1 Clazz.declarePackage ("jalview.commands");
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2 Clazz.load (["jalview.commands.CommandI", "java.lang.Enum", "java.util.ArrayList"], "jalview.commands.EditCommand", ["jalview.analysis.AlignSeq", "jalview.datamodel.AlignmentAnnotation", "$.Annotation", "$.Sequence", "$.SequenceFeature", "jalview.schemes.ResidueProperties", "jalview.util.Comparison", "$.ReverseListIterator", "$.StringUtils", "java.lang.StringBuffer", "java.util.HashMap", "$.Hashtable"], function () {
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3 c$ = Clazz.decorateAsClass (function () {
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5 this.description = null;
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6 if (!Clazz.isClassDefined ("jalview.commands.EditCommand.Edit")) {
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7 jalview.commands.EditCommand.$EditCommand$Edit$ ();
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9 Clazz.instantialize (this, arguments);
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10 }, jalview.commands, "EditCommand", null, jalview.commands.CommandI);
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11 Clazz.prepareFields (c$, function () {
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12 this.edits = new java.util.ArrayList ();
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14 Clazz.makeConstructor (c$,
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17 Clazz.makeConstructor (c$,
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18 function (description) {
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19 this.description = description;
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21 Clazz.makeConstructor (c$,
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22 function (description, command, seqs, position, number, al) {
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23 this.description = description;
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24 if (command === jalview.commands.EditCommand.Action.CUT || command === jalview.commands.EditCommand.Action.PASTE) {
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25 this.setEdit (Clazz.innerTypeInstance (jalview.commands.EditCommand.Edit, this, null, command, seqs, position, number, al));
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26 }this.performEdit (0, null);
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27 }, "~S,jalview.commands.EditCommand.Action,~A,~N,~N,jalview.datamodel.AlignmentI");
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28 Clazz.makeConstructor (c$,
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29 function (description, command, replace, seqs, position, number, al) {
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30 this.description = description;
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31 if (command === jalview.commands.EditCommand.Action.REPLACE) {
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32 this.setEdit (Clazz.innerTypeInstance (jalview.commands.EditCommand.Edit, this, null, command, seqs, position, number, al, replace));
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33 }this.performEdit (0, null);
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34 }, "~S,jalview.commands.EditCommand.Action,~S,~A,~N,~N,jalview.datamodel.AlignmentI");
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35 Clazz.defineMethod (c$, "setEdit",
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37 this.edits.clear ();
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39 }, "jalview.commands.EditCommand.Edit");
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40 Clazz.defineMethod (c$, "addEdit",
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42 if (!jalview.commands.EditCommand.expandEdit (this.edits, e)) {
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44 }}, "jalview.commands.EditCommand.Edit");
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45 c$.expandEdit = Clazz.defineMethod (c$, "expandEdit",
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46 function (edits, e) {
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47 if (edits == null || edits.isEmpty ()) {
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49 }var lastEdit = edits.get (edits.size () - 1);
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50 var action = e.command;
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51 if (lastEdit.command !== action) {
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53 }if (lastEdit.seqs.length != e.seqs.length) {
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55 }for (var i = 0; i < e.seqs.length; i++) {
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56 if (lastEdit.seqs[i].getDatasetSequence () !== e.seqs[i].getDatasetSequence ()) {
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59 var contiguous = (action === jalview.commands.EditCommand.Action.INSERT_GAP && e.position == lastEdit.position + lastEdit.number) || (action === jalview.commands.EditCommand.Action.DELETE_GAP && e.position + e.number == lastEdit.position);
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61 lastEdit.number += e.number;
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62 lastEdit.seqs = e.seqs;
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63 if (action === jalview.commands.EditCommand.Action.DELETE_GAP) {
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64 lastEdit.position--;
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67 }, "java.util.List,jalview.commands.EditCommand.Edit");
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68 Clazz.defineMethod (c$, "clearEdits",
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70 this.edits.clear ();
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72 Clazz.defineMethod (c$, "getEdit",
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74 if (i >= 0 && i < this.edits.size ()) {
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75 return this.edits.get (i);
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78 Clazz.overrideMethod (c$, "getDescription",
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80 return this.description;
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82 Clazz.overrideMethod (c$, "getSize",
