1 Clazz.declarePackage ("javajs.util");
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2 Clazz.load (["javajs.api.GenericCifDataParser", "java.util.Hashtable", "javajs.util.SB"], "javajs.util.CifDataParser", ["javajs.util.Lst", "$.PT"], function () {
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3 c$ = Clazz.decorateAsClass (function () {
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10 this.wasUnQuoted = false;
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11 this.strPeeked = null;
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13 this.fieldCount = 0;
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14 this.loopData = null;
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15 this.fileHeader = null;
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16 this.isHeader = true;
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17 this.nullString = "\0";
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19 Clazz.instantialize (this, arguments);
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20 }, javajs.util, "CifDataParser", null, javajs.api.GenericCifDataParser);
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21 Clazz.prepareFields (c$, function () {
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22 this.fileHeader = new javajs.util.SB ();
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24 Clazz.defineMethod (c$, "setNullValue",
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25 function (nullString) {
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26 this.nullString = nullString;
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28 Clazz.makeConstructor (c$,
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31 Clazz.overrideMethod (c$, "getLoopData",
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33 return this.loopData[i];
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35 Clazz.overrideMethod (c$, "getFieldCount",
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37 return this.fieldCount;
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39 Clazz.overrideMethod (c$, "getField",
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41 return this.fields[i];
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43 Clazz.overrideMethod (c$, "set",
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44 function (reader, br) {
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45 this.reader = reader;
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48 }, "javajs.api.GenericLineReader,java.io.BufferedReader");
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49 Clazz.overrideMethod (c$, "getFileHeader",
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51 return this.fileHeader.toString ();
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53 Clazz.overrideMethod (c$, "getAllCifData",
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58 var allData = new java.util.Hashtable ();
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59 var models = new javajs.util.Lst ();
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60 allData.put ("models", models);
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62 while ((key = this.getNextToken ()) != null) {
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63 if (key.startsWith ("global_") || key.startsWith ("data_")) {
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64 models.addLast (data = new java.util.Hashtable ());
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65 data.put ("name", key);
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67 }if (key.startsWith ("loop_")) {
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68 this.getAllCifLoopData (data);
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70 }if (key.charAt (0) != '_') {
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71 System.out.println ("CIF ERROR ? should be an underscore: " + key);
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73 var value = this.getNextToken ();
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74 if (value == null) {
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75 System.out.println ("CIF ERROR ? end of file; data missing: " + key);
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77 data.put (this.fixKey (key), value);
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80 if (Clazz.exceptionOf (e, Exception)) {
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86 if (this.br != null) this.br.close ();
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88 if (Clazz.exceptionOf (e, Exception)) {
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95 Clazz.defineMethod (c$, "getAllCifLoopData",
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96 ($fz = function (data) {
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98 var keyWords = new javajs.util.Lst ();
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99 while ((key = this.peekToken ()) != null && key.charAt (0) == '_') {
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100 key = this.fixKey (this.getTokenPeeked ());
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101 keyWords.addLast (key);
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102 data.put (key, new javajs.util.Lst ());
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104 this.fieldCount = keyWords.size ();
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105 if (this.fieldCount == 0) return;
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106 this.loopData = new Array (this.fieldCount);
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107 while (this.getData ()) for (var i = 0; i < this.fieldCount; i++) (data.get (keyWords.get (i))).addLast (this.loopData[i]);
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110 }, $fz.isPrivate = true, $fz), "java.util.Map");
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111 Clazz.overrideMethod (c$, "readLine",
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114 this.line = (this.reader == null ? this.br.readLine () : this.reader.readNextLine ());
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115 if (this.line == null) return null;
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116 if (this.isHeader) {
