X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=site%2Fj2s%2FJU%2FCifDataParser.js;h=fca0eb78d733a158d8a96b139d770ce92afc0392;hp=a813aab0e8470aef45e191e14465fa3fd9f8e62b;hb=b9b7a352eee79b7764c3b09c9d19663075061d8c;hpb=8ffd05b3abe52c0b6b79b011c0966361f82d5fe6

diff --git a/site/j2s/JU/CifDataParser.js b/site/j2s/JU/CifDataParser.js
index a813aab..fca0eb7 100644
--- a/site/j2s/JU/CifDataParser.js
+++ b/site/j2s/JU/CifDataParser.js
@@ -1,293 +1,293 @@
-Clazz.declarePackage ("JU");
-Clazz.load (["javajs.api.GenericCifDataParser", "java.util.Hashtable", "JU.SB"], "JU.CifDataParser", ["JU.Lst", "$.PT"], function () {
-c$ = Clazz.decorateAsClass (function () {
-this.reader = null;
-this.br = null;
-this.line = null;
-this.str = null;
-this.ich = 0;
-this.cch = 0;
-this.wasUnQuoted = false;
-this.strPeeked = null;
-this.ichPeeked = 0;
-this.fieldCount = 0;
-this.loopData = null;
-this.fileHeader = null;
-this.isHeader = true;
-this.nullString = "\0";
-this.fields = null;
-Clazz.instantialize (this, arguments);
-}, JU, "CifDataParser", null, javajs.api.GenericCifDataParser);
-Clazz.prepareFields (c$, function () {
-this.fileHeader =  new JU.SB ();
-});
-Clazz.defineMethod (c$, "setNullValue", 
-function (nullString) {
-this.nullString = nullString;
-}, "~S");
-Clazz.makeConstructor (c$, 
-function () {
-});
-Clazz.overrideMethod (c$, "getLoopData", 
-function (i) {
-return this.loopData[i];
-}, "~N");
-Clazz.overrideMethod (c$, "getFieldCount", 
-function () {
-return this.fieldCount;
-});
-Clazz.overrideMethod (c$, "getField", 
-function (i) {
-return this.fields[i];
-}, "~N");
-Clazz.overrideMethod (c$, "set", 
-function (reader, br) {
-this.reader = reader;
-this.br = br;
-return this;
-}, "javajs.api.GenericLineReader,java.io.BufferedReader");
-Clazz.overrideMethod (c$, "getFileHeader", 
-function () {
-return this.fileHeader.toString ();
-});
-Clazz.overrideMethod (c$, "getAllCifData", 
-function () {
-this.line = "";
-var key;
-var data = null;
-var allData =  new java.util.Hashtable ();
-var models =  new JU.Lst ();
-allData.put ("models", models);
-try {
-while ((key = this.getNextToken ()) != null) {
-if (key.startsWith ("global_") || key.startsWith ("data_")) {
-models.addLast (data =  new java.util.Hashtable ());
-data.put ("name", key);
-continue;
-}if (key.startsWith ("loop_")) {
-this.getAllCifLoopData (data);
-continue;
-}if (key.charAt (0) != '_') {
-System.out.println ("CIF ERROR ? should be an underscore: " + key);
-} else {
-var value = this.getNextToken ();
-if (value == null) {
-System.out.println ("CIF ERROR ? end of file; data missing: " + key);
-} else {
-data.put (this.fixKey (key), value);
-}}}
-} catch (e) {
-if (Clazz.exceptionOf (e, Exception)) {
-} else {
-throw e;
-}
-}
-try {
-if (this.br != null) this.br.close ();
-} catch (e) {
-if (Clazz.exceptionOf (e, Exception)) {
-} else {
-throw e;
-}
-}
-return allData;
-});
-Clazz.defineMethod (c$, "getAllCifLoopData", 
- function (data) {
-var key;
-var keyWords =  new JU.Lst ();
-while ((key = this.peekToken ()) != null && key.charAt (0) == '_') {
-key = this.fixKey (this.getTokenPeeked ());
-keyWords.addLast (key);
-data.put (key,  new JU.Lst ());
-}
