JAL-1807 still testing

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

diff --git a/bin/jalview/util/ShiftList.js b/bin/jalview/util/ShiftList.js
index 258fe14..29a9645 100644 (file)
--- a/bin/jalview/util/ShiftList.js
+++ b/bin/jalview/util/ShiftList.js
@@ -1,67 +1,67 @@
-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;
-});
-});
+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