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117 if (this.line.startsWith ("#")) this.fileHeader.append (this.line).appendC ('\n');
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118 else this.isHeader = false;
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121 if (Clazz.exceptionOf (e, Exception)) {
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128 Clazz.overrideMethod (c$, "getData",
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130 for (var i = 0; i < this.fieldCount; ++i) if ((this.loopData[i] = this.getNextDataToken ()) == null) return false;
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132 return (this.fieldCount > 0);
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134 Clazz.overrideMethod (c$, "skipLoop",
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135 function (doReport) {
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137 var ret = (doReport ? new javajs.util.SB () : null);
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139 while ((str = this.peekToken ()) != null && str.charAt (0) == '_') {
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140 if (ret != null) ret.append (str).append ("\n");
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141 this.getTokenPeeked ();
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145 while ((str = this.getNextDataToken ()) != null) {
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146 if (ret == null) continue;
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147 ret.append (str).append (" ");
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148 if ((++m % n) == 0) ret.append ("\n");
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150 return (ret == null ? null : ret.toString ());
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152 Clazz.overrideMethod (c$, "getNextToken",
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154 while (!this.strHasMoreTokens ()) if (this.setStringNextLine () == null) return null;
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156 return this.nextStrToken ();
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158 Clazz.overrideMethod (c$, "getNextDataToken",
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160 var str = this.peekToken ();
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161 if (str == null) return null;
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162 if (this.wasUnQuoted) if (str.charAt (0) == '_' || str.startsWith ("loop_") || str.startsWith ("data_") || str.startsWith ("stop_") || str.startsWith ("global_")) return null;
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163 return this.getTokenPeeked ();
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165 Clazz.overrideMethod (c$, "peekToken",
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167 while (!this.strHasMoreTokens ()) if (this.setStringNextLine () == null) return null;
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169 var ich = this.ich;
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170 this.strPeeked = this.nextStrToken ();
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171 this.ichPeeked = this.ich;
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173 return this.strPeeked;
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175 Clazz.overrideMethod (c$, "getTokenPeeked",
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177 this.ich = this.ichPeeked;
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178 return this.strPeeked;
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180 Clazz.overrideMethod (c$, "fullTrim",
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183 var pt1 = str.length;
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184 while (++pt0 < pt1 && javajs.util.PT.isWhitespace (str.charAt (pt0))) {
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186 while (--pt1 > pt0 && javajs.util.PT.isWhitespace (str.charAt (pt1))) {
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188 return str.substring (pt0, pt1 + 1);
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190 Clazz.overrideMethod (c$, "toUnicode",
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194 while ((pt = data.indexOf ('\\')) >= 0) {
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195 var c = data.charCodeAt (pt + 1);
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196 var ch = (c >= 65 && c <= 90 ? "ABX\u0394E\u03a6\u0393HI_K\u039bMNO\u03a0\u0398P\u03a3TY_\u03a9\u039e\u03a5Z".substring (c - 65, c - 64) : c >= 97 && c <= 122 ? "\u03b1\u03b2\u03c7\u03a4\u03a5\u03c6\u03b3\u03b7\u03b9_\u03ba\u03bb\u03bc\u03bd\u03bf\u03c0\u03b8\u03c1\u03c3\u03c4\u03c5_\u03c9\u03be\u03c5\u03b6".substring (c - 97, c - 96) : "_");
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197 data = data.substring (0, pt) + ch + data.substring (pt + 2);
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200 if (Clazz.exceptionOf (e, Exception)) {
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207 Clazz.overrideMethod (c$, "parseLoopParameters",
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208 function (fields, fieldOf, propertyOf) {
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209 var propertyCount = 0;
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210 if (fields == null) {
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211 this.fields = new Array (100);
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213 if (!javajs.util.CifDataParser.htFields.containsKey (fields[0])) for (var i = fields.length; --i >= 0; ) javajs.util.CifDataParser.htFields.put (fields[i], Integer.$valueOf (i));
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215 for (var i = fields.length; --i >= 0; ) fieldOf[i] = -1;
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217 propertyCount = fields.length;
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218 }this.fieldCount = 0;
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220 var str = this.peekToken ();
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222 this.fieldCount = 0;
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224 }if (str.charAt (0) != '_') break;
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225 var pt = this.fieldCount++;
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226 str = this.fixKey (this.getTokenPeeked ());
