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Posted to commits@airavata.apache.org by sc...@apache.org on 2015/08/24 21:28:59 UTC

[21/32] airavata-sandbox git commit: adding datacat system

http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/4231ac35/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gfinalcoord/GFinalCoordLexer.java
----------------------------------------------------------------------
diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gfinalcoord/GFinalCoordLexer.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gfinalcoord/GFinalCoordLexer.java
new file mode 100644
index 0000000..4f17b3d
--- /dev/null
+++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gfinalcoord/GFinalCoordLexer.java
@@ -0,0 +1,773 @@
+/*
+*
+* 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.gfinalcoord;/* The following code was generated by JFlex 1.4.3 on 9/10/14 9:08 AM */
+
+import java_cup.runtime.*;
+
+
+/**
+ * This class is a scanner generated by 
+ * <a href="http://www.jflex.de/">JFlex</a> 1.4.3
+ * on 9/10/14 9:08 AM from the specification file
+ * <tt>gfinalcoord.flex</tt>
+ */
+public class GFinalCoordLexer 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 INPUTF = 30;
+  public static final int ITER2 = 4;
+  public static final int INPUTE = 28;
+  public static final int INPUTD = 26;
+  public static final int INPUTC = 24;
+  public static final int INPUTB = 22;
+  public static final int INPUTA = 20;
+  public static final int INTVALUE = 8;
+  public static final int INPUT = 18;
+  public static final int IGNOREALL = 16;
+  public static final int ITER = 2;
+  public static final int YYINITIAL = 0;
+  public static final int FLOAT2 = 14;
+  public static final int FLOAT1 = 12;
+  public static final int FLOATVALUE = 10;
+  public static final int ITER3 = 6;
+
+  /**
+   * 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,  2,  2,  2,  2,  2,  2,  2,  2,  2,  2, 
+     2,  2,  3,  3,  4,  4,  5,  5,  6,  6,  7,  7,  2,  2,  2, 2
+  };
+
+  /** 
+   * 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, 
+    17,  0,  0,  0,  0,  0,  0,  0, 18,  6,  0,  3,  0, 27,  4,  0, 
+     1,  1,  1,  1,  1,  1,  1,  1,  1,  1,  0,  0,  0,  0,  0,  0, 
+     0, 13, 19,  7, 10, 15,  5, 21, 20, 11,  2,  2, 26,  2, 12,  8, 
+     2,  2,  9, 16, 14, 28,  2,  2, 22, 23, 24,  0,  0,  0,  0, 25, 
+     0,  2,  2,  2,  2,  2,  2,  2,  2,  2,  2,  2,  2,  2,  2,  2, 
+     2,  2,  2,  2,  2,  2,  2,  2,  2,  2,  2,  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 =
+    "\10\0\5\1\2\2\10\1\4\0\1\2\14\0\1\2"+
+    "\1\3\1\4\1\5\1\6\4\0\1\2\4\0\1\2"+
+    "\4\0\1\2\4\0\1\2\4\0\1\2\4\0\1\2"+
+    "\4\0\1\2\4\0\1\2\4\0\1\2\14\0\1\7"+
+    "\12\0\1\10\14\0\1\11\41\0\1\12";
+
+  private static int [] zzUnpackAction() {
+    int [] result = new int[161];
+    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\35\0\72\0\127\0\164\0\221\0\256\0\313"+
+    "\0\350\0\u0105\0\u0122\0\u013f\0\u015c\0\u0179\0\u0196\0\u01b3"+
+    "\0\u01d0\0\u01ed\0\u020a\0\u0227\0\u0244\0\u0261\0\u027e\0\u029b"+
+    "\0\u02b8\0\u02d5\0\u02f2\0\u030f\0\u01b3\0\u032c\0\u01ed\0\u0349"+
+    "\0\u0227\0\u0366\0\u0261\0\u0383\0\u03a0\0\u03bd\0\u03da\0\u03f7"+
+    "\0\u0414\0\u032c\0\u0349\0\u0366\0\u0383\0\u0431\0\u044e\0\u046b"+
+    "\0\u0488\0\u04a5\0\u04c2\0\u04df\0\u04fc\0\u0519\0\u0536\0\u0553"+