-this.fieldCount = keyWords.size ();
-if (this.fieldCount == 0) return;
-this.loopData =  new Array (this.fieldCount);
-while (this.getData ()) for (var i = 0; i < this.fieldCount; i++) (data.get (keyWords.get (i))).addLast (this.loopData[i]);
-
-
-}, "java.util.Map");
-Clazz.overrideMethod (c$, "readLine", 
-function () {
-try {
-this.line = (this.reader == null ? this.br.readLine () : this.reader.readNextLine ());
-if (this.line == null) return null;
-if (this.isHeader) {
-if (this.line.startsWith ("#")) this.fileHeader.append (this.line).appendC ('\n');
- else this.isHeader = false;
-}return this.line;
-} catch (e) {
-if (Clazz.exceptionOf (e, Exception)) {
-return null;
-} else {
-throw e;
-}
-}
-});
-Clazz.overrideMethod (c$, "getData", 
-function () {
-for (var i = 0; i < this.fieldCount; ++i) if ((this.loopData[i] = this.getNextDataToken ()) == null) return false;
-
-return (this.fieldCount > 0);
-});
-Clazz.overrideMethod (c$, "skipLoop", 
-function () {
-var str;
-while ((str = this.peekToken ()) != null && str.charAt (0) == '_') this.getTokenPeeked ();
-
-while (this.getNextDataToken () != null) {
-}
-});
-Clazz.overrideMethod (c$, "getNextToken", 
-function () {
-while (!this.strHasMoreTokens ()) if (this.setStringNextLine () == null) return null;
-
-return this.nextStrToken ();
-});
-Clazz.overrideMethod (c$, "getNextDataToken", 
-function () {
-var str = this.peekToken ();
-if (str == null) return null;
-if (this.wasUnQuoted) if (str.charAt (0) == '_' || str.startsWith ("loop_") || str.startsWith ("data_") || str.startsWith ("stop_") || str.startsWith ("global_")) return null;
-return this.getTokenPeeked ();
-});
-Clazz.overrideMethod (c$, "peekToken", 
-function () {
-while (!this.strHasMoreTokens ()) if (this.setStringNextLine () == null) return null;
-
-var ich = this.ich;
-this.strPeeked = this.nextStrToken ();
-this.ichPeeked = this.ich;
-this.ich = ich;
-return this.strPeeked;
-});
-Clazz.overrideMethod (c$, "getTokenPeeked", 
-function () {
-this.ich = this.ichPeeked;
-return this.strPeeked;
-});
-Clazz.overrideMethod (c$, "fullTrim", 
-function (str) {
-var pt0 = -1;
-var pt1 = str.length;
-while (++pt0 < pt1 && JU.PT.isWhitespace (str.charAt (pt0))) {
-}
-while (--pt1 > pt0 && JU.PT.isWhitespace (str.charAt (pt1))) {
-}
-return str.substring (pt0, pt1 + 1);
-}, "~S");
-Clazz.overrideMethod (c$, "toUnicode", 
-function (data) {
-var pt;
-try {
-while ((pt = data.indexOf ('\\')) >= 0) {
-var c = data.charCodeAt (pt + 1);
-var ch = (c >= 65 && c <= 90 ? "ABX\u0394E\u03a6\u0393HI_K\u039bMNO\u03a0\u0398P\u03a3TY_\u03a9\u039e\u03a5Z".substring (c - 65, c - 64) : c >= 97 && c <= 122 ? "\u03b1\u03b2\u03c7\u03a4\u03a5\u03c6\u03b3\u03b7\u03b9_\u03ba\u03bb\u03bc\u03bd\u03bf\u03c0\u03b8\u03c1\u03c3\u03c4\u03c5_\u03c9\u03be\u03c5\u03b6".substring (c - 97, c - 96) : "_");
-data = data.substring (0, pt) + ch + data.substring (pt + 2);
-}
-} catch (e) {
-if (Clazz.exceptionOf (e, Exception)) {
-} else {
-throw e;
-}
-}
-return data;
-}, "~S");
-Clazz.overrideMethod (c$, "parseLoopParameters", 
-function (fields, fieldOf, propertyOf) {
-var propertyCount = 0;
-if (fields == null) {
-this.fields =  new Array (100);
-} else {
