X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=bin%2Fjalview%2Futil%2FComparison.js;h=29499bb53ad547f60856379efc832f659495e8af;hp=e46a616ee33a8c03b1cfe2247cd22683829def9c;hb=8ffd05b3abe52c0b6b79b011c0966361f82d5fe6;hpb=6154cb57a6eac3bb1344b8342495f5bb701ee921

diff --git a/bin/jalview/util/Comparison.js b/bin/jalview/util/Comparison.js
index e46a616..29499bb 100644
--- a/bin/jalview/util/Comparison.js
+++ b/bin/jalview/util/Comparison.js
@@ -1,131 +1,131 @@
-Clazz.declarePackage ("jalview.util");
-Clazz.load (null, "jalview.util.Comparison", ["java.util.ArrayList"], function () {
-c$ = Clazz.declareType (jalview.util, "Comparison");
-c$.compare = Clazz.defineMethod (c$, "compare", 
-function (ii, jj) {
-return jalview.util.Comparison.compare (ii, jj, 0, ii.getLength () - 1);
-}, "jalview.datamodel.SequenceI,jalview.datamodel.SequenceI");
-c$.compare = Clazz.defineMethod (c$, "compare", 
-function (ii, jj, start, end) {
-var si = ii.getSequenceAsString ();
-var sj = jj.getSequenceAsString ();
-var ilen = si.length - 1;
-var jlen = sj.length - 1;
-while (jalview.util.Comparison.isGap (si.charAt (start + ilen))) {
-ilen--;
-}
-while (jalview.util.Comparison.isGap (sj.charAt (start + jlen))) {
-jlen--;
-}
-var count = 0;
-var match = 0;
-var pid = -1;
-if (ilen > jlen) {
-for (var j = 0; j < jlen; j++) {
-if (si.substring (start + j, start + j + 1).equals (sj.substring (start + j, start + j + 1))) {
-match++;
-}count++;
-}
-pid = match / ilen * 100;
-} else {
-for (var j = 0; j < jlen; j++) {
-if (si.substring (start + j, start + j + 1).equals (sj.substring (start + j, start + j + 1))) {
-match++;
-}count++;
-}
-pid = match / jlen * 100;
-}return pid;
-}, "jalview.datamodel.SequenceI,jalview.datamodel.SequenceI,~N,~N");
-c$.PID = Clazz.defineMethod (c$, "PID", 
-function (seq1, seq2) {
-return jalview.util.Comparison.PID (seq1, seq2, 0, seq1.length);
-}, "~S,~S");
-c$.PID = Clazz.defineMethod (c$, "PID", 
-function (seq1, seq2, start, end) {
-return jalview.util.Comparison.PID (seq1, seq2, start, end, true, false);
-}, "~S,~S,~N,~N");
-c$.PID = Clazz.defineMethod (c$, "PID", 
-function (seq1, seq2, start, end, wcGaps, ungappedOnly) {
-var s1len = seq1.length;
-var s2len = seq2.length;
-var len = Math.min (s1len, s2len);
-if (end < len) {
-len = end;
-}if (len < start) {
-start = len - 1;
-}var elen = len - start;
-var bad = 0;
-var chr1;
-var chr2;
-var agap;
-for (var i = start; i < len; i++) {
-chr1 = seq1.charAt (i);
-chr2 = seq2.charAt (i);
-agap = jalview.util.Comparison.isGap (chr1) || jalview.util.Comparison.isGap (chr2);
-if ('a' <= chr1 && chr1 <= 'z') {
-chr1 = String.fromCharCode (chr1.charCodeAt (0) - 32);
-}if ('a' <= chr2 && chr2 <= 'z') {
-chr2 = String.fromCharCode (chr2.charCodeAt (0) - 32);
-}if (chr1 != chr2) {
-if (agap) {
-if (ungappedOnly) {
-elen--;
-} else if (!wcGaps) {
-bad++;
-}} else {
-bad++;
-}}}
-if (elen < 1) {
-return 0;
