http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/4231ac35/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gscfa/GSCFaLexer.java ---------------------------------------------------------------------- diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gscfa/GSCFaLexer.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gscfa/GSCFaLexer.java new file mode 100644 index 0000000..02a4ced --- /dev/null +++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gscfa/GSCFaLexer.java @@ -0,0 +1,790 @@ +/* +* +* Licensed to the Apache Software Foundation (ASF) under one +* or more contributor license agreements. See the NOTICE file +* distributed with this work for additional information +* regarding copyright ownership. The ASF licenses this file +* to you under the Apache License, Version 2.0 (the +* "License"); you may not use this file except in compliance +* with the License. You may obtain a copy of the License at +* +* http://www.apache.org/licenses/LICENSE-2.0 +* +* Unless required by applicable law or agreed to in writing, +* software distributed under the License is distributed on an +* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY +* KIND, either express or implied. See the License for the +* specific language governing permissions and limitations +* under the License. +* +*/ +package org.apache.airavata.datacat.parsers.gridchem.gscfa;/* The following code was generated by JFlex 1.4.3 on 9/11/14 6:08 PM */ + +import java_cup.runtime.Symbol; +import org.apache.airavata.datacat.parsers.gridchem.Settings; + + +/** + * This class is a scanner generated by + * <a href="http://www.jflex.de/";>JFlex</a> 1.4.3 + * on 9/11/14 6:08 PM from the specification file + * <tt>gscfa.flex</tt> + */ +public class GSCFaLexer implements java_cup.runtime.Scanner { + + /** This character denotes the end of file */ + public static final int YYEOF = -1; + + /** initial size of the lookahead buffer */ + private static final int ZZ_BUFFERSIZE = 16384; + + /** lexical states */ + public static final int ITER2 = 6; + public static final int DASH = 10; + public static final int INTVALUE = 12; + public static final int SCF1 = 2; + public static final int IGNOREALL = 24; + public static final int ITER = 4; + public static final int YYINITIAL = 0; + public static final int ITER7 = 22; + public static final int ITER6 = 20; + public static final int ITER5 = 18; + public static final int FLOATVALUE = 14; + public static final int ITER4 = 16; + public static final int ITER3 = 8; + + /** + * ZZ_LEXSTATE[l] is the state in the DFA for the lexical state l + * ZZ_LEXSTATE[l+1] is the state in the DFA for the lexical state l + * at the beginning of a line + * l is of the form l = 2*k, k a non negative integer + */ + private static final int ZZ_LEXSTATE[] = { + 0, 0, 1, 1, 2, 2, 3, 3, 4, 4, 5, 5, 1, 1, 6, 6, + 7, 7, 8, 8, 9, 9, 10, 10, 1, 1 + }; + + /** + * Translates characters to character classes + */ + private static final char [] ZZ_CMAP = { + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 9, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 3, 0, 23, 4, 0, + 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 0, 0, 0, 0, 0, + 0, 14, 22, 19, 11, 7, 0, 17, 20, 5, 0, 0, 15, 12, 16, 13, + 0, 0, 8, 21, 6, 0, 24, 0, 10, 18, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 3, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 + }; + + /** + * Translates DFA states to action switch labels. + */ + private static final int [] ZZ_ACTION = zzUnpackAction(); + + private static final String ZZ_ACTION_PACKED_0 = + "\13\0\2\1\2\2\1\1\2\3\2\4\1\1\3\5"+ + "\10\1\3\0\1\6\15\0\1\7\1\10\1\11\1\12"+ + "\65\0\1\13\1\14\1\15\77\0\1\16\1\17"; + + private static int [] zzUnpackAction() { + int [] result = new int[174]; + int offset = 0; + offset = zzUnpackAction(ZZ_ACTION_PACKED_0, offset, result); + return result; + } + + private static int zzUnpackAction(String packed, int offset, int [] result) { + int i = 0; /* index in packed string */ + int j = offset; /* index in unpacked array */ + int l = packed.length(); + while (i < l) { + int count = packed.charAt(i++); + int value = packed.charAt(i++); + do result[j++] = value; while (--count > 0); + } + return j; + } + + + /** + * Translates a state to a row index in the transition table + */ + private static final int [] ZZ_ROWMAP = zzUnpackRowMap(); + + private static final String ZZ_ROWMAP_PACKED_0 = + "\0\0\0\31\0\62\0\113\0\144\0\175\0\226\0\257"+ + "\0\310\0\341\0\372\0\u0113\0\u012c\0\u0113\0\u0145\0\u015e"+ + "\0\u0113\0\u0177\0\u0113\0\u0190\0\u01a9\0\u0113\0\u01c2\0\u01db"+ + "\0\u01f4\0\u020d\0\u0226\0\u023f\0\u0258\0\u0271\0\u028a\0\u02a3"+ + "\0\u02bc\0\u02d5\0\u02ee\0\u01c2\0\u0307\0\u01f4\0\u0320\0\u0226"+ + "\0\u0339\0\u0258\0\u0352\0\u028a\0\u036b\0\u0384\0\u039d\0\u03b6"+ + "\0\u03cf\0\u0320\0\u0339\0\u0352\0\u036b\0\u03e8\0\u0401\0\u041a"+ + "\0\u0433\0\u044c\0\u0465\0\u047e\0\u0497\0\u04b0\0\u04c9\0\u04e2"+ + "\0\u04fb\0\u0514\0\u052d\0\u0546\0\u055f\0\u0578\0\u0591\0\u05aa"+ + "\0\u05c3\0\u05dc\0\u05f5\0\u060e\0\u0627\0\u0640\0\u0659\0\u0672"+ + "\0\u068b\0\u06a4\0\u06bd\0\u06d6\0\u06ef\0\u0708\0\u0721\0\u073a"+ + "\0\u0753\0\u076c\0\u0785\0\u079e\0\u07b7\0\u07d0\0\u07e9\0\u0802"+ + "\0\u081b\0\u0834\0\u084d\0\u0866\0\u087f\0\u0898\0\u08b1\0\u08ca"+ + "\0\u08e3\0\u08fc\0\u0113\0\u0113\0\u0113\0\u0915\0\u092e\0\u0947"+ + "\0\u0960\0\u0979\0\u0992\0\u09ab\0\u09c4\0\u09dd\0\u09f6\0\u0a0f"+ + "\0\u0a28\0\u0a41\0\u0a5a\0\u0a73\0\u0a8c\0\u0aa5\0\u0abe\0\u0ad7"+ + "\0\u0af0\0\u0b09\0\u0b22\0\u0b3b\0\u0b54\0\u0b6d\0\u0b86\0\u0b9f"+ + "\0\u0bb8\0\u0bd1\0\u0bea\0\u0c03\0\u0c1c\0\u0c35\0\u0c4e\0\u0c67"+ + "\0\u0c80\0\u0c99\0\u0cb2\0\u0ccb\0\u0ce4\0\u0cfd\0\u0d16\0\u0d2f"+ + "\0\u0d48\0\u0d61\0\u0d7a\0\u0d93\0\u0dac\0\u0dc5\0\u0dde\0\u0df7"+ + "\0\u0e10\0\u0e29\0\u0e42\0\u0e5b\0\u0e74\0\u0e8d\0\u0ea6\0\u0ebf"+ + "\0\u0ed8\0\u0ef1\0\u0f0a\0\u0f23\0\u0113\0\u0113"; + + private static int [] zzUnpackRowMap() { + int [] result = new int[174]; + int offset = 0; + offset = zzUnpackRowMap(ZZ_ROWMAP_PACKED_0, offset, result); + return result; + } + + private static int zzUnpackRowMap(String packed, int offset, int [] result) { + int i = 0; /* index in packed string */ + int j = offset; /* index in unpacked array */ + int l = packed.length(); + while (i < l) { + int high = packed.charAt(i++) << 16; + result[j++] = high | packed.charAt(i++); + } + return j; + } + + /** + * The transition table of the DFA + */ + private static final int [] ZZ_TRANS = zzUnpackTrans(); + + private static final String ZZ_TRANS_PACKED_0 = + "\5\14\1\15\55\14\1\16\1\17\24\14\1\20\2\14"+ + "\1\21\1\22\27\14\1\23\1\24\41\14\1\25\15\14"+ + "\1\26\3\27\23\26\1\30\1\26\1\14\2\31\1\32"+ + "\23\14\1\32\2\14\2\33\1\34\23\14\1\34\2\14"+ + "\2\35\1\36\23\14\1\36\2\14\2\37\1\40\23\14"+ + "\1\40\1\14\37\0\1\41\23\0\2\17\55\0\1\42"+ + "\2\0\2\22\27\0\2\24\35\0\1\43\22\0\2\44"+ + "\27\0\2\44\24\0\1\45\2\0\2\46\1\0\1\47"+ + "\25\0\2\46\27\0\2\50\1\0\1\51\25\0\2\50"+ + "\27\0\2\52\1\0\1\53\25\0\2\52\27\0\2\54"+ + "\1\0\1\55\25\0\2\54\35\0\1\56\50\0\1\57"+ + "\21\0\1\60\37\0\1\61\2\0\2\62\27\0\2\63"+ + "\27\0\2\64\27\0\2\65\36\0\1\66\47\0\1\67"+ + "\26\0\1\70\32\0\1\71\12\0\1\72\46\0\1\73"+ + "\6\0\1\74\52\0\1\75\10\0\1\76\50\0\1\77"+ + "\7\0\1\100\51\0\1\101\13\0\1\102\45\0\1\103"+ + "\23\0\1\104\35\0\1\105\12\0\1\106\46\0\1\107"+ + "\12\0\1\110\46\0\1\111\14\0\1\112\44\0\1\113"+ + "\24\0\1\114\34\0\1\115\10\0\1\116\50\0\1\117"+ + "\16\0\1\120\42\0\1\121\15\0\1\122\43\0\1\123"+ + "\21\0\1\124\37\0\1\125\12\0\1\126\46\0\1\127"+ + "\31\0\1\130\27\0\1\131\12\0\1\132\46\0\1\133"+ + "\10\0\1\134\50\0\1\135\12\0\1\136\46\0\1\137"+ + "\11\0\1\140\47\0\1\141\12\0\1\142\46\0\1\143"+ + "\22\0\1\144\36\0\1\145\7\0\1\146\51\0\1\147"+ + "\10\0\1\150\50\0\1\151\16\0\1\152\42\0\1\153"+ + "\14\0\1\154\44\0\1\155\7\0\1\156\40\0\1\157"+ + "\31\0\1\160\22\0\1\161\26\0\1\162\41\0\1\163"+ + "\17\0\1\164\31\0\1\165\41\0\1\166\31\0\1\167"+ + "\17\0\1\170\30\0\1\171\30\0\1\172\30\0\1\173"+ + "\30\0\1\174\30\0\1\175\30\0\1\176\26\0\1\177"+ + "\32\0\1\200\42\0\1\201\31\0\1\202\22\0\1\203"+ + "\32\0\1\204\31\0\1\205\16\0\1\206\32\0\1\207"+ + "\30\0\1\210\32\0\1\211\24\0\1\212\41\0\1\213"+ + "\35\0\1\214\10\0\1\215\31\0\1\216\44\0\1\217"+ + "\17\0\1\220\42\0\1\221\31\0\1\222\22\0\1\223"+ + "\32\0\1\224\31\0\1\225\16\0\1\226\32\0\1\227"+ + "\30\0\1\230\30\0\1\231\30\0\1\232\30\0\1\233"+ + "\1\0\1\234\32\0\1\235\20\0\1\236\33\0\1\237"+ + "\25\0\1\240\51\0\1\241\27\0\1\242\7\0\1\243"+ + "\35\0\1\244\30\0\1\245\26\0\1\246\42\0\1\247"+ + "\17\0\1\250\30\0\1\251\30\0\1\252\36\0\1\253"+ + "\27\0\1\254\26\0\1\255\25\0\1\256\20\0"; + + private static int [] zzUnpackTrans() { + int [] result = new int[3900]; + int offset = 0; + offset = zzUnpackTrans(ZZ_TRANS_PACKED_0, offset, result); + return result; + } + + private static int zzUnpackTrans(String packed, int offset, int [] result) { + int i = 0; /* index in packed string */ + int j = offset; /* index in unpacked array */ + int l = packed.length(); + while (i < l) { + int count = packed.charAt(i++); + int value = packed.charAt(i++); + value--; + do result[j++] = value; while (--count > 0); + } + return j; + } + + + /* error codes */ + private static final int ZZ_UNKNOWN_ERROR = 0; + private static final int ZZ_NO_MATCH = 1; + private static final int ZZ_PUSHBACK_2BIG = 2; + + /* error messages for the codes above */ + private