-Clazz.declarePackage ("jalview.datamodel");
-Clazz.load (["java.util.Iterator"], "jalview.datamodel.Mapping", ["jalview.datamodel.AlignedCodon", "$.IncompleteCodonException", "$.SequenceFeature", "jalview.util.MapList", "java.util.NoSuchElementException", "$.Vector"], function () {
-c$ = Clazz.decorateAsClass (function () {
-if (!Clazz.isClassDefined ("jalview.datamodel.Mapping.AlignedCodonIterator")) {
-jalview.datamodel.Mapping.$Mapping$AlignedCodonIterator$ ();
-}
-this.map = null;
-this.to = null;
-Clazz.instantialize (this, arguments);
-}, jalview.datamodel, "Mapping");
-Clazz.makeConstructor (c$,
-function (map) {
-this.map = map;
-}, "jalview.util.MapList");
-Clazz.makeConstructor (c$,
-function (to, map) {
-this.construct (map);
-this.to = to;
-}, "jalview.datamodel.SequenceI,jalview.util.MapList");
-Clazz.makeConstructor (c$,
-function (to, exon, is, i, j) {
-this.construct (to, new jalview.util.MapList (exon, is, i, j));
-}, "jalview.datamodel.SequenceI,~A,~A,~N,~N");
-Clazz.makeConstructor (c$,
-function (map2) {
-if (map2 !== this && map2 != null) {
-if (map2.map != null) {
-this.map = new jalview.util.MapList (map2.map);
-}this.to = map2.to;
-}}, "jalview.datamodel.Mapping");
-Clazz.defineMethod (c$, "getMap",
-function () {
-return this.map;
-});
-Clazz.defineMethod (c$, "setMap",
-function (map) {
-this.map = map;
-}, "jalview.util.MapList");
-Clazz.overrideMethod (c$, "equals",
-function (o) {
-if (o == null || !(Clazz.instanceOf (o, jalview.datamodel.Mapping))) {
-return false;
-}var other = o;
-if (other === this) {
-return true;
-}if (other.to !== this.to) {
-return false;
-}if ((this.map != null && other.map == null) || (this.map == null && other.map != null)) {
-return false;
-}if ((this.map == null && other.map == null) || this.map.equals (other.map)) {
-return true;
-}return false;
-}, "~O");
-Clazz.defineMethod (c$, "getPosition",
-function (mpos) {
-if (this.map != null) {
-var mp = this.map.shiftTo (mpos);
-if (mp != null) {
-return mp[0];
-}}return mpos;
-}, "~N");
-Clazz.defineMethod (c$, "getWord",
-function (mpos) {
-if (this.map != null) {
-return this.map.getToWord (mpos);
-}return null;
-}, "~N");
-Clazz.defineMethod (c$, "getWidth",
-function () {
-if (this.map != null) {
-return this.map.getFromRatio ();
-}return 1;
-});
-Clazz.defineMethod (c$, "getMappedWidth",
-function () {
-if (this.map != null) {
-return this.map.getToRatio ();
-}return 1;
-});
-Clazz.defineMethod (c$, "getMappedPosition",
-function (pos) {
-if (this.map != null) {
-var mp = this.map.shiftFrom (pos);
-if (mp != null) {
-return mp[0];
-}}return pos;
-}, "~N");
-Clazz.defineMethod (c$, "getMappedWord",
-function (pos) {
-if (this.map != null) {
-var mp = this.map.shiftFrom (pos);
-if (mp != null) {
-return Clazz.newIntArray (-1, [mp[0], mp[0] + mp[2] * (this.map.getToRatio () - 1)]);
-}}return null;
-}, "~N");
-Clazz.defineMethod (c$, "locateFeature",
-function (f) {
-if (true) {
-if (this.map != null) {
-var frange = this.map.locateInFrom (f.getBegin (), f.getEnd ());
-if (frange == null) {
-return null;
-}var vf = new Array (Clazz.doubleToInt (frange.length / 2));
-for (var i = 0, v = 0; i < frange.length; i += 2, v++) {
-vf[v] = new jalview.datamodel.SequenceFeature (f);
-vf[v].setBegin (frange[i]);
-vf[v].setEnd (frange[i + 1]);
-if (frange.length > 2) {
-vf[v].setDescription (f.getDescription () + "\nPart " + (v + 1));
-}}
-return vf;