-if (!JU.CifDataParser.htFields.containsKey (fields[0])) for (var i = fields.length; --i >= 0; ) JU.CifDataParser.htFields.put (fields[i], Integer.$valueOf (i));
-
-for (var i = fields.length; --i >= 0; ) fieldOf[i] = -1;
-
-propertyCount = fields.length;
-}this.fieldCount = 0;
-while (true) {
-var str = this.peekToken ();
-if (str == null) {
-this.fieldCount = 0;
-break;
-}if (str.charAt (0) != '_') break;
-var pt = this.fieldCount++;
-str = this.fixKey (this.getTokenPeeked ());
-if (fields == null) {
-this.fields[propertyOf[pt] = fieldOf[pt] = pt] = str;
-continue;
-}var iField = JU.CifDataParser.htFields.get (str);
-var i = (iField == null ? -1 : iField.intValue ());
-if ((propertyOf[pt] = i) != -1) fieldOf[i] = pt;
-}
-if (this.fieldCount > 0) this.loopData =  new Array (this.fieldCount);
-return propertyCount;
-}, "~A,~A,~A");
-Clazz.overrideMethod (c$, "fixKey", 
-function (key) {
-return (JU.PT.rep (key.startsWith ("_magnetic") ? key.substring (9) : key.startsWith ("_jana") ? key.substring (5) : key, ".", "_").toLowerCase ());
-}, "~S");
-Clazz.defineMethod (c$, "setString", 
- function (str) {
-this.str = this.line = str;
-this.cch = (str == null ? 0 : str.length);
-this.ich = 0;
-}, "~S");
-Clazz.defineMethod (c$, "setStringNextLine", 
- function () {
-this.setString (this.readLine ());
-if (this.line == null || this.line.length == 0) return this.line;
-if (this.line.charAt (0) != ';') {
-if (this.str.startsWith ("###non-st#")) this.ich = 10;
-return this.line;
-}this.ich = 1;
-var str = '\1' + this.line.substring (1) + '\n';
-while (this.readLine () != null) {
-if (this.line.startsWith (";")) {
-str = str.substring (0, str.length - 1) + '\1' + this.line.substring (1);
-break;
-}str += this.line + '\n';
-}
-this.setString (str);
-return str;
-});
-Clazz.defineMethod (c$, "strHasMoreTokens", 
- function () {
-if (this.str == null) return false;
-var ch = '#';
-while (this.ich < this.cch && ((ch = this.str.charAt (this.ich)) == ' ' || ch == '\t')) ++this.ich;
-
-return (this.ich < this.cch && ch != '#');
-});
-Clazz.defineMethod (c$, "nextStrToken", 
- function () {
-if (this.ich == this.cch) return null;
-var ichStart = this.ich;
-var ch = this.str.charAt (ichStart);
-if (ch != '\'' && ch != '"' && ch != '\1') {
-this.wasUnQuoted = true;
-while (this.ich < this.cch && (ch = this.str.charAt (this.ich)) != ' ' && ch != '\t') ++this.ich;
-
-if (this.ich == ichStart + 1) if (this.nullString != null && (this.str.charAt (ichStart) == '.' || this.str.charAt (ichStart) == '?')) return this.nullString;
-var s = this.str.substring (ichStart, this.ich);
-return s;
-}this.wasUnQuoted = false;
-var chOpeningQuote = ch;
-var previousCharacterWasQuote = false;
-while (++this.ich < this.cch) {
-ch = this.str.charAt (this.ich);
-if (previousCharacterWasQuote && (ch == ' ' || ch == '\t')) break;
-previousCharacterWasQuote = (ch == chOpeningQuote);
-}
-if (this.ich == this.cch) {
-if (previousCharacterWasQuote) return this.str.substring (ichStart + 1, this.ich - 1);
-return this.str.substring (ichStart, this.ich);
-}++this.ich;
-return this.str.substring (ichStart + 1, this.ich - 2);
-});
-c$.htFields = c$.prototype.htFields =  new java.util.Hashtable ();