-}return (100 * (elen - bad)) / elen;
-}, "~S,~S,~N,~N,~B,~B");
-c$.isGap = Clazz.defineMethod (c$, "isGap", 
-function (c) {
-return (c == '-' || c == '.' || c == ' ') ? true : false;
-}, "~S");
-c$.isNucleotide = Clazz.defineMethod (c$, "isNucleotide", 
-function (seqs) {
-if (seqs == null) {
-return false;
-}var ntCount = 0;
-var aaCount = 0;
-for (var seq, $seq = 0, $$seq = seqs; $seq < $$seq.length && ((seq = $$seq[$seq]) || true); $seq++) {
-if (seq == null) {
-continue;
-}for (var c, $c = 0, $$c = seq.getSequence (); $c < $$c.length && ((c = $$c[$c]) || true); $c++) {
-if ('a' <= c && c <= 'z') {
-c = String.fromCharCode (c.charCodeAt (0) - 32);
-}if (c == 'A' || c == 'G' || c == 'C' || c == 'T' || c == 'U') {
-ntCount++;
-} else if (!jalview.util.Comparison.isGap (c)) {
-aaCount++;
-}}
-}
-if (ntCount * 100 > 85 * (ntCount + aaCount)) {
-return true;
-} else {
-return false;
-}}, "~A");
-c$.isNucleotide2 = Clazz.defineMethod (c$, "isNucleotide2", 
-function (seqs) {
-if (seqs == null) {
-return false;
-}var flattened =  new java.util.ArrayList ();
-for (var ss, $ss = 0, $$ss = seqs; $ss < $$ss.length && ((ss = $$ss[$ss]) || true); $ss++) {
-for (var s, $s = 0, $$s = ss; $s < $$s.length && ((s = $$s[$s]) || true); $s++) {
-flattened.add (s);
-}
-}
-var oneDArray = flattened.toArray ( new Array (flattened.size ()));
-return jalview.util.Comparison.isNucleotide (oneDArray);
-}, "~A");
-Clazz.defineStatics (c$,
-"EIGHTY_FIVE", 85,
-"TO_UPPER_CASE", 32,
-"GAP_SPACE", ' ',
-"GAP_DOT", '.',
-"GAP_DASH", '-');
-c$.GapChars = c$.prototype.GapChars =  String.instantialize ( Clazz.newCharArray (-1, [' ', '.', '-']));
-Clazz.defineStatics (c$,
-"caseShift", 32);
-});
+Clazz.declarePackage ("jalview.util");
+Clazz.load (null, "jalview.util.Comparison", ["java.util.ArrayList"], function () {
+c$ = Clazz.declareType (jalview.util, "Comparison");
+c$.compare = Clazz.defineMethod (c$, "compare", 
+function (ii, jj) {
+return jalview.util.Comparison.compare (ii, jj, 0, ii.getLength () - 1);
+}, "jalview.datamodel.SequenceI,jalview.datamodel.SequenceI");
+c$.compare = Clazz.defineMethod (c$, "compare", 
+function (ii, jj, start, end) {
+var si = ii.getSequenceAsString ();
+var sj = jj.getSequenceAsString ();
+var ilen = si.length - 1;
+var jlen = sj.length - 1;
+while (jalview.util.Comparison.isGap (si.charAt (start + ilen))) {
+ilen--;
+}
+while (jalview.util.Comparison.isGap (sj.charAt (start + jlen))) {
+jlen--;
+}
+var count = 0;
+var match = 0;
+var pid = -1;
+if (ilen > jlen) {
+for (var j = 0; j < jlen; j++) {
+if (si.substring (start + j, start + j + 1).equals (sj.substring (start + j, start + j + 1))) {
+match++;
+}count++;
+}
+pid = match / ilen * 100;
+} else {
+for (var j = 0; j < jlen; j++) {
+if (si.substring (start + j, start + j + 1).equals (sj.substring (start + j, start + j + 1))) {
+match++;
+}count++;
+}
+pid = match / jlen * 100;
+}return pid;
