) {
\r
1656 var Width = this.viewport.getAlignment ().getWidth ();
\r
1657 for (var i = 0; i < this.viewport.getAlignment ().getSequences ().size (); i++) {
\r
1658 current = this.viewport.getAlignment ().getSequenceAt (i);
\r
1659 if (current.getLength () < Width) {
\r
1660 current.insertCharAt (Width - 1, this.viewport.getGapCharacter ());
\r
1662 this.alignPanel.paintAlignment (true);
\r
1663 }if ((this.viewport.getSelectionGroup () != null && this.viewport.getSelectionGroup ().getSize () > 1) || (this.viewport.getAlignment ().getHeight () > 1)) {
\r
1664 var tp = new jalview.appletgui.TreePanel (this.alignPanel, type, pwType);
\r
1665 this.addTreeMenuItem (tp, title);
\r
1666 jalview.bin.JalviewLite.addFrame (tp, title, 600, 500);
\r
1668 Clazz.defineMethod (c$, "loadTree_actionPerformed",
\r
1670 var cap = new jalview.appletgui.CutAndPasteTransfer (true, this);
\r
1671 cap.setText (jalview.util.MessageManager.getString ("label.paste_newick_tree_file"));
\r
1672 cap.setTreeImport ();
\r
1673 var frame = new awt2swing.Frame ();
\r
1675 jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.getString ("label.paste_newick_file"), 400, 300);
\r
1677 Clazz.defineMethod (c$, "loadTree",
\r
1678 function (tree, treeFile) {
\r
1679 var tp = new jalview.appletgui.TreePanel (this.alignPanel, treeFile, jalview.util.MessageManager.getString ("label.load_tree_from_file"), tree);
\r
1680 jalview.bin.JalviewLite.addFrame (tp, treeFile, 600, 500);
\r
1681 this.addTreeMenuItem (tp, treeFile);
\r
1682 }, "jalview.io.NewickFile,~S");
\r
1683 Clazz.defineMethod (c$, "sortByTree",
\r
1684 function (treePanel, title) {
\r
1685 var oldOrder = this.viewport.getAlignment ().getSequencesArray ();
\r
1686 jalview.analysis.AlignmentSorter.sortByTree (this.viewport.getAlignment (), treePanel.getTree ());
\r
1687 this.addHistoryItem ( new jalview.commands.OrderCommand (jalview.util.MessageManager.formatMessage ("label.order_by_params", Clazz.newArray (-1, [title])), oldOrder, this.viewport.getAlignment ()));
\r
1688 this.alignPanel.paintAlignment (true);
\r
1689 }, "jalview.appletgui.TreePanel,~S");
\r
1690 Clazz.defineMethod (c$, "addTreeMenuItem",
\r
1691 function (treePanel, title) {
\r
1692 var item = new awt2swing.MenuItem (title);
\r
1693 this.sortByTreeMenu.add (item);
\r
1694 item.addActionListener (((Clazz.isClassDefined ("jalview.appletgui.AlignFrame$2") ? 0 : jalview.appletgui.AlignFrame.$AlignFrame$2$ ()), Clazz.innerTypeInstance (jalview.appletgui.AlignFrame$2, this, Clazz.cloneFinals ("treePanel", treePanel, "title", title))));
\r
1695 treePanel.addWindowListener (((Clazz.isClassDefined ("jalview.appletgui.AlignFrame$3") ? 0 : jalview.appletgui.AlignFrame.$AlignFrame$3$ ()), Clazz.innerTypeInstance (jalview.appletgui.AlignFrame$3, this, Clazz.cloneFinals ("treePanel", treePanel, "title", title, "item", item))));
\r
1696 }, "jalview.appletgui.TreePanel,~S");
\r
1697 Clazz.defineMethod (c$, "sortBy",
\r
1698 function (alorder, undoname) {
\r
1699 var oldOrder = this.viewport.getAlignment ().getSequencesArray ();
\r
1700 if ((this.viewport.applet, jalview.bin.JalviewLite).debug) {
\r
1701 System.err.println ("Sorting " + alorder.getOrder ().size () + " in alignment '" + this.getTitle () + "'");
\r
1702 }jalview.analysis.AlignmentSorter.sortBy (this.viewport.getAlignment (), alorder);
\r
1703 if (undoname != null) {
\r
1704 this.addHistoryItem ( new jalview.commands.OrderCommand (undoname, oldOrder, this.viewport.getAlignment ()));
\r
1705 }this.alignPanel.paintAlignment (true);
\r
1707 }, "jalview.datamodel.AlignmentOrder,~S");
\r
1708 Clazz.defineMethod (c$, "documentation_actionPerformed",
\r
1710 this.alignPanel.av.applet.openJalviewHelpUrl ();
\r
1712 Clazz.defineMethod (c$, "about_actionPerformed",
\r
1714 if (!Clazz.isClassDefined ("jalview.appletgui.AlignFrame$1AboutPanel")) {
\r
1715 jalview.appletgui.AlignFrame.$AlignFrame$1AboutPanel$ ();
\r
1717 var frame = new awt2swing.Frame ();
\r
1718 frame.add (Clazz.innerTypeInstance (jalview.appletgui.AlignFrame$1AboutPanel, this, null, jalview.bin.JalviewLite.getVersion (), jalview.bin.JalviewLite.getBuildDate ()));
\r
1719 jalview.bin.JalviewLite.addFrame (frame, jalview.util.MessageManager.getString ("label.jalview"), 580, 220);
\r
1721 Clazz.defineMethod (c$, "showURL",
\r
1722 function (url, target) {
\r
1723 if (this.viewport.applet == null) {
\r
1724 System.out.println ("Not running as applet - no browser available.");
\r
1726 this.viewport.applet.showURL (url, target);
\r
1728 Clazz.defineMethod (c$, "jbInit",
\r
1730 this.setMenuBar (this.alignFrameMenuBar);
\r
1731 this.inputText.setLabel (jalview.util.MessageManager.getString ("label.input_from_textbox"));
\r
1732 this.inputText.addActionListener (this);
\r
1733 var outputTextboxMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("label.out_to_textbox"));
\r
1734 for (var i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++) {
\r
1735 var item = new awt2swing.MenuItem (jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
\r
1736 item.addActionListener (((Clazz.isClassDefined ("jalview.appletgui.AlignFrame$4") ? 0 : jalview.appletgui.AlignFrame.$AlignFrame$4$ ()), Clazz.innerTypeInstance (jalview.appletgui.AlignFrame$4, this, null)));
\r
1737 outputTextboxMenu.add (item);
