-Clazz.declarePackage ("jalview.datamodel");
-Clazz.load (null, "jalview.datamodel.CigarBase", ["jalview.util.MessageManager", "java.lang.Error", "$.Exception", "$.StringBuffer", "java.util.Vector", "javajs.util.AU"], function () {
-c$ = Clazz.decorateAsClass (function () {
-this.length = 0;
-this._inc_length = 10;
-this.operation = null;
-this.range = null;
-Clazz.instantialize (this, arguments);
-}, jalview.datamodel, "CigarBase");
-Clazz.makeConstructor (c$,
-function () {
-});
-Clazz.defineMethod (c$, "getSequenceAndDeletions",
-function (reference, GapChar) {
-var rlength = 0;
-var deletions = javajs.util.AU.newInt2 (this.length);
-var trunc_deletions = null;
-var sq = new StringBuffer ();
-var cursor = 0;
-var alcursor = 0;
-var start = 0;
-var startpos = 0;
-var end = 0;
-var endpos = 0;
-var delcount = -1;
-var consecutive_del = false;
-if (this.length == 0) {
-return null;
-}if (reference != null) {
-rlength = reference.length;
-}var modstart = true;
-for (var i = 0; i < this.length; i++) {
-switch (this.operation[i]) {
-case 'D':
-if (!consecutive_del) {
-deletions[++delcount] = Clazz.newIntArray (-1, [cursor, 0, alcursor]);
-}cursor += this.range[i];
-deletions[delcount][1] = cursor - 1;
-consecutive_del = true;
-break;
-case 'I':
-consecutive_del = false;
-for (var r = 0; r < this.range[i]; r++) {
-sq.append (GapChar);
-alcursor++;
-}
-break;
-case 'M':
-consecutive_del = false;
-if (modstart) {
-start = cursor;
-startpos = alcursor;
-modstart = false;
-}if (reference != null) {
-var sbend = cursor + this.range[i];
-if (sbend > rlength) {
-sq.append (reference.substring (cursor, rlength));
-while (sbend-- >= rlength) {
-sq.append (GapChar);
-}
-} else {
-sq.append (reference.substring (cursor, sbend));
-}}alcursor += this.range[i];
-cursor += this.range[i];
-end = cursor - 1;
-endpos = alcursor;
-break;
-default:
-throw new Error (jalview.util.MessageManager.formatMessage ("error.unknown_seq_cigar_operation", Clazz.newArray (-1, [ new StringBuffer (this.operation[i].charCodeAt (0)).toString ()])));
-}
-}
-if (++delcount > 0) {
-trunc_deletions = Clazz.newIntArray (delcount, 0);
-System.arraycopy (deletions, 0, trunc_deletions, 0, delcount);
-}deletions = null;
-return Clazz.newArray (-1, [((reference != null) ? sq.toString () : null), Clazz.newIntArray (-1, [start, startpos, end, endpos]), trunc_deletions]);
-}, "~S,~S");
-Clazz.defineMethod (c$, "compact_operations",
-function () {
-var i = 1;
-if (this.operation == null) {
-return;
-}var last = this.operation[0];
-while (i < this.length) {
-if (last == this.operation[i]) {
-this.range[i - 1] += this.range[i];
-var r = this.length - i;
-if (r > 0) {
-System.arraycopy (this.range, i + 1, this.range, i, r);
-System.arraycopy (this.operation, i + 1, this.operation, i, r);
-}this.length--;
-} else {
-last = this.operation[i++];
-}}
-});
-c$.parseCigarString = Clazz.defineMethod (c$, "parseCigarString",
-function (cigarString) {
-var ops = 0;
-for (var i = 0, l = cigarString.length; i < l; i++) {
-var c = cigarString.charAt (i);
-if (c == 'M' || c.charCodeAt (0) == (45) || c == 'I' || c.charCodeAt (0) == (41) || c == 'D' || c.charCodeAt (0) == (36)) {
-ops++;
-}}
-var operation = Clazz.newCharArray (ops, '\0');