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84 return this.edits.size ();
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86 Clazz.defineMethod (c$, "getAlignment",
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88 return (this.edits.isEmpty () ? null : this.edits.get (0).al);
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90 Clazz.defineMethod (c$, "appendEdit",
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91 function (command, seqs, position, number, al, performEdit) {
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92 this.appendEdit (command, seqs, position, number, al, performEdit, null);
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93 }, "jalview.commands.EditCommand.Action,~A,~N,~N,jalview.datamodel.AlignmentI,~B");
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94 Clazz.defineMethod (c$, "appendEdit",
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95 function (command, seqs, position, number, al, performEdit, views) {
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96 var edit = Clazz.innerTypeInstance (jalview.commands.EditCommand.Edit, this, null, command, seqs, position, number, al.getGapCharacter ());
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97 if (al.getHeight () == seqs.length) {
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99 edit.fullAlignmentHeight = true;
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100 }this.addEdit (edit);
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102 jalview.commands.EditCommand.performEdit (edit, views);
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103 }}, "jalview.commands.EditCommand.Action,~A,~N,~N,jalview.datamodel.AlignmentI,~B,~A");
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104 Clazz.defineMethod (c$, "appendEdit",
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105 function (edit, al, performEdit, views) {
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106 if (al.getHeight () == edit.seqs.length) {
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108 edit.fullAlignmentHeight = true;
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109 }this.addEdit (edit);
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111 jalview.commands.EditCommand.performEdit (edit, views);
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112 }}, "jalview.commands.EditCommand.Edit,jalview.datamodel.AlignmentI,~B,~A");
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113 Clazz.defineMethod (c$, "performEdit",
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114 function (commandIndex, views) {
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115 var iterator = this.edits.listIterator (commandIndex);
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116 while (iterator.hasNext ()) {
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117 var edit = iterator.next ();
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118 jalview.commands.EditCommand.performEdit (edit, views);
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121 c$.performEdit = Clazz.defineMethod (c$, "performEdit",
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122 function (edit, views) {
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123 switch (edit.command) {
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124 case jalview.commands.EditCommand.Action.INSERT_GAP:
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125 jalview.commands.EditCommand.insertGap (edit);
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127 case jalview.commands.EditCommand.Action.DELETE_GAP:
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128 jalview.commands.EditCommand.deleteGap (edit);
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130 case jalview.commands.EditCommand.Action.CUT:
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131 jalview.commands.EditCommand.cut (edit, views);
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133 case jalview.commands.EditCommand.Action.PASTE:
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134 jalview.commands.EditCommand.paste (edit, views);
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136 case jalview.commands.EditCommand.Action.REPLACE:
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137 jalview.commands.EditCommand.replace (edit);
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139 case jalview.commands.EditCommand.Action.INSERT_NUC:
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144 }, "jalview.commands.EditCommand.Edit,~A");
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145 Clazz.overrideMethod (c$, "doCommand",
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147 this.performEdit (0, views);
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149 Clazz.overrideMethod (c$, "undoCommand",
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151 var iterator = this.edits.listIterator (this.edits.size ());
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152 while (iterator.hasPrevious ()) {
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153 var e = iterator.previous ();
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154 switch (e.command) {
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155 case jalview.commands.EditCommand.Action.INSERT_GAP:
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156 jalview.commands.EditCommand.deleteGap (e);
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158 case jalview.commands.EditCommand.Action.DELETE_GAP:
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159 jalview.commands.EditCommand.insertGap (e);
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161 case jalview.commands.EditCommand.Action.CUT:
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162 jalview.commands.EditCommand.paste (e, views);
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164 case jalview.commands.EditCommand.Action.PASTE:
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165 jalview.commands.EditCommand.cut (e, views);
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167 case jalview.commands.EditCommand.Action.REPLACE:
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168 jalview.commands.EditCommand.replace (e);