\r
1739 this.closeMenuItem.addActionListener (this);
\r
1740 this.loadApplication.addActionListener (this);
\r
1741 this.$loadTree.addActionListener (this);
\r
1742 this.$loadAnnotations.addActionListener (this);
\r
1743 this.$outputFeatures.addActionListener (this);
\r
1744 this.$outputAnnotations.addActionListener (this);
\r
1745 this.undoMenuItem.setEnabled (false);
\r
1746 this.undoMenuItem.setLabel (jalview.util.MessageManager.getString ("action.undo"));
\r
1747 this.undoMenuItem.addActionListener (this);
\r
1748 this.redoMenuItem.setEnabled (false);
\r
1749 this.redoMenuItem.setLabel (jalview.util.MessageManager.getString ("action.redo"));
\r
1750 this.redoMenuItem.addActionListener (this);
\r
1751 this.copy.setLabel (jalview.util.MessageManager.getString ("action.copy"));
\r
1752 this.copy.addActionListener (this);
\r
1753 this.cut.setLabel (jalview.util.MessageManager.getString ("action.cut"));
\r
1754 this.cut.addActionListener (this);
\r
1755 this.$delete.setLabel (jalview.util.MessageManager.getString ("action.delete"));
\r
1756 this.$delete.addActionListener (this);
\r
1757 this.pasteMenu.setLabel (jalview.util.MessageManager.getString ("action.paste"));
\r
1758 this.pasteNew.setLabel (jalview.util.MessageManager.getString ("label.to_new_alignment"));
\r
1759 this.pasteNew.addActionListener (this);
\r
1760 this.pasteThis.setLabel (jalview.util.MessageManager.getString ("label.to_this_alignment"));
\r
1761 this.pasteThis.addActionListener (this);
\r
1762 this.remove2LeftMenuItem.setLabel (jalview.util.MessageManager.getString ("action.remove_left"));
\r
1763 this.remove2LeftMenuItem.addActionListener (this);
\r
1764 this.remove2RightMenuItem.setLabel (jalview.util.MessageManager.getString ("action.remove_right"));
\r
1765 this.remove2RightMenuItem.addActionListener (this);
\r
1766 this.removeGappedColumnMenuItem.setLabel (jalview.util.MessageManager.getString ("action.remove_empty_columns"));
\r
1767 this.removeGappedColumnMenuItem.addActionListener (this);
\r
1768 this.removeAllGapsMenuItem.setLabel (jalview.util.MessageManager.getString ("action.remove_all_gaps"));
\r
1769 this.removeAllGapsMenuItem.addActionListener (this);
\r
1770 this.removeRedundancyMenuItem.setLabel (jalview.util.MessageManager.getString ("action.remove_redundancy").concat ("..."));
\r
1771 this.removeRedundancyMenuItem.addActionListener (this);
\r
1772 this.findMenuItem.setLabel (jalview.util.MessageManager.getString ("action.find"));
\r
1773 this.findMenuItem.addActionListener (this);
\r
1774 this.selectAllSequenceMenuItem.addActionListener (this);
\r
1775 this.deselectAllSequenceMenuItem.addActionListener (this);
\r
1776 this.invertSequenceMenuItem.setLabel (jalview.util.MessageManager.getString ("action.invert_sequence_selection"));
\r
1777 this.invertSequenceMenuItem.addActionListener (this);
\r
1778 this.invertColSel.setLabel (jalview.util.MessageManager.getString ("action.invert_column_selection"));
\r
1779 this.invertColSel.addActionListener (this);
\r
1780 this.deleteGroups.setLabel (jalview.util.MessageManager.getString ("action.undefine_groups"));
\r
1781 this.deleteGroups.addActionListener (this);
\r
1782 this.grpsFromSelection.setLabel (jalview.util.MessageManager.getString ("action.make_groups_selection"));
\r
1783 this.grpsFromSelection.addActionListener (this);
\r
1784 this.createGroup.setLabel (jalview.util.MessageManager.getString ("action.create_group"));
\r
1785 this.unGroup.setLabel (jalview.util.MessageManager.getString ("action.remove_group"));
\r
1786 this.annotationColumnSelection.setLabel ("Select by Annotation");
\r
1787 this.annotationColumnSelection.addActionListener (this);
\r
1788 this.$newView.setLabel (jalview.util.MessageManager.getString ("action.new_view"));
\r
1789 this.$newView.addActionListener (this);
\r
1790 var showMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.show"));
\r
1791 this.showColumns.setLabel (jalview.util.MessageManager.getString ("label.all_columns"));
\r
1792 this.showSeqs.setLabel (jalview.util.MessageManager.getString ("label.all_sequences"));
\r
1793 var hideMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.hide"));
\r
1794 this.hideColumns.setLabel (jalview.util.MessageManager.getString ("label.selected_columns"));
\r
1795 this.hideSequences.setLabel (jalview.util.MessageManager.getString ("label.selected_sequences"));
\r
1796 this.hideAllButSelection.setLabel (jalview.util.MessageManager.getString ("label.all_but_selected_region"));
\r
1797 this.hideAllSelection.setLabel (jalview.util.MessageManager.getString ("label.selected_region"));
\r
1798 this.showAllHidden.setLabel (jalview.util.MessageManager.getString ("label.all_sequences_columns"));
\r
1799 this.showColumns.addActionListener (this);
\r
1800 this.showSeqs.addActionListener (this);
\r
1801 this.hideColumns.addActionListener (this);
\r
1802 this.hideSequences.addActionListener (this);
\r
1803 this.hideAllButSelection.addActionListener (this);
\r
1804 this.hideAllSelection.addActionListener (this);
\r
1805 this.showAllHidden.addActionListener (this);
\r
1806 this.featureSettings.setLabel (jalview.util.MessageManager.getString ("label.feature_settings"));
\r
1807 this.featureSettings.addActionListener (this);
\r