-Clazz.defineStatics (c$,
-"grABC", "ABX\u0394E\u03a6\u0393HI_K\u039bMNO\u03a0\u0398P\u03a3TY_\u03a9\u039e\u03a5Z",
-"grabc", "\u03b1\u03b2\u03c7\u03a4\u03a5\u03c6\u03b3\u03b7\u03b9_\u03ba\u03bb\u03bc\u03bd\u03bf\u03c0\u03b8\u03c1\u03c3\u03c4\u03c5_\u03c9\u03be\u03c5\u03b6");
-});
+Clazz.declarePackage ("JU");
+Clazz.load (["javajs.api.GenericCifDataParser", "java.util.Hashtable", "JU.SB"], "JU.CifDataParser", ["JU.Lst", "$.PT"], function () {
+c$ = Clazz.decorateAsClass (function () {
+this.reader = null;
+this.br = null;
+this.line = null;
+this.str = null;
+this.ich = 0;
+this.cch = 0;
+this.wasUnQuoted = false;
+this.strPeeked = null;
+this.ichPeeked = 0;
+this.fieldCount = 0;
+this.loopData = null;
+this.fileHeader = null;
+this.isHeader = true;
+this.nullString = "\0";
+this.fields = null;
+Clazz.instantialize (this, arguments);
+}, JU, "CifDataParser", null, javajs.api.GenericCifDataParser);
+Clazz.prepareFields (c$, function () {
+this.fileHeader =  new JU.SB ();
+});
+Clazz.defineMethod (c$, "setNullValue", 
+function (nullString) {
+this.nullString = nullString;
+}, "~S");
+Clazz.makeConstructor (c$, 
+function () {
+});
+Clazz.overrideMethod (c$, "getLoopData", 
+function (i) {
+return this.loopData[i];
+}, "~N");
+Clazz.overrideMethod (c$, "getFieldCount", 
+function () {
+return this.fieldCount;
+});
+Clazz.overrideMethod (c$, "getField", 
+function (i) {
+return this.fields[i];
+}, "~N");
+Clazz.overrideMethod (c$, "set", 
+function (reader, br) {
+this.reader = reader;
+this.br = br;
+return this;
+}, "javajs.api.GenericLineReader,java.io.BufferedReader");
+Clazz.overrideMethod (c$, "getFileHeader", 
+function () {
+return this.fileHeader.toString ();
+});
+Clazz.overrideMethod (c$, "getAllCifData", 
+function () {
+this.line = "";
+var key;
+var data = null;
+var allData =  new java.util.Hashtable ();
+var models =  new JU.Lst ();
+allData.put ("models", models);
+try {
+while ((key = this.getNextToken ()) != null) {
+if (key.startsWith ("global_") || key.startsWith ("data_")) {
+models.addLast (data =  new java.util.Hashtable ());
+data.put ("name", key);
+continue;
+}if (key.startsWith ("loop_")) {
+this.getAllCifLoopData (data);
+continue;
+}if (key.charAt (0) != '_') {
+System.out.println ("CIF ERROR ? should be an underscore: " + key);
+} else {
+var value = this.getNextToken ();
+if (value == null) {
+System.out.println ("CIF ERROR ? end of file; data missing: " + key);
+} else {
+data.put (this.fixKey (key), value);
+}}}
+} catch (e) {
+if (Clazz.exceptionOf (e, Exception)) {
+} else {
+throw e;
+}
+}
+try {
+if (this.br != null) this.br.close ();
+} catch (e) {
+if (Clazz.exceptionOf (e, Exception)) {
+} else {
+throw e;
+}
+}
+return allData;
+});
+Clazz.defineMethod (c$, "getAllCifLoopData", 
+ function (data) {
+var key;
+var keyWords =  new JU.Lst ();
+while ((key = this.peekToken ()) != null && key.charAt (0) == '_') {
+key = this.fixKey (this.getTokenPeeked ());
+keyWords.addLast (key);
+data.put (key,  new JU.Lst ());
+}
+this.fieldCount = keyWords.size ();
+if (this.fieldCount == 0) return;
+this.loopData =  new Array (this.fieldCount);
+while (this.getData ()) for (var i = 0; i < this.fieldCount; i++) (data.get (keyWords.get (i))).addLast (this.loopData[i]);
