JAL-1807 test

[jalviewjs.git] / bin / jalview / util / ShiftList.js

diff --git a/bin/jalview/util/ShiftList.js b/bin/jalview/util/ShiftList.js
index 29a9645..258fe14 100644 (file)
--- a/bin/jalview/util/ShiftList.js
+++ b/bin/jalview/util/ShiftList.js
@@ -1,67 +1,67 @@
-Clazz.declarePackage ("jalview.util");\r
-Clazz.load (null, "jalview.util.ShiftList", ["java.util.ArrayList"], function () {\r
-c$ = Clazz.decorateAsClass (function () {\r
-this.shifts = null;\r
-Clazz.instantialize (this, arguments);\r
-}, jalview.util, "ShiftList");\r
-Clazz.makeConstructor (c$, \r
-function () {\r
-this.shifts =  new java.util.ArrayList ();\r
-});\r
-Clazz.defineMethod (c$, "addShift", \r
-function (pos, shift) {\r
-{\r
-var sidx = 0;\r
-var rshift = null;\r
-while (sidx < this.shifts.size () && (rshift = this.shifts.get (sidx))[0] < pos) {\r
-sidx++;\r
-}\r
-if (sidx == this.shifts.size ()) {\r
-this.shifts.add (sidx,  Clazz.newIntArray (-1, [pos, shift]));\r
-} else {\r
-rshift[1] += shift;\r
-}}}, "~N,~N");\r
-Clazz.defineMethod (c$, "shift", \r
-function (pos) {\r
-if (this.shifts.size () == 0) {\r
-return pos;\r
-}var shifted = pos;\r
-var sidx = 0;\r
-var rshift;\r
-while (sidx < this.shifts.size () && (rshift = (this.shifts.get (sidx++)))[0] <= pos) {\r
-shifted += rshift[1];\r
-}\r
-return shifted;\r
-}, "~N");\r
-Clazz.defineMethod (c$, "clear", \r
-function () {\r
-this.shifts.clear ();\r
-});\r
-Clazz.defineMethod (c$, "getInverse", \r
-function () {\r
-var inverse =  new jalview.util.ShiftList ();\r
-{\r
-if (this.shifts != null) {\r
-for (var sh, $sh = this.shifts.iterator (); $sh.hasNext () && ((sh = $sh.next ()) || true);) {\r
-if (sh != null) {\r
-inverse.shifts.add ( Clazz.newIntArray (-1, [sh[0], -sh[1]]));\r
-}}\r
-}}return inverse;\r
-});\r
-c$.parseMap = Clazz.defineMethod (c$, "parseMap", \r
-function (gapMap) {\r
-var shiftList = null;\r
-if (gapMap != null && gapMap.length > 0) {\r
-shiftList =  new jalview.util.ShiftList ();\r
-for (var i = 0, p = 0; i < gapMap.length; p++, i++) {\r
-if (p != gapMap[i]) {\r
-shiftList.addShift (p, gapMap[i] - p);\r
-p = gapMap[i];\r
-}}\r
-}return shiftList;\r
-}, "~A");\r
-Clazz.defineMethod (c$, "getShifts", \r
-function () {\r
-return this.shifts;\r
-});\r
-});\r
+Clazz.declarePackage ("jalview.util");
+Clazz.load (null, "jalview.util.ShiftList", ["java.util.ArrayList"], function () {
+c$ = Clazz.decorateAsClass (function () {
+this.shifts = null;
+Clazz.instantialize (this, arguments);
+}, jalview.util, "ShiftList");
+Clazz.makeConstructor (c$, 
+function () {
+this.shifts =  new java.util.ArrayList ();
+});
+Clazz.defineMethod (c$, "addShift", 
+function (pos, shift) {
+{
+var sidx = 0;
+var rshift = null;
+while (sidx < this.shifts.size () && (rshift = this.shifts.get (sidx))[0] < pos) {
+sidx++;
+}
+if (sidx == this.shifts.size ()) {
+this.shifts.add (sidx,  Clazz.newIntArray (-1, [pos, shift]));
+} else {
+rshift[1] += shift;
+}}}, "~N,~N");
+Clazz.defineMethod (c$, "shift", 
+function (pos) {
+if (this.shifts.size () == 0) {
+return pos;
+}var shifted = pos;
+var sidx = 0;
+var rshift;
+while (sidx < this.shifts.size () && (rshift = (this.shifts.get (sidx++)))[0] <= pos) {
+shifted += rshift[1];
+}
+return shifted;
+}, "~N");
+Clazz.defineMethod (c$, "clear", 
+function () {
+this.shifts.clear ();
+});
+Clazz.defineMethod (c$, "getInverse", 
+function () {
+var inverse =  new jalview.util.ShiftList ();
+{
+if (this.shifts != null) {
+for (var sh, $sh = this.shifts.iterator (); $sh.hasNext () && ((sh = $sh.next ()) || true);) {
+if (sh != null) {
+inverse.shifts.add ( Clazz.newIntArray (-1, [sh[0], -sh[1]]));
+}}
+}}return inverse;
+});
+c$.parseMap = Clazz.defineMethod (c$, "parseMap", 
+function (gapMap) {
+var shiftList = null;
+if (gapMap != null && gapMap.length > 0) {
+shiftList =  new jalview.util.ShiftList ();
+for (var i = 0, p = 0; i < gapMap.length; p++, i++) {
+if (p != gapMap[i]) {
+shiftList.addShift (p, gapMap[i] - p);
+p = gapMap[i];
+}}
+}return shiftList;
+}, "~A");
+Clazz.defineMethod (c$, "getShifts", 
+function () {
+return this.shifts;
+});
+});