-var range = Clazz.newIntArray (ops, 0);
-var op = 0;
-var i = 0;
-var l = cigarString.length;
-while (i < l) {
-var c;
-var j = i;
-do {
-c = cigarString.charAt (j++);
-} while (c >= '0' && c <= '9' && j < l);
-if (j >= l && c >= '0' && c <= '9') {
-throw new Exception (jalview.util.MessageManager.getString ("exception.unterminated_cigar_string"));
-}try {
-var rangeint = cigarString.substring (i, j - 1);
-range[op] = Integer.parseInt (rangeint);
-i = j;
-} catch (e) {
-if (Clazz.exceptionOf (e, Exception)) {
-throw new Error (jalview.util.MessageManager.getString ("error.implementation_bug_parse_cigar_string"));
-} else {
-throw e;
-}
-}
-if (c >= 'a' && c <= 'z') {
-c = String.fromCharCode (c.charCodeAt (0) - 32);
-}if ((c == 'M' || c == 'I' || c == 'D')) {
-operation[op++] = c;
-} else {
-throw new Exception (jalview.util.MessageManager.formatMessage ("exception.unexpected_operation_cigar_string_pos", Clazz.newArray (-1, [ new StringBuffer (c.charCodeAt (0)).toString (), Integer.$valueOf (i).toString (), cigarString])));
-}}
-return Clazz.newArray (-1, [operation, range]);
-}, "~S");
-Clazz.defineMethod (c$, "addOperation",
-function (op, range) {
-if (op >= 'a' && op <= 'z') {
-op = String.fromCharCode (op.charCodeAt (0) - 32);
-}if (op != 'M' && op != 'D' && op != 'I') {
-throw new Error (jalview.util.MessageManager.getString ("error.implementation_error_invalid_operation_string"));
-}if (range == 0) {
-return;
-}if (range < 0) {
-throw new Error (jalview.util.MessageManager.getString ("error.invalid_range_string"));
-}var lngth = 0;
-if (this.operation == null) {
-this.operation = Clazz.newCharArray (this._inc_length, '\0');
-this.range = Clazz.newIntArray (this._inc_length, 0);
-}if (this.length + 1 == this.operation.length) {
-var ops = this.operation;
-this.operation = Clazz.newCharArray (this.length + 1 + this._inc_length, '\0');
-System.arraycopy (ops, 0, this.operation, 0, this.length);
-ops = null;
-var rng = this.range;
-this.range = Clazz.newIntArray (this.length + 1 + this._inc_length, 0);
-System.arraycopy (rng, 0, this.range, 0, this.length);
-rng = null;
-}if ((this.length > 0) && (this.operation[this.length - 1] == op)) {
-this.length--;
-} else {
-this.range[this.length] = 0;
-}this.operation[this.length] = op;
-this.range[this.length++] += range;
-}, "~S,~N");
-Clazz.defineMethod (c$, "deleteRange",
-function (start, end) {
-var deleted = 0;
-if (this.length == 0) {
-return deleted;
-}if (start < 0 || start > end) {
-throw new Error (jalview.util.MessageManager.getString ("error.implementation_error_delete_range_out_of_bounds"));
-}var cursor = 0;
-var rlength = 1 + end - start;
-var oldlen = this.length;
-var o = 0;
-var editing = false;
-var oldops = this.operation;
-var oldrange = this.range;
-this.length = 0;
-this.operation = null;
-this.range = null;
-this.compact_operations ();
-while (o < oldlen && cursor <= end && rlength > 0) {
-if (oldops[o] == 'D') {
-this.addDeleted (oldrange[o++]);
-continue;
-}var remain = oldrange[o];
-if (!editing) {
-if ((cursor + remain) <= start) {
-this.addOperation (oldops[o], oldrange[o]);
-cursor += oldrange[o++];
-continue;
-}editing = true;
-if (start - cursor > 0) {
