X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=site%2Fj2s%2Fjalview%2Futil%2FShiftList.js;fp=site%2Fj2s%2Fjalview%2Futil%2FShiftList.js;h=258fe1493d1abf5ebe81e7196aefd29c0f866355;hp=29a96450cd345ed784724decb0f8eb2d503e9a18;hb=b9b7a352eee79b7764c3b09c9d19663075061d8c;hpb=7301a2415adab88038b291fc54caeeb3a5a47a44

diff --git a/site/j2s/jalview/util/ShiftList.js b/site/j2s/jalview/util/ShiftList.js
index 29a9645..258fe14 100644
--- a/site/j2s/jalview/util/ShiftList.js
+++ b/site/j2s/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");
+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;
+});
+});