+
+
+}, "java.util.Map");
+Clazz.overrideMethod (c$, "readLine", 
+function () {
+try {
+this.line = (this.reader == null ? this.br.readLine () : this.reader.readNextLine ());
+if (this.line == null) return null;
+if (this.isHeader) {
+if (this.line.startsWith ("#")) this.fileHeader.append (this.line).appendC ('\n');
+ else this.isHeader = false;
+}return this.line;
+} catch (e) {
+if (Clazz.exceptionOf (e, Exception)) {
+return null;
+} else {
+throw e;
+}
+}
+});
+Clazz.overrideMethod (c$, "getData", 
+function () {
+for (var i = 0; i < this.fieldCount; ++i) if ((this.loopData[i] = this.getNextDataToken ()) == null) return false;
+
+return (this.fieldCount > 0);
+});
+Clazz.overrideMethod (c$, "skipLoop", 
+function () {
+var str;
+while ((str = this.peekToken ()) != null && str.charAt (0) == '_') this.getTokenPeeked ();
+
+while (this.getNextDataToken () != null) {
+}
+});
+Clazz.overrideMethod (c$, "getNextToken", 
+function () {
+while (!this.strHasMoreTokens ()) if (this.setStringNextLine () == null) return null;
+
+return this.nextStrToken ();
+});
+Clazz.overrideMethod (c$, "getNextDataToken", 
+function () {
+var str = this.peekToken ();
+if (str == null) return null;
+if (this.wasUnQuoted) if (str.charAt (0) == '_' || str.startsWith ("loop_") || str.startsWith ("data_") || str.startsWith ("stop_") || str.startsWith ("global_")) return null;
+return this.getTokenPeeked ();
+});
+Clazz.overrideMethod (c$, "peekToken", 
+function () {
+while (!this.strHasMoreTokens ()) if (this.setStringNextLine () == null) return null;
+
+var ich = this.ich;
+this.strPeeked = this.nextStrToken ();
+this.ichPeeked = this.ich;
+this.ich = ich;
+return this.strPeeked;
+});
+Clazz.overrideMethod (c$, "getTokenPeeked", 
+function () {
+this.ich = this.ichPeeked;
+return this.strPeeked;
+});
+Clazz.overrideMethod (c$, "fullTrim", 
+function (str) {
+var pt0 = -1;
+var pt1 = str.length;
+while (++pt0 < pt1 && JU.PT.isWhitespace (str.charAt (pt0))) {
+}
+while (--pt1 > pt0 && JU.PT.isWhitespace (str.charAt (pt1))) {
+}
+return str.substring (pt0, pt1 + 1);
+}, "~S");
+Clazz.overrideMethod (c$, "toUnicode", 
+function (data) {
+var pt;
+try {
+while ((pt = data.indexOf ('\\')) >= 0) {
+var c = data.charCodeAt (pt + 1);
+var ch = (c >= 65 && c <= 90 ? "ABX\u0394E\u03a6\u0393HI_K\u039bMNO\u03a0\u0398P\u03a3TY_\u03a9\u039e\u03a5Z".substring (c - 65, c - 64) : c >= 97 && c <= 122 ? "\u03b1\u03b2\u03c7\u03a4\u03a5\u03c6\u03b3\u03b7\u03b9_\u03ba\u03bb\u03bc\u03bd\u03bf\u03c0\u03b8\u03c1\u03c3\u03c4\u03c5_\u03c9\u03be\u03c5\u03b6".substring (c - 97, c - 96) : "_");
+data = data.substring (0, pt) + ch + data.substring (pt + 2);
+}
+} catch (e) {
+if (Clazz.exceptionOf (e, Exception)) {
+} else {
+throw e;
+}
+}
+return data;
+}, "~S");
+Clazz.overrideMethod (c$, "parseLoopParameters", 
+function (fields, fieldOf, propertyOf) {
+var propertyCount = 0;
+if (fields == null) {
+this.fields =  new Array (100);
+} else {
+if (!JU.CifDataParser.htFields.containsKey (fields[0])) for (var i = fields.length; --i >= 0; ) JU.CifDataParser.htFields.put (fields[i], Integer.$valueOf (i));
+