1808 this.sequenceFeatures.setLabel (jalview.util.MessageManager.getString ("label.show_sequence_features"));
\r
1809 this.sequenceFeatures.addItemListener (this);
\r
1810 this.sequenceFeatures.setState (false);
\r
1811 this.followMouseOverFlag.setLabel (jalview.util.MessageManager.getString ("label.automatic_scrolling"));
\r
1812 this.followMouseOverFlag.addItemListener (this);
\r
1813 this.alProperties.addActionListener (this);
\r
1814 this.overviewMenuItem.setLabel (jalview.util.MessageManager.getString ("label.overview_window"));
\r
1815 this.overviewMenuItem.addActionListener (this);
\r
1816 this.annotationPanelMenuItem.setLabel (jalview.util.MessageManager.getString ("label.show_annotations"));
\r
1817 this.annotationPanelMenuItem.addItemListener (this);
\r
1818 this.showGroupConsensus.setLabel (jalview.util.MessageManager.getString ("label.group_consensus"));
\r
1819 this.showGroupConservation.setLabel (jalview.util.MessageManager.getString ("label.group_conservation"));
\r
1820 this.showConsensusHistogram.setLabel (jalview.util.MessageManager.getString ("label.show_consensus_histogram"));
\r
1821 this.showSequenceLogo.setLabel (jalview.util.MessageManager.getString ("label.show_consensus_logo"));
\r
1822 this.normSequenceLogo.setLabel (jalview.util.MessageManager.getString ("label.norm_consensus_logo"));
\r
1823 this.applyAutoAnnotationSettings.setLabel (jalview.util.MessageManager.getString ("label.apply_all_groups"));
\r
1824 this.applyAutoAnnotationSettings.setState (true);
\r
1825 var autoAnnMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("label.autocalculated_annotation"));
\r
1826 this.showGroupConsensus.addItemListener (this);
\r
1827 this.showGroupConservation.addItemListener (this);
\r
1828 this.showConsensusHistogram.addItemListener (this);
\r
1829 this.showSequenceLogo.addItemListener (this);
\r
1830 this.normSequenceLogo.addItemListener (this);
\r
1831 this.applyAutoAnnotationSettings.addItemListener (this);
\r
1832 this.showAlignmentAnnotations = new awt2swing.CheckboxMenuItem (jalview.util.MessageManager.getString ("label.show_all_al_annotations"));
\r
1833 this.showSequenceAnnotations = new awt2swing.CheckboxMenuItem (jalview.util.MessageManager.getString ("label.show_all_seq_annotations"));
\r
1834 this.sortAnnBySequence = new awt2swing.CheckboxMenuItem (jalview.util.MessageManager.getString ("label.sort_annotations_by_sequence"));
\r
1835 this.sortAnnByLabel = new awt2swing.CheckboxMenuItem (jalview.util.MessageManager.getString ("label.sort_annotations_by_label"));
\r
1836 this.showAutoFirst = new awt2swing.CheckboxMenuItem (jalview.util.MessageManager.getString ("label.show_first"));
\r
1837 this.showAutoLast = new awt2swing.CheckboxMenuItem (jalview.util.MessageManager.getString ("label.show_last"));
\r
1838 this.showAlignmentAnnotations.addItemListener (this);
\r
1839 this.showSequenceAnnotations.addItemListener (this);
\r
1840 this.sortAnnBySequence.addItemListener (this);
\r
1841 this.sortAnnByLabel.addItemListener (this);
\r
1842 this.showAutoFirst.addItemListener (this);
\r
1843 this.showAutoLast.addItemListener (this);
\r
1844 this.$font.setLabel (jalview.util.MessageManager.getString ("action.font"));
\r
1845 this.$font.addActionListener (this);
\r
1846 this.scaleAbove.setLabel (jalview.util.MessageManager.getString ("action.scale_above"));
\r
1847 this.scaleAbove.setState (true);
\r
1848 this.scaleAbove.setEnabled (false);
\r
1849 this.scaleAbove.addItemListener (this);
\r
1850 this.scaleLeft.setEnabled (false);
\r
1851 this.scaleLeft.setState (true);
\r
1852 this.scaleLeft.setLabel (jalview.util.MessageManager.getString ("action.scale_left"));
\r
1853 this.scaleLeft.addItemListener (this);
\r
1854 this.scaleRight.setEnabled (false);
\r
1855 this.scaleRight.setState (true);
\r
1856 this.scaleRight.setLabel (jalview.util.MessageManager.getString ("action.scale_right"));
\r
1857 this.scaleRight.addItemListener (this);
\r
1858 this.viewBoxesMenuItem.setLabel (jalview.util.MessageManager.getString ("action.boxes"));
\r
1859 this.viewBoxesMenuItem.setState (true);
\r
1860 this.viewBoxesMenuItem.addItemListener (this);
\r
1861 this.viewTextMenuItem.setLabel (jalview.util.MessageManager.getString ("action.text"));
\r
1862 this.viewTextMenuItem.setState (true);
\r
1863 this.viewTextMenuItem.addItemListener (this);
\r
1864 this.colourTextMenuItem.setLabel (jalview.util.MessageManager.getString ("label.colour_text"));
\r
1865 this.colourTextMenuItem.addItemListener (this);
\r
1866 this.displayNonconservedMenuItem.setLabel (jalview.util.MessageManager.getString ("label.show_non_conversed"));
\r
1867 this.displayNonconservedMenuItem.addItemListener (this);
\r
1868 this.wrapMenuItem.setLabel (jalview.util.MessageManager.getString ("action.wrap"));
\r
1869 this.wrapMenuItem.addItemListener (this);
\r
1870 this.renderGapsMenuItem.setLabel (jalview.util.MessageManager.getString ("action.show_gaps"));
\r
1871 this.renderGapsMenuItem.setState (true);
\r
1872 this.renderGapsMenuItem.addItemListener (this);
\r
1873 this.centreColumnLabelFlag.setLabel (jalview.util.MessageManager.getString ("label.centre_column_labels"));
\r
1874 this.centreColumnLabelFlag.addItemListener (this);
\r
1875 this.seqLimits.setState (true);
\r