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170 case jalview.commands.EditCommand.Action.INSERT_NUC:
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177 c$.insertGap = Clazz.defineMethod (c$, "insertGap",
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178 ($fz = function (command) {
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179 for (var s = 0; s < command.seqs.length; s++) {
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180 command.seqs[s].insertCharAt (command.position, command.number, command.gapChar);
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182 jalview.commands.EditCommand.adjustAnnotations (command, true, false, null);
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183 }, $fz.isPrivate = true, $fz), "jalview.commands.EditCommand.Edit");
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184 c$.deleteGap = Clazz.defineMethod (c$, "deleteGap",
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185 ($fz = function (command) {
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186 for (var s = 0; s < command.seqs.length; s++) {
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187 command.seqs[s].deleteChars (command.position, command.position + command.number);
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189 jalview.commands.EditCommand.adjustAnnotations (command, false, false, null);
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190 }, $fz.isPrivate = true, $fz), "jalview.commands.EditCommand.Edit");
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191 c$.cut = Clazz.defineMethod (c$, "cut",
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192 function (command, views) {
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193 var seqDeleted = false;
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194 command.string = Clazz.newCharArray (command.seqs.length, '\0');
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195 for (var i = 0; i < command.seqs.length; i++) {
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196 var sequence = command.seqs[i];
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197 if (sequence.getLength () > command.position) {
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198 command.string[i] = sequence.getSequence (command.position, command.position + command.number);
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199 var oldds = sequence.getDatasetSequence ();
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200 if (command.oldds != null && command.oldds[i] != null) {
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201 sequence.setDatasetSequence (null);
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202 }sequence.deleteChars (command.position, command.position + command.number);
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203 if (command.oldds != null && command.oldds[i] != null) {
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204 sequence.setDatasetSequence (command.oldds[i]);
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205 command.oldds[i] = oldds;
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207 if (oldds !== sequence.getDatasetSequence () || sequence.getSequenceFeatures () != null) {
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208 if (command.oldds == null) {
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209 command.oldds = new Array (command.seqs.length);
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210 }command.oldds[i] = oldds;
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211 jalview.commands.EditCommand.adjustFeatures (command, i, sequence.findPosition (command.position), sequence.findPosition (command.position + command.number), false);
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212 }}}if (sequence.getLength () < 1) {
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213 command.al.deleteSequence (sequence);
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216 jalview.commands.EditCommand.adjustAnnotations (command, false, seqDeleted, views);
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217 }, "jalview.commands.EditCommand.Edit,~A");
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218 c$.paste = Clazz.defineMethod (c$, "paste",
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219 function (command, views) {
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222 var newDSWasNeeded;
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225 var seqWasDeleted = false;
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228 for (var i = 0; i < command.seqs.length; i++) {
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229 newDSNeeded = false;
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230 newDSWasNeeded = command.oldds != null && command.oldds[i] != null;
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231 if (command.seqs[i].getLength () < 1) {
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232 if (command.alIndex[i] < command.al.getHeight ()) {
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235 if (!(command.alIndex[i] < 0)) {
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236 sequences.add (command.alIndex[i], command.seqs[i]);
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238 command.al.addSequence (command.seqs[i]);
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239 }seqWasDeleted = true;
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240 }newstart = command.seqs[i].getStart ();
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241 newend = command.seqs[i].getEnd ();
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242 tmp = new StringBuffer ();
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243 tmp.append (command.seqs[i].getSequence ());
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244 if (command.string != null && command.string[i] != null) {
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245 if (command.position >= tmp.length ()) {
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246 var length = command.position - tmp.length ();
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247 while (length > 0) {
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248 tmp.append (command.gapChar);
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251 }tmp.insert (command.position, command.string[i]);