+    "\0\u0570\0\u058d\0\u05aa\0\u05c7\0\u05e4\0\u0601\0\u061e\0\u063b"+
+    "\0\u0658\0\u0675\0\u0692\0\u06af\0\u06cc\0\u06e9\0\u0706\0\u0723"+
+    "\0\u0740\0\u075d\0\u077a\0\u0797\0\u07b4\0\u07d1\0\u07ee\0\u080b"+
+    "\0\u0828\0\u0845\0\u0862\0\u087f\0\u089c\0\u08b9\0\u08d6\0\u08f3"+
+    "\0\u0910\0\u092d\0\u094a\0\u0967\0\u0984\0\u09a1\0\u09be\0\u09db"+
+    "\0\u09f8\0\u0a15\0\u0a32\0\u0a4f\0\u0a6c\0\u0a89\0\350\0\u0aa6"+
+    "\0\u0ac3\0\u0ae0\0\u0afd\0\u0b1a\0\u0b37\0\u0b54\0\u0b71\0\u0b8e"+
+    "\0\u0bab\0\350\0\u0bc8\0\u0be5\0\u0c02\0\u0c1f\0\u0c3c\0\u0c59"+
+    "\0\u0c76\0\u0c93\0\u0cb0\0\u0ccd\0\u0cea\0\u0d07\0\350\0\u0d24"+
+    "\0\u0d41\0\u0d5e\0\u0d7b\0\u0d98\0\u0db5\0\u0dd2\0\u0def\0\u0e0c"+
+    "\0\u0e29\0\u0e46\0\u0e63\0\u0e80\0\u0e9d\0\u0eba\0\u0ed7\0\u0ef4"+
+    "\0\u0f11\0\u0f2e\0\u0f4b\0\u0f68\0\u0f85\0\u0fa2\0\u0fbf\0\u0fdc"+
+    "\0\u0ff9\0\u1016\0\u1033\0\u1050\0\u106d\0\u108a\0\u10a7\0\u10c4"+
+    "\0\350";
+
+  private static int [] zzUnpackRowMap() {
+    int [] result = new int[161];
+    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 =
+    "\7\11\1\12\34\11\1\13\6\11\1\14\14\11\1\15"+
+    "\40\11\1\16\2\11\1\16\1\11\4\16\1\17\5\16"+
+    "\2\11\10\16\1\11\1\16\1\11\1\20\1\11\1\21"+
+    "\27\11\1\21\2\11\1\22\1\11\1\23\27\11\1\23"+
+    "\2\11\1\24\1\11\1\25\27\11\1\25\2\11\1\26"+
+    "\1\11\1\27\27\11\1\27\1\11\45\0\1\30\50\0"+
+    "\1\31\34\0\1\32\43\0\1\33\2\0\2\16\2\0"+
+    "\1\16\1\0\12\16\2\0\10\16\1\0\1\16\1\0"+
+    "\2\16\2\0\1\16\1\0\5\16\1\34\4\16\2\0"+
+    "\10\16\1\0\1\16\1\0\1\35\2\0\1\36\31\0"+
+    "\1\35\34\0\1\37\2\0\1\40\31\0\1\37\34\0"+
+    "\1\41\2\0\1\42\31\0\1\41\34\0\1\43\2\0"+
+    "\1\44\31\0\1\43\43\0\1\45\41\0\1\46\36\0"+
+    "\1\47\50\0\1\50\2\0\2\16\2\0\1\16\1\0"+
+    "\7\16\1\51\2\16\2\0\10\16\1\0\1\16\1\0"+
+    "\1\52\34\0\1\53\34\0\1\54\34\0\1\55\44\0"+
+    "\1\56\34\0\1\57\54\0\1\60\36\0\1\61\2\0"+
+    "\2\16\2\0\1\16\1\0\10\16\1\62\1\16\2\0"+
+    "\10\16\1\0\1\16\12\0\1\63\47\0\1\64\26\0"+
+    "\1\65\50\0\1\66\2\0\2\16\2\0\1\16\1\0"+
+    "\2\16\1\67\7\16\2\0\10\16\1\0\1\16\13\0"+
+    "\1\70\40\0\1\71\31\0\1\72\53\0\1\73\2\0"+
+    "\2\16\2\0\1\16\1\0\5\16\1\74\4\16\2\0"+
+    "\10\16\1\0\1\16\14\0\1\75\41\0\1\76\25\0"+
+    "\1\77\55\0\1\100\2\0\2\16\2\0\1\16\1\0"+
+    "\12\16\2\0\10\16\1\0\1\101\15\0\1\102\40\0"+
+    "\1\103\44\0\1\104\36\0\1\105\2\0\2\16\2\0"+
+    "\1\16\1\0\1\106\11\16\2\0\10\16\1\0\1\16"+
+    "\16\0\1\107\37\0\1\110\23\0\1\111\57\0\1\112"+
+    "\2\0\2\16\2\0\1\16\1\0\12\16\2\0\7\16"+
+    "\1\113\1\0\1\16\17\0\1\114\36\0\1\115\20\0"+
+    "\1\116\62\0\1\117\2\0\2\16\2\0\1\16\1\0"+
+    "\10\16\1\120\1\16\2\0\10\16\1\0\1\16\20\0"+
+    "\1\121\35\0\1\122\44\0\1\123\36\0\1\124\2\0"+
+    "\2\16\2\0\1\16\1\0\6\16\1\125\3\16\2\0"+
+    "\10\16\1\0\1\16\21\0\1\126\34\0\1\127\20\0"+
+    "\1\130\62\0\1\131\2\0\2\16\2\0\1\16\1\0"+
+    "\2\16\1\132\7\16\2\0\10\16\1\0\1\16\22\0"+
+    "\1\133\33\0\1\134\26\0\1\135\54\0\1\136\2\0"+
+    "\2\16\2\0\1\16\1\0\12\16\1\137\1\0\10\16"+
+    "\1\0\1\16\23\0\1\140\32\0\1\141\45\0\1\142"+
+    "\35\0\1\143\13\0\1\144\32\0\1\145\45\0\1\146"+
+    "\32\0\1\147\50\0\1\150\14\0\1\151\45\0\1\152"+
+    "\36\0\1\153\41\0\1\154\21\0\1\155\25\0\1\156"+
+    "\44\0\1\157\46\0\1\160\17\0\1\161\24\0\1\162"+
+    "\47\0\1\163\46\0\1\164\16\0\1\165\40\0\1\166"+
