Merge branch 'master' of https://source.jalview.org/git/jalviewjs.git

[jalviewjs.git] / site / j2s / jalview / analysis / Grouping.js

diff --git a/site/j2s/jalview/analysis/Grouping.js b/site/j2s/jalview/analysis/Grouping.js
index 60e2571..49d4004 100644 (file)
--- a/site/j2s/jalview/analysis/Grouping.js
+++ b/site/j2s/jalview/analysis/Grouping.js
@@ -1,88 +1,88 @@
-Clazz.declarePackage ("jalview.analysis");\r
-Clazz.load (null, "jalview.analysis.Grouping", ["jalview.datamodel.SequenceGroup", "java.lang.StringBuilder", "java.util.ArrayList", "$.HashMap"], function () {\r
-c$ = Clazz.declareType (jalview.analysis, "Grouping");\r
-c$.makeGroupsFrom = Clazz.defineMethod (c$, "makeGroupsFrom", \r
-function (sequences, selectedChars, list) {\r
-var gps =  new java.util.HashMap ();\r
-var width = 0;\r
-var i;\r
-var pgroup =  new java.util.HashMap ();\r
-if (list != null) {\r
-for (var sg, $sg = list.iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) {\r
-for (var sq, $sq = sg.getSequences (null).iterator (); $sq.hasNext () && ((sq = $sq.next ()) || true);) {\r
-pgroup.put (sq.toString (), sg);\r
-}\r
-}\r
-}for (i = 0; i < sequences.length; i++) {\r
-var schar = selectedChars[i];\r
-var pgp = pgroup.get ((sequences[i]).toString ());\r
-if (pgp != null) {\r
-schar = pgp.getName () + ":" + schar;\r
-}var svec = gps.get (schar);\r
-if (svec == null) {\r
-svec =  new java.util.ArrayList ();\r
-gps.put (schar, svec);\r
-}if (width < sequences[i].getLength ()) {\r
-width = sequences[i].getLength ();\r
-}svec.add (sequences[i]);\r
-}\r
-var groups =  new Array (gps.size ());\r
-i = 0;\r
-for (var key, $key = gps.keySet ().iterator (); $key.hasNext () && ((key = $key.next ()) || true);) {\r
-var group =  new jalview.datamodel.SequenceGroup (gps.get (key), "Subseq: " + key, null, true, true, false, 0, width - 1);\r
-groups[i++] = group;\r
-}\r
-gps.clear ();\r
-pgroup.clear ();\r
-return groups;\r
-}, "~A,~A,java.util.List");\r
-c$.makeGroupsFromCols = Clazz.defineMethod (c$, "makeGroupsFromCols", \r
-function (sequences, cs, list) {\r
-var gps =  new java.util.HashMap ();\r
-var pgroup =  new java.util.HashMap ();\r
-if (list != null) {\r
-for (var sg, $sg = list.iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) {\r
-for (var sq, $sq = sg.getSequences (null).iterator (); $sq.hasNext () && ((sq = $sq.next ()) || true);) {\r
-pgroup.put (sq.toString (), sg);\r
-}\r
-}\r
-}var spos =  Clazz.newIntArray (cs.getSelected ().size (), 0);\r
-var width = -1;\r
-var i = 0;\r
-for (var pos, $pos = cs.getSelected ().iterator (); $pos.hasNext () && ((pos = $pos.next ()) || true);) {\r
-spos[i++] = pos.intValue ();\r
-}\r
-;for (i = 0; i < sequences.length; i++) {\r
-var slen = sequences[i].getLength ();\r
-if (width < slen) {\r
-width = slen;\r
-}var pgp = pgroup.get ((sequences[i]).toString ());\r
-var schar =  new StringBuilder ();\r
-if (pgp != null) {\r
-schar.append (pgp.getName () + ":");\r
-}for (var p, $p = 0, $$p = spos; $p < $$p.length && ((p = $$p[$p]) || true); $p++) {\r
-if (p >= slen) {\r
-schar.append ("~");\r
-} else {\r
-schar.append (sequences[i].getCharAt (p));\r
-}}\r
-var svec = gps.get (schar.toString ());\r
-if (svec == null) {\r
-svec =  new java.util.ArrayList ();\r
-gps.put (schar.toString (), svec);\r
-}svec.add (sequences[i]);\r
-}\r
-var groups =  new Array (gps.size ());\r
-i = 0;\r
-for (var key, $key = gps.keySet ().iterator (); $key.hasNext () && ((key = $key.next ()) || true);) {\r
-var group =  new jalview.datamodel.SequenceGroup (gps.get (key), "Subseq: " + key, null, true, true, false, 0, width - 1);\r
-groups[i++] = group;\r
-}\r
-gps.clear ();\r
-pgroup.clear ();\r
-return groups;\r