-}}if (false) {
-var word = this.getWord (f.getBegin ());
-if (word[0] < word[1]) {
-f.setBegin (word[0]);
-} else {
-f.setBegin (word[1]);
-}word = this.getWord (f.getEnd ());
-if (word[0] > word[1]) {
-f.setEnd (word[0]);
-} else {
-f.setEnd (word[1]);
-}}return Clazz.newArray (-1, [f]);
-}, "jalview.datamodel.SequenceFeature");
-Clazz.defineMethod (c$, "locateRange",
-function (from, to) {
-if (this.map != null) {
-if (from <= to) {
-from = (this.map.getToLowest () < from) ? from : this.map.getToLowest ();
-to = (this.map.getToHighest () > to) ? to : this.map.getToHighest ();
-if (from > to) {
-return null;
-}} else {
-from = (this.map.getToHighest () > from) ? from : this.map.getToHighest ();
-to = (this.map.getToLowest () < to) ? to : this.map.getToLowest ();
-if (from < to) {
-return null;
-}}return this.map.locateInFrom (from, to);
-}return Clazz.newIntArray (-1, [from, to]);
-}, "~N,~N");
-Clazz.defineMethod (c$, "locateMappedRange",
-function (from, to) {
-if (this.map != null) {
-if (from <= to) {
-from = (this.map.getFromLowest () < from) ? from : this.map.getFromLowest ();
-to = (this.map.getFromHighest () > to) ? to : this.map.getFromHighest ();
-if (from > to) {
-return null;
-}} else {
-from = (this.map.getFromHighest () > from) ? from : this.map.getFromHighest ();
-to = (this.map.getFromLowest () < to) ? to : this.map.getFromLowest ();
-if (from < to) {
-return null;
-}}return this.map.locateInTo (from, to);
-}return Clazz.newIntArray (-1, [from, to]);
-}, "~N,~N");
-Clazz.defineMethod (c$, "intersectVisContigs",
-function (viscontigs) {
-var copy = new jalview.datamodel.Mapping (this);
-if (this.map != null) {
-var vpos = 0;
-var apos = 0;
-var toRange = new java.util.Vector ();
-var fromRange = new java.util.Vector ();
-for (var vc = 0; vc < viscontigs.length; vc += 2) {
-var mpr = this.locateMappedRange (1 + viscontigs[vc], viscontigs[vc + 1] - 1);
-if (mpr != null) {
-for (var m = 0; m < mpr.length; m += 2) {
-toRange.addElement ( Clazz.newIntArray (-1, [mpr[m], mpr[m + 1]]));
-var xpos = this.locateRange (mpr[m], mpr[m + 1]);
-for (var x = 0; x < xpos.length; x += 2) {
-fromRange.addElement ( Clazz.newIntArray (-1, [xpos[x], xpos[x + 1]]));
-}
-}
-}}
-var from = Clazz.newIntArray (fromRange.size () * 2, 0);
-var to = Clazz.newIntArray (toRange.size () * 2, 0);
-var r;
-for (var f = 0, fSize = fromRange.size (); f < fSize; f++) {
-r = fromRange.elementAt (f);
-from[f * 2] = r[0];
-from[f * 2 + 1] = r[1];
-}
-for (var f = 0, fSize = toRange.size (); f < fSize; f++) {
-r = toRange.elementAt (f);
-to[f * 2] = r[0];
-to[f * 2 + 1] = r[1];
-}
-copy.setMap ( new jalview.util.MapList (from, to, this.map.getFromRatio (), this.map.getToRatio ()));
-}return copy;
-}, "~A");
-Clazz.defineMethod (c$, "getTo",
-function () {
-return this.to;
-});
-Clazz.defineMethod (c$, "setTo",
-function (tto) {
-this.to = tto;
-}, "jalview.datamodel.SequenceI");
-Clazz.defineMethod (c$, "finalize",
-function () {
-this.map = null;
-this.to = null;
-Clazz.superCall (this, jalview.datamodel.Mapping, "finalize", []);
-});
-Clazz.defineMethod (c$, "getCodonIterator",
-function (seq, gapChar) {
-return Clazz.innerTypeInstance (jalview.datamodel.Mapping.AlignedCodonIterator, this, null, seq.getSequence (), gapChar);
-}, "jalview.datamodel.SequenceI,~S");
-c$.$Mapping$AlignedCodonIterator$ = function () {
-Clazz.pu$h ();
-c$ = Clazz.decorateAsClass (function () {
