X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=site%2Fj2s%2Fjalview%2Futil%2FDBRefUtils.js;h=71833dba28134df1ce8c4d9722d689cea74ee102;hp=b82a1e9160e4792974ddd24242ccc420d35e8fb2;hb=b9b7a352eee79b7764c3b09c9d19663075061d8c;hpb=7301a2415adab88038b291fc54caeeb3a5a47a44 diff --git a/site/j2s/jalview/util/DBRefUtils.js b/site/j2s/jalview/util/DBRefUtils.js index b82a1e9..71833db 100644 --- a/site/j2s/jalview/util/DBRefUtils.js +++ b/site/j2s/jalview/util/DBRefUtils.js @@ -1,184 +1,184 @@ -Clazz.declarePackage ("jalview.util"); -Clazz.load (["java.util.HashMap"], "jalview.util.DBRefUtils", ["jalview.datamodel.DBRefEntry", "$.DBRefSource", "$.PDBEntry", "jalview.jsdev.RegExp", "java.util.ArrayList", "$.Hashtable"], function () { -c$ = Clazz.declareType (jalview.util, "DBRefUtils"); -c$.selectRefs = Clazz.defineMethod (c$, "selectRefs", -function (dbrefs, sources) { -if (dbrefs == null) { -return null; -}if (sources == null) { -return dbrefs; -}var srcs = new java.util.HashMap (); -var res = new java.util.ArrayList (); -for (var i = 0; i < sources.length; i++) { -srcs.put ( String.instantialize (sources[i]), new Integer (i)); -} -for (var i = 0, j = dbrefs.length; i < j; i++) { -if (srcs.containsKey (dbrefs[i].getSource ())) { -res.add (dbrefs[i]); -}} -if (res.size () > 0) { -var reply = new Array (res.size ()); -return res.toArray (reply); -}res = null; -return null; -}, "~A,~A"); -c$.isDasCoordinateSystem = Clazz.defineMethod (c$, "isDasCoordinateSystem", -function (string, dBRefEntry) { -if (string == null || dBRefEntry == null) { -return false; -}var coordsys = jalview.util.DBRefUtils.dasCoordinateSystemsLookup.get (string.toLowerCase ()); -return coordsys == null ? false : coordsys.equals (dBRefEntry.getSource ()); -}, "~S,jalview.datamodel.DBRefEntry"); -c$.getCanonicalName = Clazz.defineMethod (c$, "getCanonicalName", -function (source) { -if (source == null) { -return null; -}var canonical = jalview.util.DBRefUtils.canonicalSourceNameLookup.get (source.toLowerCase ()); -return canonical == null ? source : canonical; -}, "~S"); -c$.searchRefs = Clazz.defineMethod (c$, "searchRefs", -function (ref, entry) { -return jalview.util.DBRefUtils.searchRefs (ref, entry, jalview.util.DBRefUtils.matchDbAndIdAndEitherMapOrEquivalentMapList); -}, "~A,jalview.datamodel.DBRefEntry"); -c$.searchRefs = Clazz.defineMethod (c$, "searchRefs", -function (refs, entry, comparator) { -if (refs == null || entry == null) { -return null; -}var rfs = new java.util.ArrayList (); -for (var i = 0; i < refs.length; i++) { -if (comparator.matches (entry, refs[i])) { -rfs.add (refs[i]); -}} -return rfs.size () == 0 ? null : rfs.toArray ( new Array (rfs.size ())); -}, "~A,jalview.datamodel.DBRefEntry,jalview.util.DBRefUtils.DbRefComp"); -c$.parseToDbRef = Clazz.defineMethod (c$, "parseToDbRef", -function (seq, dbname, version, acn) { -var ref = null; -if (dbname != null) { -var locsrc = jalview.util.DBRefUtils.getCanonicalName (dbname); -if (locsrc.equals (jalview.datamodel.DBRefSource.PDB)) { -var r = jalview.jsdev.RegExp.newRegex (["([0-9][0-9A-Za-z]{3})\\s*(.?)