X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=site%2Fj2s%2Fjalview%2Fanalysis%2FSeqsetUtils.js;h=f8914e1f54f6c8c9b678284f11c86ee0340c1afd;hp=a93feddbba12664203699a62303c8d10e157c95e;hb=b9b7a352eee79b7764c3b09c9d19663075061d8c;hpb=8ffd05b3abe52c0b6b79b011c0966361f82d5fe6

diff --git a/site/j2s/jalview/analysis/SeqsetUtils.js b/site/j2s/jalview/analysis/SeqsetUtils.js
index a93fedd..f8914e1 100644
--- a/site/j2s/jalview/analysis/SeqsetUtils.js
+++ b/site/j2s/jalview/analysis/SeqsetUtils.js
@@ -1,124 +1,124 @@
-Clazz.declarePackage ("jalview.analysis");
-Clazz.load (null, "jalview.analysis.SeqsetUtils", ["jalview.analysis.AlignSeq", "$.SequenceIdMatcher", "jalview.datamodel.Sequence", "jalview.util.Comparison", "java.util.Hashtable", "$.Vector"], function () {
-c$ = Clazz.declareType (jalview.analysis, "SeqsetUtils");
-c$.SeqCharacterHash = Clazz.defineMethod (c$, "SeqCharacterHash", 
-function (seq) {
-var sqinfo =  new java.util.Hashtable ();
-sqinfo.put ("Name", seq.getName ());
-sqinfo.put ("Start",  new Integer (seq.getStart ()));
-sqinfo.put ("End",  new Integer (seq.getEnd ()));
-if (seq.getDescription () != null) {
-sqinfo.put ("Description", seq.getDescription ());
-}var sfeat =  new java.util.Vector ();
-var sfarray = seq.getSequenceFeatures ();
-if (sfarray != null && sfarray.length > 0) {
-for (var i = 0; i < sfarray.length; i++) {
-sfeat.addElement (sfarray[i]);
-}
-}sqinfo.put ("SeqFeatures", sfeat);
-sqinfo.put ("PdbId", (seq.getPDBId () != null) ? seq.getPDBId () :  new java.util.Vector ());
-sqinfo.put ("datasetSequence", (seq.getDatasetSequence () != null) ? seq.getDatasetSequence () :  new jalview.datamodel.Sequence ("THISISAPLACEHOLDER", ""));
-return sqinfo;
-}, "jalview.datamodel.SequenceI");
-c$.SeqCharacterUnhash = Clazz.defineMethod (c$, "SeqCharacterUnhash", 
-function (sq, sqinfo) {
-var namePresent = true;
-if (sqinfo == null) {
-return false;
-}var oldname = sqinfo.get ("Name");
-var start = sqinfo.get ("Start");
-var end = sqinfo.get ("End");
-var sfeatures = sqinfo.get ("SeqFeatures");
-var pdbid = sqinfo.get ("PdbId");
-var description = sqinfo.get ("Description");
-var seqds = sqinfo.get ("datasetSequence");
-if (oldname == null) {
-namePresent = false;
-} else {
-sq.setName (oldname);
-}if (pdbid != null && pdbid.size () > 0) {
-sq.setPDBId (pdbid);
-}if ((start != null) && (end != null)) {
-sq.setStart (start.intValue ());
-sq.setEnd (end.intValue ());
-}if ((sfeatures != null) && (sfeatures.size () > 0)) {
-var sfarray =  new Array (sfeatures.size ());
-for (var is = 0, isize = sfeatures.size (); is < isize; is++) {
-sfarray[is] = sfeatures.elementAt (is);
-}
-sq.setSequenceFeatures (sfarray);
-}if (description != null) {
-sq.setDescription (description);
-}if ((seqds != null) && !(seqds.getName ().equals ("THISISAPLACEHOLDER") && seqds.getLength () == 0)) {
-sq.setDatasetSequence (seqds);
-}return namePresent;
-}, "jalview.datamodel.SequenceI,java.util.Hashtable");
-c$.unique_name = Clazz.defineMethod (c$, "unique_name", 
-function (i) {
-return  String.instantialize ("Sequence" + i);
-}, "~N");
-c$.uniquify = Clazz.defineMethod (c$, "uniquify", 
-function (sequences, write_names) {
-var map =  new java.util.Hashtable ();
-for (var i = 0; i < sequences.length; i++) {
-var safename = jalview.analysis.SeqsetUtils.unique_name (i);
-map.put (safename, jalview.analysis.SeqsetUtils.SeqCharacterHash (sequences[i]));