-this.addOperation (oldops[o], start - cursor);
-remain -= start - cursor;
-}}if (o < oldlen && editing && rlength > 0 && remain > 0) {
-switch (oldops[o]) {
-case 'M':
-if (rlength > remain) {
-this.addDeleted (remain);
-deleted += remain;
-} else {
-deleted += rlength;
-this.addDeleted (rlength);
-if (remain - rlength > 0) {
-this.addOperation ('M', remain - rlength);
-}rlength = 0;
-remain = 0;
-}break;
-case 'I':
-if (remain - rlength > 0) {
-this.addInsertion (remain - rlength);
-rlength = 0;
-}break;
-case 'D':
-throw new Error (jalview.util.MessageManager.getString ("error.implementation_error"));
-default:
-throw new Error (jalview.util.MessageManager.formatMessage ("error.implementation_error_unknown_operation", Clazz.newArray (-1, [ new StringBuffer (oldops[o].charCodeAt (0)).toString ()])));
-}
-rlength -= remain;
-remain = oldrange[++o];
-}}
-while (o < oldlen) {
-this.addOperation (oldops[o], oldrange[o++]);
-}
-return deleted;
-}, "~N,~N");
-Clazz.defineMethod (c$, "hasDeletedRegions",
-function () {
-for (var i = 0; i < this.length; i++) {
-if (this.operation[i] == 'D') {
-return true;
-}}
-return false;
-});
-Clazz.defineMethod (c$, "getDeletedRegions",
-function () {
-if (this.length == 0) {
-return null;
-}var dr = new java.util.Vector ();
-var cursor = 0;
-var vcursor = 0;
-for (var i = 0; i < this.length; i++) {
-switch (this.operation[i]) {
-case 'M':
-cursor += this.range[i];
-case 'I':
-vcursor += this.range[i];
-break;
-case 'D':
-dr.addElement ( Clazz.newIntArray (-1, [vcursor, cursor, this.range[i]]));
-cursor += this.range[i];
-}
-}
-if (dr.size () == 0) {
-return null;
-}var delregions = Clazz.newIntArray (dr.size () * 3, 0);
-for (var i = 0, l = dr.size (); i < l; i++) {
-var reg = dr.elementAt (i);
-delregions[i * 3] = reg[0];
-delregions[i * 3 + 1] = reg[1];
-delregions[i * 3 + 2] = reg[2];
-}
-return delregions;
-});
-Clazz.defineMethod (c$, "getFullWidth",
-function () {
-var w = 0;
-if (this.range != null) {
-for (var i = 0; i < this.length; i++) {
-w += this.range[i];
-}
-}return w;
-});
-Clazz.defineMethod (c$, "getWidth",
-function () {
-var w = 0;
-if (this.range != null) {
-for (var i = 0; i < this.length; i++) {
-if (this.operation[i] == 'M' || this.operation[i] == 'I') {
-w += this.range[i];
-}}
-}return w;
-});
-Clazz.defineMethod (c$, "addInsertion",
-function (range) {
-this.addOperation ('I', range);
-}, "~N");
-Clazz.defineMethod (c$, "addDeleted",
-function (range) {
-this.addOperation ('D', range);
-}, "~N");
-Clazz.defineMethod (c$, "getCigarstring",
-function () {
-var cigarString = new StringBuffer ();
-for (var i = 0; i < this.length; i++) {
-cigarString.append ("" + this.range[i]);
-cigarString.append (this.operation[i]);
-}
-return cigarString.toString ();
-});
-Clazz.defineStatics (c$,
-"D", 'D',
-"I", 'I',
-"M", 'M',
-"_case_shift", String.fromCharCode (32));
-});
+Clazz.declarePackage ("jalview.datamodel");\r
+Clazz.load (null, "jalview.datamodel.CigarBase", ["jalview.util.MessageManager", "java.lang.Error", "$.Exception", "$.StringBuffer", "java.util.Vector", "javajs.util.AU"], function () {\r
+c$ = Clazz.decorateAsClass (function () {\r
+this.length = 0;\r
+this._inc_length = 10;\r
+this.operation = null;\r