\\s*;\\s*([0-9]+)-([0-9]+)"]); -if (r.search (acn.trim ())) { -var pdbid = r.stringMatchedI (1); -var chaincode = r.stringMatchedI (2); -if (chaincode == null) { -chaincode = " "; -}if (chaincode.equals (" ")) { -chaincode = "_"; -}ref = new jalview.datamodel.DBRefEntry (locsrc, version, pdbid + chaincode); -var pdbr = new jalview.datamodel.PDBEntry (); -pdbr.setId (pdbid); -pdbr.setType (jalview.datamodel.PDBEntry.Type.PDB); -pdbr.setProperty ( new java.util.Hashtable ()); -pdbr.setChainCode (chaincode); -seq.addPDBId (pdbr); -} else { -System.err.println ("Malformed PDB DR line:" + acn); -}} else { -ref = new jalview.datamodel.DBRefEntry (locsrc, version, acn); -}}if (ref != null) { -seq.addDBRef (ref); -}return ref; -}, "jalview.datamodel.SequenceI,~S,~S,~S"); -c$.$DBRefUtils$1$ = function () { -Clazz.pu$h(self.c$); -c$ = Clazz.declareAnonymous (jalview.util, "DBRefUtils$1", null, jalview.util.DBRefUtils.DbRefComp); -Clazz.defineMethod (c$, "matches", -function (refa, refb) { -if (refa.getSource () == null || refb.getSource ().equals (refa.getSource ())) { -if (refa.getVersion () == null || refb.getVersion ().equals (refa.getVersion ())) { -if (refa.getAccessionId () == null || refb.getAccessionId ().equals (refa.getAccessionId ())) { -if (refa.getMap () == null || (refb.getMap () != null && refb.getMap ().equals (refa.getMap ()))) { -return true; -}}}}return false; -}, "jalview.datamodel.DBRefEntry,jalview.datamodel.DBRefEntry"); -c$ = Clazz.p0p (); -}; -c$.$DBRefUtils$2$ = function () { -Clazz.pu$h(self.c$); -c$ = Clazz.declareAnonymous (jalview.util, "DBRefUtils$2", null, jalview.util.DBRefUtils.DbRefComp); -Clazz.defineMethod (c$, "matches", -function (refa, refb) { -if ((refa.getSource () == null || refb.getSource () == null) || refb.getSource ().equals (refa.getSource ())) { -if ((refa.getVersion () == null || refb.getVersion () == null) || refb.getVersion ().equals (refa.getVersion ())) { -if ((refa.getAccessionId () == null || refb.getAccessionId () == null) || refb.getAccessionId ().equals (refa.getAccessionId ())) { -if ((refa.getMap () == null || refb.getMap () == null) || (refb.getMap () != null && refb.getMap ().equals (refa.getMap ()))) { -return true; -}}}}return false; -}, "jalview.datamodel.DBRefEntry,jalview.datamodel.DBRefEntry"); -c$ = Clazz.p0p (); -}; -c$.$DBRefUtils$3$ = function () { -Clazz.pu$h(self.c$); -c$ = Clazz.declareAnonymous (jalview.util, "DBRefUtils$3", null, jalview.util.DBRefUtils.DbRefComp); -Clazz.defineMethod (c$, "matches", -function (refa, refb) { -if (refa.getSource () != null && refb.getSource () != null && refb.getSource ().equals (refa.getSource ())) { -if (refa.getAccessionId () != null && refb.getAccessionId () != null || refb.getAccessionId ().equals (refa.getAccessionId ())) { -if ((refa.getMap () == null || refb.getMap () == null) || (refa.getMap () != null && refb.getMap () != null && refb.getMap ().equals (refa.getMap ()))) { -return true; -}}}return false; -}, "jalview.datamodel.DBRefEntry,jalview.datamodel.DBRefEntry"); -c$ = Clazz.p0p (); -}; -c$.