X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=bin%2Fjalview%2Fdatamodel%2FCigarBase.js;h=5b88b3f3e20cb3f4999f615dfd9d5ae634d0d490;hp=bd75085fa13ba4faf18c0fd32bafb3e92f305cc7;hb=7301a2415adab88038b291fc54caeeb3a5a47a44;hpb=6154cb57a6eac3bb1344b8342495f5bb701ee921

diff --git a/bin/jalview/datamodel/CigarBase.js b/bin/jalview/datamodel/CigarBase.js
index bd75085..5b88b3f 100644
--- a/bin/jalview/datamodel/CigarBase.js
+++ b/bin/jalview/datamodel/CigarBase.js
@@ -1,310 +1,310 @@
-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");
+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));
+});