+this.range = null;\r
+Clazz.instantialize (this, arguments);\r
+}, jalview.datamodel, "CigarBase");\r
+Clazz.makeConstructor (c$, \r
+function () {\r
+});\r
+Clazz.defineMethod (c$, "getSequenceAndDeletions", \r
+function (reference, GapChar) {\r
+var rlength = 0;\r
+var deletions = javajs.util.AU.newInt2 (this.length);\r
+var trunc_deletions = null;\r
+var sq = new StringBuffer ();\r
+var cursor = 0;\r
+var alcursor = 0;\r
+var start = 0;\r
+var startpos = 0;\r
+var end = 0;\r
+var endpos = 0;\r
+var delcount = -1;\r
+var consecutive_del = false;\r
+if (this.length == 0) {\r
+return null;\r
+}if (reference != null) {\r
+rlength = reference.length;\r
+}var modstart = true;\r
+for (var i = 0; i < this.length; i++) {\r
+switch (this.operation[i]) {\r
+case 'D':\r
+if (!consecutive_del) {\r
+deletions[++delcount] = Clazz.newIntArray (-1, [cursor, 0, alcursor]);\r
+}cursor += this.range[i];\r
+deletions[delcount][1] = cursor - 1;\r
+consecutive_del = true;\r
+break;\r
+case 'I':\r
+consecutive_del = false;\r
+for (var r = 0; r < this.range[i]; r++) {\r
+sq.append (GapChar);\r
+alcursor++;\r
+}\r
+break;\r
+case 'M':\r
+consecutive_del = false;\r
+if (modstart) {\r
+start = cursor;\r
+startpos = alcursor;\r
+modstart = false;\r
+}if (reference != null) {\r
+var sbend = cursor + this.range[i];\r
+if (sbend > rlength) {\r
+sq.append (reference.substring (cursor, rlength));\r
+while (sbend-- >= rlength) {\r
+sq.append (GapChar);\r
+}\r
+} else {\r
+sq.append (reference.substring (cursor, sbend));\r
+}}alcursor += this.range[i];\r
+cursor += this.range[i];\r
+end = cursor - 1;\r
+endpos = alcursor;\r
+break;\r
+default:\r
+throw new Error (jalview.util.MessageManager.formatMessage ("error.unknown_seq_cigar_operation", Clazz.newArray (-1, [ new StringBuffer (this.operation[i].charCodeAt (0)).toString ()])));\r
+}\r
+}\r
+if (++delcount > 0) {\r
+trunc_deletions = Clazz.newIntArray (delcount, 0);\r
+System.arraycopy (deletions, 0, trunc_deletions, 0, delcount);\r
+}deletions = null;\r
+return Clazz.newArray (-1, [((reference != null) ? sq.toString () : null), Clazz.newIntArray (-1, [start, startpos, end, endpos]), trunc_deletions]);\r
+}, "~S,~S");\r
+Clazz.defineMethod (c$, "compact_operations", \r
+function () {\r
+var i = 1;\r
+if (this.operation == null) {\r
+return;\r
+}var last = this.operation[0];\r
+while (i < this.length) {\r
+if (last == this.operation[i]) {\r
+this.range[i - 1] += this.range[i];\r
+var r = this.length - i;\r
+if (r > 0) {\r
+System.arraycopy (this.range, i + 1, this.range, i, r);\r
+System.arraycopy (this.operation, i + 1, this.operation, i, r);\r
+}this.length--;\r
+} else {\r
+last = this.operation[i++];\r
+}}\r
+});\r
+c$.parseCigarString = Clazz.defineMethod (c$, "parseCigarString", \r
+function (cigarString) {\r
+var ops = 0;\r
+for (var i = 0, l = cigarString.length; i < l; i++) {\r
+var c = cigarString.charAt (i);\r
+if (c == 'M' || c.charCodeAt (0) == (45) || c == 'I' || c.charCodeAt (0) == (41) || c == 'D' || c.charCodeAt (0) == (36)) {\r
+ops++;\r
+}}\r
+var operation = Clazz.newCharArray (ops, '\0');\r
+var range = Clazz.newIntArray (ops, 0);\r
+var op = 0;\r
+var i = 0;\r
+var l = cigarString.length;\r