+    "\46\0\1\167\15\0\1\170\41\0\1\171\46\0\1\172"+
+    "\10\0\1\173\46\0\1\174\46\0\1\147\20\0\1\175"+
+    "\36\0\1\176\33\0\1\177\35\0\1\200\34\0\1\201"+
+    "\34\0\1\202\34\0\1\203\34\0\1\204\34\0\1\205"+
+    "\34\0\1\206\34\0\1\207\34\0\1\210\34\0\1\211"+
+    "\34\0\1\212\34\0\1\213\34\0\1\214\42\0\1\215"+
+    "\26\0\1\216\34\0\1\217\34\0\1\220\34\0\1\221"+
+    "\34\0\1\222\34\0\1\223\34\0\1\224\34\0\1\225"+
+    "\34\0\1\226\34\0\1\227\34\0\1\230\34\0\1\231"+
+    "\34\0\1\232\34\0\1\233\34\0\1\234\34\0\1\235"+
+    "\34\0\1\236\34\0\1\237\34\0\1\240\43\0\1\241"+
+    "\4\0";
+
+  private static int [] zzUnpackTrans() {
+    int [] result = new int[4321];
+    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 =
+    "\10\0\1\11\16\1\4\0\1\1\14\0\5\1\4\0"+
+    "\1\1\4\0\1\1\4\0\1\1\4\0\1\1\4\0"+
+    "\1\1\4\0\1\1\4\0\1\1\4\0\1\1\4\0"+
+    "\1\1\14\0\1\11\12\0\1\11\14\0\1\11\41\0"+
+    "\1\11";
+
+  private static int [] zzUnpackAttribute() {
+    int [] result = new int[161];
+    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 GFinalCoordLexer(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 GFinalCoordLexer(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 2: 
+          { yybegin (INPUTA);
+   return new Symbol(GFinalCoordSym.INPUT2);
+          }
+        case 11: break;
+        case 5: 
+          { yybegin (INPUTD);
+   return new Symbol(GFinalCoordSym.INPUT5, new Float(yytext()));
+          }
+        case 12: break;
+        case 6: 
+          { yybegin (INPUT);
+   return new Symbol(GFinalCoordSym.INPUT6, new Float(yytext()));
+          }
+        case 13: break;
+        case 9: 
+          { yybegin (IGNOREALL);
+   return new Symbol(GFinalCoordSym.SCFDONE);
+          }
+        case 14: break;
+        case 8: 
+          { yybegin(ITER);
+	   return new Symbol(GFinalCoordSym.FOUNDITER);
+          }
+        case 15: break;
+        case 10: 
+          { yybegin(INPUT);
+            return new Symbol(GFinalCoordSym.INPUT1);
+          }
+        case 16: break;
+        case 7: 
+          { yybegin(IGNOREALL);
+      return new Symbol(GFinalCoordSym.SCFDONE);
+          }
+        case 17: break;
+        case 4: 
+          { yybegin (INPUTC);
+   return new Symbol(GFinalCoordSym.INPUT4, new Float(yytext()));
+          }
+        case 18: break;
+        case 3: 
+          { yybegin (INPUTB);
+   return new Symbol(GFinalCoordSym.INPUT3, new Float(yytext()));
+          }
+        case 19: break;
+        case 1: 
+          { 
+          }
+        case 20: break;
+        default: 
+          if (zzInput == YYEOF && zzStartRead == zzCurrentPos) {
+            zzAtEOF = true;
+            zzDoEOF();
+              { return new java_cup.runtime.Symbol(GFinalCoordSym.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 <me...@yahoo.com>
+   */
+  private String getTokenName(int token) {
+    try {
+      java.lang.reflect.Field [] classFields = GFinalCoordSym.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 <me...@yahoo.com>
+   */
+  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 GFinalCoordLexer <inputfile>");
+    }
+    else {
+      for (int i = 0; i < argv.length; i++) {
+        GFinalCoordLexer scanner = null;
+        try {
+          scanner = new GFinalCoordLexer( 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/gfinalcoord/GFinalCoordParser.java