1876 this.seqLimits.setLabel (jalview.util.MessageManager.getString ("label.show_sequence_limits"));
\r
1877 this.seqLimits.addItemListener (this);
\r
1878 this.applyToAllGroups.setLabel (jalview.util.MessageManager.getString ("label.apply_colour_to_all_groups"));
\r
1879 this.applyToAllGroups.setState (true);
\r
1880 this.applyToAllGroups.addItemListener (this);
\r
1881 this.clustalColour.setLabel (jalview.util.MessageManager.getString ("label.clustalx"));
\r
1882 this.clustalColour.addActionListener (this);
\r
1883 this.zappoColour.setLabel (jalview.util.MessageManager.getString ("label.zappo"));
\r
1884 this.zappoColour.addActionListener (this);
\r
1885 this.taylorColour.setLabel (jalview.util.MessageManager.getString ("label.taylor"));
\r
1886 this.taylorColour.addActionListener (this);
\r
1887 this.hydrophobicityColour.setLabel (jalview.util.MessageManager.getString ("label.hydrophobicity"));
\r
1888 this.hydrophobicityColour.addActionListener (this);
\r
1889 this.helixColour.setLabel (jalview.util.MessageManager.getString ("label.helix_propensity"));
\r
1890 this.helixColour.addActionListener (this);
\r
1891 this.strandColour.setLabel (jalview.util.MessageManager.getString ("label.strand_propensity"));
\r
1892 this.strandColour.addActionListener (this);
\r
1893 this.turnColour.setLabel (jalview.util.MessageManager.getString ("label.turn_propensity"));
\r
1894 this.turnColour.addActionListener (this);
\r
1895 this.buriedColour.setLabel (jalview.util.MessageManager.getString ("label.buried_index"));
\r
1896 this.buriedColour.addActionListener (this);
\r
1897 this.purinePyrimidineColour.setLabel (jalview.util.MessageManager.getString ("label.purine_pyrimidine"));
\r
1898 this.purinePyrimidineColour.addActionListener (this);
\r
1899 this.RNAInteractionColour.setLabel (jalview.util.MessageManager.getString ("label.rna_interaction"));
\r
1900 this.RNAInteractionColour.addActionListener (this);
\r
1901 this.RNAHelixColour.setLabel (jalview.util.MessageManager.getString ("action.by_rna_helixes"));
\r
1902 this.RNAHelixColour.addActionListener (this);
\r
1903 this.userDefinedColour.setLabel (jalview.util.MessageManager.getString ("action.user_defined"));
\r
1904 this.userDefinedColour.addActionListener (this);
\r
1905 this.PIDColour.setLabel (jalview.util.MessageManager.getString ("label.percentage_identity"));
\r
1906 this.PIDColour.addActionListener (this);
\r
1907 this.BLOSUM62Colour.setLabel (jalview.util.MessageManager.getString ("label.blosum62_score"));
\r
1908 this.BLOSUM62Colour.addActionListener (this);
\r
1909 this.tcoffeeColour.setLabel (jalview.util.MessageManager.getString ("label.tcoffee_scores"));
\r
1910 this.tcoffeeColour.setEnabled (false);
\r
1911 this.tcoffeeColour.addActionListener (this);
\r
1912 this.conservationMenuItem.setLabel (jalview.util.MessageManager.getString ("action.by_conservation"));
\r
1913 this.conservationMenuItem.addItemListener (this);
\r
1914 this.noColourmenuItem.setLabel (jalview.util.MessageManager.getString ("label.none"));
\r
1915 this.noColourmenuItem.addActionListener (this);
\r
1916 this.abovePIDThreshold.setLabel (jalview.util.MessageManager.getString ("label.above_identity_threshold"));
\r
1917 this.abovePIDThreshold.addItemListener (this);
\r
1918 this.nucleotideColour.setLabel (jalview.util.MessageManager.getString ("label.nucleotide"));
\r
1919 this.nucleotideColour.addActionListener (this);
\r
1920 this.modifyPID.setLabel (jalview.util.MessageManager.getString ("label.modify_identity_thereshold"));
\r
1921 this.modifyPID.addActionListener (this);
\r
1922 this.modifyConservation.setLabel (jalview.util.MessageManager.getString ("label.modify_conservation_thereshold"));
\r
1923 this.modifyConservation.addActionListener (this);
\r
1924 this.annotationColour.setLabel (jalview.util.MessageManager.getString ("action.by_annotation"));
\r
1925 this.annotationColour.addActionListener (this);
\r
1926 this.sortPairwiseMenuItem.setLabel (jalview.util.MessageManager.getString ("action.by_pairwise_id"));
\r
1927 this.sortPairwiseMenuItem.addActionListener (this);
\r
1928 this.sortIDMenuItem.setLabel (jalview.util.MessageManager.getString ("action.by_id"));
\r
1929 this.sortIDMenuItem.addActionListener (this);
\r
1930 this.sortLengthMenuItem.setLabel (jalview.util.MessageManager.getString ("action.by_length"));
\r
1931 this.sortLengthMenuItem.addActionListener (this);
\r
1932 this.sortGroupMenuItem.setLabel (jalview.util.MessageManager.getString ("action.by_group"));
\r
1933 this.sortGroupMenuItem.addActionListener (this);
\r
1934 this.pairwiseAlignmentMenuItem.setLabel (jalview.util.MessageManager.getString ("action.pairwise_alignment"));
\r
1935 this.pairwiseAlignmentMenuItem.addActionListener (this);
\r
1936 this.PCAMenuItem.setLabel (jalview.util.MessageManager.getString ("label.principal_component_analysis"));
\r
1937 this.PCAMenuItem.addActionListener (this);
\r
1938 this.autoCalculate = new awt2swing.CheckboxMenuItem (jalview.util.MessageManager.getString ("label.autocalculate_consensus"), true);
\r
1939 this.averageDistanceTreeMenuItem.setLabel (jalview.util.MessageManager.getString ("label.average_distance_identity"));
\r
1940 this.averageDistanceTreeMenuItem.addActionListener (this);
\r
1941 this.neighbourTreeMenuItem.setLabel (jalview.util.MessageManager.getString ("label.neighbour_joining_identity"));