$DBRefUtils$4$ = function () { -Clazz.pu$h(self.c$); -c$ = Clazz.declareAnonymous (jalview.util, "DBRefUtils$4", null, jalview.util.DBRefUtils.DbRefComp); -Clazz.defineMethod (c$, "matches", -function (refa, refb) { -if (refa.getSource () != null && refb.getSource () != null && refb.getSource ().equals (refa.getSource ())) { -if (refa.getAccessionId () != null && refb.getAccessionId () != null || refb.getAccessionId ().equals (refa.getAccessionId ())) { -if ((refa.getMap () == null && refb.getMap () == null) || (refa.getMap () != null && refb.getMap () != null)) { -if ((refb.getMap ().getMap () == null && refa.getMap ().getMap () == null) || (refb.getMap ().getMap () != null && refa.getMap ().getMap () != null && refb.getMap ().getMap ().getInverse ().equals (refa.getMap ().getMap ()))) { -return true; -}}}}return false; -}, "jalview.datamodel.DBRefEntry,jalview.datamodel.DBRefEntry"); -c$ = Clazz.p0p (); -}; -c$.$DBRefUtils$5$ = function () { -Clazz.pu$h(self.c$); -c$ = Clazz.declareAnonymous (jalview.util, "DBRefUtils$5", null, jalview.util.DBRefUtils.DbRefComp); -Clazz.defineMethod (c$, "matches", -function (refa, refb) { -if (refa.getSource () != null && refb.getSource () != null && refb.getSource ().equals (refa.getSource ())) { -if (refa.getAccessionId () != null && refb.getAccessionId () != null || refb.getAccessionId ().equals (refa.getAccessionId ())) { -if (refa.getMap () == null && refb.getMap () == null) { -return true; -}if (refa.getMap () != null && refb.getMap () != null && ((refb.getMap ().getMap () == null && refa.getMap ().getMap () == null) || (refb.getMap ().getMap () != null && refa.getMap ().getMap () != null && refb.getMap ().getMap ().equals (refa.getMap ().getMap ())))) { -return true; -}}}return false; -}, "jalview.datamodel.DBRefEntry,jalview.datamodel.DBRefEntry"); -c$ = Clazz.p0p (); -}; -c$.$DBRefUtils$6$ = function () { -Clazz.pu$h(self.c$); -c$ = Clazz.declareAnonymous (jalview.util, "DBRefUtils$6", null, jalview.util.DBRefUtils.DbRefComp); -Clazz.defineMethod (c$, "matches", -function (refa, refb) { -if (refa.getSource () != null && refb.getSource () != null && refb.getSource ().equals (refa.getSource ())) { -if (refa.getAccessionId () != null && refb.getAccessionId () != null && refb.getAccessionId ().equals (refa.getAccessionId ())) { -if (refa.getMap () == null || refb.getMap () == null) { -return true; -}if ((refa.getMap () != null && refb.getMap () != null) && (refb.getMap ().getMap () == null && refa.getMap ().getMap () == null) || (refb.getMap ().getMap () != null && refa.getMap ().getMap () != null && (refb.getMap ().getMap ().equals (refa.getMap ().getMap ())))) { -return true; -}}}return false; -}, "jalview.datamodel.DBRefEntry,jalview.datamodel.DBRefEntry"); -c$ = Clazz.p0p (); -}; -Clazz.declareInterface (jalview.util.DBRefUtils, "DbRefComp"); -c$.canonicalSourceNameLookup = c$.prototype.canonicalSourceNameLookup = new java.util.HashMap (); -c$.dasCoordinateSystemsLookup = c$.prototype.dasCoordinateSystemsLookup = new java.util.HashMap (); -{ -jalview.util.DBRefUtils.canonicalSourceNameLookup.put ("uniprotkb/swiss-prot", jalview.datamodel.DBRefSource.UNIPROT); -jalview.util.DBRefUtils.canonicalSourceNameLookup.put ("uniprotkb/trembl", jalview.datamodel.DBRefSource.UNIPROT); -jalview.util.DBRefUtils.canonicalSourceNameLookup.put ("pdb", jalview.datamodel.DBRefSource.PDB); -jalview.util.DBRefUtils.dasCoordinateSystemsLookup.put ("pdbresnum", jalview.datamodel.DBRefSource.PDB); -jalview.util.DBRefUtils.dasCoordinateSystemsLookup.put ("uniprot", jalview.datamodel.DBRefSource.UNIPROT); -jalview.util.DBRefUtils.dasCoordinateSystemsLookup.put ("embl", jalview.datamodel.DBRefSource.EMBL); -}c$.matchNonNullonA = c$.prototype.matchNonNullonA = ((Clazz.isClassDefined ("jalview.util.DBRefUtils$1") ? 