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252 for (var s = 0; s < command.string[i].length; s++) {
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253 if (jalview.schemes.ResidueProperties.aaIndex[command.string[i][s].charCodeAt (0)] != 23) {
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254 if (!newDSNeeded) {
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255 newDSNeeded = true;
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256 start = command.seqs[i].findPosition (command.position);
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257 end = command.seqs[i].findPosition (command.position + command.number);
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258 }if (command.seqs[i].getStart () == start) {
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263 command.string[i] = null;
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264 }command.seqs[i].setSequence (tmp.toString ());
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265 command.seqs[i].setStart (newstart);
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266 command.seqs[i].setEnd (newend);
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268 if (command.seqs[i].getDatasetSequence () != null) {
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270 if (newDSWasNeeded) {
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271 ds = command.oldds[i];
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273 ds = new jalview.datamodel.Sequence (command.seqs[i].getName (), jalview.analysis.AlignSeq.extractGaps (jalview.util.Comparison.GapChars, command.seqs[i].getSequenceAsString ()), command.seqs[i].getStart (), command.seqs[i].getEnd ());
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274 ds.setDescription (command.seqs[i].getDescription ());
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275 }if (command.oldds == null) {
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276 command.oldds = new Array (command.seqs.length);
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277 }command.oldds[i] = command.seqs[i].getDatasetSequence ();
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278 command.seqs[i].setDatasetSequence (ds);
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279 }jalview.commands.EditCommand.adjustFeatures (command, i, start, end, true);
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281 jalview.commands.EditCommand.adjustAnnotations (command, true, seqWasDeleted, views);
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282 command.string = null;
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283 }, "jalview.commands.EditCommand.Edit,~A");
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284 c$.replace = Clazz.defineMethod (c$, "replace",
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285 function (command) {
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288 var start = command.position;
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289 var end = command.number;
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290 command.number = start + command.string[0].length;
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291 for (var i = 0; i < command.seqs.length; i++) {
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292 var newDSWasNeeded = command.oldds != null && command.oldds[i] != null;
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293 oldstring = command.seqs[i].getSequenceAsString ();
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294 tmp = new StringBuffer (oldstring.substring (0, start));
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295 tmp.append (command.string[i]);
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296 var nogaprep = jalview.analysis.AlignSeq.extractGaps (jalview.util.Comparison.GapChars, String.instantialize (command.string[i]));
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297 var ipos = command.seqs[i].findPosition (start) - command.seqs[i].getStart ();
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298 tmp.append (oldstring.substring (end));
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299 command.seqs[i].setSequence (tmp.toString ());
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300 command.string[i] = oldstring.substring (start, end).toCharArray ();
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301 var nogapold = jalview.analysis.AlignSeq.extractGaps (jalview.util.Comparison.GapChars, String.instantialize (command.string[i]));
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302 if (!nogaprep.toLowerCase ().equals (nogapold.toLowerCase ())) {
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303 if (newDSWasNeeded) {
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304 var oldds = command.seqs[i].getDatasetSequence ();
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305 command.seqs[i].setDatasetSequence (command.oldds[i]);
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306 command.oldds[i] = oldds;
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308 if (command.oldds == null) {
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309 command.oldds = new Array (command.seqs.length);
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310 }command.oldds[i] = command.seqs[i].getDatasetSequence ();
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311 var newds = new jalview.datamodel.Sequence (command.seqs[i].getDatasetSequence ());
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313 var osp = newds.getSequenceAsString ();
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314 fullseq = osp.substring (0, ipos) + nogaprep + osp.substring (ipos + nogaprep.length);
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315 newds.setSequence (fullseq.toUpperCase ());
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316 command.seqs[i].setDatasetSequence (newds);
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320 }, "jalview.commands.EditCommand.Edit");
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321 c$.adjustAnnotations = Clazz.defineMethod (c$, "adjustAnnotations",
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322 function (command, insert, modifyVisibility, views) {
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323 var annotations = null;
