Merge branch 'master' of https://source.jalview.org/git/jalviewjs.git

[jalviewjs.git] / site / j2s / jalview / commands / RemoveGapsCommand.js

diff --git a/site/j2s/jalview/commands/RemoveGapsCommand.js b/site/j2s/jalview/commands/RemoveGapsCommand.js
index 7097db3..3cc233d 100644 (file)
--- a/site/j2s/jalview/commands/RemoveGapsCommand.js
+++ b/site/j2s/jalview/commands/RemoveGapsCommand.js
@@ -1,56 +1,56 @@
-Clazz.declarePackage ("jalview.commands");\r
-Clazz.load (["jalview.commands.EditCommand"], "jalview.commands.RemoveGapsCommand", ["jalview.util.Comparison"], function () {\r
-c$ = Clazz.declareType (jalview.commands, "RemoveGapsCommand", jalview.commands.EditCommand);\r
-Clazz.makeConstructor (c$, \r
-function (description, seqs, al) {\r
-Clazz.superConstructor (this, jalview.commands.RemoveGapsCommand, []);\r
-this.description = description;\r
-var width = 0;\r
-for (var i = 0; i < seqs.length; i++) {\r
-if (seqs[i].getLength () > width) {\r
-width = seqs[i].getLength ();\r
-}}\r
-this.findGaps (seqs, 0, width, al);\r
-}, "~S,~A,jalview.datamodel.AlignmentI");\r
-Clazz.makeConstructor (c$, \r
-function (description, seqs, start, end, al) {\r
-Clazz.superConstructor (this, jalview.commands.RemoveGapsCommand, []);\r
-this.description = description;\r
-this.findGaps (seqs, start, end, al);\r
-}, "~S,~A,~N,~N,jalview.datamodel.AlignmentI");\r
-Clazz.defineMethod (c$, "findGaps", \r
-function (seqs, start, end, al) {\r
-var startCol = -1;\r
-var endCol = -1;\r
-var deletedCols = 0;\r
-var j;\r
-var jSize;\r
-this.clearEdits ();\r
-var $delete = true;\r
-var sequence;\r
-for (var s = 0; s < seqs.length; s++) {\r
-deletedCols = 0;\r
-startCol = -1;\r
-endCol = -1;\r
-sequence = seqs[s].getSequence (start, end + 1);\r
-jSize = sequence.length;\r
-for (j = 0; j < jSize; j++) {\r
-$delete = true;\r
-if (!jalview.util.Comparison.isGap (sequence[j])) {\r
-if ($delete) {\r
-endCol = j;\r
-}$delete = false;\r
-}if ($delete && startCol == -1) {\r
-startCol = j;\r
-}if (!$delete && startCol > -1) {\r
-this.appendEdit (jalview.commands.EditCommand.Action.DELETE_GAP,  Clazz.newArray (-1, [seqs[s]]), start + startCol - deletedCols, endCol - startCol, al, false, null);\r
-deletedCols += (endCol - startCol);\r
-startCol = -1;\r
-endCol = -1;\r
-}}\r
-if ($delete && startCol > -1) {\r
-this.appendEdit (jalview.commands.EditCommand.Action.DELETE_GAP,  Clazz.newArray (-1, [seqs[s]]), start + startCol - deletedCols, jSize - startCol, al, false, null);\r
-}}\r
-this.performEdit (0, null);\r
-}, "~A,~N,~N,jalview.datamodel.AlignmentI");\r
-});\r
+Clazz.declarePackage ("jalview.commands");
+Clazz.load (["jalview.commands.EditCommand"], "jalview.commands.RemoveGapsCommand", ["jalview.util.Comparison"], function () {
+c$ = 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");
+});