0 : jalview.util.DBRefUtils.$DBRefUtils$1$ ()), Clazz.innerTypeInstance (jalview.util.DBRefUtils$1, this, null)); -c$.matchEitherNonNull = c$.prototype.matchEitherNonNull = ((Clazz.isClassDefined ("jalview.util.DBRefUtils$2") ? 0 : jalview.util.DBRefUtils.$DBRefUtils$2$ ()), Clazz.innerTypeInstance (jalview.util.DBRefUtils$2, this, null)); -c$.matchDbAndIdAndEitherMap = c$.prototype.matchDbAndIdAndEitherMap = ((Clazz.isClassDefined ("jalview.util.DBRefUtils$3") ? 0 : jalview.util.DBRefUtils.$DBRefUtils$3$ ()), Clazz.innerTypeInstance (jalview.util.DBRefUtils$3, this, null)); -c$.matchDbAndIdAndComplementaryMapList = c$.prototype.matchDbAndIdAndComplementaryMapList = ((Clazz.isClassDefined ("jalview.util.DBRefUtils$4") ? 0 : jalview.util.DBRefUtils.$DBRefUtils$4$ ()), Clazz.innerTypeInstance (jalview.util.DBRefUtils$4, this, null)); -c$.matchDbAndIdAndEquivalentMapList = c$.prototype.matchDbAndIdAndEquivalentMapList = ((Clazz.isClassDefined ("jalview.util.DBRefUtils$5") ? 0 : jalview.util.DBRefUtils.$DBRefUtils$5$ ()), Clazz.innerTypeInstance (jalview.util.DBRefUtils$5, this, null)); -c$.matchDbAndIdAndEitherMapOrEquivalentMapList = c$.prototype.matchDbAndIdAndEitherMapOrEquivalentMapList = ((Clazz.isClassDefined ("jalview.util.DBRefUtils$6") ? 0 : jalview.util.DBRefUtils.$DBRefUtils$6$ ()), Clazz.innerTypeInstance (jalview.util.DBRefUtils$6, this, null)); -}); +Clazz.declarePackage ("jalview.util"); +Clazz.load (["java.util.HashMap"], "jalview.util.DBRefUtils", ["jalview.datamodel.DBRefEntry", "$.DBRefSource", "$.PDBEntry", "jalview.jsdev.RegExp", "java.util.ArrayList", "$.Hashtable"], function () { +c$ = Clazz.declareType (jalview.util, "DBRefUtils"); +c$.selectRefs = Clazz.defineMethod (c$, "selectRefs", +function (dbrefs, sources) { +if (dbrefs == null) { +return null; +}if (sources == null) { +return dbrefs; +}var srcs = new java.util.HashMap (); +var res = new java.util.ArrayList (); +for (var i = 0; i < sources.length; i++) { +srcs.put ( String.instantialize (sources[i]), new Integer (i)); +} +for (var i = 0, j = dbrefs.length; i < j; i++) { +if (srcs.containsKey (dbrefs[i].getSource ())) { +res.add (dbrefs[i]); +}} +if (res.size () > 0) { +var reply = new Array (res.size ()); +return res.toArray (reply); +}res = null; +return null; +}, "~A,~A"); +c$.isDasCoordinateSystem = Clazz.defineMethod (c$, "isDasCoordinateSystem", +function (string, dBRefEntry) { +if (string == null || dBRefEntry == null) { +return false; +}var coordsys = jalview.util.DBRefUtils.dasCoordinateSystemsLookup.get (string.toLowerCase ()); +return coordsys == null ? false : coordsys.equals (dBRefEntry.getSource ()); +}, "~S,jalview.datamodel.DBRefEntry"); +c$.getCanonicalName = Clazz.defineMethod (c$, "getCanonicalName", +function (source) { +if (source == null) { +return null; +}var canonical = jalview.util.DBRefUtils.canonicalSourceNameLookup.get (source.toLowerCase ()); +return canonical == null ? source : canonical; +}, "~S"); +c$.searchRefs = Clazz.defineMethod (c$, "searchRefs", +function (ref, entry) { +return jalview.util.DBRefUtils.searchRefs (ref, entry, jalview.util.DBRefUtils.matchDbAndIdAndEitherMapOrEquivalentMapList); +}, "~A,jalview.datamodel.DBRefEntry"); +c$.searchRefs = Clazz.defineMethod (c$, "searchRefs", +function (refs, entry, comparator) { +if (refs == null || entry == null) { +return null; +}var rfs = new java.util.ArrayList (); +for (var i = 0; i < refs.length; i++) { +if (comparator.matches (entry, refs[i])) { +rfs.add (refs[i]); +}} +return rfs.size () == 0 ? null : rfs.toArray ( new Array (rfs.size ())); +}, "~A,jalview.datamodel.DBRefEntry,jalview.util.DBRefUtils.DbRefComp"); +c$.parseToDbRef = Clazz.defineMethod (c$, "parseToDbRef", +function (seq, dbname, version, acn) { +var ref = null; +if (dbname != null) { +var locsrc = jalview.util.DBRefUtils.getCanonicalName (dbname); +if (locsrc.equals (jalview.datamodel.DBRefSource.PDB)) { +var r = jalview.jsdev.RegExp.newRegex (["([0-9][0-9A-Za-z]{3})\\s*(.?)\\s*;\\s*([0-9]+)-([0-9]+)"]); +if (r.search (acn.trim ())) { +var pdbid = r.stringMatchedI (1); +var chaincode = r.stringMatchedI (2); +if (chaincode == null) { +chaincode = " "; +}if (chaincode.equals (" ")) { +chaincode = "_"; +}ref = new jalview.datamodel.DBRefEntry (locsrc, version, pdbid + chaincode); +var pdbr = new jalview.datamodel.PDBEntry (); +pdbr.setId (pdbid); +pdbr.setType (jalview.datamodel.PDBEntry.Type.PDB); +pdbr.setProperty ( new java.util.Hashtable ()); +pdbr.setChainCode (chaincode); +seq.addPDBId (pdbr); +} else { +System.err.println ("Malformed PDB DR line:" + acn); +}} else { +ref = new jalview.datamodel.DBRefEntry (locsrc, version, acn); +}}if (ref != null) { +seq.addDBRef (ref); +}return ref; +}, "jalview.datamodel.SequenceI,~S,~S,~S"); +c$.$DBRefUtils$1$ = function () { +Clazz.pu$h(self.c$); +c$ = Clazz.declareAnonymous (jalview.util, "DBRefUtils$1", null, jalview.util.DBRefUtils.DbRefComp); +Clazz.defineMethod (c$, "matches", +function (refa, refb) { +if (refa.getSource () == null || refb.getSource ().equals (refa.getSource ())) { +if (refa.getVersion () == null || refb.getVersion ().equals (refa.getVersion ())) { +if (refa.getAccessionId () == null || refb.getAccessionId ().equals (refa.getAccessionId ())) { +if (refa.getMap () == null || (refb.getMap () != null && refb.getMap ().equals (refa.getMap ()))) { +return true; +}}}}return false; +}, "jalview.datamodel.DBRefEntry,jalview.datamodel.DBRefEntry"); +c$ = Clazz.p0p (); +}; +c$.$DBRefUtils$2$ = function () { +Clazz.pu$h(self.c$); +c$ = Clazz.declareAnonymous (jalview.util, "DBRefUtils$2", null, jalview.util.DBRefUtils.DbRefComp); +Clazz.defineMethod (c$, "matches", +function (refa, refb) { +if ((refa.getSource () == null || refb.getSource () == null) || refb.getSource ().equals (refa.getSource ())) { +if ((refa.getVersion () == null || refb.getVersion () == null) || refb.getVersion ().equals (refa.getVersion ())) { +if ((refa.getAccessionId () == null || refb.getAccessionId () == null) || refb.getAccessionId ().equals (refa.getAccessionId ())) { +if ((refa.getMap () == null || refb.getMap () == null) || (refb.getMap () != null && refb.getMap ().equals (refa.getMap ()))) { +return true; +}}}}return false; +}, "jalview.datamodel.DBRefEntry,jalview.datamodel.DBRefEntry"); +c$ = Clazz.p0p (); +}; +c$.