\r
1942 this.neighbourTreeMenuItem.addActionListener (this);
\r
1943 this.avDistanceTreeBlosumMenuItem.setLabel (jalview.util.MessageManager.getString ("label.average_distance_bloslum62"));
\r
1944 this.avDistanceTreeBlosumMenuItem.addActionListener (this);
\r
1945 this.njTreeBlosumMenuItem.setLabel (jalview.util.MessageManager.getString ("label.neighbour_blosum62"));
\r
1946 this.njTreeBlosumMenuItem.addActionListener (this);
\r
1947 this.sortByTreeMenu.setLabel (jalview.util.MessageManager.getString ("action.by_tree_order"));
\r
1948 var sortMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.sort"));
\r
1949 var calculateTreeMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.calculate_tree"));
\r
1950 this.autoCalculate.addItemListener (this);
\r
1951 this.$sortByTree.addItemListener (this);
\r
1952 var helpMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.help"));
\r
1953 this.documentation.setLabel (jalview.util.MessageManager.getString ("label.documentation"));
\r
1954 this.documentation.addActionListener (this);
\r
1955 this.about.setLabel (jalview.util.MessageManager.getString ("label.about"));
\r
1956 this.about.addActionListener (this);
\r
1957 this.alignFrameMenuBar.add (this.fileMenu);
\r
1958 var editMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.edit"));
\r
1959 this.alignFrameMenuBar.add (editMenu);
\r
1960 var selectMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.select"));
\r
1961 this.alignFrameMenuBar.add (selectMenu);
\r
1962 var viewMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.view"));
\r
1963 this.alignFrameMenuBar.add (viewMenu);
\r
1964 var annotationsMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.annotations"));
\r
1965 this.alignFrameMenuBar.add (annotationsMenu);
\r
1966 var formatMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.format"));
\r
1967 this.alignFrameMenuBar.add (formatMenu);
\r
1968 var colourMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.colour"));
\r
1969 this.alignFrameMenuBar.add (colourMenu);
\r
1970 var calculateMenu = new awt2swing.Menu (jalview.util.MessageManager.getString ("action.calculate"));
\r
1971 this.alignFrameMenuBar.add (calculateMenu);
\r
1972 this.alignFrameMenuBar.add (helpMenu);
\r
1973 this.fileMenu.add (this.inputText);
\r
1974 this.fileMenu.add (this.$loadTree);
\r
1975 this.fileMenu.add (this.$loadAnnotations);
\r
1976 this.fileMenu.addSeparator ();
\r
1977 this.fileMenu.add (outputTextboxMenu);
\r
1978 this.fileMenu.add (this.$outputFeatures);
\r
1979 this.fileMenu.add (this.$outputAnnotations);
\r
1980 if (this.jalviewServletURL != null) {
\r
1981 this.fileMenu.add (this.loadApplication);
\r
1982 }this.fileMenu.addSeparator ();
\r
1983 this.fileMenu.add (this.closeMenuItem);
\r
1984 editMenu.add (this.undoMenuItem);
\r
1985 editMenu.add (this.redoMenuItem);
\r
1986 editMenu.add (this.cut);
\r
1987 editMenu.add (this.copy);
\r
1988 this.pasteMenu.add (this.pasteNew);
\r
1989 this.pasteMenu.add (this.pasteThis);
\r
1990 editMenu.add (this.pasteMenu);
\r
1991 editMenu.add (this.$delete);
\r
1992 editMenu.addSeparator ();
\r
1993 editMenu.add (this.remove2LeftMenuItem);
\r
1994 editMenu.add (this.remove2RightMenuItem);
\r
1995 editMenu.add (this.removeGappedColumnMenuItem);
\r
1996 editMenu.add (this.removeAllGapsMenuItem);
\r
1997 editMenu.add (this.removeRedundancyMenuItem);
\r
1998 selectMenu.add (this.findMenuItem);
\r
1999 selectMenu.addSeparator ();
\r
2000 selectMenu.add (this.selectAllSequenceMenuItem);
\r
2001 selectMenu.add (this.deselectAllSequenceMenuItem);
\r
2002 selectMenu.add (this.invertSequenceMenuItem);
\r
2003 selectMenu.add (this.invertColSel);
\r
2004 selectMenu.add (this.createGroup);
\r
2005 selectMenu.add (this.unGroup);
\r
2006 selectMenu.add (this.grpsFromSelection);
\r
2007 selectMenu.add (this.deleteGroups);
\r
2008 selectMenu.add (this.annotationColumnSelection);
\r
2009 viewMenu.add (this.$newView);
\r
2010 viewMenu.addSeparator ();
\r
2011 showMenu.add (this.showColumns);
\r
2012 showMenu.add (this.showSeqs);
\r
2013 showMenu.add (this.showAllHidden);
\r
2014 viewMenu.add (showMenu);
\r
2015 hideMenu.add (this.hideColumns);
\r
2016 hideMenu.add (this.hideSequences);
\r
2017 hideMenu.add (this.hideAllSelection);
\r
2018 hideMenu.add (this.hideAllButSelection);
\r
2019 viewMenu.add (hideMenu);
\r
2020 viewMenu.addSeparator ();
\r
2021 viewMenu.add (this.followMouseOverFlag);
\r
2022 viewMenu.addSeparator ();
\r
2023 viewMenu.add (this.sequenceFeatures);
\r
2024 viewMenu.add (this.featureSettings);
\r
2025 viewMenu.addSeparator ();
\r
2026 viewMenu.add (this.alProperties);
\r
2027 viewMenu.addSeparator ();
\r
2028 viewMenu.add (this.overviewMenuItem);
\r
2029 annotationsMenu.add (this.annotationPanelMenuItem);
\r
2030 annotationsMenu.addSeparator ();
\r
2031 annotationsMenu.add (this.showAlignmentAnnotations);
\r
2032 annotationsMenu.add (this.showSequenceAnnotations);
\r
2033 annotationsMenu.add (this.sortAnnBySequence);
\r
2034 annotationsMenu.add (this.sortAnnByLabel);
\r
2035 annotationsMenu.addSeparator ();
\r
2036 autoAnnMenu.add (this.showAutoFirst);
\r
2037 autoAnnMenu.add (this.showAutoLast);
\r
2038 autoAnnMenu.addSeparator ();
\r
