X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=bin%2Fjalview%2Fcommands%2FRemoveGapsCommand.js;h=3cc233d6ef6df2c3a7e06636e95d1051f4ee6865;hp=7097db390dcc36bf522335acc41c2d0a5a5558aa;hb=7301a2415adab88038b291fc54caeeb3a5a47a44;hpb=6154cb57a6eac3bb1344b8342495f5bb701ee921

diff --git a/bin/jalview/commands/RemoveGapsCommand.js b/bin/jalview/commands/RemoveGapsCommand.js
index 7097db3..3cc233d 100644
--- a/bin/jalview/commands/RemoveGapsCommand.js
+++ b/bin/jalview/commands/RemoveGapsCommand.js
@@ -1,56 +1,56 @@
-Clazz.declarePackage ("jalview.commands");
-Clazz.load (["jalview.commands.EditCommand"], "jalview.commands.RemoveGapsCommand", ["jalview.util.Comparison"], function () {
-c$ = Clazz.declareType (jalview.commands, "RemoveGapsCommand", jalview.commands.EditCommand);
-Clazz.makeConstructor (c$, 
-function (description, seqs, al) {
-Clazz.superConstructor (this, jalview.commands.RemoveGapsCommand, []);
-this.description = description;
-var width = 0;
-for (var i = 0; i < seqs.length; i++) {
-if (seqs[i].getLength () > width) {
-width = seqs[i].getLength ();
-}}
-this.findGaps (seqs, 0, width, al);
-}, "~S,~A,jalview.datamodel.AlignmentI");
-Clazz.makeConstructor (c$, 
-function (description, seqs, start, end, al) {
-Clazz.superConstructor (this, jalview.commands.RemoveGapsCommand, []);
-this.description = description;
-this.findGaps (seqs, start, end, al);
-}, "~S,~A,~N,~N,jalview.datamodel.AlignmentI");
-Clazz.defineMethod (c$, "findGaps", 
-function (seqs, start, end, al) {
-var startCol = -1;
-var endCol = -1;
-var deletedCols = 0;
-var j;
-var jSize;
-this.clearEdits ();
-var $delete = true;
-var sequence;
-for (var s = 0; s < seqs.length; s++) {
-deletedCols = 0;
-startCol = -1;
-endCol = -1;
-sequence = seqs[s].getSequence (start, end + 1);
-jSize = sequence.length;
-for (j = 0; j < jSize; j++) {
-$delete = true;
-if (!jalview.util.Comparison.isGap (sequence[j])) {
-if ($delete) {
-endCol = j;
-}$delete = false;
-}if ($delete && startCol == -1) {
-startCol = j;
-}if (!$delete && startCol > -1) {
-this.appendEdit (jalview.commands.EditCommand.Action.DELETE_GAP,  Clazz.newArray (-1, [seqs[s]]), start + startCol - deletedCols, endCol - startCol, al, false, null);
-deletedCols += (endCol - startCol);
-startCol = -1;
-endCol = -1;
-}}
-if ($delete && startCol > -1) {
-this.appendEdit (jalview.commands.EditCommand.Action.DELETE_GAP,  Clazz.newArray (-1, [seqs[s]]), start + startCol - deletedCols, jSize - startCol, al, false, null);
-}}
-this.performEdit (0, null);
-}, "~A,~N,~N,jalview.datamodel.AlignmentI");
-});
+Clazz.declarePackage ("jalview.commands");
+Clazz.load (["jalview.commands.EditCommand"], "jalview.commands.RemoveGapsCommand", ["jalview.util.Comparison"], function () {
+c$ = Clazz.declareType (jalview.commands, "RemoveGapsCommand", jalview.commands.EditCommand);
+Clazz.makeConstructor (c$, 
+function (description, seqs, al) {
+Clazz.superConstructor (this, jalview.commands.RemoveGapsCommand, []);
+this.description = description;
+var width = 0;
+for (var i = 0; i < seqs.length; i++) {
+if (seqs[i].getLength () > width) {
+width = seqs[i].getLength ();
+}}
+this.findGaps (seqs, 0, width, al);
+}, "~S,~A,jalview.datamodel.AlignmentI");
+Clazz.makeConstructor (c$, 
+function (description, seqs, start, end, al) {
+Clazz.superConstructor (this, jalview.commands.RemoveGapsCommand, []);
+this.description = description;
+this.findGaps (seqs, start, end, al);
+}, "~S,~A,~N,~N,jalview.datamodel.AlignmentI");
+Clazz.defineMethod (c$, "findGaps", 
+function (seqs, start, end, al) {
+var startCol = -1;
+var endCol = -1;
+var deletedCols = 0;
+var j;
+var jSize;
+this.clearEdits ();
+var $delete = true;
+var sequence;
+for (var s = 0; s < seqs.length; s++) {
+deletedCols = 0;
+startCol = -1;
+endCol = -1;
+sequence = seqs[s].getSequence (start, end + 1);
+jSize = sequence.length;
+for (j = 0; j < jSize; j++) {
+$delete = true;
+if (!jalview.util.Comparison.isGap (sequence[j])) {
+if ($delete) {
+endCol = j;
+}$delete = false;
+}if ($delete && startCol == -1) {
+startCol = j;
+}if (!$delete && startCol > -1) {
+this.appendEdit (jalview.commands.EditCommand.Action.DELETE_GAP,  Clazz.newArray (-1, [seqs[s]]), start + startCol - deletedCols, endCol - startCol, al, false, null);
+deletedCols += (endCol - startCol);
+startCol = -1;
+endCol = -1;
+}}
+if ($delete && startCol > -1) {
+this.appendEdit (jalview.commands.EditCommand.Action.DELETE_GAP,  Clazz.newArray (-1, [seqs[s]]), start + startCol - deletedCols, jSize - startCol, al, false, null);
+}}
+this.performEdit (0, null);
+}, "~A,~N,~N,jalview.datamodel.AlignmentI");
+});