-Clazz.prepareCallback (this, arguments);
-this.gap = '\0';
-this.alignedSeq = null;
-this.alignedColumn = 0;
-this.alignedBases = 0;
-this.fromRanges = null;
-this.toRanges = null;
-this.currentFromRange = null;
-this.currentToRange = null;
-this.fromPosition = 0;
-this.toPosition = 0;
-Clazz.instantialize (this, arguments);
-}, jalview.datamodel.Mapping, "AlignedCodonIterator", null, java.util.Iterator);
-Clazz.makeConstructor (c$,
-function (a, b) {
-this.alignedSeq = a;
-this.gap = b;
-this.fromRanges = this.b$["jalview.datamodel.Mapping"].map.getFromRanges ().iterator ();
-this.toRanges = this.b$["jalview.datamodel.Mapping"].map.getToRanges ().iterator ();
-if (this.fromRanges.hasNext ()) {
-this.currentFromRange = this.fromRanges.next ();
-this.fromPosition = this.currentFromRange[0];
-}if (this.toRanges.hasNext ()) {
-this.currentToRange = this.toRanges.next ();
-this.toPosition = this.currentToRange[0];
-}}, "~A,~S");
-Clazz.defineMethod (c$, "hasNext",
-function () {
-if (this.fromRanges.hasNext ()) {
-return true;
-}if (this.currentFromRange == null || this.fromPosition >= this.currentFromRange[1]) {
-return false;
-}return true;
-});
-Clazz.overrideMethod (c$, "next",
-function () {
-if (!this.hasNext ()) {
-throw new java.util.NoSuchElementException ();
-}var a = this.getNextCodon ();
-var b = this.getAlignedCodon (a);
-var c = this.getPeptide ();
-return new jalview.datamodel.AlignedCodon (b[0], b[1], b[2], c);
-});
-Clazz.defineMethod (c$, "getPeptide",
-($fz = function () {
-if (this.toPosition <= this.currentToRange[1]) {
-var a = this.b$["jalview.datamodel.Mapping"].to.getSequence ()[this.toPosition - 1];
-this.toPosition++;
-return String.valueOf (a);
-}if (!this.toRanges.hasNext ()) {
-throw new java.util.NoSuchElementException ("Ran out of peptide at position " + this.toPosition);
-}this.currentToRange = this.toRanges.next ();
-this.toPosition = this.currentToRange[0];
-return this.getPeptide ();
-}, $fz.isPrivate = true, $fz));
-Clazz.defineMethod (c$, "getNextCodon",
-($fz = function () {
-var a = Clazz.newIntArray (3, 0);
-var b = 0;
-while (b < 3) {
-if (this.fromPosition <= this.currentFromRange[1]) {
-a[b++] = this.fromPosition++;
-} else {
-if (!this.fromRanges.hasNext ()) {
-throw new jalview.datamodel.IncompleteCodonException ();
-}this.currentFromRange = this.fromRanges.next ();
-this.fromPosition = this.currentFromRange[0];
-}}
-return a;
-}, $fz.isPrivate = true, $fz));
-Clazz.defineMethod (c$, "getAlignedCodon",
-($fz = function (a) {
-var b = Clazz.newIntArray (a.length, 0);
-for (var c = 0; c < a.length; c++) {
-b[c] = this.getAlignedColumn (a[c]);
-}
-return b;
-}, $fz.isPrivate = true, $fz), "~A");
-Clazz.defineMethod (c$, "getAlignedColumn",
-($fz = function (a) {
-while (this.alignedBases < a && this.alignedColumn < this.alignedSeq.length) {
-if (this.alignedSeq[this.alignedColumn++] != this.gap) {
-this.alignedBases++;
-}}
-return this.alignedColumn - 1;
-}, $fz.isPrivate = true, $fz), "~N");
-Clazz.overrideMethod (c$, "remove",
-function () {
-});
-c$ = Clazz.p0p ();
-};
-});
+Clazz.declarePackage ("jalview.datamodel");\r
+Clazz.load (["java.util.Iterator"], "jalview.datamodel.Mapping", ["jalview.datamodel.AlignedCodon", "$.IncompleteCodonException", "$.SequenceFeature", "jalview.util.MapList", "java.util.NoSuchElementException", "$.Vector"], function () {\r
+c$ = Clazz.decorateAsClass (function () {\r