-if (write_names) {
-sequences[i].setName (safename);
-}}
-return map;
-}, "~A,~B");
-c$.deuniquify = Clazz.defineMethod (c$, "deuniquify", 
-function (map, sequences) {
-return jalview.analysis.SeqsetUtils.deuniquify (map, sequences, true);
-}, "java.util.Hashtable,~A");
-c$.deuniquify = Clazz.defineMethod (c$, "deuniquify", 
-function (map, sequences, quiet) {
-var matcher =  new jalview.analysis.SequenceIdMatcher (sequences);
-var msq = null;
-var keys = map.keys ();
-var unmatched =  new java.util.Vector ();
-for (var i = 0, j = sequences.length; i < j; i++) {
-unmatched.addElement (sequences[i]);
-}
-while (keys.hasMoreElements ()) {
-var key = keys.nextElement ();
-if (Clazz.instanceOf (key, String)) {
-if ((msq = matcher.findIdMatch (key)) != null) {
-var sqinfo = map.get (key);
-unmatched.removeElement (msq);
-jalview.analysis.SeqsetUtils.SeqCharacterUnhash (msq, sqinfo);
-} else {
-if (!quiet) {
-System.err.println ("Can't find '" + (key) + "' in uniquified alignment");
-}}}}
-if (unmatched.size () > 0 && !quiet) {
-System.err.println ("Did not find matches for :");
-for (var i = unmatched.elements (); i.hasMoreElements (); System.out.println ((i.nextElement ()).getName ())) {
-;}
-return false;
-}return true;
-}, "java.util.Hashtable,~A,~B");
-c$.getNonEmptySequenceSet = Clazz.defineMethod (c$, "getNonEmptySequenceSet", 
-function (sequences) {
-var ungapped =  Clazz.newBooleanArray (sequences.length, false);
-var msflen = 0;
-for (var i = 0, j = sequences.length; i < j; i++) {
-var tempseq = jalview.analysis.AlignSeq.extractGaps (jalview.util.Comparison.GapChars, sequences[i].getSequenceAsString ());
-if (tempseq.length == 0) {
-ungapped[i] = false;
-} else {
-ungapped[i] = true;
-msflen++;
-}}
-if (msflen == 0) {
-return null;
-}var mset =  new Array (msflen);
-for (var i = 0, j = sequences.length, k = 0; i < j; i++) {
-if (ungapped[i]) {
-mset[k++] = sequences[i];
-}}
-ungapped = null;
-return mset;
-}, "~A");
-});
+Clazz.declarePackage ("jalview.analysis");
+Clazz.load (null, "jalview.analysis.SeqsetUtils", ["jalview.analysis.AlignSeq", "$.SequenceIdMatcher", "jalview.datamodel.Sequence", "jalview.util.Comparison", "java.util.Hashtable", "$.Vector"], function () {
+c$ = Clazz.declareType (jalview.analysis, "SeqsetUtils");
+c$.SeqCharacterHash = Clazz.defineMethod (c$, "SeqCharacterHash", 
+function (seq) {
+var sqinfo =  new java.util.Hashtable ();
+sqinfo.put ("Name", seq.getName ());
+sqinfo.put ("Start",  new Integer (seq.getStart ()));
+sqinfo.put ("End",  new Integer (seq.getEnd ()));
+if (seq.getDescription () != null) {
+sqinfo.put ("Description", seq.getDescription ());
+}var sfeat =  new java.util.Vector ();
+var sfarray = seq.getSequenceFeatures ();
+if (sfarray != null && sfarray.length > 0) {
+for (var i = 0; i < sfarray.length; i++) {
+sfeat.addElement (sfarray[i]);
+}
+}sqinfo.put ("SeqFeatures", sfeat);
+sqinfo.put ("PdbId", (seq.getPDBId () != null) ? seq.getPDBId () :  new java.util.Vector ());
+sqinfo.put ("datasetSequence", (seq.getDatasetSequence () != null) ? seq.getDatasetSequence () :  new jalview.datamodel.Sequence ("THISISAPLACEHOLDER", ""));
+return sqinfo;
+}, "jalview.datamodel.SequenceI");
+c$.SeqCharacterUnhash = Clazz.defineMethod (c$, "SeqCharacterUnhash", 
+function (sq, sqinfo) {
+var namePresent = true;
+if (sqinfo == null) {
+return false;
+}var oldname = sqinfo.get ("Name");
+var start = sqinfo.get ("Start");