static final String ZZ_ERROR_MSG[] = { + "Unkown internal scanner error", + "Error: could not match input", + "Error: pushback value was too large" + }; + + /** + * ZZ_ATTRIBUTE[aState] contains the attributes of state <code>aState</code> + */ + private static final int [] ZZ_ATTRIBUTE = zzUnpackAttribute(); + + private static final String ZZ_ATTRIBUTE_PACKED_0 = + "\13\0\1\11\1\1\1\11\2\1\1\11\1\1\1\11"+ + "\2\1\1\11\12\1\3\0\1\1\15\0\4\1\65\0"+ + "\3\11\77\0\2\11"; + + private static int [] zzUnpackAttribute() { + int [] result = new int[174]; + int offset = 0; + offset = zzUnpackAttribute(ZZ_ATTRIBUTE_PACKED_0, offset, result); + return result; + } + + private static int zzUnpackAttribute(String packed, int offset, int [] result) { + int i = 0; /* index in packed string */ + int j = offset; /* index in unpacked array */ + int l = packed.length(); + while (i < l) { + int count = packed.charAt(i++); + int value = packed.charAt(i++); + do result[j++] = value; while (--count > 0); + } + return j; + } + + /** the input device */ + private java.io.Reader zzReader; + + /** the current state of the DFA */ + private int zzState; + + /** the current lexical state */ + private int zzLexicalState = YYINITIAL; + + /** this buffer contains the current text to be matched and is + the source of the yytext() string */ + private char zzBuffer[] = new char[ZZ_BUFFERSIZE]; + + /** the textposition at the last accepting state */ + private int zzMarkedPos; + + /** the current text position in the buffer */ + private int zzCurrentPos; + + /** startRead marks the beginning of the yytext() string in the buffer */ + private int zzStartRead; + + /** endRead marks the last character in the buffer, that has been read + from input */ + private int zzEndRead; + + /** number of newlines encountered up to the start of the matched text */ + private int yyline; + + /** the number of characters up to the start of the matched text */ + private int yychar; + + /** + * the number of characters from the last newline up to the start of the + * matched text + */ + private int yycolumn; + + /** + * zzAtBOL == true <=> the scanner is currently at the beginning of a line + */ + private boolean zzAtBOL = true; + + /** zzAtEOF == true <=> the scanner is at the EOF */ + private boolean zzAtEOF; + + /** denotes if the user-EOF-code has already been executed */ + private boolean zzEOFDone; + + /* user code: */ + public static boolean DEBUG = false; + + + /** + * Creates a new scanner + * There is also a java.io.InputStream version of this constructor. + * + * @param in the java.io.Reader to read input from. + */ + public GSCFaLexer(java.io.Reader in) { + this.zzReader = in; + } + + /** + * Creates a new scanner. + * There is also java.io.Reader version of this constructor. + * + * @param in the java.io.Inputstream to read input from. + */ + public GSCFaLexer(java.io.InputStream in) { + this(new java.io.InputStreamReader(in)); + } + + + /** + * Refills the input buffer. + * + * @return <code>false</code>, iff there was new input. + * + * @exception java.io.IOException if any I/O-Error occurs + */ + private boolean zzRefill() throws java.io.IOException { + + /* first: make room (if you can) */ + if (zzStartRead > 0) { + System.arraycopy(zzBuffer, zzStartRead, + zzBuffer, 0, + zzEndRead-zzStartRead); + + /* translate stored positions */ + zzEndRead-= zzStartRead; + zzCurrentPos-= zzStartRead; + zzMarkedPos-= zzStartRead; + zzStartRead = 0; + } + + /* is the buffer big enough? */ + if (zzCurrentPos >= zzBuffer.length) { + /* if not: blow it up */ + char newBuffer[] = new char[zzCurrentPos*2]; + System.arraycopy(zzBuffer, 0, newBuffer, 0, zzBuffer.length); + zzBuffer = newBuffer; + } + + /* finally: fill the buffer with new input */ + int numRead = zzReader.read(zzBuffer, zzEndRead, + zzBuffer.length-zzEndRead); + + if (numRead > 0) { + zzEndRead+= numRead; + return false; + } + // unlikely but not impossible: read 0 characters, but not at end of stream + if (numRead == 0) { + int c = zzReader.read(); + if (c == -1) { + return true; + } else { + zzBuffer[zzEndRead++] = (char) c; + return false; + } + } + + // numRead < 0 + return true; + } + + + /** + * Closes the input stream. + */ + public final void yyclose() throws java.io.IOException { + zzAtEOF = true; /* indicate end of file */ + zzEndRead = zzStartRead; /* invalidate buffer */ + + if (zzReader != null) + zzReader.close(); + } + + + /** + * Resets the scanner to read from a new input stream. + * Does not close the old reader. + * + * All internal variables are reset, the old input stream + * <b>cannot</b> be reused (internal buffer is discarded and lost). + * Lexical state is set to <tt>ZZ_INITIAL</tt>. + * + * @param reader the new input stream + */ + public final void yyreset(java.io.Reader reader) { + zzReader = reader; + zzAtBOL = true; + zzAtEOF = false; + zzEOFDone = false; + zzEndRead = zzStartRead = 0; + zzCurrentPos = zzMarkedPos = 0; + yyline = yychar = yycolumn = 0; + zzLexicalState = YYINITIAL; + } + + + /** + * Returns the current lexical state. + */ + public final int yystate() { + return zzLexicalState; + } + + + /** + * Enters a new lexical state + * + * @param newState the new lexical state + */ + public final void yybegin(int newState) { + zzLexicalState = newState; + } + + + /** + * Returns the text matched by the current regular expression. + */ + public final String yytext() { + return new String( zzBuffer, zzStartRead, zzMarkedPos-zzStartRead ); + } + + + /** + * Returns the character at position <tt>pos</tt> from the + * matched text. + * + * It is equivalent to yytext().charAt(pos), but faster + * + * @param pos the position of the character to fetch. + * A value from 0 to yylength()-1. + * + * @return the character at position pos + */ + public final char yycharat(int pos) { + return zzBuffer[zzStartRead+pos]; + } + + + /** + * Returns the length of the matched text region. + */ + public final int yylength() { + return zzMarkedPos-zzStartRead; + } + + + /** + * Reports an error that occured while scanning. + * + * In a wellformed scanner (no or only correct usage of + * yypushback(int) and a match-all fallback rule) this method + * will only be called with things that "Can't Possibly Happen". + * If this method is called, something is seriously wrong + * (e.g. a JFlex bug producing a faulty scanner etc.). + * + * Usual syntax/scanner level error handling should be done + * in error fallback rules. + * + * @param errorCode the code of the errormessage to display + */ + private void zzScanError(int errorCode) { + String message; + try { + message = ZZ_ERROR_MSG[errorCode]; + } + catch (ArrayIndexOutOfBoundsException e) { + message = ZZ_ERROR_MSG[ZZ_UNKNOWN_ERROR]; + } + + throw new Error(message); + } + + + /** + * Pushes the specified amount of characters back into the input stream. + * + * They will be read again by then next call of the scanning method + * + * @param number the number of characters to be read again. + * This number must not be greater than yylength()! + */ + public void yypushback(int number) { + if ( number > yylength() ) + zzScanError(ZZ_PUSHBACK_2BIG); + + zzMarkedPos -= number; + } + + + /** + * Contains user EOF-code, which will be executed exactly once, + * when the end of file is reached + */ + private void zzDoEOF() throws java.io.IOException { + if (!zzEOFDone) { + zzEOFDone = true; + yyclose(); + } + } + + + /** + * Resumes scanning until the next regular expression is matched, + * the end of input is encountered or an I/O-Error occurs. + * + * @return the next token + * @exception java.io.IOException if any I/O-Error occurs + */ + public java_cup.runtime.Symbol next_token() throws java.io.IOException { + int zzInput; + int zzAction; + + // cached fields: + int zzCurrentPosL; + int zzMarkedPosL; + int zzEndReadL = zzEndRead; + char [] zzBufferL = zzBuffer; + char [] zzCMapL = ZZ_CMAP; + + int [] zzTransL = ZZ_TRANS; + int [] zzRowMapL = ZZ_ROWMAP; + int [] zzAttrL = ZZ_ATTRIBUTE; + + while (true) { + zzMarkedPosL = zzMarkedPos; + + zzAction = -1; + + zzCurrentPosL = zzCurrentPos = zzStartRead = zzMarkedPosL; + + zzState = ZZ_LEXSTATE[zzLexicalState]; + + + zzForAction: { + while (true) { + + if (zzCurrentPosL < zzEndReadL) + zzInput = zzBufferL[zzCurrentPosL++]; + else if (zzAtEOF) { + zzInput = YYEOF; + break zzForAction; + } + else { + // store back cached positions + zzCurrentPos = zzCurrentPosL; + zzMarkedPos = zzMarkedPosL; + boolean eof = zzRefill(); + // get translated positions and possibly new buffer + zzCurrentPosL = zzCurrentPos; + zzMarkedPosL = zzMarkedPos; + zzBufferL = zzBuffer; + zzEndReadL = zzEndRead; + if (eof) { + zzInput = YYEOF; + break zzForAction; + } + else { + zzInput = zzBufferL[zzCurrentPosL++]; + } + } + int zzNext = zzTransL[ zzRowMapL[zzState] + zzCMapL[zzInput] ]; + if (zzNext == -1) break zzForAction; + zzState = zzNext; + + int zzAttributes = zzAttrL[zzState]; + if ( (zzAttributes & 1) == 1 ) { + zzAction = zzState; + zzMarkedPosL = zzCurrentPosL; + if ( (zzAttributes & 8) == 8 ) break zzForAction; + } + + } + } + + // store back cached position + zzMarkedPos = zzMarkedPosL; + + switch (zzAction < 0 ? zzAction : ZZ_ACTION[zzAction]) { + case 11: + { if (Settings.DEBUG) System.out.println("GSCFaFlex: Found the dash"); + yybegin(DASH); + } + case 16: break; + case 13: + { yybegin(DASH); + } + case 17: break; + case 4: + { if (Settings.DEBUG) System.out.println("GSCFaFlex: Found the third integer in the iteration"); + if (Settings.DEBUG) System.out.println(yytext()); + yybegin(ITER4); + return new Symbol(GSCFaSym.INT2, new Integer(yytext())); + } + case 18: break; + case 3: + { if (Settings.DEBUG) System.out.println("GSCFaFlex: Found the second integer in the iteration"); + if (Settings.DEBUG) System.out.println(yytext()); + yybegin(ITER3); + return new Symbol(GSCFaSym.INT1, new Integer(yytext())); + } + case 19: break; + case 14: + { if (Settings.DEBUG) System.out.println("GSCFaFlex: Found ITER EX DEM etc"); + yybegin(ITER); + return new Symbol(GSCFaSym.FOUNDITER); + } + case 20: break; + case 2: + { if (Settings.DEBUG) System.out.println("GSCFaFlex: Found the first integer in the iteration"); + if (Settings.DEBUG) System.out.println(yytext()); + yybegin(ITER2); + return new Symbol(GSCFaSym.INTCycle, new Integer(yytext())); + } + case 21: break; + case 9: + { if (Settings.DEBUG) System.out.println("GSCFaFlex: Found float2"); + yybegin (ITER7); + return new Symbol(GSCFaSym.FLOAT2); + } + case 22: break; + case 7: + { if (Settings.DEBUG) System.out.println("GSCFaFlex: Found the energy"); + if (Settings.DEBUG) System.out.println(yytext()); + yybegin(ITER5); + return new Symbol(GSCFaSym.ENERGY, new Float(yytext())); + } + case 23: break; + case 5: + { if (Settings.DEBUG) System.out.println("GSCFaFlex: Found new line"); + } + case 24: break; + case 12: + { yybegin(IGNOREALL); + return new Symbol(GSCFaSym.SCFDONE); + } + case 25: break; + case 8: + { if (Settings.DEBUG) System.out.println("GSCFaFlex: ITER5"); + if (Settings.DEBUG) System.out.println("GSCFaFlex: Found float1"); + yybegin (ITER6); + return new Symbol(GSCFaSym.FLOAT1); + } + case 26: break; + case 6: + { if (Settings.DEBUG) System.out.println("GSCFaFlex: Found float value"); + yybegin(ITER); + } + case 27: break; + case 15: + { if (Settings.DEBUG) System.out.println("GSCFaFlex: Found ITER EX DEM etc"); + yybegin(ITER); + return new Symbol(GSCFaSym.FOUNDITER); + } + case 28: break; + case 10: + { if (Settings.DEBUG) System.out.println("GSCFaFlex: Found float3"); + yybegin(ITER); + return new Symbol(GSCFaSym.FLOAT3); + } + case 29: break; + case 1: + { + } + case 30: break; + default: + if (zzInput == YYEOF && zzStartRead == zzCurrentPos) { + zzAtEOF = true; + zzDoEOF(); + { return new java_cup.runtime.Symbol(GSCFaSym.EOF); } + } + else { + zzScanError(ZZ_NO_MATCH); + } + } + } + } + + /** + * Converts an int token code into the name of the + * token by reflection on the cup symbol class/interface sym + * + * This code was contributed by Karl Meissner <[email protected]> + */ + private String getTokenName(int token) { + try { + java.lang.reflect.Field [] classFields = GSCFaSym.class.getFields(); + for (int i = 0; i < classFields.length; i++) { + if (classFields[i].getInt(null) == token) { + return classFields[i].getName(); + } + } + } catch (Exception e) { + e.printStackTrace(System.err); + } + + return "UNKNOWN TOKEN"; + } + + /** + * Same as next_token but also prints the token to standard out + * for debugging. + * + * This code was contributed by Karl Meissner <[email protected]> + */ + public java_cup.runtime.Symbol debug_next_token() throws java.io.IOException { + java_cup.runtime.Symbol s = next_token(); + System.out.println( " --"+ yytext() + "--" + getTokenName(s.sym) + "--"); + return s; + } + + /** + * Runs the scanner on input files. + * + * This is a standalone scanner, it will print any unmatched + * text to System.out unchanged. + * + * @param argv the command line, contains the filenames to run + * the scanner on. + */ + public static void main(String argv[]) { + if (argv.length == 0) { + System.out.println("Usage : java GSCFaLexer <inputfile>"); + } + else { + for (int i = 0; i < argv.length; i++) { + GSCFaLexer scanner = null; + try { + scanner = new GSCFaLexer( new java.io.FileReader(argv[i]) ); + while ( !scanner.zzAtEOF ) scanner.next_token(); + } + catch (java.io.FileNotFoundException e) { + System.out.println("File not found : \""+argv[i]+"\""); + } + catch (java.io.IOException e) { + System.out.println("IO error scanning file \""+argv[i]+"\""); + System.out.println(e); + } + catch (Exception e) { + System.out.println("Unexpected exception:"); + e.printStackTrace(); + } + } + } + } + + +}
http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/4231ac35/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gscfa/GSCFaSym.java ---------------------------------------------------------------------- diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gscfa/GSCFaSym.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gscfa/GSCFaSym.java new file mode 100644 index 0000000..9ae3a32 --- /dev/null +++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gscfa/GSCFaSym.java @@ -0,0 +1,44 @@ +/* +* +* Licensed to the Apache Software Foundation (ASF) under one +* or more contributor license agreements. See the NOTICE file +* distributed with this work for additional information +* regarding copyright ownership. The ASF licenses this file +* to you under the Apache License, Version 2.0 (the +* "License"); you may not use this file except in compliance +* with the License. You may obtain a copy of the License at +* +* http://www.apache.org/licenses/LICENSE-2.0 +* +* Unless required by applicable law or agreed to in writing, +* software distributed under the License is distributed on an +* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY +* KIND, either express or implied. See the License for the +* specific language governing permissions and limitations +* under the License. +* +*/ +package org.apache.airavata.datacat.parsers.gridchem.gscfa; +//---------------------------------------------------- +// The following code was generated by CUP v0.10k +// Thu Sep 11 18:08:50 IST 2014 +//---------------------------------------------------- + +/** CUP generated class containing symbol constants. */ +public class GSCFaSym { + /* terminals */ + public static final int INTCycle = 7; + public static final int ENERGY = 12; + public static final int EOF = 0; + public static final int INT3 = 6; + public static final int INT2 = 5; + public static final int INT1 = 4; + public static final int error = 1; + public static final int FLOAT3 = 11; + public static final int FLOAT2 = 10; + public static final int SCFDONE = 3; + public static final int FLOAT1 = 9; + public static final int FOUNDITER = 2; + public static final int FLOAT = 8; +} + http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/4231ac35/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gscfa/GscfaParser.java ---------------------------------------------------------------------- diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gscfa/GscfaParser.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gscfa/GscfaParser.java new file mode 100644 index 0000000..900a0cd --- /dev/null +++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gscfa/GscfaParser.java @@ -0,0 +1,336 @@ +/* +* +* Licensed to the Apache Software Foundation (ASF) under one +* or more contributor license agreements. See the NOTICE file +* distributed with this work for additional information +* regarding copyright ownership. The ASF licenses this file +* to you under the Apache License, Version 2.0 (the +* "License"); you may not use this file except in compliance +* with the License. You may obtain a copy of the License at +* +* http://www.apache.org/licenses/LICENSE-2.0 +* +* Unless required by applicable law or agreed to in writing, +* software distributed under the License is distributed on an +* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY +* KIND, either express or implied. See the License for the +* specific language governing permissions and limitations +* under the License. +* +*/ +package org.apache.airavata.datacat.parsers.gridchem.gscfa; + + +import java_cup.runtime.lr_parser; +import org.apache.airavata.datacat.parsers.gridchem.GridChemQueueParser; + +import javax.swing.