$DBRefUtils$3$ = function () { +Clazz.pu$h(self.c$); +c$ = Clazz.declareAnonymous (jalview.util, "DBRefUtils$3", null, jalview.util.DBRefUtils.DbRefComp); +Clazz.defineMethod (c$, "matches", +function (refa, refb) { +if (refa.getSource () != null && refb.getSource () != null && refb.getSource ().equals (refa.getSource ())) { +if (refa.getAccessionId () != null && refb.getAccessionId () != null || refb.getAccessionId ().equals (refa.getAccessionId ())) { +if ((refa.getMap () == null || refb.getMap () == null) || (refa.getMap () != null && refb.getMap () != null && refb.getMap ().equals (refa.getMap ()))) { +return true; +}}}return false; +}, "jalview.datamodel.DBRefEntry,jalview.datamodel.DBRefEntry"); +c$ = Clazz.p0p (); +}; +c$.$DBRefUtils$4$ = function () { +Clazz.pu$h(self.c$); +c$ = Clazz.declareAnonymous (jalview.util, "DBRefUtils$4", null, jalview.util.DBRefUtils.DbRefComp); +Clazz.defineMethod (c$, "matches", +function (refa, refb) { +if (refa.getSource () != null && refb.getSource () != null && refb.getSource ().equals (refa.getSource ())) { +if (refa.getAccessionId () != null && refb.getAccessionId () != null || refb.getAccessionId ().equals (refa.getAccessionId ())) { +if ((refa.getMap () == null && refb.getMap () == null) || (refa.getMap () != null && refb.getMap () != null)) { +if ((refb.getMap ().getMap () == null && refa.getMap ().getMap () == null) || (refb.getMap ().getMap () != null && refa.getMap ().getMap () != null && refb.getMap ().getMap ().getInverse ().equals (refa.getMap ().getMap ()))) { +return true; +}}}}return false; +}, "jalview.datamodel.DBRefEntry,jalview.datamodel.DBRefEntry"); +c$ = Clazz.p0p (); +}; +c$.$DBRefUtils$5$ = function () { +Clazz.pu$h(self.c$); +c$ = Clazz.declareAnonymous (jalview.util, "DBRefUtils$5", null, jalview.util.DBRefUtils.DbRefComp); +Clazz.defineMethod (c$, "matches", +function (refa, refb) { +if (refa.getSource () != null && refb.getSource () != null && refb.getSource ().equals (refa.getSource ())) { +if (refa.getAccessionId () != null && refb.getAccessionId () != null || refb.getAccessionId ().equals (refa.getAccessionId ())) { +if (refa.getMap () == null && refb.getMap () == null) { +return true; +}if (refa.getMap () != null && refb.getMap () != null && ((refb.getMap ().getMap () == null && refa.getMap ().getMap () == null) || (refb.getMap ().getMap () != null && refa.getMap ().getMap () != null && refb.getMap ().getMap ().equals (refa.getMap ().getMap ())))) { +return true; +}}}return false; +}, "jalview.datamodel.DBRefEntry,jalview.datamodel.DBRefEntry"); +c$ = Clazz.p0p (); +}; +c$.