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324 if (modifyVisibility && !insert) {
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325 command.deletedAnnotationRows = new java.util.Hashtable ();
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326 }if (command.fullAlignmentHeight) {
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327 annotations = command.al.getAlignmentAnnotation ();
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331 for (var s = 0; s < command.seqs.length; s++) {
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332 if (modifyVisibility) {
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334 tmp = command.seqs[s].getAnnotation ();
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336 var alen = tmp.length;
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337 for (var aa = 0; aa < tmp.length; aa++) {
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338 if (!command.al.deleteAnnotation (tmp[aa])) {
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342 command.seqs[s].setAlignmentAnnotation (null);
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343 if (alen != tmp.length) {
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344 var saved = new Array (alen);
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345 for (var aa = 0, aapos = 0; aa < tmp.length; aa++) {
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346 if (tmp[aa] != null) {
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347 saved[aapos++] = tmp[aa];
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351 command.deletedAnnotationRows.put (command.seqs[s], saved);
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352 for (var alview = 0; views != null && alview < views.length; alview++) {
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353 if (views[alview] !== command.al) {
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354 var toremove = views[alview].getAlignmentAnnotation ();
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355 if (toremove == null || toremove.length == 0) {
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357 }for (var aa = 0; aa < toremove.length; aa++) {
\r
358 if (toremove[aa].sequenceRef === command.seqs[s]) {
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359 views[alview].deleteAnnotation (toremove[aa]);
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363 command.deletedAnnotationRows.put (command.seqs[s], tmp);
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365 if (command.deletedAnnotationRows != null && command.deletedAnnotationRows.containsKey (command.seqs[s])) {
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366 var revealed = command.deletedAnnotationRows.get (command.seqs[s]);
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367 command.seqs[s].setAlignmentAnnotation (revealed);
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368 if (revealed != null) {
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369 for (var aa = 0; aa < revealed.length; aa++) {
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370 command.al.addAnnotation (revealed[aa]);
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372 for (var aa = 0; aa < revealed.length; aa++) {
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373 command.al.setAnnotationIndex (revealed[aa], aa);
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375 for (var vnum = 0; views != null && vnum < views.length; vnum++) {
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376 if (views[vnum] !== command.al) {
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377 var avwidth = views[vnum].getWidth () + 1;
\r
378 for (var a = 0; a < revealed.length; a++) {
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379 var newann = new jalview.datamodel.AlignmentAnnotation (revealed[a]);
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380 command.seqs[s].addAlignmentAnnotation (newann);
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381 newann.padAnnotation (avwidth);
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382 views[vnum].addAnnotation (newann);
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383 views[vnum].setAnnotationIndex (newann, a);
\r
387 }if (command.seqs[s].getAnnotation () == null) {
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390 annotations = command.seqs[s].getAnnotation ();
\r
392 tmp = new Array (aSize + command.seqs[s].getAnnotation ().length);
\r
393 System.arraycopy (annotations, 0, tmp, 0, aSize);
\r
394 System.arraycopy (command.seqs[s].getAnnotation (), 0, tmp, aSize, command.seqs[s].getAnnotation ().length);
\r
396 }aSize = annotations.length;
\r
398 }if (annotations == null) {
\r
401 command.deletedAnnotations = new java.util.Hashtable ();
\r
404 for (var a = 0; a < annotations.length; a++) {
\r
405 if (annotations[a].autoCalculated || annotations[a].annotations == null) {
\r
408 aSize = annotations[a].annotations.length;
\r
410 temp = new Array (aSize + command.number);
\r
411 if (annotations[a].padGaps) {
\r
412 for (var aa = 0; aa < temp.length; aa++) {
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413 temp[aa] = new jalview.datamodel.Annotation (command.gapChar + "", null, ' ', 0);
\r
416 if (command.position < aSize) {
\r
417 if (command.position + command.number >= aSize) {
\r
420 tSize = aSize - command.number;
\r
425 }temp = new Array (tSize);
\r
427 if (command.position < annotations[a].annotations.length) {
\r
428 System.arraycopy (annotations[a].annotations, 0, temp, 0, command.position);
\r
429 if (command.deletedAnnotations != null && command.deletedAnnotations.containsKey (annotations[a].annotationId)) {
\r
430 var restore = command.deletedAnnotations.get (annotations[a].annotationId);
\r
431 System.arraycopy (restore, 0, temp, command.position, command.number);
\r
432 }System.arraycopy (annotations[a].annotations, command.position, temp, command.position + command.number, aSize - command.position);
\r
434 if (command.deletedAnnotations != null && command.deletedAnnotations.containsKey (annotations[a].annotationId)) {
\r
435 var restore = command.deletedAnnotations.get (annotations[a].annotationId);
\r
436 temp = new Array (annotations[a].annotations.length + restore.length);
\r