*; +import java.io.FileReader; +import java.util.ArrayList; +import java.util.HashMap; + +public class GscfaParser extends java_cup.runtime.lr_parser implements GridChemQueueParser{ + + /** Default constructor. */ + public GscfaParser() {super();} + + /** Constructor which sets the default scanner. */ + public GscfaParser(java_cup.runtime.Scanner s) {super(s);} + + /** + * Constructor which uses a file reader. + */ + public GscfaParser(final FileReader fileReader) { + super(new GSCFaLexer(fileReader)); + } + + + /** Production table. */ + protected static final short _production_table[][] = + lr_parser.unpackFromStrings(new String[]{ + "\000\010\000\002\003\005\000\002\002\004\000\002\004" + + "\003\000\002\005\004\000\002\005\003\000\002\010\002" + + "\000\002\006\012\000\002\007\003"}); + + /** Access to production table. */ + public short[][] production_table() {return _production_table;} + + /** Parse-action table. */ + protected static final short[][] _action_table = + lr_parser.unpackFromStrings(new String[]{ + "\000\022\000\004\004\005\001\002\000\004\011\012\001" + + "\002\000\004\011\uffff\001\002\000\004\002\007\001\002" + + "\000\004\002\000\001\002\000\006\005\023\011\012\001" + + "\002\000\006\005\ufffd\011\ufffd\001\002\000\004\006\ufffc" + + "\001\002\000\004\006\014\001\002\000\004\007\015\001" + + "\002\000\004\016\017\001\002\000\004\013\020\001\002" + + "\000\004\013\ufffa\001\002\000\004\014\021\001\002\000" + + "\004\015\022\001\002\000\006\005\ufffb\011\ufffb\001\002" + + "\000\004\002\001\001\002\000\006\005\ufffe\011\ufffe\001" + + "\002"}); + + /** Access to parse-action table. */ + public short[][] action_table() {return _action_table;} + + /** <code>reduce_goto</code> table. */ + protected static final short[][] _reduce_table = + lr_parser.unpackFromStrings(new String[]{ + "\000\022\000\006\003\005\004\003\001\001\000\006\005" + + "\007\006\010\001\001\000\002\001\001\000\002\001\001" + + "\000\002\001\001\000\004\006\023\001\001\000\002\001" + + "\001\000\004\010\012\001\001\000\002\001\001\000\002" + + "\001\001\000\004\007\015\001\001\000\002\001\001\000" + + "\002\001\001\000\002\001\001\000\002\001\001\000\002" + + "\001\001\000\002\001\001\000\002\001\001"}); + + /** Access to <code>reduce_goto</code> table. */ + public short[][] reduce_table() {return _reduce_table;} + + /** Instance of action encapsulation class. */ + protected CUP$parser$actions action_obj; + + //Each string is of the format + //energy and iteraction + private ArrayList<String> result = new ArrayList<String>(); + private String tempStr = ""; + + + public ArrayList<String> getResult() { + return result; + } + + public void addToResult(String value) { + result.add(value); + } + + public String getTempStr() { + return tempStr; + } + + public void setTempStr(String s) { + this.tempStr = s; + } + + /*Adding the parsed data to the hash map */ + @Override + public HashMap<String, String> getParsedData() throws Exception { + parse(); + HashMap<String,String> results= new HashMap<String,String>(); + int energyCount=0; + int iterationCount=0; + for(int i=0;i<result.size();i++){ + String singleString= result.get(i); + String[] temp=singleString.split(" "); + if(temp.length>1){ + String keyString=temp[0]; + String dataString=temp[1]; + if(keyString.equals("ENERGY")){ + results.put("GscfaParser_ENERGY_"+energyCount,dataString); + energyCount++; + }else if(keyString.equals("ITERATION")){ + results.put("GscfaParser_ITERATION_"+iterationCount,dataString); + iterationCount++; + } + } + } + return results; + } + /** Action encapsulation object initializer. */ + protected void init_actions() + { + action_obj = new CUP$parser$actions(this); + } + + /** Invoke a user supplied parse action. */ + public java_cup.runtime.Symbol do_action( + int act_num, + java_cup.runtime.lr_parser parser, + java.util.Stack stack, + int top) + throws java.lang.Exception + { + /* call code in generated class */ + return action_obj.CUP$parser$do_action(act_num, parser, stack, top); + } + + /** Indicates start state. */ + public int start_state() {return 0;} + /** Indicates start production. */ + public int start_production() {return 1;} + + /** <code>EOF</code> Symbol index. */ + public int EOF_sym() {return 0;} + + /** <code>error</code> Symbol index. */ + public int error_sym() {return 1;} + + +} + +/** Cup generated class to encapsulate user supplied action code.*/ +class CUP$parser$actions { + + + //__________________________________ + public static boolean DEBUG = true; + private static JTable table; + private static final String tableLabel = "SCF Intermediate Results:"; +// private static String cycle = "0"; + + + public static JTable getTable() { + return table; + } + + public static String getTableLabel() { + return tableLabel; + } + +/* public static void main(String[] args) throws IOException { + File temp = new File("temporary"); + boolean append = true; + try{ + FileWriter temp1 = new FileWriter(temp, append); + PrintWriter temp2 = new PrintWriter(temp1);} + + catch (FileNotFoundException e) { + System.out.println("no file, dude!"); + } */ +// } + + private final GscfaParser GscfaParser; + + /** Constructor */ + CUP$parser$actions(GscfaParser GscfaParser) { + this.GscfaParser = GscfaParser; + } + + /** Method with the actual generated action code. */ + public final java_cup.runtime.Symbol CUP$parser$do_action( + int CUP$parser$act_num, + java_cup.runtime.lr_parser CUP$parser$parser, + java.util.Stack CUP$parser$stack, + int CUP$parser$top) + throws java.lang.Exception + { + /* Symbol object for return from actions */ + java_cup.runtime.Symbol CUP$parser$result; + + /* select the action based on the action number */ + switch (CUP$parser$act_num) + { + /*. . . . . . . . . . . . . . . . . . . .*/ + case 7: // en ::= ENERGY + { + Object RESULT = null; + int eleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left; + int eright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right; + Float e = (Float)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value; + //___________________________________________________________________ + if (DEBUG) System.out.println("CUP:gscfa:scfcycle: ENERGY "+e); + GscfaParser.addToResult("ENERGY "+e); +// temp2.println(e); +// parseSCF.putField("iteration "+cycle, "energy", e); + + CUP$parser$result = new java_cup.runtime.Symbol(5/*en*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT); + } + return CUP$parser$result; + + /*. . . . . . . . . . . . . . . . . . . .*/ + case 6: // scfcycle ::= INTCycle NT$0 INT1 INT2 en FLOAT1 FLOAT2 FLOAT3 + { + Object RESULT = null; + // propagate RESULT from NT$0 + if ( ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-6)).value != null ) + RESULT = (Object) ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-6)).value; + int cleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-7)).left; + int cright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-7)).right; + Integer c = (Integer)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-7)).value; + + CUP$parser$result = new java_cup.runtime.Symbol(4/*scfcycle*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-7)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT); + } + return CUP$parser$result; + + /*. . . . . . . . . . . . . . . . . . . .*/ + case 5: // NT$0 ::= + { + Object RESULT = null; + int cleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left; + int cright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right; + Integer c = (Integer)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value; + //___________________________________________________________________ + if (DEBUG) System.out.println("CUP:gscfa:scfcycle: ITERATION "+c); + GscfaParser.addToResult("ITERATION "+c); +// temp2.print(c); +// temp2.print(" "); +// cycle = c; + +// parseSCF.putField("iteration "+cycle, cycle); + + CUP$parser$result = new java_cup.runtime.Symbol(6/*NT$0*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT); + } + return CUP$parser$result; + + /*. . . . . . . . . . . . . . . . . . . .*/ + case 4: // scfpat ::= scfcycle + { + Object RESULT = null; + + CUP$parser$result = new java_cup.runtime.Symbol(3/*scfpat*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT); + } + return CUP$parser$result; + + /*. . . . . . . . . . . . . . . . . . . .*/ + case 3: // scfpat ::= scfpat scfcycle + { + Object RESULT = null; + if (DEBUG) System.out.println("CUP:gscfa: in scfpat"); + CUP$parser$result = new java_cup.runtime.Symbol(3/*scfpat*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-1)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT); + } + return CUP$parser$result; + + /*. . . . . . . . . . . . . . . . . . . .*/ + case 2: // scfintro ::= FOUNDITER + { + Object RESULT = null; + if (DEBUG) System.out.println("CUP:gscfa: found start of SCF Iteration"); + CUP$parser$result = new java_cup.runtime.Symbol(2/*scfintro*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT); + } + return CUP$parser$result; + + /*. . . . . . . . . . . . . . . . . . . .*/ + case 1: // $START ::= startpt EOF + { + Object RESULT = null; + int start_valleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-1)).left; + int start_valright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-1)).right; + Object start_val = (Object)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-1)).value; + RESULT = start_val; + CUP$parser$result = new java_cup.runtime.Symbol(0/*$START*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-1)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT); + } + /* ACCEPT */ + CUP$parser$parser.done_parsing(); + return CUP$parser$result; + + /*. . . . . . . . . . . . . . . . . . . .*/ + case 0: // startpt ::= scfintro scfpat SCFDONE + { + Object RESULT = null; + if (DEBUG) System.out.println("CUP:gscfa: end of parse tree "); + table = new JTable(); + +// table = parseSCF.getTable(); + + CUP$parser$result = new java_cup.runtime.Symbol(1/*startpt*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-2)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT); + } + return CUP$parser$result; + + /* . . . . . .*/ + default: + throw new Exception( + "Invalid action number found in internal parse table"); + + } + } +} + http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/4231ac35/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gvb/GVBLexer.java ---------------------------------------------------------------------- diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gvb/GVBLexer.