+if (!Clazz.isClassDefined ("jalview.datamodel.Mapping.AlignedCodonIterator")) {\r
+jalview.datamodel.Mapping.$Mapping$AlignedCodonIterator$ ();\r
+}\r
+this.map = null;\r
+this.to = null;\r
+Clazz.instantialize (this, arguments);\r
+}, jalview.datamodel, "Mapping");\r
+Clazz.makeConstructor (c$, \r
+function (map) {\r
+this.map = map;\r
+}, "jalview.util.MapList");\r
+Clazz.makeConstructor (c$, \r
+function (to, map) {\r
+this.construct (map);\r
+this.to = to;\r
+}, "jalview.datamodel.SequenceI,jalview.util.MapList");\r
+Clazz.makeConstructor (c$, \r
+function (to, exon, is, i, j) {\r
+this.construct (to, new jalview.util.MapList (exon, is, i, j));\r
+}, "jalview.datamodel.SequenceI,~A,~A,~N,~N");\r
+Clazz.makeConstructor (c$, \r
+function (map2) {\r
+if (map2 !== this && map2 != null) {\r
+if (map2.map != null) {\r
+this.map = new jalview.util.MapList (map2.map);\r
+}this.to = map2.to;\r
+}}, "jalview.datamodel.Mapping");\r
+Clazz.defineMethod (c$, "getMap", \r
+function () {\r
+return this.map;\r
+});\r
+Clazz.defineMethod (c$, "setMap", \r
+function (map) {\r
+this.map = map;\r
+}, "jalview.util.MapList");\r
+Clazz.overrideMethod (c$, "equals", \r
+function (o) {\r
+if (o == null || !(Clazz.instanceOf (o, jalview.datamodel.Mapping))) {\r
+return false;\r
+}var other = o;\r
+if (other === this) {\r
+return true;\r
+}if (other.to !== this.to) {\r
+return false;\r
+}if ((this.map != null && other.map == null) || (this.map == null && other.map != null)) {\r
+return false;\r
+}if ((this.map == null && other.map == null) || this.map.equals (other.map)) {\r
+return true;\r
+}return false;\r
+}, "~O");\r
+Clazz.defineMethod (c$, "getPosition", \r
+function (mpos) {\r
+if (this.map != null) {\r
+var mp = this.map.shiftTo (mpos);\r
+if (mp != null) {\r
+return mp[0];\r
+}}return mpos;\r
+}, "~N");\r
+Clazz.defineMethod (c$, "getWord", \r
+function (mpos) {\r
+if (this.map != null) {\r
+return this.map.getToWord (mpos);\r
+}return null;\r
+}, "~N");\r
+Clazz.defineMethod (c$, "getWidth", \r
+function () {\r
+if (this.map != null) {\r
+return this.map.getFromRatio ();\r
+}return 1;\r
+});\r
+Clazz.defineMethod (c$, "getMappedWidth", \r
+function () {\r
+if (this.map != null) {\r
+return this.map.getToRatio ();\r
+}return 1;\r
+});\r
+Clazz.defineMethod (c$, "getMappedPosition", \r
+function (pos) {\r
+if (this.map != null) {\r
+var mp = this.map.shiftFrom (pos);\r
+if (mp != null) {\r
+return mp[0];\r
+}}return pos;\r
+}, "~N");\r
+Clazz.defineMethod (c$, "getMappedWord", \r
+function (pos) {\r
+if (this.map != null) {\r
+var mp = this.map.shiftFrom (pos);\r
+if (mp != null) {\r
+return Clazz.newIntArray (-1, [mp[0], mp[0] + mp[2] * (this.map.getToRatio () - 1)]);\r
+}}return null;\r
+}, "~N");\r
+Clazz.defineMethod (c$, "locateFeature", \r
+function (f) {\r
+if (true) {\r
+if (this.map != null) {\r
+var frange = this.map.locateInFrom (f.getBegin (), f.getEnd ());\r
+if (frange == null) {\r
+return null;\r
+}var vf = new Array (Clazz.doubleToInt (frange.length / 2));\r
+for (var i = 0, v = 0; i < frange.length; i += 2, v++) {\r
+vf[v] = new jalview.datamodel.SequenceFeature (f);\r
+vf[v].setBegin (frange[i]);\r
+vf[v].setEnd (frange[i + 1]);\r
+if (frange.length > 2) {\r
+vf[v].setDescription (f.getDescription () + "\nPart " + (v + 1));\r
+}}\r
+return vf;\r
+}}if (false) {\r
+var word = this.getWord (f.getBegin ());\r
+if (word[0] < word[1]) {\r
+f.setBegin (word[0]);\r