2039 autoAnnMenu.add (this.applyAutoAnnotationSettings);
\r
2040 autoAnnMenu.add (this.showConsensusHistogram);
\r
2041 autoAnnMenu.add (this.showSequenceLogo);
\r
2042 autoAnnMenu.add (this.normSequenceLogo);
\r
2043 autoAnnMenu.addSeparator ();
\r
2044 autoAnnMenu.add (this.showGroupConservation);
\r
2045 autoAnnMenu.add (this.showGroupConsensus);
\r
2046 annotationsMenu.add (autoAnnMenu);
\r
2047 formatMenu.add (this.$font);
\r
2048 formatMenu.add (this.seqLimits);
\r
2049 formatMenu.add (this.wrapMenuItem);
\r
2050 formatMenu.add (this.scaleAbove);
\r
2051 formatMenu.add (this.scaleLeft);
\r
2052 formatMenu.add (this.scaleRight);
\r
2053 formatMenu.add (this.viewBoxesMenuItem);
\r
2054 formatMenu.add (this.viewTextMenuItem);
\r
2055 formatMenu.add (this.colourTextMenuItem);
\r
2056 formatMenu.add (this.displayNonconservedMenuItem);
\r
2057 formatMenu.add (this.renderGapsMenuItem);
\r
2058 formatMenu.add (this.centreColumnLabelFlag);
\r
2059 colourMenu.add (this.applyToAllGroups);
\r
2060 colourMenu.addSeparator ();
\r
2061 colourMenu.add (this.noColourmenuItem);
\r
2062 colourMenu.add (this.clustalColour);
\r
2063 colourMenu.add (this.BLOSUM62Colour);
\r
2064 colourMenu.add (this.PIDColour);
\r
2065 colourMenu.add (this.zappoColour);
\r
2066 colourMenu.add (this.taylorColour);
\r
2067 colourMenu.add (this.hydrophobicityColour);
\r
2068 colourMenu.add (this.helixColour);
\r
2069 colourMenu.add (this.strandColour);
\r
2070 colourMenu.add (this.turnColour);
\r
2071 colourMenu.add (this.buriedColour);
\r
2072 colourMenu.add (this.nucleotideColour);
\r
2073 colourMenu.add (this.purinePyrimidineColour);
\r
2074 colourMenu.add (this.tcoffeeColour);
\r
2075 colourMenu.add (this.userDefinedColour);
\r
2076 colourMenu.addSeparator ();
\r
2077 colourMenu.add (this.conservationMenuItem);
\r
2078 colourMenu.add (this.modifyConservation);
\r
2079 colourMenu.add (this.abovePIDThreshold);
\r
2080 colourMenu.add (this.modifyPID);
\r
2081 colourMenu.add (this.annotationColour);
\r
2082 colourMenu.add (this.RNAHelixColour);
\r
2083 sortMenu.add (this.sortIDMenuItem);
\r
2084 sortMenu.add (this.sortLengthMenuItem);
\r
2085 sortMenu.add (this.sortByTreeMenu);
\r
2086 sortMenu.add (this.sortGroupMenuItem);
\r
2087 sortMenu.add (this.sortPairwiseMenuItem);
\r
2088 calculateMenu.add (sortMenu);
\r
2089 calculateTreeMenu.add (this.averageDistanceTreeMenuItem);
\r
2090 calculateTreeMenu.add (this.neighbourTreeMenuItem);
\r
2091 calculateTreeMenu.add (this.avDistanceTreeBlosumMenuItem);
\r
2092 calculateTreeMenu.add (this.njTreeBlosumMenuItem);
\r
2093 calculateMenu.add (calculateTreeMenu);
\r
2094 calculateMenu.addSeparator ();
\r
2095 calculateMenu.add (this.pairwiseAlignmentMenuItem);
\r
2096 calculateMenu.add (this.PCAMenuItem);
\r
2097 calculateMenu.add (this.autoCalculate);
\r
2098 calculateMenu.add (this.$sortByTree);
\r
2099 helpMenu.add (this.documentation);
\r
2100 helpMenu.add (this.about);
\r
2101 this.statusBar.setBackground (java.awt.Color.white);
\r
2102 this.statusBar.setFont ( new java.awt.Font ("Verdana", 0, 11));
\r
2103 this.setStatus (jalview.util.MessageManager.getString ("label.status_bar"));
\r
2104 this.add (this.statusBar, "South");
\r
2106 Clazz.overrideMethod (c$, "setStatus",
\r
2107 function (string) {
\r
2108 this.statusBar.setText (string);
\r
2110 Clazz.defineMethod (c$, "createAlignFrameWindow",
\r
2111 function (reallyEmbedded) {
\r
2112 if (reallyEmbedded) {
\r
2113 this.embedAlignFrameInApplet (this.viewport.applet);
\r
2115 if (this.embedMenuIfNeeded (this.alignPanel)) {
\r
2116 this.alignPanel.setSize (this.getSize ().width, this.getSize ().height - this.statusBar.getHeight ());
\r
2117 }this.add (this.statusBar, "South");
\r
2118 this.add (this.alignPanel, "Center");
\r
2119 jalview.bin.JalviewLite.addFrame (this, this.getTitle (), this.frameWidth, this.frameHeight);
\r
2121 Clazz.defineMethod (c$, "embedAlignFrameInApplet",
\r
2122 function (theApplet) {
\r
2123 this.fileMenu.remove (this.closeMenuItem);
\r
2124 this.fileMenu.remove (3);
\r
2125 this.embeddedMenu = this.makeEmbeddedPopupMenu (this.alignFrameMenuBar, false, false);
\r
2126 theApplet.setLayout ( new java.awt.BorderLayout ());
\r
2127 theApplet.add (this.embeddedMenu, "North");
\r
2128 theApplet.add (this.statusBar, "South");
\r
2129 this.alignPanel.setSize (theApplet.getSize ().width, theApplet.getSize ().height - this.embeddedMenu.getHeight () - this.statusBar.getHeight ());
\r
2130 theApplet.add (this.alignPanel, "Center");
\r
2132 theApplet.addFocusListener (((Clazz.isClassDefined ("jalview.appletgui.AlignFrame$5") ? 0 : jalview.appletgui.AlignFrame.$AlignFrame$5$ ()), Clazz.innerTypeInstance (jalview.appletgui.AlignFrame$5, this, Clazz.cloneFinals ("theApplet", theApplet, "me", me))));
\r
2133 theApplet.validate ();
\r
2134 }, "jalview.bin.JalviewLite");
\r
2135 Clazz.defineMethod (c$, "addStructureViewInstance",
\r
2136 function (jmolviewer, sequenceIds) {
\r
2139 Clazz.defineMethod (c$, "addPdbFile",
\r
2140 function (sequenceId, pdbEntryString, pdbFile) {
\r
2141 var toaddpdb = this.viewport.getAlignment ().findName (sequenceId);
\r
2142 var needtoadd = false;
\r
2143 if (toaddpdb != null) {
\r
2144 var pdbe = toaddpdb.getPDBId ();
\r
2145 var pdbentry = null;
\r
2146 if (pdbe != null && pdbe.size () > 0) {