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gvb/GVBLexer.java new file mode 100644 index 0000000..eaa2a0c --- /dev/null +++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gvb/GVBLexer.java @@ -0,0 +1,777 @@ +/* +* +* Licensed to the Apache Software Foundation (ASF) under one +* or more contributor license agreements. See the NOTICE file +* distributed with this work for additional information +* regarding copyright ownership. The ASF licenses this file +* to you under the Apache License, Version 2.0 (the +* "License"); you may not use this file except in compliance +* with the License. You may obtain a copy of the License at +* +* http://www.apache.org/licenses/LICENSE-2.0 +* +* Unless required by applicable law or agreed to in writing, +* software distributed under the License is distributed on an +* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY +* KIND, either express or implied. See the License for the +* specific language governing permissions and limitations +* under the License. +* +*/ +package org.apache.airavata.datacat.parsers.gridchem.gvb;/* The following code was generated by JFlex 1.4.3 on 9/11/14 6:26 PM */ + +import java_cup.runtime.Symbol; +import org.apache.airavata.datacat.parsers.gridchem.Settings; + + +/** + * This class is a scanner generated by + * <a href="http://www.jflex.de/";>JFlex</a> 1.4.3 + * on 9/11/14 6:26 PM from the specification file + * <tt>gvb.flex</tt> + */ +public class GVBLexer implements java_cup.runtime.Scanner { + + /** This character denotes the end of file */ + public static final int YYEOF = -1; + + /** initial size of the lookahead buffer */ + private static final int ZZ_BUFFERSIZE = 16384; + + /** lexical states */ + public static final int ITER2 = 6; + public static final int DASH = 10; + public static final int INTVALUE = 12; + public static final int SCF1 = 2; + public static final int IGNOREALL = 24; + public static final int ITER = 4; + public static final int YYINITIAL = 0; + public static final int ITER8 = 8; + public static final int ITER7 = 22; + public static final int ITER6 = 20; + public static final int ITER5 = 18; + public static final int FLOATVALUE = 14; + public static final int ITER4 = 16; + + /** + * ZZ_LEXSTATE[l] is the state in the DFA for the lexical state l + * ZZ_LEXSTATE[l+1] is the state in the DFA for the lexical state l + * at the beginning of a line + * l is of the form l = 2*k, k a non negative integer + */ + private static final int ZZ_LEXSTATE[] = { + 0, 0, 1, 1, 2, 2, 3, 3, 4, 4, 5, 5, 1, 1, 6, 6, + 7, 7, 8, 8, 9, 9, 10, 10, 1, 1 + }; + + /** + * Translates characters to character classes + */ + private static final char [] ZZ_CMAP = { + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 10, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 3, 0, 24, 4, 0, + 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 0, 0, 0, 0, 0, 0, + 0, 13, 23, 18, 22, 8, 5, 16, 19, 6, 0, 0, 14, 0, 15, 12, + 0, 21, 9, 20, 7, 0, 25, 0, 11, 17, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 3, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 + }; + + /** + * Translates DFA states to action switch labels. + */ + private static final int [] ZZ_ACTION = zzUnpackAction(); + + private static final String ZZ_ACTION_PACKED_0 = + "\13\0\2\1\2\2\1\1\2\3\3\1\3\4\10\1"+ + "\5\0\1\5\13\0\1\6\2\0\1\7\1\10\1\11"+ + "\1\12\65\0\1\13\1\14\1\15\62\0\1\16"; + + private static int [] zzUnpackAction() { + int [] result = new int[163]; + int offset = 0; + offset = zzUnpackAction(ZZ_ACTION_PACKED_0, offset, result); + return result; + } + + private static int zzUnpackAction(String packed, int offset, int [] result) { + int i = 0; /* index in packed string */ + int j = offset; /* index in unpacked array */ + int l = packed.length(); + while (i < l) { + int count = packed.charAt(i++); + int value = packed.charAt(i++); + do result[j++] = value; while (--count > 0); + } + return j; + } + + + /** + * Translates a state to a row index in the transition table + */ + private static final int [] ZZ_ROWMAP = zzUnpackRowMap(); + + private static final String ZZ_ROWMAP_PACKED_0 = + "\0\0\0\32\0\64\0\116\0\150\0\202\0\234\0\266"+ + "\0\320\0\352\0\u0104\0\u011e\0\u0138\0\u011e\0\u0152\0\u016c"+ + "\0\u011e\0\u0186\0\u01a0\0\u01ba\0\u01d4\0\u011e\0\u01ee\0\u0208"+ + "\0\u0222\0\u023c\0\u0256\0\u0270\0\u028a\0\u02a4\0\u02be\0\u02d8"+ + "\0\u02f2\0\u030c\0\u01a0\0\u0326\0\u0340\0\u01ee\0\u035a\0\u0222"+ + "\0\u0374\0\u0256\0\u038e\0\u028a\0\u03a8\0\u02be\0\u03c2\0\u03dc"+ + "\0\u03f6\0\u0326\0\u0410\0\u042a\0\u0374\0\u038e\0\u03a8\0\u03c2"+ + "\0\u0444\0\u045e\0\u0478\0\u0492\0\u04ac\0\u04c6\0\u04e0\0\u04fa"+ + "\0\u0514\0\u052e\0\u0548\0\u0562\0\u057c\0\u0596\0\u05b0\0\u05ca"+ + "\0\u05e4\0\u05fe\0\u0618\0\u0632\0\u064c\0\u0666\0\u0680\0\u069a"+ + "\0\u06b4\0\u06ce\0\u06e8\0\u0702\0\u071c\0\u0736\0\u0750\0\u076a"+ + "\0\u0784\0\u079e\0\u07b8\0\u07d2\0\u07ec\0\u0806\0\u0820\0\u083a"+ + "\0\u0854\0\u086e\0\u0888\0\u08a2\0\u08bc\0\u08d6\0\u08f0\0\u090a"+ + "\0\u0924\0\u093e\0\u0958\0\u0972\0\u098c\0\u011e\0\u011e\0\u011e"+ + "\0\u09a6\0\u09c0\0\u09da\0\u09f4\0\u0a0e\0\u0a28\0\u0a42\0\u0a5c"+ + "\0\u0a76\0\u0a90\0\u0aaa\0\u0ac4\0\u0ade\0\u0af8\0\u0b12\0\u0b2c"+ + "\0\u0b46\0\u0b60\0\u0b7a\0\u0b94\0\u0bae\0\u0bc8\0\u0be2\0\u0bfc"+ + "\0\u0c16\0\u0c30\0\u0c4a\0\u0c64\0\u0c7e\0\u0c98\0\u0cb2\0\u0ccc"+ + "\0\u0ce6\0\u0d00\0\u0d1a\0\u0d34\0\u0d4e\0\u0d68\0\u0d82\0\u0d9c"+ + "\0\u0db6\0\u0dd0\0\u0dea\0\u0e04\0\u0e1e\0\u0e38\0\u0e52\0\u0e6c"+ + "\0\u0e86\0\u0ea0\0\u011e"; + + private static int [] zzUnpackRowMap() { + int [] result = new int[163]; + int offset = 0; + offset = zzUnpackRowMap(ZZ_ROWMAP_PACKED_0, offset, result); + return result; + } + + private static int zzUnpackRowMap(String packed, int offset, int [] result) { + int i = 0; /* index in packed string */ + int j = offset; /* index in unpacked array */ + int l = packed.length(); + while (i < l) { + int high = packed.charAt(i++) << 16; + result[j++] = high | packed.charAt(i++); + } + return j; + } + + /** + * The transition table of the DFA + */ + private static final int [] ZZ_TRANS = zzUnpackTrans(); + + private static final String ZZ_TRANS_PACKED_0 = + "\6\14\1\15\56\14\1\16\1\17\25\14\1\20\2\14"+ + "\1\21\1\22\30\14\2\23\1\24\24\14\1\24\27\14"+ + "\1\25\3\14\1\26\3\27\24\26\1\30\1\26\1\14"+ + "\2\31\1\32\24\14\1\32\2\14\2\33\1\34\24\14"+ + "\1\34\2\14\2\35\1\36\24\14\1\36\2\14\2\37"+ + "\1\40\24\14\1\40\1\14\41\0\1\41\23\0\2\17"+ + "\57\0\1\42\2\0\2\22\30\0\2\43\1\0\1\44"+ + "\26\0\2\43\37\0\1\45\22\0\2\46\30\0\2\46"+ + "\25\0\1\47\2\0\2\50\1\0\1\51\26\0\2\50"+ + "\30\0\2\52\1\0\1\53\26\0\2\52\30\0\2\54"+ + "\1\0\1\55\26\0\2\54\30\0\2\56\1\0\1\57"+ + "\26\0\2\56\37\0\1\60\51\0\1\61\2\0\2\62"+ + "\46\0\1\63\42\0\1\64\2\0\2\65\30\0\2\66"+ + "\30\0\2\67\30\0\2\70\40\0\1\71\50\0\1\72"+ + "\25\0\1\73\35\0\1\74\13\0\1\75\47\0\1\76"+ + "\7\0\1\77\53\0\1\100\11\0\1\101\51\0\1\102"+ + "\10\0\1\103\52\0\1\104\14\0\1\105\46\0\1\106"+ + "\22\0\1\107\40\0\1\110\13\0\1\111\47\0\1\112"+ + "\13\0\1\113\47\0\1\114\13\0\1\115\47\0\1\116"+ + "\23\0\1\117\37\0\1\120\13\0\1\121\47\0\1\122"+ + "\15\0\1\123\45\0\1\124\13\0\1\125\47\0\1\126"+ + "\20\0\1\127\42\0\1\130\13\0\1\131\47\0\1\132"+ + "\32\0\1\133\30\0\1\134\10\0\1\135\52\0\1\136"+ + "\11\0\1\137\51\0\1\140\15\0\1\141\45\0\1\142"+ + "\12\0\1\143\50\0\1\144\10\0\1\145\52\0\1\146"+ + "\21\0\1\147\41\0\1\150\16\0\1\151\44\0\1\152"+ + "\11\0\1\153\51\0\1\154\17\0\1\155\43\0\1\156"+ + "\27\0\1\157\33\0\1\160\13\0\1\161\27\0\1\162"+ + "\40\0\1\163\22\0\1\164\32\0\1\165\40\0\1\166"+ + "\32\0\1\167\22\0\1\170\31\0\1\171\31\0\1\172"+ + "\31\0\1\173\31\0\1\174\31\0\1\175\31\0\1\176"+ + "\27\0\1\177\33\0\1\200\41\0\1\201\32\0\1\202"+ + "\23\0\1\203\33\0\1\204\32\0\1\205\21\0\1\206"+ + "\33\0\1\207\31\0\1\210\31\0\1\211\31\0\1\212"+ + "\31\0\1\213\31\0\1\214\31\0\1\215\31\0\1\216"+ + "\43\0\1\217\32\0\1\220\26\0\1\221\35\0\1\222"+ + "\10\0\1\223\36\0\1\224\31\0\1\225\31\0\1\226"+ + "\31\0\1\227\31\0\1\230\31\0\1\231\31\0\1\232"+ + "\33\0\1\233\26\0\1\234\47\0\1\235\6\0\1\236"+ + "\37\0\1\237\37\0\1\240\22\0\1\241\35\0\1\242"+ + "\42\0\1\243\3\0"; + + private static int [] zzUnpackTrans() { + int [] result = new int[3770]; + int offset = 0; + offset = zzUnpackTrans(ZZ_TRANS_PACKED_0, offset, result); + return result; + } + + private static int zzUnpackTrans(String packed, int offset, int [] result) { + int i = 0; /* index in packed string */ + int j = offset; /* index in unpacked array */ + int l = packed.length(); + while (i < l) { + int count = packed.charAt(i++); + int value = packed.charAt(i++); + value--; + do result[j++] = value; while (--count > 0); + } + return j; + } + + + /* error codes */ + private static final int ZZ_UNKNOWN_ERROR = 0; + private static final int ZZ_NO_MATCH = 1; + private static final int ZZ_PUSHBACK_2BIG = 2; + + /* error messages for the codes above */ + private static final String ZZ_ERROR_MSG[] = { + "Unkown internal scanner error", + "Error: could not match input", + "Error: pushback value was too large" + }; + + /** + * ZZ_ATTRIBUTE[aState] contains the attributes of state <code>aState</code> + */ + private static final int [] ZZ_ATTRIBUTE = zzUnpackAttribute(); + + private static final String ZZ_ATTRIBUTE_PACKED_0 = + "\13\0\1\11\1\1\1\11\2\1\1\11\4\1\1\11"+ + "\12\1\5\0\1\1\13\0\1\1\2\0\4\1\65\0"+ + "\3\11\62\0\1\11"; + + private static int [] zzUnpackAttribute() { + int [] result = new int[163]; + int offset = 0; + offset = zzUnpackAttribute(ZZ_ATTRIBUTE_PACKED_0, offset, result); + return result; + } + + private static int zzUnpackAttribute(String packed, int offset, int [] result) { + int i = 0; /* index in packed string */ + int j = offset; /* index in unpacked array */ + int l = packed.length(); + while (i < l) { + int count = packed.charAt(i++); + int value = packed.charAt(i++); + do result[j++] = value; while (--count > 0); + } + return j; + } + + /** the input device */ + private java.io.Reader zzReader; + + /** the current state of the DFA */ + private int zzState; + + /** the current lexical state */ + private int zzLexicalState = YYINITIAL; + + /** this buffer contains the current text to be matched and is + the source of the yytext() string */ + private char zzBuffer[] = new char[ZZ_BUFFERSIZE]; + + /** the textposition at the last accepting state */ + private int zzMarkedPos; + + /** the current text position in the buffer */ + private int zzCurrentPos; + + /** startRead marks the beginning of the yytext() string in the buffer */ + private int zzStartRead; + + /** endRead marks the last character in the buffer, that has been read + from input */ + private int zzEndRead; + + /** number of newlines encountered up to the start of the matched text */ + private int yyline; + + /** the number of characters up to the start of the matched text */ + private int yychar; + + /** + * the number of characters from the last newline up to the start of the + * matched text + */ + private int yycolumn; + + /** + * zzAtBOL == true <=> the scanner is currently at the beginning of a line + */ + private boolean zzAtBOL = true; + + /** zzAtEOF == true <=> the scanner is at the EOF */ + private boolean zzAtEOF; + + /** denotes if the user-EOF-code has already been executed */ + private boolean zzEOFDone; + + /* user code: */ + public static boolean DEBUG = false; + + + /** + * Creates a new scanner + * There is also a java.io.InputStream version of this constructor. + * + * @param in the java.io.Reader to read input from. + */ + public GVBLexer(java.io.Reader in) { + this.zzReader = in; + } + + /** + * Creates a new scanner. + * There is also java.io.Reader version of this constructor. + * + * @param in the java.io.Inputstream to read input from. + */ + public GVBLexer(java.io.InputStream in) { + this(new java.io.InputStreamReader(in)); + } + + + /** + * Refills the input buffer. + * + * @return <code>false</code>, iff there was new input. + * + * @exception java.io.IOException if any I/O-Error occurs + */ + private boolean zzRefill() throws java.io.IOException { + + /* first: make room (if you can) */ + if (zzStartRead > 0) { + System.arraycopy(zzBuffer, zzStartRead, + zzBuffer, 0, + zzEndRead-zzStartRead); + + /* translate stored positions */ + zzEndRead-= zzStartRead; + zzCurrentPos-= zzStartRead; + zzMarkedPos-= zzStartRead; + zzStartRead = 0; + } + + /* is the buffer big enough? */ + if (zzCurrentPos >= zzBuffer.length) { + /* if not: blow it up */ + char newBuffer[] = new char[zzCurrentPos*2]; + System.arraycopy(zzBuffer, 0, newBuffer, 0, zzBuffer.length); + zzBuffer = newBuffer; + } + + /* finally: fill the buffer with new input */ + int numRead = zzReader.read(zzBuffer, zzEndRead, + zzBuffer.length-zzEndRead); + + if (numRead > 0) { + zzEndRead+= numRead; + return false; + } + // unlikely but not impossible: read 0 characters, but not at end of stream + if (numRead == 0) { + int c = zzReader.read(); + if (c == -1) { + return true; + } else { + zzBuffer[zzEndRead++] = (char) c; + return false; + } + } + + // numRead < 0 + return true; + } + + + /** + * Closes the input stream. + */ + public final void yyclose() throws java.io.IOException { + zzAtEOF = true; /* indicate end of file */ + zzEndRead = zzStartRead; /* invalidate buffer */ + + if (zzReader != null) + zzReader.close(); + } + + + /** + * Resets the scanner to read from a new input stream. + * Does not close the old reader. + * + * All internal variables are reset, the old input stream + * <b>cannot</b> be reused (internal buffer is discarded and lost). + * Lexical state is set to <tt>ZZ_INITIAL</tt>. + * + * @param reader the new input stream + */ + public final void yyreset(java.io.Reader reader) { + zzReader = reader; + zzAtBOL = true; + zzAtEOF = false; + zzEOFDone = false; + zzEndRead = zzStartRead = 0; + zzCurrentPos = zzMarkedPos = 0; + yyline = yychar = yycolumn = 0; + zzLexicalState = YYINITIAL; + } + + + /** + * Returns the current lexical state. + */ + public final int yystate() { + return zzLexicalState; + } + + + /** + * Enters a new lexical state + * + * @param newState the new lexical state + */ + public final void yybegin(int newState) { + zzLexicalState = newState; + } + + + /** + * Returns the text matched by the current regular expression. + */ + public final String yytext() { + return new String( zzBuffer, zzStartRead, zzMarkedPos-zzStartRead ); + } + + + /** + * Returns the character at position <tt>pos</tt> from the + * matched text. + * + * It is equivalent to yytext().charAt(pos), but faster + * + * @param pos the position of the character to fetch. + * A value from 0 to yylength()-1. + * + * @return the character at position pos + */ + public final char yycharat(int pos) { + return zzBuffer[zzStartRead+pos]; + } + + + /** + * Returns the length of the matched text region. + */ + public final int yylength() { + return zzMarkedPos-zzStartRead; + } + + + /** + * Reports an error that occured while scanning. + * + * In a wellformed scanner (no or only correct usage of + * yypushback(int) and a match-all fallback rule) this method + * will only be called with things that "Can't Possibly Happen". + * If this method is called, something is seriously wrong + * (e.g. a JFlex bug producing a faulty scanner etc.). + * + * Usual syntax/scanner level error handling should be done + * in error fallback rules. + * + * @param errorCode the code of the errormessage to display + */ + private void zzScanError(int errorCode) { + String message; + try { + message = ZZ_ERROR_MSG[errorCode]; + } + catch (ArrayIndexOutOfBoundsException e) { + message = ZZ_ERROR_MSG[ZZ_UNKNOWN_ERROR]; + } + + throw new Error(message); + } + + + /** + * Pushes the specified amount of characters back into the input stream. + * + * They will be read again by then next call of the scanning method + * + * @param number the number of characters to be read again. + * This number must not be greater than yylength()! + */ + public void yypushback(int number) { + if ( number > yylength() ) + zzScanError(ZZ_PUSHBACK_2BIG); + + zzMarkedPos -= number; + } + + + /** + * Contains user EOF-code, which will be executed exactly once, + * when the end of file is reached + */ + private void zzDoEOF() throws java.io.IOException { + if (!zzEOFDone) { + zzEOFDone = true; + yyclose(); + } + } + + + /** + * Resumes scanning until the next regular expression is matched, + * the end of input is encountered or an I/O-Error occurs. + * + * @return the next token + * @exception java.io.IOException if any I/O-Error occurs + */ + public java_cup.runtime.Symbol next_token() throws java.io.IOException { + int zzInput; + int zzAction; + + // cached fields: + int zzCurrentPosL; + int zzMarkedPosL; + int zzEndReadL = zzEndRead; + char [] zzBufferL = zzBuffer; + char [] zzCMapL = ZZ_CMAP; + + int [] zzTransL = ZZ_TRANS; + int [] zzRowMapL = ZZ_ROWMAP; + int [] zzAttrL = ZZ_ATTRIBUTE; + + while (true) { + zzMarkedPosL = zzMarkedPos; + + zzAction = -1; + + zzCurrentPosL = zzCurrentPos = zzStartRead = zzMarkedPosL; + + zzState = ZZ_LEXSTATE[zzLexicalState]; + + + zzForAction: { + while (true) { + + if (zzCurrentPosL < zzEndReadL) + zzInput = zzBufferL[zzCurrentPosL++]; + else if (zzAtEOF) { + zzInput = YYEOF; + break zzForAction; + } + else { + // store back cached positions + zzCurrentPos = zzCurrentPosL; + zzMarkedPos = zzMarkedPosL; + boolean eof = zzRefill(); + // get translated positions and possibly new buffer + zzCurrentPosL = zzCurrentPos; + zzMarkedPosL = zzMarkedPos; + zzBufferL = zzBuffer; + zzEndReadL = zzEndRead; + if (eof) { + zzInput = YYEOF; + break zzForAction; + } + else { + zzInput = zzBufferL[zzCurrentPosL++]; + } + } + int zzNext = zzTransL[ zzRowMapL[zzState] + zzCMapL[zzInput] ]; + if (zzNext == -1) break zzForAction; + zzState = zzNext; + + int zzAttributes = zzAttrL[zzState]; + if ( (zzAttributes & 1) == 1 ) { + zzAction = zzState; + zzMarkedPosL = zzCurrentPosL; + if ( (zzAttributes & 8) == 8 ) break zzForAction; + } + + } + } + + // store back cached position + zzMarkedPos = zzMarkedPosL; + + switch (zzAction < 0 ? zzAction : ZZ_ACTION[zzAction]) { + case 10: + { if (Settings.DEBUG) System.out.println("GVBFlex: Found float3"); + yybegin(ITER); + return new Symbol(GVBSym.FLOAT3); + } + case 15: break; + case 11: + { if (Settings.DEBUG) System.out.println("GVBFlex: Found the dash"); + yybegin(DASH); + } + case 16: break; + case 13: + { yybegin(DASH); + } + case 17: break; + case 14: + { if (Settings.DEBUG) System.out.println("GVBFlex: Found START OF"); + yybegin(ITER); + return new Symbol(GVBSym.FOUNDITER); + } + case 18: break; + case 7: + { if (Settings.DEBUG) System.out.println("GVBFlex: Found the energy"); + if (Settings.DEBUG) System.out.println(yytext()); + yybegin(ITER5); + return new Symbol(GVBSym.ENERGY, new Float(yytext())); + } + case 19: break; + case 6: + { if (Settings.DEBUG) System.out.println("GVBFlex: Found float4"); + yybegin(ITER); + return new Symbol(GVBSym.FLOAT4); + } + case 20: break; + case 12: + { yybegin(IGNOREALL); + return new Symbol(GVBSym.SCFDONE); + } + case 21: break; + case 9: + { if (Settings.DEBUG) System.out.println("GVBFlex: Found float2"); + yybegin (ITER7); + return new Symbol(GVBSym.FLOAT2); + } + case 22: break; + case 2: + { if (Settings.DEBUG) System.out.println("GVBFlex: Found the first integer in the iteration"); + if (Settings.DEBUG) System.out.println(yytext()); + yybegin(ITER2); + return new Symbol(GVBSym.INTCycle, new Integer(yytext())); + } + case 23: break; + case 8: + { if (Settings.DEBUG) System.out.println("GVBFlex: ITER5"); + if (Settings.DEBUG) System.out.println("GVBFlex: Found float1"); + yybegin (ITER6); + return new Symbol(GVBSym.FLOAT1); + } + case 24: break; + case 5: + { if (Settings.DEBUG) System.out.println("GVBFlex: Found float value"); + yybegin(ITER); + } + case 25: break; + case 4: + { if (Settings.DEBUG) System.out.println("GVBFlex: Found new line"); + } + case 26: break; + case 1: + { + } + case 27: break; + case 3: + { if (Settings.DEBUG) System.out.println("GVBFlex: Found the second integer in the iteration"); if (Settings.DEBUG) System.out.println(yytext()); yybegin(ITER4); return new Symbol(GVBSym.INT1, new Integer(yytext())); + } + case 28: break; + default: + if (zzInput == YYEOF && zzStartRead == zzCurrentPos) { + zzAtEOF = true; + zzDoEOF(); + { return new java_cup.runtime.Symbol(GVBSym.EOF); } + } + else { + zzScanError(ZZ_NO_MATCH); + } + } + } + } + + /** + * Converts an int token code into the name of the + * token by reflection on the cup symbol class/interface sym + * + * This code was contributed by Karl Meissner <[email protected]> + */ + private String getTokenName(int token) { + try { + java.lang.reflect.Field [] classFields = GVBSym.class.getFields(); + for (int i = 0; i < classFields.length; i++) { + if (classFields[i].getInt(null) == token) { + return classFields[i].getName(); + } + } + } catch (Exception e) { + e.printStackTrace(System.err); + } + + return "UNKNOWN TOKEN"; + } + + /** + * Same as next_token but also prints the token to standard out + * for debugging. + * + * This code was contributed by Karl Meissner <[email protected]> + */ + public java_cup.runtime.Symbol debug_next_token() throws java.io.IOException { + java_cup.runtime.Symbol s = next_token(); + System.out.println( " --"+ yytext() + "--" + getTokenName(s.sym) + "--"); + return s; + } + + /** + * Runs the scanner on input files. + * + * This is a standalone scanner, it will print any unmatched + * text to System.out unchanged. + * + * @param argv the command line, contains the filenames to run + * the scanner on. + */ + public static void main(String argv[]) { + if (argv.length == 0) { + System.out.println("Usage : java GVBLexer <inputfile>"); + } + else { + for (int i = 0; i < argv.length; i++) { + GVBLexer scanner = null; + try { + scanner = new GVBLexer( new java.io.FileReader(argv[i]) ); + while ( !scanner.zzAtEOF ) scanner.next_token(); + } + catch (java.io.FileNotFoundException e) { + System.out.println("File not found : \""+argv[i]+"\""); + } + catch (java.io.IOException e) { + System.out.println("IO error scanning file \""+argv[i]+"\""); + System.out.println(e); + } + catch (Exception e) { + System.out.println("Unexpected exception:"); + e.printStackTrace(); + } + } + } + } + + +} http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/4231ac35/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gvb/GVBParser.java ---------------------------------------------------------------------- diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gvb/GVBParser.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gvb/GVBParser.java new file mode 100644 index 0000000..507da25 --- /dev/null +++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gvb/GVBParser.java @@ -0,0 +1,335 @@ +/* +* +* Licensed to the Apache Software Foundation (ASF) under one +* or more contributor license agreements. See the NOTICE file +* distributed with this work for additional information +* regarding copyright ownership. The ASF licenses this file +* to you under the Apache License, Version 2.0 (the +* "License"); you may not use this file except in compliance +* with the License. You may obtain a copy of the License at +* +* http://www.apache.org/licenses/LICENSE-2.0 +* +* Unless required by applicable law or agreed to in writing, +* software distributed under the License is distributed on an +* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY +* KIND, either express or implied. See the License for the +* specific language governing permissions and limitations +* under the License. +* +*/ +package org.apache.airavata.datacat.parsers.gridchem.gvb; + + +import java_cup.runtime.lr_parser; +import org.apache.airavata.datacat.parsers.gridchem.GridChemQueueParser; + +import javax.swing.*; +import java.io.FileReader; +import java.util.ArrayList; +import java.util.HashMap; + + +public class GVBParser extends java_cup.runtime.lr_parser implements GridChemQueueParser { + + /** Default constructor. */ + public GVBParser() {super();} + + /** Constructor which sets the default scanner. */ + public GVBParser(java_cup.runtime.Scanner s) {super(s);} + + /** + * Constructor which uses a file reader. + */ + public GVBParser(final FileReader fileReader) { + super(new GVBLexer(fileReader)); + } + /** Production table. */ + protected static final short[][] _production_table = + lr_parser.unpackFromStrings(new String[]{ + "\000\010\000\002\003\005\000\002\002\004\000\002\004" + + "\003\000\002\005\004\000\002\005\003\000\002\010\002" + + "\000\002\006\011\000\002\007\003"}); + + /** Access to production table. */ + public short[][] production_table() {return _production_table;} + + /** Parse-action table. */ + protected static final short[][] _action_table = + lr_parser.unpackFromStrings(new String[]{ + "\000\021\000\004\004\005\001\002\000\004\011\012\001" + + "\002\000\004\011\uffff\001\002\000\004\002\007\001\002" + + "\000\004\002\000\001\002\000\006\005\022\011\012\001" + + "\002\000\006\005\ufffd\011\ufffd\001\002\000\004\006\ufffc" + + "\001\002\000\004\006\014\001\002\000\004\016\016\001" + + "\002\000\004\013\017\001\002\000\004\013\ufffa\001\002" + + "\000\004\014\020\001\002\000\004\015\021\001\002\000" + + "\006\005\ufffb\011\ufffb\001\002\000\004\002\001\001\002" + + "\000\006\005\ufffe\011\ufffe\001\002"}); + + /** Access to parse-action table. */ + public short[][] action_table() {return _action_table;} + + /** <code>reduce_goto</code> table. */ + protected static final short[][] _reduce_table = + lr_parser.unpackFromStrings(new String[]{ + "\000\021\000\006\003\005\004\003\001\001\000\006\005" + + "\007\006\010\001\001\000\002\001\001\000\002\001\001" + + "\000\002\001\001\000\004\006\022\001\001\000\002\001" + + "\001\000\004\010\012\001\001\000\002\001\001\000\004" + + "\007\014\001\001\000\002\001\001\000\002\001\001\000" + + "\002\001\001\000\002\001\001\000\002\001\001\000\002" + + "\001\001\000\002\001\001"}); + + /** Access to <code>reduce_goto</code> table. */ + public short[][] reduce_table() {return _reduce_table;} + + /** Instance of action encapsulation class. */ + protected CUP$parser$actions action_obj; + + //Each string is of the format + //energy and iteraction + private ArrayList<String> result = new ArrayList<String>(); + private String tempStr = ""; + + + public ArrayList<String> getResult() { + return result; + } + + public void addToResult(String value) { + result.add(value); + } + + public String getTempStr() { + return tempStr; + } + + public void setTempStr(String s) { + this.tempStr = s; + } + + /*Adding the parsed data to the hash map */ + @Override + public HashMap<String, String> getParsedData() throws Exception { + parse(); + HashMap<String,String> results= new HashMap<String,String>(); + int energyCount=0; + int iterationCount=0; + for(int i=0;i<result.size();i++){ + String singleString= result.get(i); + String[] temp=singleString.split(" "); + if(temp.length>1){ + String keyString=temp[0]; + String dataString=temp[1]; + if(keyString.equals("ENERGY")){ + results.put("GVBParser_ENERGY_"+energyCount,dataString); + energyCount++; + }else if(keyString.equals("ITERATION")){ + results.put("GVBParser_ITERATION_"+iterationCount,dataString); + iterationCount++; + } + } + } + return results; + } + + /** Action encapsulation object initializer. */ + protected void init_actions() + { + action_obj = new CUP$parser$actions(this); + } + + /** Invoke a user supplied parse action. */ + public java_cup.runtime.Symbol do_action( + int act_num, + java_cup.runtime.lr_parser parser, + java.util.Stack stack, + int top) + throws java.lang.Exception + { + /* call code in generated class */ + return action_obj.CUP$parser$do_action(act_num, parser, stack, top); + } + + /** Indicates start state. */ + public int start_state() {return 0;} + /** Indicates start production. */ + public int start_production() {return 1;} + + /** <code>EOF</code> Symbol index. */ + public int EOF_sym() {return 0;} + + /** <code>error</code> Symbol index. */ + public int error_sym() {return 1;} + + +} + +/** Cup generated class to encapsulate user supplied action code.