437 System.arraycopy (annotations[a].annotations, 0, temp, 0, annotations[a].annotations.length);
\r
438 System.arraycopy (restore, 0, temp, annotations[a].annotations.length, restore.length);
\r
440 temp = annotations[a].annotations;
\r
442 if (tSize != aSize || command.position < 2) {
\r
443 var copylen = Math.min (command.position, annotations[a].annotations.length);
\r
445 System.arraycopy (annotations[a].annotations, 0, temp, 0, copylen);
\r
446 }var deleted = new Array (command.number);
\r
447 if (copylen >= command.position) {
\r
448 copylen = Math.min (command.number, annotations[a].annotations.length - command.position);
\r
450 System.arraycopy (annotations[a].annotations, command.position, deleted, 0, copylen);
\r
451 }}command.deletedAnnotations.put (annotations[a].annotationId, deleted);
\r
452 if (annotations[a].annotations.length > command.position + command.number) {
\r
453 System.arraycopy (annotations[a].annotations, command.position + command.number, temp, command.position, annotations[a].annotations.length - command.position - command.number);
\r
455 var dSize = aSize - command.position;
\r
457 var deleted = new Array (command.number);
\r
458 System.arraycopy (annotations[a].annotations, command.position, deleted, 0, dSize);
\r
459 command.deletedAnnotations.put (annotations[a].annotationId, deleted);
\r
460 tSize = Math.min (annotations[a].annotations.length, command.position);
\r
461 temp = new Array (tSize);
\r
462 System.arraycopy (annotations[a].annotations, 0, temp, 0, tSize);
\r
464 temp = annotations[a].annotations;
\r
465 }}}annotations[a].annotations = temp;
\r
467 }, "jalview.commands.EditCommand.Edit,~B,~B,~A");
\r
468 c$.adjustFeatures = Clazz.defineMethod (c$, "adjustFeatures",
\r
469 function (command, index, i, j, insert) {
\r
470 var seq = command.seqs[index];
\r
471 var sequence = seq.getDatasetSequence ();
\r
472 if (sequence == null) {
\r
475 if (command.editedFeatures != null && command.editedFeatures.containsKey (seq)) {
\r
476 sequence.setSequenceFeatures (command.editedFeatures.get (seq));
\r
478 }var sf = sequence.getSequenceFeatures ();
\r
481 }var oldsf = new Array (sf.length);
\r
483 for (var s = 0; s < sf.length; s++) {
\r
484 var copy = new jalview.datamodel.SequenceFeature (sf[s]);
\r
486 if (sf[s].getEnd () < i) {
\r
488 }if (sf[s].getBegin () > j) {
\r
489 sf[s].setBegin (copy.getBegin () - cSize);
\r
490 sf[s].setEnd (copy.getEnd () - cSize);
\r
492 }if (sf[s].getBegin () >= i) {
\r
493 sf[s].setBegin (i);
\r
494 }if (sf[s].getEnd () < j) {
\r
495 sf[s].setEnd (j - 1);
\r
496 }sf[s].setEnd (sf[s].getEnd () - (cSize));
\r
497 if (sf[s].getBegin () > sf[s].getEnd ()) {
\r
498 sequence.deleteFeature (sf[s]);
\r
500 if (command.editedFeatures == null) {
\r
501 command.editedFeatures = new java.util.Hashtable ();
\r
502 }command.editedFeatures.put (seq, oldsf);
\r
503 }, "jalview.commands.EditCommand.Edit,~N,~N,~N,~B");
\r
504 Clazz.defineMethod (c$, "getEdits",
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508 Clazz.defineMethod (c$, "priorState",
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509 function (forUndo) {
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510 var result = new java.util.HashMap ();
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511 if (this.getEdits () == null) {
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514 for (var e, $e = this.getEdits ().iterator (); $e.hasNext () && ((e = $e.next ()) || true);) {
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515 for (var seq, $seq = 0, $$seq = e.getSequences (); $seq < $$seq.length && ((seq = $$seq[$seq]) || true); $seq++) {
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516 var ds = seq.getDatasetSequence ();
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517 var preEdit = result.get (ds);
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518 if (preEdit == null) {
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519 preEdit = new jalview.datamodel.Sequence ("", seq.getSequenceAsString ());
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520 preEdit.setDatasetSequence (ds);
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521 result.put (ds, preEdit);
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525 }var edits = new jalview.util.ReverseListIterator (this.getEdits ());
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526 while (edits.hasNext ()) {
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527 var oldEdit = edits.next ();
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528 var action = oldEdit.getAction ();
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529 var position = oldEdit.getPosition ();
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530 var number = oldEdit.getNumber ();
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531 var gap = oldEdit.getGapCharacter ();
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532 for (var seq, $seq = 0, $$seq = oldEdit.getSequences (); $seq < $$seq.length && ((seq = $$seq[$seq]) || true); $seq++) {
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533 var ds = seq.getDatasetSequence ();
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534 var preEdit = result.get (ds);
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535 if (preEdit == null) {
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536 preEdit = new jalview.datamodel.Sequence ("", seq.getSequenceAsString ());
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537 preEdit.setDatasetSequence (ds);
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538 result.put (ds, preEdit);
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540 if (action === jalview.commands.EditCommand.Action.DELETE_GAP) {
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541 preEdit.setSequence ( String.instantialize (jalview.util.StringUtils.insertCharAt (preEdit.getSequence (), position, number, gap)));
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542 } else if (action === jalview.commands.EditCommand.Action.INSERT_GAP) {
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543 preEdit.setSequence ( String.instantialize (jalview.util.StringUtils.deleteChars (preEdit.getSequence (), position, position + number)));
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545 System.err.println ("Can't undo edit action " + action);
