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