1 Clazz.declarePackage ("jalview.commands");
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2 Clazz.load (["jalview.commands.EditCommand"], "jalview.commands.RemoveGapColCommand", ["jalview.util.Comparison"], function () {
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3 c$ = Clazz.decorateAsClass (function () {
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4 this.columnsDeleted = 0;
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5 Clazz.instantialize (this, arguments);
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6 }, jalview.commands, "RemoveGapColCommand", jalview.commands.EditCommand);
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7 Clazz.makeConstructor (c$,
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8 function (description, seqs, start, end, al) {
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9 Clazz.superConstructor (this, jalview.commands.RemoveGapColCommand, []);
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10 this.description = description;
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12 var jSize = seqs.length;
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15 this.columnsDeleted = 0;
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18 for (var i = start; i <= end; i++) {
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20 for (j = 0; j < jSize; j++) {
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21 if (seqs[j].getLength () > i) {
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22 if (!jalview.util.Comparison.isGap (seqs[j].getCharAt (i))) {
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28 if ($delete && startCol == -1) {
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30 }if (!$delete && startCol > -1) {
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31 this.appendEdit (jalview.commands.EditCommand.Action.DELETE_GAP, seqs, startCol - this.columnsDeleted, endCol - startCol, al, false, null);
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32 this.columnsDeleted += (endCol - startCol);
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36 if ($delete && startCol > -1) {
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37 this.appendEdit (jalview.commands.EditCommand.Action.DELETE_GAP, seqs, startCol - this.columnsDeleted, end - startCol + 1, al, false, null);
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38 this.columnsDeleted += (end - startCol + 1);
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39 }this.performEdit (0, null);
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40 }, "~S,~A,~N,~N,jalview.datamodel.AlignmentI");
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41 Clazz.overrideMethod (c$, "getSize",
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43 return this.columnsDeleted;
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