+}, "jalview.datamodel.SequenceI,jalview.datamodel.SequenceI,~N,~N");
+c$.PID = Clazz.defineMethod (c$, "PID", 
+function (seq1, seq2) {
+return jalview.util.Comparison.PID (seq1, seq2, 0, seq1.length);
+}, "~S,~S");
+c$.PID = Clazz.defineMethod (c$, "PID", 
+function (seq1, seq2, start, end) {
+return jalview.util.Comparison.PID (seq1, seq2, start, end, true, false);
+}, "~S,~S,~N,~N");
+c$.PID = Clazz.defineMethod (c$, "PID", 
+function (seq1, seq2, start, end, wcGaps, ungappedOnly) {
+var s1len = seq1.length;
+var s2len = seq2.length;
+var len = Math.min (s1len, s2len);
+if (end < len) {
+len = end;
+}if (len < start) {
+start = len - 1;
+}var elen = len - start;
+var bad = 0;
+var chr1;
+var chr2;
+var agap;
+for (var i = start; i < len; i++) {
+chr1 = seq1.charAt (i);
+chr2 = seq2.charAt (i);
+agap = jalview.util.Comparison.isGap (chr1) || jalview.util.Comparison.isGap (chr2);
+if ('a' <= chr1 && chr1 <= 'z') {
+chr1 = String.fromCharCode (chr1.charCodeAt (0) - 32);
+}if ('a' <= chr2 && chr2 <= 'z') {
+chr2 = String.fromCharCode (chr2.charCodeAt (0) - 32);
+}if (chr1 != chr2) {
+if (agap) {
+if (ungappedOnly) {
+elen--;
+} else if (!wcGaps) {
+bad++;
+}} else {
+bad++;
+}}}
+if (elen < 1) {
+return 0;
+}return (100 * (elen - bad)) / elen;
+}, "~S,~S,~N,~N,~B,~B");
+c$.isGap = Clazz.defineMethod (c$, "isGap", 
+function (c) {
+return (c == '-' || c == '.' || c == ' ') ? true : false;
+}, "~S");
+c$.isNucleotide = Clazz.defineMethod (c$, "isNucleotide", 
+function (seqs) {
+if (seqs == null) {
+return false;
+}var ntCount = 0;
+var aaCount = 0;
+for (var seq, $seq = 0, $$seq = seqs; $seq < $$seq.length && ((seq = $$seq[$seq]) || true); $seq++) {
+if (seq == null) {
+continue;
+}for (var c, $c = 0, $$c = seq.getSequence (); $c < $$c.length && ((c = $$c[$c]) || true); $c++) {
+if ('a' <= c && c <= 'z') {
+c = String.fromCharCode (c.charCodeAt (0) - 32);
+}if (c == 'A' || c == 'G' || c == 'C' || c == 'T' || c == 'U') {
+ntCount++;
+} else if (!jalview.util.Comparison.isGap (c)) {
+aaCount++;
+}}
+}
+if (ntCount * 100 > 85 * (ntCount + aaCount)) {
+return true;
+} else {
+return false;
+}}, "~A");
+c$.isNucleotide2 = Clazz.defineMethod (c$, "isNucleotide2", 
+function (seqs) {
+if (seqs == null) {
+return false;
+}var flattened =  new java.util.ArrayList ();
+for (var ss, $ss = 0, $$ss = seqs; $ss < $$ss.length && ((ss = $$ss[$ss]) || true); $ss++) {
+for (var s, $s = 0, $$s = ss; $s < $$s.length && ((s = $$s[$s]) || true); $s++) {
+flattened.add (s);
+}
+}
+var oneDArray = flattened.toArray ( new Array (flattened.size ()));
+return jalview.util.Comparison.isNucleotide (oneDArray);
+}, "~A");
+Clazz.defineStatics (c$,
+"EIGHTY_FIVE", 85,
+"TO_UPPER_CASE", 32,
+"GAP_SPACE", ' ',
+"GAP_DOT", '.',
+"GAP_DASH", '-');
+c$.GapChars = c$.prototype.GapChars =  String.instantialize ( Clazz.newCharArray (-1, [' ', '.', '-']));
+Clazz.defineStatics (c$,
+"caseShift", 32);
+});