-}, "~A,jalview.datamodel.ColumnSelection,java.util.List");\r
-c$.divideByFeature = Clazz.defineMethod (c$, "divideByFeature", \r
-function (featureLabels, groupLabels, start, stop, sequences, exgroups, method) {\r
-}, "~A,~A,~N,~N,~A,java.util.Vector,~S");\r
-});\r
+Clazz.declarePackage ("jalview.analysis");
+Clazz.load (null, "jalview.analysis.Grouping", ["jalview.datamodel.SequenceGroup", "java.lang.StringBuilder", "java.util.ArrayList", "$.HashMap"], function () {
+c$ = Clazz.declareType (jalview.analysis, "Grouping");
+c$.makeGroupsFrom = Clazz.defineMethod (c$, "makeGroupsFrom", 
+function (sequences, selectedChars, list) {
+var gps =  new java.util.HashMap ();
+var width = 0;
+var i;
+var pgroup =  new java.util.HashMap ();
+if (list != null) {
+for (var sg, $sg = list.iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) {
+for (var sq, $sq = sg.getSequences (null).iterator (); $sq.hasNext () && ((sq = $sq.next ()) || true);) {
+pgroup.put (sq.toString (), sg);
+}
+}
+}for (i = 0; i < sequences.length; i++) {
+var schar = selectedChars[i];
+var pgp = pgroup.get ((sequences[i]).toString ());
+if (pgp != null) {
+schar = pgp.getName () + ":" + schar;
+}var svec = gps.get (schar);
+if (svec == null) {
+svec =  new java.util.ArrayList ();
+gps.put (schar, svec);
+}if (width < sequences[i].getLength ()) {
+width = sequences[i].getLength ();
+}svec.add (sequences[i]);
+}
+var groups =  new Array (gps.size ());
+i = 0;
+for (var key, $key = gps.keySet ().iterator (); $key.hasNext () && ((key = $key.next ()) || true);) {
+var group =  new jalview.datamodel.SequenceGroup (gps.get (key), "Subseq: " + key, null, true, true, false, 0, width - 1);
+groups[i++] = group;
+}
+gps.clear ();
+pgroup.clear ();
+return groups;
+}, "~A,~A,java.util.List");
+c$.makeGroupsFromCols = Clazz.defineMethod (c$, "makeGroupsFromCols", 
+function (sequences, cs, list) {
+var gps =  new java.util.HashMap ();
+var pgroup =  new java.util.HashMap ();
+if (list != null) {
+for (var sg, $sg = list.iterator (); $sg.hasNext () && ((sg = $sg.next ()) || true);) {
+for (var sq, $sq = sg.getSequences (null).iterator (); $sq.hasNext () && ((sq = $sq.next ()) || true);) {
+pgroup.put (sq.toString (), sg);
+}
+}
+}var spos =  Clazz.newIntArray (cs.getSelected ().size (), 0);
+var width = -1;
+var i = 0;
+for (var pos, $pos = cs.getSelected ().iterator (); $pos.hasNext () && ((pos = $pos.next ()) || true);) {
+spos[i++] = pos.intValue ();
+}
+;for (i = 0; i < sequences.length; i++) {
+var slen = sequences[i].getLength ();
+if (width < slen) {
+width = slen;
+}var pgp = pgroup.get ((sequences[i]).toString ());
+var schar =  new StringBuilder ();
+if (pgp != null) {
+schar.append (pgp.getName () + ":");
+}for (var p, $p = 0, $$p = spos; $p < $$p.length && ((p = $$p[$p]) || true); $p++) {
+if (p >= slen) {
+schar.append ("~");
+} else {
+schar.append (sequences[i].getCharAt (p));
+}}
+var svec = gps.get (schar.toString ());
+if (svec == null) {
+svec =  new java.util.ArrayList ();
+gps.put (schar.toString (), svec);
+}svec.add (sequences[i]);
+}
+var groups =  new Array (gps.size ());
+i = 0;
+for (var key, $key = gps.keySet ().iterator (); $key.hasNext () && ((key = $key.next ()) || true);) {
+var group =  new jalview.datamodel.SequenceGroup (gps.get (key), "Subseq: " + key, null, true, true, false, 0, width - 1);
+groups[i++] = group;
+}
+gps.clear ();
+pgroup.clear ();
+return groups;
+}, "~A,jalview.datamodel.ColumnSelection,java.util.List");
+c$.divideByFeature = Clazz.defineMethod (c$, "divideByFeature", 
+function (featureLabels, groupLabels, start, stop, sequences, exgroups, method) {
+}, "~A,~A,~N,~N,~A,java.util.Vector,~S");
+});