1 Clazz.declarePackage ("jalview.util");
2 Clazz.load (["java.util.HashMap"], "jalview.util.DBRefUtils", ["jalview.datamodel.DBRefEntry", "$.DBRefSource", "$.PDBEntry", "jalview.jsdev.RegExp", "java.util.ArrayList", "$.Hashtable"], function () {
3 c$ = Clazz.declareType (jalview.util, "DBRefUtils");
4 c$.selectRefs = Clazz.defineMethod (c$, "selectRefs",
5 function (dbrefs, sources) {
8 }if (sources == null) {
10 }var srcs = new java.util.HashMap ();
11 var res = new java.util.ArrayList ();
12 for (var i = 0; i < sources.length; i++) {
13 srcs.put ( String.instantialize (sources[i]), new Integer (i));
15 for (var i = 0, j = dbrefs.length; i < j; i++) {
16 if (srcs.containsKey (dbrefs[i].getSource ())) {
19 if (res.size () > 0) {
20 var reply = new Array (res.size ());
21 return res.toArray (reply);
25 c$.isDasCoordinateSystem = Clazz.defineMethod (c$, "isDasCoordinateSystem",
26 function (string, dBRefEntry) {
27 if (string == null || dBRefEntry == null) {
29 }var coordsys = jalview.util.DBRefUtils.dasCoordinateSystemsLookup.get (string.toLowerCase ());
30 return coordsys == null ? false : coordsys.equals (dBRefEntry.getSource ());
31 }, "~S,jalview.datamodel.DBRefEntry");
32 c$.getCanonicalName = Clazz.defineMethod (c$, "getCanonicalName",
36 }var canonical = jalview.util.DBRefUtils.canonicalSourceNameLookup.get (source.toLowerCase ());
37 return canonical == null ? source : canonical;
39 c$.searchRefs = Clazz.defineMethod (c$, "searchRefs",
40 function (ref, entry) {
41 return jalview.util.DBRefUtils.searchRefs (ref, entry, jalview.util.DBRefUtils.matchDbAndIdAndEitherMapOrEquivalentMapList);
42 }, "~A,jalview.datamodel.DBRefEntry");
43 c$.searchRefs = Clazz.defineMethod (c$, "searchRefs",
44 function (refs, entry, comparator) {
45 if (refs == null || entry == null) {
47 }var rfs = new java.util.ArrayList ();
48 for (var i = 0; i < refs.length; i++) {
49 if (comparator.matches (entry, refs[i])) {
52 return rfs.size () == 0 ? null : rfs.toArray ( new Array (rfs.size ()));
53 }, "~A,jalview.datamodel.DBRefEntry,jalview.util.DBRefUtils.DbRefComp");
54 c$.parseToDbRef = Clazz.defineMethod (c$, "parseToDbRef",
55 function (seq, dbname, version, acn) {
58 var locsrc = jalview.util.DBRefUtils.getCanonicalName (dbname);
59 if (locsrc.equals (jalview.datamodel.DBRefSource.PDB)) {
60 var r = jalview.jsdev.RegExp.newRegex (["([0-9][0-9A-Za-z]{3})\\s*(.?)\\s*;\\s*([0-9]+)-([0-9]+)"]);
61 if (r.search (acn.trim ())) {
62 var pdbid = r.stringMatchedI (1);
63 var chaincode = r.stringMatchedI (2);
64 if (chaincode == null) {
66 }if (chaincode.equals (" ")) {
68 }ref = new jalview.datamodel.DBRefEntry (locsrc, version, pdbid + chaincode);
69 var pdbr = new jalview.datamodel.PDBEntry ();
71 pdbr.setType (jalview.datamodel.PDBEntry.Type.PDB);
72 pdbr.setProperty ( new java.util.Hashtable ());
73 pdbr.setChainCode (chaincode);
76 System.err.println ("Malformed PDB DR line:" + acn);
78 ref = new jalview.datamodel.DBRefEntry (locsrc, version, acn);
82 }, "jalview.datamodel.SequenceI,~S,~S,~S");
83 c$.$DBRefUtils$1$ = function () {
85 c$ = Clazz.declareAnonymous (jalview.util, "DBRefUtils$1", null, jalview.util.DBRefUtils.DbRefComp);
86 Clazz.defineMethod (c$, "matches",