+} else {\r
+f.setBegin (word[1]);\r
+}word = this.getWord (f.getEnd ());\r
+if (word[0] > word[1]) {\r
+f.setEnd (word[0]);\r
+} else {\r
+f.setEnd (word[1]);\r
+}}return Clazz.newArray (-1, [f]);\r
+}, "jalview.datamodel.SequenceFeature");\r
+Clazz.defineMethod (c$, "locateRange", \r
+function (from, to) {\r
+if (this.map != null) {\r
+if (from <= to) {\r
+from = (this.map.getToLowest () < from) ? from : this.map.getToLowest ();\r
+to = (this.map.getToHighest () > to) ? to : this.map.getToHighest ();\r
+if (from > to) {\r
+return null;\r
+}} else {\r
+from = (this.map.getToHighest () > from) ? from : this.map.getToHighest ();\r
+to = (this.map.getToLowest () < to) ? to : this.map.getToLowest ();\r
+if (from < to) {\r
+return null;\r
+}}return this.map.locateInFrom (from, to);\r
+}return Clazz.newIntArray (-1, [from, to]);\r
+}, "~N,~N");\r
+Clazz.defineMethod (c$, "locateMappedRange", \r
+function (from, to) {\r
+if (this.map != null) {\r
+if (from <= to) {\r
+from = (this.map.getFromLowest () < from) ? from : this.map.getFromLowest ();\r
+to = (this.map.getFromHighest () > to) ? to : this.map.getFromHighest ();\r
+if (from > to) {\r
+return null;\r
+}} else {\r
+from = (this.map.getFromHighest () > from) ? from : this.map.getFromHighest ();\r
+to = (this.map.getFromLowest () < to) ? to : this.map.getFromLowest ();\r
+if (from < to) {\r
+return null;\r
+}}return this.map.locateInTo (from, to);\r
+}return Clazz.newIntArray (-1, [from, to]);\r
+}, "~N,~N");\r
+Clazz.defineMethod (c$, "intersectVisContigs", \r
+function (viscontigs) {\r
+var copy = new jalview.datamodel.Mapping (this);\r
+if (this.map != null) {\r
+var vpos = 0;\r
+var apos = 0;\r
+var toRange = new java.util.Vector ();\r
+var fromRange = new java.util.Vector ();\r
+for (var vc = 0; vc < viscontigs.length; vc += 2) {\r
+var mpr = this.locateMappedRange (1 + viscontigs[vc], viscontigs[vc + 1] - 1);\r
+if (mpr != null) {\r
+for (var m = 0; m < mpr.length; m += 2) {\r
+toRange.addElement ( Clazz.newIntArray (-1, [mpr[m], mpr[m + 1]]));\r
+var xpos = this.locateRange (mpr[m], mpr[m + 1]);\r
+for (var x = 0; x < xpos.length; x += 2) {\r
+fromRange.addElement ( Clazz.newIntArray (-1, [xpos[x], xpos[x + 1]]));\r
+}\r
+}\r
+}}\r
+var from = Clazz.newIntArray (fromRange.size () * 2, 0);\r
+var to = Clazz.newIntArray (toRange.size () * 2, 0);\r
+var r;\r
+for (var f = 0, fSize = fromRange.size (); f < fSize; f++) {\r
+r = fromRange.elementAt (f);\r
+from[f * 2] = r[0];\r
+from[f * 2 + 1] = r[1];\r
+}\r
+for (var f = 0, fSize = toRange.size (); f < fSize; f++) {\r
+r = toRange.elementAt (f);\r
+to[f * 2] = r[0];\r
+to[f * 2 + 1] = r[1];\r
+}\r
+copy.setMap ( new jalview.util.MapList (from, to, this.map.getFromRatio (), this.map.getToRatio ()));\r
+}return copy;\r
+}, "~A");\r
+Clazz.defineMethod (c$, "getTo", \r
+function () {\r
+return this.to;\r
+});\r
+Clazz.defineMethod (c$, "setTo", \r
+function (tto) {\r
+this.to = tto;\r
+}, "jalview.datamodel.SequenceI");\r
+Clazz.defineMethod (c$, "finalize", \r
+function () {\r
+this.map = null;\r
+this.to = null;\r
+Clazz.superCall (this, jalview.datamodel.Mapping, "finalize", []);\r
+});\r
+Clazz.defineMethod (c$, "getCodonIterator", \r
+function (seq, gapChar) {\r
+return Clazz.innerTypeInstance (jalview.datamodel.Mapping.AlignedCodonIterator, this, null, seq.getSequence (), gapChar);\r
+}, "jalview.datamodel.SequenceI,~S");\r