\r
2147 for (var pe = 0, peSize = pdbe.size (); pe < peSize; pe++) {
\r
2148 pdbentry = pdbe.elementAt (pe);
\r
2149 if (!pdbentry.getId ().equals (pdbEntryString) && !pdbentry.getFile ().equals (pdbFile)) {
\r
2154 }if (pdbentry == null) {
\r
2155 pdbentry = new jalview.datamodel.PDBEntry ();
\r
2156 pdbentry.setId (pdbEntryString);
\r
2157 pdbentry.setFile (pdbFile);
\r
2159 }var protocol = jalview.io.AppletFormatAdapter.resolveProtocol (pdbFile, "PDB");
\r
2160 if (protocol == null) {
\r
2163 if (pdbentry.getProperty () == null) {
\r
2164 pdbentry.setProperty ( new java.util.Hashtable ());
\r
2165 }pdbentry.getProperty ().put ("protocol", protocol);
\r
2166 toaddpdb.addPDBId (pdbentry);
\r
2167 this.alignPanel.getStructureSelectionManager ().registerPDBEntry (pdbentry);
\r
2170 Clazz.defineMethod (c$, "cleanSeqChainArrays",
\r
2171 function (seqs, chains) {
\r
2172 if (seqs != null) {
\r
2173 var sequences = new java.util.Vector ();
\r
2174 for (var i = 0; i < seqs.length; i++) {
\r
2175 if (seqs[i] != null) {
\r
2176 sequences.addElement ( Clazz.newArray (-1, [seqs[i], (chains != null) ? chains[i] : null]));
\r
2178 seqs = new Array (sequences.size ());
\r
2179 chains = new Array (sequences.size ());
\r
2180 for (var i = 0, isize = sequences.size (); i < isize; i++) {
\r
2181 var oj = sequences.elementAt (i);
\r
2183 chains[i] = oj[1];
\r
2185 }return Clazz.newArray (-1, [seqs, chains]);
\r
2187 Clazz.defineMethod (c$, "newStructureView",
\r
2188 function (applet, pdb, seqs, chains, protocol) {
\r
2189 var sqch = this.cleanSeqChainArrays (seqs, chains);
\r
2192 if (seqs == null || seqs.length == 0) {
\r
2193 System.err.println ("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
\r
2194 }if (protocol == null || protocol.trim ().length == 0 || protocol.equals ("null")) {
\r
2195 protocol = pdb.getProperty ().get ("protocol");
\r
2196 if (protocol == null) {
\r
2197 System.err.println ("Couldn't work out protocol to open structure: " + pdb.getId ());
\r
2199 }}if (applet.useXtrnalSviewer) {
\r
2200 if (jalview.structure.StructureSelectionManager.getStructureSelectionManager (applet).setMapping (seqs, chains, pdb.getFile (), protocol) == null) {
\r
2201 System.err.println ("Failed to map " + pdb.getFile () + " (" + protocol + ") to any sequences");
\r
2203 }if (applet.isAlignPdbStructures () && applet.jmolAvailable) {
\r
2206 var jmols = applet.getAppletWindow (jalview.appletgui.AppletJmol);
\r
2207 for (var i = 0, iSize = jmols.size (); i < iSize; i++) {
\r
2208 tajm = jmols.elementAt (i);
\r
2209 if (tajm.ap.alignFrame === this) {
\r
2213 if (ajm != null) {
\r
2214 System.err.println ("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
\r
2216 }} new jalview.appletgui.AppletJmol (pdb, seqs, chains, this.alignPanel, protocol);
\r
2217 jalview.bin.JalviewLite.lastFrameX += 40;
\r
2218 jalview.bin.JalviewLite.lastFrameY += 40;
\r
2219 }, "jalview.bin.JalviewLite,jalview.datamodel.PDBEntry,~A,~A,~S");
\r
2220 Clazz.defineMethod (c$, "alignedStructureView",
\r
2221 function (applet, pdb, seqs, chains, protocols) {
\r
2222 System.err.println ("Aligned Structure View: Not yet implemented.");
\r
2223 }, "jalview.bin.JalviewLite,~A,~A,~A,~A");
\r
2224 Clazz.defineMethod (c$, "select",
\r
2225 function (sel, csel) {
\r
2226 this.alignPanel.seqPanel.selection (sel, csel, null);
\r
2227 }, "jalview.datamodel.SequenceGroup,jalview.datamodel.ColumnSelection");
\r
2228 Clazz.defineMethod (c$, "scrollTo",
\r
2229 function (row, column) {
\r
2230 this.alignPanel.seqPanel.scrollTo (row, column);
\r
2232 Clazz.defineMethod (c$, "scrollToRow",
\r
2234 this.alignPanel.seqPanel.scrollToRow (row);
\r
2236 Clazz.defineMethod (c$, "scrollToColumn",
\r
2237 function (column) {
\r
2238 this.alignPanel.seqPanel.scrollToColumn (column);
\r
2240 Clazz.defineMethod (c$, "getSequenceSetId",
\r
2242 return this.viewport.getSequenceSetId ();
\r
2244 Clazz.defineMethod (c$, "loadScoreFile",
\r
2245 function (inFile) {
\r
2246 var file = jalview.jsdev.GenericFileAdapter.getFile ("TCoffeeScoreFile", [inFile, jalview.io.AppletFormatAdapter.checkProtocol (inFile)]);
\r
2247 if (!file.isValid ()) {
\r
2248 System.err.println ("Problems parsing T-Coffee scores: " + file.getWarningMessage ());
\r
2249 System.err.println ("Origin was:\n" + inFile);
\r
2252 if ((aln = this.viewport.getAlignment ()) != null && (aln.getHeight () != file.getHeight () || aln.getWidth () != file.getWidth ())) {
\r
2253 System.err.println ("The scores matrix does not match the alignment dimensions");
\r
2254 }if (file.annotateAlignment (this.alignPanel.getAlignment (), false)) {
\r
2255 this.alignPanel.fontChanged ();
\r
2256 this.tcoffeeColour.setEnabled (true);
\r
2257 this.changeColour ( new jalview.schemes.TCoffeeColourScheme (this.alignPanel.getAlignment ()));
\r
2260 System.err.println ("Problems resolving T-Coffee scores:");
\r
2261 if (file.getWarningMessage () != null) {
\r
2262 System.err.println (file.getWarningMessage ());
\r
2265 Clazz.defineMethod (c$, "getSplitFrame",
\r
2267 return this.splitFrame;
\r
2269 Clazz.defineMethod (c$, "setSplitFrame",
\r
2271 this.splitFrame = sf;
\r
2272 }, "jalview.appletgui.SplitFrame");
\r
2273 Clazz.overrideMethod (c$, "setShowSeqFeatures",
\r