+var end = sqinfo.get ("End");
+var sfeatures = sqinfo.get ("SeqFeatures");
+var pdbid = sqinfo.get ("PdbId");
+var description = sqinfo.get ("Description");
+var seqds = sqinfo.get ("datasetSequence");
+if (oldname == null) {
+namePresent = false;
+} else {
+sq.setName (oldname);
+}if (pdbid != null && pdbid.size () > 0) {
+sq.setPDBId (pdbid);
+}if ((start != null) && (end != null)) {
+sq.setStart (start.intValue ());
+sq.setEnd (end.intValue ());
+}if ((sfeatures != null) && (sfeatures.size () > 0)) {
+var sfarray =  new Array (sfeatures.size ());
+for (var is = 0, isize = sfeatures.size (); is < isize; is++) {
+sfarray[is] = sfeatures.elementAt (is);
+}
+sq.setSequenceFeatures (sfarray);
+}if (description != null) {
+sq.setDescription (description);
+}if ((seqds != null) && !(seqds.getName ().equals ("THISISAPLACEHOLDER") && seqds.getLength () == 0)) {
+sq.setDatasetSequence (seqds);
+}return namePresent;
+}, "jalview.datamodel.SequenceI,java.util.Hashtable");
+c$.unique_name = Clazz.defineMethod (c$, "unique_name", 
+function (i) {
+return  String.instantialize ("Sequence" + i);
+}, "~N");
+c$.uniquify = Clazz.defineMethod (c$, "uniquify", 
+function (sequences, write_names) {
+var map =  new java.util.Hashtable ();
+for (var i = 0; i < sequences.length; i++) {
+var safename = jalview.analysis.SeqsetUtils.unique_name (i);
+map.put (safename, jalview.analysis.SeqsetUtils.SeqCharacterHash (sequences[i]));
+if (write_names) {
+sequences[i].setName (safename);
+}}
+return map;
+}, "~A,~B");
+c$.deuniquify = Clazz.defineMethod (c$, "deuniquify", 
+function (map, sequences) {
+return jalview.analysis.SeqsetUtils.deuniquify (map, sequences, true);
+}, "java.util.Hashtable,~A");
+c$.deuniquify = Clazz.defineMethod (c$, "deuniquify", 
+function (map, sequences, quiet) {
+var matcher =  new jalview.analysis.SequenceIdMatcher (sequences);
+var msq = null;
+var keys = map.keys ();
+var unmatched =  new java.util.Vector ();
+for (var i = 0, j = sequences.length; i < j; i++) {
+unmatched.addElement (sequences[i]);
+}
+while (keys.hasMoreElements ()) {
+var key = keys.nextElement ();
+if (Clazz.instanceOf (key, String)) {
+if ((msq = matcher.findIdMatch (key)) != null) {
+var sqinfo = map.get (key);
+unmatched.removeElement (msq);
+jalview.analysis.SeqsetUtils.SeqCharacterUnhash (msq, sqinfo);
+} else {
+if (!quiet) {
+System.err.println ("Can't find '" + (key) + "' in uniquified alignment");
+}}}}
+if (unmatched.size () > 0 && !quiet) {
+System.err.println ("Did not find matches for :");
+for (var i = unmatched.elements (); i.hasMoreElements (); System.out.println ((i.nextElement ()).getName ())) {
+;}
+return false;
+}return true;
+}, "java.util.Hashtable,~A,~B");
+c$.getNonEmptySequenceSet = Clazz.defineMethod (c$, "getNonEmptySequenceSet", 
+function (sequences) {
+var ungapped =  Clazz.newBooleanArray (sequences.length, false);
+var msflen = 0;
+for (var i = 0, j = sequences.length; i < j; i++) {
+var tempseq = jalview.analysis.AlignSeq.extractGaps (jalview.util.Comparison.GapChars, sequences[i].getSequenceAsString ());
+if (tempseq.length == 0) {
+ungapped[i] = false;
+} else {
+ungapped[i] = true;
+msflen++;
+}}
+if (msflen == 0) {
+return null;
+}var mset =  new Array (msflen);
+for (var i = 0, j = sequences.length, k = 0; i < j; i++) {
+if (ungapped[i]) {
+mset[k++] = sequences[i];
+}}
+ungapped = null;
+return mset;
+}, "~A");
+});