87 function (refa, refb) {
88 if (refa.getSource () == null || refb.getSource ().equals (refa.getSource ())) {
89 if (refa.getVersion () == null || refb.getVersion ().equals (refa.getVersion ())) {
90 if (refa.getAccessionId () == null || refb.getAccessionId ().equals (refa.getAccessionId ())) {
91 if (refa.getMap () == null || (refb.getMap () != null && refb.getMap ().equals (refa.getMap ()))) {
94 }, "jalview.datamodel.DBRefEntry,jalview.datamodel.DBRefEntry");
97 c$.$DBRefUtils$2$ = function () {
99 c$ = Clazz.declareAnonymous (jalview.util, "DBRefUtils$2", null, jalview.util.DBRefUtils.DbRefComp);
100 Clazz.defineMethod (c$, "matches",
101 function (refa, refb) {
102 if ((refa.getSource () == null || refb.getSource () == null) || refb.getSource ().equals (refa.getSource ())) {
103 if ((refa.getVersion () == null || refb.getVersion () == null) || refb.getVersion ().equals (refa.getVersion ())) {
104 if ((refa.getAccessionId () == null || refb.getAccessionId () == null) || refb.getAccessionId ().equals (refa.getAccessionId ())) {
105 if ((refa.getMap () == null || refb.getMap () == null) || (refb.getMap () != null && refb.getMap ().equals (refa.getMap ()))) {
108 }, "jalview.datamodel.DBRefEntry,jalview.datamodel.DBRefEntry");
111 c$.$DBRefUtils$3$ = function () {
113 c$ = Clazz.declareAnonymous (jalview.util, "DBRefUtils$3", null, jalview.util.DBRefUtils.DbRefComp);
114 Clazz.defineMethod (c$, "matches",
115 function (refa, refb) {
116 if (refa.getSource () != null && refb.getSource () != null && refb.getSource ().equals (refa.getSource ())) {
117 if (refa.getAccessionId () != null && refb.getAccessionId () != null || refb.getAccessionId ().equals (refa.getAccessionId ())) {
118 if ((refa.getMap () == null || refb.getMap () == null) || (refa.getMap () != null && refb.getMap () != null && refb.getMap ().equals (refa.getMap ()))) {
121 }, "jalview.datamodel.DBRefEntry,jalview.datamodel.DBRefEntry");
124 c$.$DBRefUtils$4$ = function () {
126 c$ = Clazz.declareAnonymous (jalview.util, "DBRefUtils$4", null, jalview.util.DBRefUtils.DbRefComp);
127 Clazz.defineMethod (c$, "matches",
128 function (refa, refb) {
129 if (refa.getSource () != null && refb.getSource () != null && refb.getSource ().equals (refa.getSource ())) {
130 if (refa.getAccessionId () != null && refb.getAccessionId () != null || refb.getAccessionId ().equals (refa.getAccessionId ())) {
131 if ((refa.getMap () == null && refb.getMap () == null) || (refa.getMap () != null && refb.getMap () != null)) {
132 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 ()))) {
135 }, "jalview.datamodel.DBRefEntry,jalview.datamodel.DBRefEntry");
138 c$.$DBRefUtils$5$ = function () {
140 c$ = Clazz.declareAnonymous (jalview.util, "DBRefUtils$5", null, jalview.util.DBRefUtils.DbRefComp);
141 Clazz.defineMethod (c$, "matches",
142 function (refa, refb) {
143 if (refa.getSource () != null && refb.getSource () != null && refb.getSource ().equals (refa.getSource ())) {
144 if (refa.getAccessionId () != null && refb.getAccessionId () != null || refb.getAccessionId ().equals (refa.getAccessionId ())) {
145 if (refa.getMap () == null && refb.getMap () == null) {
147 }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 ())))) {