$DBRefUtils$6$ = function () { +Clazz.pu$h(self.c$); +c$ = Clazz.declareAnonymous (jalview.util, "DBRefUtils$6", null, jalview.util.DBRefUtils.DbRefComp); +Clazz.defineMethod (c$, "matches", +function (refa, refb) { +if (refa.getSource () != null && refb.getSource () != null && refb.getSource ().equals (refa.getSource ())) { +if (refa.getAccessionId () != null && refb.getAccessionId () != null && refb.getAccessionId ().equals (refa.getAccessionId ())) { +if (refa.getMap () == null || refb.getMap () == null) { +return true; +}if ((refa.getMap () != null && refb.getMap () != null) && (refb.getMap ().getMap () == null && refa.getMap ().getMap () == null) || (refb.getMap ().getMap () != null && refa.getMap ().getMap () != null && (refb.getMap ().getMap ().equals (refa.getMap ().getMap ())))) { +return true; +}}}return false; +}, "jalview.datamodel.DBRefEntry,jalview.datamodel.DBRefEntry"); +c$ = Clazz.p0p (); +}; +Clazz.declareInterface (jalview.util.DBRefUtils, "DbRefComp"); +c$.canonicalSourceNameLookup = c$.prototype.canonicalSourceNameLookup = new java.util.HashMap (); +c$.dasCoordinateSystemsLookup = c$.prototype.dasCoordinateSystemsLookup = new java.util.HashMap (); +{ +jalview.util.DBRefUtils.canonicalSourceNameLookup.put ("uniprotkb/swiss-prot", jalview.datamodel.DBRefSource.UNIPROT); +jalview.util.DBRefUtils.canonicalSourceNameLookup.put ("uniprotkb/trembl", jalview.datamodel.DBRefSource.UNIPROT); +jalview.util.DBRefUtils.canonicalSourceNameLookup.put ("pdb", jalview.datamodel.DBRefSource.PDB); +jalview.util.DBRefUtils.dasCoordinateSystemsLookup.put ("pdbresnum", jalview.datamodel.DBRefSource.PDB); +jalview.util.DBRefUtils.dasCoordinateSystemsLookup.put ("uniprot", jalview.datamodel.DBRefSource.UNIPROT); +jalview.util.DBRefUtils.dasCoordinateSystemsLookup.put ("embl", jalview.datamodel.DBRefSource.EMBL); +}c$.matchNonNullonA = c$.prototype.matchNonNullonA = ((Clazz.isClassDefined ("jalview.util.DBRefUtils$1") ? 0 : jalview.util.DBRefUtils.$DBRefUtils$1$ ()), Clazz.innerTypeInstance (jalview.util.DBRefUtils$1, this, null)); +c$.matchEitherNonNull = c$.prototype.matchEitherNonNull = ((Clazz.isClassDefined ("jalview.util.DBRefUtils$2") ? 0 : jalview.util.DBRefUtils.$DBRefUtils$2$ ()), Clazz.innerTypeInstance (jalview.util.DBRefUtils$2, this, null)); +c$.matchDbAndIdAndEitherMap = c$.prototype.matchDbAndIdAndEitherMap = ((Clazz.isClassDefined ("jalview.util.DBRefUtils$3") ? 0 : jalview.util.DBRefUtils.$DBRefUtils$3$ ()), Clazz.innerTypeInstance (jalview.util.DBRefUtils$3, this, null)); +c$.matchDbAndIdAndComplementaryMapList = c$.prototype.matchDbAndIdAndComplementaryMapList = ((Clazz.isClassDefined ("jalview.util.DBRefUtils$4") ? 0 : jalview.util.DBRefUtils.$DBRefUtils$4$ ()), Clazz.innerTypeInstance (jalview.util.DBRefUtils$4, this, null)); +c$.matchDbAndIdAndEquivalentMapList = c$.prototype.matchDbAndIdAndEquivalentMapList = ((Clazz.isClassDefined ("jalview.util.DBRefUtils$5") ? 0 : jalview.util.DBRefUtils.$DBRefUtils$5$ ()), Clazz.innerTypeInstance (jalview.util.DBRefUtils$5, this, null)); +c$.matchDbAndIdAndEitherMapOrEquivalentMapList = c$.prototype.matchDbAndIdAndEitherMapOrEquivalentMapList = ((Clazz.isClassDefined ("jalview.util.DBRefUtils$6") ? 0 : jalview.util.DBRefUtils.$DBRefUtils$6$ ()), Clazz.innerTypeInstance (jalview.util.DBRefUtils$6, this, null)); +});