+while (i < l) {\r
+var c;\r
+var j = i;\r
+do {\r
+c = cigarString.charAt (j++);\r
+} while (c >= '0' && c <= '9' && j < l);\r
+if (j >= l && c >= '0' && c <= '9') {\r
+throw new Exception (jalview.util.MessageManager.getString ("exception.unterminated_cigar_string"));\r
+}try {\r
+var rangeint = cigarString.substring (i, j - 1);\r
+range[op] = Integer.parseInt (rangeint);\r
+i = j;\r
+} catch (e) {\r
+if (Clazz.exceptionOf (e, Exception)) {\r
+throw new Error (jalview.util.MessageManager.getString ("error.implementation_bug_parse_cigar_string"));\r
+} else {\r
+throw e;\r
+}\r
+}\r
+if (c >= 'a' && c <= 'z') {\r
+c = String.fromCharCode (c.charCodeAt (0) - 32);\r
+}if ((c == 'M' || c == 'I' || c == 'D')) {\r
+operation[op++] = c;\r
+} else {\r
+throw new Exception (jalview.util.MessageManager.formatMessage ("exception.unexpected_operation_cigar_string_pos", Clazz.newArray (-1, [ new StringBuffer (c.charCodeAt (0)).toString (), Integer.$valueOf (i).toString (), cigarString])));\r
+}}\r
+return Clazz.newArray (-1, [operation, range]);\r
+}, "~S");\r
+Clazz.defineMethod (c$, "addOperation", \r
+function (op, range) {\r
+if (op >= 'a' && op <= 'z') {\r
+op = String.fromCharCode (op.charCodeAt (0) - 32);\r
+}if (op != 'M' && op != 'D' && op != 'I') {\r
+throw new Error (jalview.util.MessageManager.getString ("error.implementation_error_invalid_operation_string"));\r
+}if (range == 0) {\r
+return;\r
+}if (range < 0) {\r
+throw new Error (jalview.util.MessageManager.getString ("error.invalid_range_string"));\r
+}var lngth = 0;\r
+if (this.operation == null) {\r
+this.operation = Clazz.newCharArray (this._inc_length, '\0');\r
+this.range = Clazz.newIntArray (this._inc_length, 0);\r
+}if (this.length + 1 == this.operation.length) {\r
+var ops = this.operation;\r
+this.operation = Clazz.newCharArray (this.length + 1 + this._inc_length, '\0');\r
+System.arraycopy (ops, 0, this.operation, 0, this.length);\r
+ops = null;\r
+var rng = this.range;\r
+this.range = Clazz.newIntArray (this.length + 1 + this._inc_length, 0);\r
+System.arraycopy (rng, 0, this.range, 0, this.length);\r
+rng = null;\r
+}if ((this.length > 0) && (this.operation[this.length - 1] == op)) {\r
+this.length--;\r
+} else {\r
+this.range[this.length] = 0;\r
+}this.operation[this.length] = op;\r
+this.range[this.length++] += range;\r
+}, "~S,~N");\r
+Clazz.defineMethod (c$, "deleteRange", \r
+function (start, end) {\r
+var deleted = 0;\r
+if (this.length == 0) {\r
+return deleted;\r
+}if (start < 0 || start > end) {\r
+throw new Error (jalview.util.MessageManager.getString ("error.implementation_error_delete_range_out_of_bounds"));\r
+}var cursor = 0;\r
+var rlength = 1 + end - start;\r
+var oldlen = this.length;\r
+var o = 0;\r
+var editing = false;\r
+var oldops = this.operation;\r
+var oldrange = this.range;\r
+this.length = 0;\r
+this.operation = null;\r
+this.range = null;\r
+this.compact_operations ();\r
+while (o < oldlen && cursor <= end && rlength > 0) {\r
+if (oldops[o] == 'D') {\r
+this.addDeleted (oldrange[o++]);\r
+continue;\r
+}var remain = oldrange[o];\r
+if (!editing) {\r
+if ((cursor + remain) <= start) {\r
+this.addOperation (oldops[o], oldrange[o]);\r
+cursor += oldrange[o++];\r
+continue;\r