*/ +class CUP$parser$actions { + + + //__________________________________ + public static boolean DEBUG = true; + private static JTable table; + private static final String tableLabel = "SCF Intermediate Results:"; +// private static String cycle = "0"; + + + public static JTable getTable() { + return table; + } + + public static String getTableLabel() { + return tableLabel; + } + +/* public static void main(String[] args) throws IOException { + File temp = new File("temporary"); + boolean append = true; + try{ + FileWriter temp1 = new FileWriter(temp, append); + PrintWriter temp2 = new PrintWriter(temp1);} + + catch (FileNotFoundException e) { + System.out.println("no file, dude!"); + } */ +// } + + private final GVBParser GVBParser; + + /** Constructor */ + CUP$parser$actions(GVBParser GVBParser) { + this.GVBParser = GVBParser; + } + + /** Method with the actual generated action code. */ + public final java_cup.runtime.Symbol CUP$parser$do_action( + int CUP$parser$act_num, + java_cup.runtime.lr_parser CUP$parser$parser, + java.util.Stack CUP$parser$stack, + int CUP$parser$top) + throws java.lang.Exception + { + /* Symbol object for return from actions */ + java_cup.runtime.Symbol CUP$parser$result; + + /* select the action based on the action number */ + switch (CUP$parser$act_num) + { + /*. . . . . . . . . . . . . . . . . . . .*/ + case 7: // en ::= ENERGY + { + Object RESULT = null; + int eleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left; + int eright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right; + Float e = (Float)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value; + //___________________________________________________________________ + if (DEBUG) System.out.println("CUP:gscfa:scfcycle: ENERGY "+e); + GVBParser.addToResult("ENERGY "+e); +// temp2.println(e); +// parseSCF.putField("iteration "+cycle, "energy", e); + + CUP$parser$result = new java_cup.runtime.Symbol(5/*en*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT); + } + return CUP$parser$result; + + /*. . . . . . . . . . . . . . . . . . . .*/ + case 6: // scfcycle ::= INTCycle NT$0 INT1 en FLOAT1 FLOAT2 FLOAT3 + { + Object RESULT = null; + // propagate RESULT from NT$0 + if ( ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-5)).value != null ) + RESULT = (Object) ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-5)).value; + int cleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-6)).left; + int cright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-6)).right; + Integer c = (Integer)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-6)).value; + + CUP$parser$result = new java_cup.runtime.Symbol(4/*scfcycle*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-6)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT); + } + return CUP$parser$result; + + /*. . . . . . . . . . . . . . . . . . . .*/ + case 5: // NT$0 ::= + { + Object RESULT = null; + int cleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left; + int cright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right; + Integer c = (Integer)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value; + //___________________________________________________________________ + if (DEBUG) System.out.println("CUP:gscfa:scfcycle: ITERATION "+c); + GVBParser.addToResult("ITERATION "+c); +// temp2.print(c); +// temp2.print(" "); +// cycle = c; + +// parseSCF.putField("iteration "+cycle, cycle); + + CUP$parser$result = new java_cup.runtime.Symbol(6/*NT$0*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT); + } + return CUP$parser$result; + + /*. . . . . . . . . . . . . . . . . . . .*/ + case 4: // scfpat ::= scfcycle + { + Object RESULT = null; + + CUP$parser$result = new java_cup.runtime.Symbol(3/*scfpat*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT); + } + return CUP$parser$result; + + /*. . . . . . . . . . . . . . . . . . . .*/ + case 3: // scfpat ::= scfpat scfcycle + { + Object RESULT = null; + if (DEBUG) System.out.println("CUP:gscfa: in scfpat"); + CUP$parser$result = new java_cup.runtime.Symbol(3/*scfpat*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-1)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT); + } + return CUP$parser$result; + + /*. . . . . . . . . . . . . . . . . . . .*/ + case 2: // scfintro ::= FOUNDITER + { + Object RESULT = null; + if (DEBUG) System.out.println("CUP:gscfa: found start of SCF Iteration"); + CUP$parser$result = new java_cup.runtime.Symbol(2/*scfintro*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT); + } + return CUP$parser$result; + + /*. . . . . . . . . . . . . . . . . . . .*/ + case 1: // $START ::= startpt EOF + { + Object RESULT = null; + int start_valleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-1)).left; + int start_valright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-1)).right; + Object start_val = (Object)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-1)).value; + RESULT = start_val; + CUP$parser$result = new java_cup.runtime.Symbol(0/*$START*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-1)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT); + } + /* ACCEPT */ + CUP$parser$parser.done_parsing(); + return CUP$parser$result; + + /*. . . . . . . . . . . . . . . . . . . .*/ + case 0: // startpt ::= scfintro scfpat SCFDONE + { + Object RESULT = null; + if (DEBUG) System.out.println("CUP:gscfa: end of parse tree "); + table = new JTable(); + +// table = parseSCF.getTable(); + + CUP$parser$result = new java_cup.runtime.Symbol(1/*startpt*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-2)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT); + } + return CUP$parser$result; + + /* . . . . . .*/ + default: + throw new Exception( + "Invalid action number found in internal parse table"); + + } + } +} + http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/4231ac35/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gvb/GVBSym.java ---------------------------------------------------------------------- diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gvb/GVBSym.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gvb/GVBSym.java new file mode 100644 index 0000000..b398de2 --- /dev/null +++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gvb/GVBSym.java @@ -0,0 +1,45 @@ +/* +* +* Licensed to the Apache Software Foundation (ASF) under one +* or more contributor license agreements. See the NOTICE file +* distributed with this work for additional information +* regarding copyright ownership. The ASF licenses this file +* to you under the Apache License, Version 2.0 (the +* "License"); you may not use this file except in compliance +* with the License. You may obtain a copy of the License at +* +* http://www.apache.org/licenses/LICENSE-2.0 +* +* Unless required by applicable law or agreed to in writing, +* software distributed under the License is distributed on an +* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY +* KIND, either express or implied. See the License for the +* specific language governing permissions and limitations +* under the License. +* +*/ +package org.apache.airavata.datacat.parsers.gridchem.gvb; +//---------------------------------------------------- +// The following code was generated by CUP v0.10k +// Thu Sep 11 18:26:09 IST 2014 +//---------------------------------------------------- + +/** CUP generated class containing symbol constants. */ +public class GVBSym { + /* terminals */ + public static final int INTCycle = 7; + public static final int ENERGY = 12; + public static final int EOF = 0; + public static final int INT3 = 6; + public static final int INT2 = 5; + public static final int INT1 = 4; + public static final int error = 1; + public static final int FLOAT4 = 13; + public static final int FLOAT3 = 11; + public static final int FLOAT2 = 10; + public static final int SCFDONE = 3; + public static final int FLOAT1 = 9; + public static final int FOUNDITER = 2; + public static final int FLOAT = 8; +} + http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/4231ac35/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/inchi/InChI.java ---------------------------------------------------------------------- diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/inchi/InChI.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/inchi/InChI.java new file mode 100644 index 0000000..9c2dd80 --- /dev/null +++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/inchi/InChI.java @@ -0,0 +1,47 @@ +/* +* +* Licensed to the Apache Software Foundation (ASF) under one +* or more contributor license agreements. See the NOTICE file +* distributed with this work for additional information +* regarding copyright ownership. The ASF licenses this file +* to you under the Apache License, Version 2.0 (the +* "License"); you may not use this file except in compliance +* with the License. You may obtain a copy of the License at +* +* http://www.apache.org/licenses/LICENSE-2.0 +* +* Unless required by applicable law or agreed to in writing, +* software distributed under the License is distributed on an +* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY +* KIND, either express or implied. See the License for the +* specific language governing permissions and limitations +* under the License. +* +*/ +package org.apache.airavata.datacat.parsers.gridchem.inchi; + +public class InChI { + private String inchi; + private String inchiKey; + + public InChI(String inchi, String inchiKey) { + this.inchi = inchi; + this.inchiKey = inchiKey; + } + + public String getInchiKey() { + return inchiKey; + } + + public void setInchiKey(String inchiKey) { + this.inchiKey = inchiKey; + } + + public String getInchi() { + return inchi; + } + + public void setInchi(String inchi) { + this.inchi = inchi; + } +}