2275 this.viewport.setShowSequenceFeatures (b);
\r
2277 Clazz.overrideMethod (c$, "setMenusForViewport",
\r
2280 Clazz.overrideMethod (c$, "refreshFeatureUI",
\r
2281 function (enableIfNecessary) {
\r
2282 if (enableIfNecessary) {
\r
2283 this.sequenceFeatures.setState (true);
\r
2284 this.alignPanel.av.setShowSequenceFeatures (true);
\r
2286 Clazz.overrideMethod (c$, "getFeatureSettingsUI",
\r
2288 return this.alignPanel.av.featureSettings;
\r
2290 c$.$AlignFrame$1$ = function () {
\r
2291 Clazz.pu$h(self.c$);
\r
2292 c$ = Clazz.declareAnonymous (jalview.appletgui, "AlignFrame$1", java.awt.event.WindowAdapter);
\r
2293 Clazz.overrideMethod (c$, "windowClosing",
\r
2295 if (this.f$.ap != null) {
\r
2296 this.f$.ap.setOverviewPanel (null);
\r
2297 }}, "java.awt.event.WindowEvent");
\r
2298 c$ = Clazz.p0p ();
\r
2300 c$.$AlignFrame$2$ = function () {
\r
2301 Clazz.pu$h(self.c$);
\r
2302 c$ = Clazz.declareAnonymous (jalview.appletgui, "AlignFrame$2", null, java.awt.event.ActionListener);
\r
2303 Clazz.overrideMethod (c$, "actionPerformed",
\r
2305 this.b$["jalview.appletgui.AlignFrame"].sortByTree (this.f$.treePanel, this.f$.title);
\r
2306 }, "java.awt.event.ActionEvent");
\r
2307 c$ = Clazz.p0p ();
\r
2309 c$.$AlignFrame$3$ = function () {
\r
2310 Clazz.pu$h(self.c$);
\r
2311 c$ = Clazz.declareAnonymous (jalview.appletgui, "AlignFrame$3", java.awt.event.WindowAdapter);
\r
2312 Clazz.defineMethod (c$, "windowOpened",
\r
2314 if (this.b$["jalview.appletgui.AlignFrame"].viewport.sortByTree) {
\r
2315 this.b$["jalview.appletgui.AlignFrame"].sortByTree (this.f$.treePanel, this.f$.title);
\r
2316 }Clazz.superCall (this, jalview.appletgui.AlignFrame$3, "windowOpened", [e]);
\r
2317 }, "java.awt.event.WindowEvent");
\r
2318 Clazz.overrideMethod (c$, "windowClosing",
\r
2320 this.b$["jalview.appletgui.AlignFrame"].sortByTreeMenu.remove (this.f$.item);
\r
2321 }, "java.awt.event.WindowEvent");
\r
2322 c$ = Clazz.p0p ();
\r
2324 c$.$AlignFrame$1AboutPanel$ = function () {
\r
2325 Clazz.pu$h(self.c$);
\r
2326 c$ = Clazz.decorateAsClass (function () {
\r
2327 Clazz.prepareCallback (this, arguments);
\r
2328 this.version = null;
\r
2329 this.builddate = null;
\r
2330 Clazz.instantialize (this, arguments);
\r
2331 }, jalview.appletgui, "AlignFrame$1AboutPanel", awt2swing.Canvas);
\r
2332 Clazz.makeConstructor (c$,
\r
2334 Clazz.superConstructor (this, jalview.appletgui.AlignFrame$1AboutPanel, []);
\r
2336 this.builddate = b;
\r
2338 Clazz.overrideMethod (c$, "paintComponent",
\r
2340 a.setColor (java.awt.Color.white);
\r
2341 a.fillRect (0, 0, this.getSize ().width, this.getSize ().height);
\r
2342 a.setFont ( new java.awt.Font ("Helvetica", 0, 12));
\r
2343 var b = a.getFontMetrics ();
\r
2344 var c = b.getHeight ();
\r
2347 a.setColor (java.awt.Color.black);
\r
2348 a.setFont ( new java.awt.Font ("Helvetica", 1, 14));
\r
2349 a.drawString (jalview.util.MessageManager.formatMessage ("label.jalviewLite_release", Clazz.newArray (-1, [this.version])), e, d += c);
\r
2350 a.setFont ( new java.awt.Font ("Helvetica", 1, 12));
\r
2351 a.drawString (jalview.util.MessageManager.formatMessage ("label.jaview_build_date", Clazz.newArray (-1, [this.builddate])), e, d += c);
\r
2352 a.setFont ( new java.awt.Font ("Helvetica", 0, 12));
\r
2353 a.drawString (jalview.util.MessageManager.getString ("label.jalview_authors_1"), e, d += c * 1.5);
\r
2354 a.drawString (jalview.util.MessageManager.getString ("label.jalview_authors_2"), e + 50, d += c + 8);
\r
2355 a.drawString (jalview.util.MessageManager.getString ("label.jalview_dev_managers"), e, d += c);
\r
2356 a.drawString (jalview.util.MessageManager.getString ("label.jalview_distribution_lists"), e, d += c);
\r
2357 a.drawString (jalview.util.MessageManager.getString ("label.jalview_please_cite"), e, d += c + 8);
\r
2358 a.drawString (jalview.util.MessageManager.getString ("label.jalview_cite_1_authors"), e, d += c);
\r
2359 a.drawString (jalview.util.MessageManager.getString ("label.jalview_cite_1_title"), e, d += c);
\r
2360 a.drawString (jalview.util.MessageManager.getString ("label.jalview_cite_1_ref"), e, d += c);
\r
2361 }, "java.awt.Graphics");
\r
2362 c$ = Clazz.p0p ();
\r
2364 c$.$AlignFrame$4$ = function () {
\r
2365 Clazz.pu$h(self.c$);
\r
2366 c$ = Clazz.declareAnonymous (jalview.appletgui, "AlignFrame$4", null, java.awt.event.ActionListener);
\r
2367 Clazz.overrideMethod (c$, "actionPerformed",
\r
2369 this.b$["jalview.appletgui.AlignFrame"].outputText_actionPerformed (e);
\r
2370 }, "java.awt.event.ActionEvent");
\r
2371 c$ = Clazz.p0p ();
\r
2373 c$.$AlignFrame$5$ = function () {
\r
2374 Clazz.pu$h(self.c$);
\r
2375 c$ = Clazz.declareAnonymous (jalview.appletgui, "AlignFrame$5", null, java.awt.event.FocusListener);
\r
2376 Clazz.overrideMethod (c$, "focusLost",
\r
2378 if (this.f$.theApplet.currentAlignFrame === this.f$.me) {
\r
2379 this.f$.theApplet.currentAlignFrame = null;
\r
2380 }}, "java.awt.event.FocusEvent");
\r
2381 Clazz.overrideMethod (c$, "focusGained",
\r
2383 this.f$.theApplet.currentAlignFrame = this.f$.me;
\r
2384 }, "java.awt.event.FocusEvent");
\r
2385 c$ = Clazz.p0p ();
\r
2387 Clazz.defineStatics (c$,
\r
2388 "copiedSequences", null,
\r
2389 "copiedHiddenColumns", null);
\r
git://source.jalview.org / jalviewjs.git / blob