+}editing = true;\r
+if (start - cursor > 0) {\r
+this.addOperation (oldops[o], start - cursor);\r
+remain -= start - cursor;\r
+}}if (o < oldlen && editing && rlength > 0 && remain > 0) {\r
+switch (oldops[o]) {\r
+case 'M':\r
+if (rlength > remain) {\r
+this.addDeleted (remain);\r
+deleted += remain;\r
+} else {\r
+deleted += rlength;\r
+this.addDeleted (rlength);\r
+if (remain - rlength > 0) {\r
+this.addOperation ('M', remain - rlength);\r
+}rlength = 0;\r
+remain = 0;\r
+}break;\r
+case 'I':\r
+if (remain - rlength > 0) {\r
+this.addInsertion (remain - rlength);\r
+rlength = 0;\r
+}break;\r
+case 'D':\r
+throw new Error (jalview.util.MessageManager.getString ("error.implementation_error"));\r
+default:\r
+throw new Error (jalview.util.MessageManager.formatMessage ("error.implementation_error_unknown_operation", Clazz.newArray (-1, [ new StringBuffer (oldops[o].charCodeAt (0)).toString ()])));\r
+}\r
+rlength -= remain;\r
+remain = oldrange[++o];\r
+}}\r
+while (o < oldlen) {\r
+this.addOperation (oldops[o], oldrange[o++]);\r
+}\r
+return deleted;\r
+}, "~N,~N");\r
+Clazz.defineMethod (c$, "hasDeletedRegions", \r
+function () {\r
+for (var i = 0; i < this.length; i++) {\r
+if (this.operation[i] == 'D') {\r
+return true;\r
+}}\r
+return false;\r
+});\r
+Clazz.defineMethod (c$, "getDeletedRegions", \r
+function () {\r
+if (this.length == 0) {\r
+return null;\r
+}var dr = new java.util.Vector ();\r
+var cursor = 0;\r
+var vcursor = 0;\r
+for (var i = 0; i < this.length; i++) {\r
+switch (this.operation[i]) {\r
+case 'M':\r
+cursor += this.range[i];\r
+case 'I':\r
+vcursor += this.range[i];\r
+break;\r
+case 'D':\r
+dr.addElement ( Clazz.newIntArray (-1, [vcursor, cursor, this.range[i]]));\r
+cursor += this.range[i];\r
+}\r
+}\r
+if (dr.size () == 0) {\r
+return null;\r
+}var delregions = Clazz.newIntArray (dr.size () * 3, 0);\r
+for (var i = 0, l = dr.size (); i < l; i++) {\r
+var reg = dr.elementAt (i);\r
+delregions[i * 3] = reg[0];\r
+delregions[i * 3 + 1] = reg[1];\r
+delregions[i * 3 + 2] = reg[2];\r
+}\r
+return delregions;\r
+});\r
+Clazz.defineMethod (c$, "getFullWidth", \r
+function () {\r
+var w = 0;\r
+if (this.range != null) {\r
+for (var i = 0; i < this.length; i++) {\r
+w += this.range[i];\r
+}\r
+}return w;\r
+});\r
+Clazz.defineMethod (c$, "getWidth", \r
+function () {\r
+var w = 0;\r
+if (this.range != null) {\r
+for (var i = 0; i < this.length; i++) {\r
+if (this.operation[i] == 'M' || this.operation[i] == 'I') {\r
+w += this.range[i];\r
+}}\r
+}return w;\r
+});\r
+Clazz.defineMethod (c$, "addInsertion", \r
+function (range) {\r
+this.addOperation ('I', range);\r
+}, "~N");\r
+Clazz.defineMethod (c$, "addDeleted", \r
+function (range) {\r
+this.addOperation ('D', range);\r
+}, "~N");\r
+Clazz.defineMethod (c$, "getCigarstring", \r
+function () {\r
+var cigarString = new StringBuffer ();\r
+for (var i = 0; i < this.length; i++) {\r
+cigarString.append ("" + this.range[i]);\r
+cigarString.append (this.operation[i]);\r
+}\r
+return cigarString.toString ();\r
+});\r
+Clazz.defineStatics (c$,\r
+"D", 'D',\r
+"I", 'I',\r
+"M", 'M',\r
+"_case_shift", String.fromCharCode (32));\r
+});\r
git://source.jalview.org / jalviewjs.git / blobdiff