+for (var i = fields.length; --i >= 0; ) fieldOf[i] = -1;
+
+propertyCount = fields.length;
+}this.fieldCount = 0;
+while (true) {
+var str = this.peekToken ();
+if (str == null) {
+this.fieldCount = 0;
+break;
+}if (str.charAt (0) != '_') break;
+var pt = this.fieldCount++;
+str = this.fixKey (this.getTokenPeeked ());
+if (fields == null) {
+this.fields[propertyOf[pt] = fieldOf[pt] = pt] = str;
+continue;
+}var iField = JU.CifDataParser.htFields.get (str);
+var i = (iField == null ? -1 : iField.intValue ());
+if ((propertyOf[pt] = i) != -1) fieldOf[i] = pt;
+}
+if (this.fieldCount > 0) this.loopData =  new Array (this.fieldCount);
+return propertyCount;
+}, "~A,~A,~A");
+Clazz.overrideMethod (c$, "fixKey", 
+function (key) {
+return (JU.PT.rep (key.startsWith ("_magnetic") ? key.substring (9) : key.startsWith ("_jana") ? key.substring (5) : key, ".", "_").toLowerCase ());
+}, "~S");
+Clazz.defineMethod (c$, "setString", 
+ function (str) {
+this.str = this.line = str;
+this.cch = (str == null ? 0 : str.length);
+this.ich = 0;
+}, "~S");
+Clazz.defineMethod (c$, "setStringNextLine", 
+ function () {
+this.setString (this.readLine ());
+if (this.line == null || this.line.length == 0) return this.line;
+if (this.line.charAt (0) != ';') {
+if (this.str.startsWith ("###non-st#")) this.ich = 10;
+return this.line;
+}this.ich = 1;
+var str = '\1' + this.line.substring (1) + '\n';
+while (this.readLine () != null) {
+if (this.line.startsWith (";")) {
+str = str.substring (0, str.length - 1) + '\1' + this.line.substring (1);
+break;
+}str += this.line + '\n';
+}
+this.setString (str);
+return str;
+});
+Clazz.defineMethod (c$, "strHasMoreTokens", 
+ function () {
+if (this.str == null) return false;
+var ch = '#';
+while (this.ich < this.cch && ((ch = this.str.charAt (this.ich)) == ' ' || ch == '\t')) ++this.ich;
+
+return (this.ich < this.cch && ch != '#');
+});
+Clazz.defineMethod (c$, "nextStrToken", 
+ function () {
+if (this.ich == this.cch) return null;
+var ichStart = this.ich;
+var ch = this.str.charAt (ichStart);
+if (ch != '\'' && ch != '"' && ch != '\1') {
+this.wasUnQuoted = true;
+while (this.ich < this.cch && (ch = this.str.charAt (this.ich)) != ' ' && ch != '\t') ++this.ich;
+
+if (this.ich == ichStart + 1) if (this.nullString != null && (this.str.charAt (ichStart) == '.' || this.str.charAt (ichStart) == '?')) return this.nullString;
+var s = this.str.substring (ichStart, this.ich);
+return s;
+}this.wasUnQuoted = false;
+var chOpeningQuote = ch;
+var previousCharacterWasQuote = false;
+while (++this.ich < this.cch) {
+ch = this.str.charAt (this.ich);
+if (previousCharacterWasQuote && (ch == ' ' || ch == '\t')) break;
+previousCharacterWasQuote = (ch == chOpeningQuote);
+}
+if (this.ich == this.cch) {
+if (previousCharacterWasQuote) return this.str.substring (ichStart + 1, this.ich - 1);
+return this.str.substring (ichStart, this.ich);
+}++this.ich;
+return this.str.substring (ichStart + 1, this.ich - 2);
+});
+c$.htFields = c$.prototype.htFields =  new java.util.Hashtable ();
+Clazz.defineStatics (c$,
+"grABC", "ABX\u0394E\u03a6\u0393HI_K\u039bMNO\u03a0\u0398P\u03a3TY_\u03a9\u039e\u03a5Z",
+"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");
+});