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550 Clazz.defineMethod (c$, "getEditIterator",
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551 function (forwards) {
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553 return this.getEdits ().iterator ();
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555 return new jalview.util.ReverseListIterator (this.getEdits ());
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557 c$.$EditCommand$Edit$ = function () {
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559 c$ = Clazz.decorateAsClass (function () {
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560 Clazz.prepareCallback (this, arguments);
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562 this.fullAlignmentHeight = false;
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563 this.deletedAnnotationRows = null;
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564 this.deletedAnnotations = null;
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565 this.editedFeatures = null;
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567 this.command = null;
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568 this.string = null;
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570 this.alIndex = null;
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573 this.gapChar = '\0';
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574 Clazz.instantialize (this, arguments);
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575 }, jalview.commands.EditCommand, "Edit");
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576 Clazz.makeConstructor (c$,
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577 function (a, b, c, d, e) {
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583 }, "jalview.commands.EditCommand.Action,~A,~N,~N,~S");
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584 Clazz.makeConstructor (c$,
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585 function (a, b, c, d, e) {
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586 this.gapChar = e.getGapCharacter ();
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592 this.alIndex = Clazz.newIntArray (b.length, 0);
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593 for (var f = 0; f < b.length; f++) {
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594 this.alIndex[f] = e.findIndex (b[f]);
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596 this.fullAlignmentHeight = (e.getHeight () == b.length);
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597 }, "jalview.commands.EditCommand.Action,~A,~N,~N,jalview.datamodel.AlignmentI");
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598 Clazz.makeConstructor (c$,
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599 function (a, b, c, d, e, f) {
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605 this.gapChar = e.getGapCharacter ();
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606 this.string = Clazz.newCharArray (b.length, '\0');
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607 for (var g = 0; g < b.length; g++) {
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608 this.string[g] = f.toCharArray ();
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610 this.fullAlignmentHeight = (e.getHeight () == b.length);
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611 }, "jalview.commands.EditCommand.Action,~A,~N,~N,jalview.datamodel.AlignmentI,~S");
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612 Clazz.defineMethod (c$, "getSequences",
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616 Clazz.defineMethod (c$, "getPosition",
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618 return this.position;
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620 Clazz.defineMethod (c$, "getAction",
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622 return this.command;
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624 Clazz.defineMethod (c$, "getNumber",
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626 return this.number;
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628 Clazz.defineMethod (c$, "getGapCharacter",
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630 return this.gapChar;
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635 c$ = Clazz.declareType (jalview.commands.EditCommand, "Action", Enum);
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636 Clazz.defineMethod (c$, "getUndoAction",
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639 case jalview.commands.EditCommand.Action.INSERT_GAP:
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640 return jalview.commands.EditCommand.Action.DELETE_GAP;
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641 case jalview.commands.EditCommand.Action.CUT:
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642 return jalview.commands.EditCommand.Action.PASTE;
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643 case jalview.commands.EditCommand.Action.DELETE_GAP:
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644 return jalview.commands.EditCommand.Action.INSERT_GAP;
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645 case jalview.commands.EditCommand.Action.INSERT_NUC:
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647 case jalview.commands.EditCommand.Action.PASTE:
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648 return jalview.commands.EditCommand.Action.CUT;
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649 case jalview.commands.EditCommand.Action.REPLACE:
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650 return jalview.commands.EditCommand.Action.REPLACE;
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654 Clazz.defineEnumConstant (c$, "INSERT_GAP", 0, []);
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655 Clazz.defineEnumConstant (c$, "DELETE_GAP", 1, []);
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656 Clazz.defineEnumConstant (c$, "CUT", 2, []);
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657 Clazz.defineEnumConstant (c$, "PASTE", 3, []);
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658 Clazz.defineEnumConstant (c$, "REPLACE", 4, []);
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659 Clazz.defineEnumConstant (c$, "INSERT_NUC", 5, []);
\r