150 }, "jalview.datamodel.DBRefEntry,jalview.datamodel.DBRefEntry");
153 c$.$DBRefUtils$6$ = function () {
155 c$ = Clazz.declareAnonymous (jalview.util, "DBRefUtils$6", null, jalview.util.DBRefUtils.DbRefComp);
156 Clazz.defineMethod (c$, "matches",
157 function (refa, refb) {
158 if (refa.getSource () != null && refb.getSource () != null && refb.getSource ().equals (refa.getSource ())) {
159 if (refa.getAccessionId () != null && refb.getAccessionId () != null && refb.getAccessionId ().equals (refa.getAccessionId ())) {
160 if (refa.getMap () == null || refb.getMap () == null) {
162 }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 ())))) {
165 }, "jalview.datamodel.DBRefEntry,jalview.datamodel.DBRefEntry");
168 Clazz.declareInterface (jalview.util.DBRefUtils, "DbRefComp");
169 c$.canonicalSourceNameLookup = c$.prototype.canonicalSourceNameLookup = new java.util.HashMap ();
170 c$.dasCoordinateSystemsLookup = c$.prototype.dasCoordinateSystemsLookup = new java.util.HashMap ();
172 jalview.util.DBRefUtils.canonicalSourceNameLookup.put ("uniprotkb/swiss-prot", jalview.datamodel.DBRefSource.UNIPROT);
173 jalview.util.DBRefUtils.canonicalSourceNameLookup.put ("uniprotkb/trembl", jalview.datamodel.DBRefSource.UNIPROT);
174 jalview.util.DBRefUtils.canonicalSourceNameLookup.put ("pdb", jalview.datamodel.DBRefSource.PDB);
175 jalview.util.DBRefUtils.dasCoordinateSystemsLookup.put ("pdbresnum", jalview.datamodel.DBRefSource.PDB);
176 jalview.util.DBRefUtils.dasCoordinateSystemsLookup.put ("uniprot", jalview.datamodel.DBRefSource.UNIPROT);
177 jalview.util.DBRefUtils.dasCoordinateSystemsLookup.put ("embl", jalview.datamodel.DBRefSource.EMBL);
178 }c$.matchNonNullonA = c$.prototype.matchNonNullonA = ((Clazz.isClassDefined ("jalview.util.DBRefUtils$1") ? 0 : jalview.util.DBRefUtils.$DBRefUtils$1$ ()), Clazz.innerTypeInstance (jalview.util.DBRefUtils$1, this, null));
179 c$.matchEitherNonNull = c$.prototype.matchEitherNonNull = ((Clazz.isClassDefined ("jalview.util.DBRefUtils$2") ? 0 : jalview.util.DBRefUtils.$DBRefUtils$2$ ()), Clazz.innerTypeInstance (jalview.util.DBRefUtils$2, this, null));
180 c$.matchDbAndIdAndEitherMap = c$.prototype.matchDbAndIdAndEitherMap = ((Clazz.isClassDefined ("jalview.util.DBRefUtils$3") ? 0 : jalview.util.DBRefUtils.$DBRefUtils$3$ ()), Clazz.innerTypeInstance (jalview.util.DBRefUtils$3, this, null));
181 c$.matchDbAndIdAndComplementaryMapList = c$.prototype.matchDbAndIdAndComplementaryMapList = ((Clazz.isClassDefined ("jalview.util.DBRefUtils$4") ? 0 : jalview.util.DBRefUtils.$DBRefUtils$4$ ()), Clazz.innerTypeInstance (jalview.util.DBRefUtils$4, this, null));
182 c$.matchDbAndIdAndEquivalentMapList = c$.prototype.matchDbAndIdAndEquivalentMapList = ((Clazz.isClassDefined ("jalview.util.DBRefUtils$5") ? 0 : jalview.util.DBRefUtils.$DBRefUtils$5$ ()), Clazz.innerTypeInstance (jalview.util.DBRefUtils$5, this, null));
183 c$.matchDbAndIdAndEitherMapOrEquivalentMapList = c$.prototype.matchDbAndIdAndEitherMapOrEquivalentMapList = ((Clazz.isClassDefined ("jalview.util.DBRefUtils$6") ? 0 : jalview.util.DBRefUtils.$DBRefUtils$6$ ()), Clazz.innerTypeInstance (jalview.util.DBRefUtils$6, this, null));