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227 if (fields == null) {
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228 this.fields[propertyOf[pt] = fieldOf[pt] = pt] = str;
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230 }var iField = javajs.util.CifDataParser.htFields.get (str);
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231 var i = (iField == null ? -1 : iField.intValue ());
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232 if ((propertyOf[pt] = i) != -1) fieldOf[i] = pt;
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234 if (this.fieldCount > 0) this.loopData = new Array (this.fieldCount);
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235 return propertyCount;
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237 Clazz.overrideMethod (c$, "fixKey",
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239 return (javajs.util.PT.rep (key.startsWith ("_magnetic") ? key.substring (9) : key.startsWith ("_jana") ? key.substring (5) : key, ".", "_").toLowerCase ());
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241 Clazz.defineMethod (c$, "setString",
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242 ($fz = function (str) {
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243 this.str = this.line = str;
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244 this.cch = (str == null ? 0 : str.length);
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246 }, $fz.isPrivate = true, $fz), "~S");
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247 Clazz.defineMethod (c$, "setStringNextLine",
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248 ($fz = function () {
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249 this.setString (this.readLine ());
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250 if (this.line == null || this.line.length == 0) return this.line;
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251 if (this.line.charAt (0) != ';') {
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252 if (this.str.startsWith ("###non-st#")) this.ich = 10;
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255 var str = '\1' + this.line.substring (1) + '\n';
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256 while (this.readLine () != null) {
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257 if (this.line.startsWith (";")) {
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258 str = str.substring (0, str.length - 1) + '\1' + this.line.substring (1);
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260 }str += this.line + '\n';
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262 this.setString (str);
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264 }, $fz.isPrivate = true, $fz));
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265 Clazz.defineMethod (c$, "strHasMoreTokens",
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266 ($fz = function () {
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267 if (this.str == null) return false;
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269 while (this.ich < this.cch && ((ch = this.str.charAt (this.ich)) == ' ' || ch == '\t')) ++this.ich;
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271 return (this.ich < this.cch && ch != '#');
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272 }, $fz.isPrivate = true, $fz));
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273 Clazz.defineMethod (c$, "nextStrToken",
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274 ($fz = function () {
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275 if (this.ich == this.cch) return null;
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276 var ichStart = this.ich;
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277 var ch = this.str.charAt (ichStart);
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278 if (ch != '\'' && ch != '"' && ch != '\1') {
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279 this.wasUnQuoted = true;
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280 while (this.ich < this.cch && (ch = this.str.charAt (this.ich)) != ' ' && ch != '\t') ++this.ich;
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282 if (this.ich == ichStart + 1) if (this.nullString != null && (this.str.charAt (ichStart) == '.' || this.str.charAt (ichStart) == '?')) return this.nullString;
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283 var s = this.str.substring (ichStart, this.ich);
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285 }this.wasUnQuoted = false;
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286 var chOpeningQuote = ch;
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287 var previousCharacterWasQuote = false;
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288 while (++this.ich < this.cch) {
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289 ch = this.str.charAt (this.ich);
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290 if (previousCharacterWasQuote && (ch == ' ' || ch == '\t')) break;
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291 previousCharacterWasQuote = (ch == chOpeningQuote);
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293 if (this.ich == this.cch) {
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294 if (previousCharacterWasQuote) return this.str.substring (ichStart + 1, this.ich - 1);
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295 return this.str.substring (ichStart, this.ich);
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297 return this.str.substring (ichStart + 1, this.ich - 2);
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298 }, $fz.isPrivate = true, $fz));
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299 c$.htFields = c$.prototype.htFields = new java.util.Hashtable ();
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300 Clazz.defineStatics (c$,
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301 "grABC", "ABX\u0394E\u03a6\u0393HI_K\u039bMNO\u03a0\u0398P\u03a3TY_\u03a9\u039e\u03a5Z",
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302 "grabc", "\u03b1\u03b2\u03c7\u03a4\u03a5\u03c6\u03b3\u03b7\u03b9_\u03ba\u03bb\u03bc\u03bd\u03bf\u03c0\u03b8\u03c1\u03c3\u03c4\u03c5_\u03c9\u03be\u03c5\u03b6");
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