+c$.$Mapping$AlignedCodonIterator$ = function () {\r
+Clazz.pu$h ();\r
+c$ = Clazz.decorateAsClass (function () {\r
+Clazz.prepareCallback (this, arguments);\r
+this.gap = '\0';\r
+this.alignedSeq = null;\r
+this.alignedColumn = 0;\r
+this.alignedBases = 0;\r
+this.fromRanges = null;\r
+this.toRanges = null;\r
+this.currentFromRange = null;\r
+this.currentToRange = null;\r
+this.fromPosition = 0;\r
+this.toPosition = 0;\r
+Clazz.instantialize (this, arguments);\r
+}, jalview.datamodel.Mapping, "AlignedCodonIterator", null, java.util.Iterator);\r
+Clazz.makeConstructor (c$, \r
+function (a, b) {\r
+this.alignedSeq = a;\r
+this.gap = b;\r
+this.fromRanges = this.b$["jalview.datamodel.Mapping"].map.getFromRanges ().iterator ();\r
+this.toRanges = this.b$["jalview.datamodel.Mapping"].map.getToRanges ().iterator ();\r
+if (this.fromRanges.hasNext ()) {\r
+this.currentFromRange = this.fromRanges.next ();\r
+this.fromPosition = this.currentFromRange[0];\r
+}if (this.toRanges.hasNext ()) {\r
+this.currentToRange = this.toRanges.next ();\r
+this.toPosition = this.currentToRange[0];\r
+}}, "~A,~S");\r
+Clazz.defineMethod (c$, "hasNext", \r
+function () {\r
+if (this.fromRanges.hasNext ()) {\r
+return true;\r
+}if (this.currentFromRange == null || this.fromPosition >= this.currentFromRange[1]) {\r
+return false;\r
+}return true;\r
+});\r
+Clazz.overrideMethod (c$, "next", \r
+function () {\r
+if (!this.hasNext ()) {\r
+throw new java.util.NoSuchElementException ();\r
+}var a = this.getNextCodon ();\r
+var b = this.getAlignedCodon (a);\r
+var c = this.getPeptide ();\r
+return new jalview.datamodel.AlignedCodon (b[0], b[1], b[2], c);\r
+});\r
+Clazz.defineMethod (c$, "getPeptide", \r
+($fz = function () {\r
+if (this.toPosition <= this.currentToRange[1]) {\r
+var a = this.b$["jalview.datamodel.Mapping"].to.getSequence ()[this.toPosition - 1];\r
+this.toPosition++;\r
+return String.valueOf (a);\r
+}if (!this.toRanges.hasNext ()) {\r
+throw new java.util.NoSuchElementException ("Ran out of peptide at position " + this.toPosition);\r
+}this.currentToRange = this.toRanges.next ();\r
+this.toPosition = this.currentToRange[0];\r
+return this.getPeptide ();\r
+}, $fz.isPrivate = true, $fz));\r
+Clazz.defineMethod (c$, "getNextCodon", \r
+($fz = function () {\r
+var a = Clazz.newIntArray (3, 0);\r
+var b = 0;\r
+while (b < 3) {\r
+if (this.fromPosition <= this.currentFromRange[1]) {\r
+a[b++] = this.fromPosition++;\r
+} else {\r
+if (!this.fromRanges.hasNext ()) {\r
+throw new jalview.datamodel.IncompleteCodonException ();\r
+}this.currentFromRange = this.fromRanges.next ();\r
+this.fromPosition = this.currentFromRange[0];\r
+}}\r
+return a;\r
+}, $fz.isPrivate = true, $fz));\r
+Clazz.defineMethod (c$, "getAlignedCodon", \r
+($fz = function (a) {\r
+var b = Clazz.newIntArray (a.length, 0);\r
+for (var c = 0; c < a.length; c++) {\r
+b[c] = this.getAlignedColumn (a[c]);\r
+}\r
+return b;\r
+}, $fz.isPrivate = true, $fz), "~A");\r
+Clazz.defineMethod (c$, "getAlignedColumn", \r
+($fz = function (a) {\r
+while (this.alignedBases < a && this.alignedColumn < this.alignedSeq.length) {\r
+if (this.alignedSeq[this.alignedColumn++] != this.gap) {\r
+this.alignedBases++;\r
+}}\r
+return this.alignedColumn - 1;\r
+}, $fz.isPrivate = true, $fz), "~N");\r
+Clazz.overrideMethod (c$, "remove", \r
+function () {\r
+});\r
+c$ = Clazz.p0p ();\r
+};\r
+});\r
git://source.jalview.org / jalviewjs.git / blobdiff