----------------------------------------------------------------------
diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gfinalcoord/GFinalCoordParser.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gfinalcoord/GFinalCoordParser.java
new file mode 100644
index 0000000..8889053
--- /dev/null
+++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gfinalcoord/GFinalCoordParser.java
@@ -0,0 +1,339 @@
+/*
+*
+* 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.gfinalcoord;
+
+
+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 GFinalCoordParser extends java_cup.runtime.lr_parser implements GridChemQueueParser {
+
+  /** Default constructor. */
+  public GFinalCoordParser() {super();}
+
+  /** Constructor which sets the default scanner. */
+  public GFinalCoordParser(java_cup.runtime.Scanner s) {super(s);}
+
+    /**
+     * Constructor which uses a file reader.
+     */
+    public GFinalCoordParser(final FileReader fileReader) {
+        super(new GFinalCoordLexer(fileReader));
+    }
+
+  /** Production table. */
+  protected static final short _production_table[][] = 
+    lr_parser.unpackFromStrings(new String[]{
+            "\000\012\000\002\003\005\000\002\002\004\000\002\004" +
+                    "\004\000\002\005\004\000\002\005\003\000\002\006\007" +
+                    "\000\002\007\003\000\002\010\003\000\002\011\003\000" +
+                    "\002\012\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\023\000\004\006\005\001\002\000\004\005\011\001" +
+                    "\002\000\004\004\010\001\002\000\004\002\007\001\002" +
+                    "\000\004\002\000\001\002\000\004\005\uffff\001\002\000" +
+                    "\004\010\017\001\002\000\006\005\011\007\014\001\002" +
+                    "\000\006\005\ufffd\007\ufffd\001\002\000\004\002\001\001" +
+                    "\002\000\006\005\ufffe\007\ufffe\001\002\000\004\011\020" +
+                    "\001\002\000\004\011\ufffb\001\002\000\004\012\ufffa\001" +
+                    "\002\000\004\012\022\001\002\000\004\013\ufff9\001\002" +
+                    "\000\004\013\024\001\002\000\006\005\ufff8\007\ufff8\001" +
+                    "\002\000\006\005\ufffc\007\ufffc\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\023\000\006\003\005\004\003\001\001\000\006\005" +
+                    "\011\006\012\001\001\000\002\001\001\000\002\001\001" +
+                    "\000\002\001\001\000\002\001\001\000\004\007\015\001" +
+                    "\001\000\004\006\014\001\001\000\002\001\001\000\002" +
+                    "\001\001\000\002\001\001\000\004\010\020\001\001\000" +
+                    "\002\001\001\000\002\001\001\000\004\011\022\001\001" +
+                    "\000\002\001\001\000\004\012\024\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
+    //center# atomic# x_coord y_coord z_coord
+    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();
+        int e6Count=0;
+        int e5Count=0;
+        int e4Count=0;
+        int e=0;
+        HashMap<String, String> results = new HashMap<String, String>();
+        for (int i = 0; i < result.size(); i++) {
+            String singleString= result.get(i);
+            String[] temp= singleString.split(" ");
+            String firstElement=temp[0];
+            String dataElement=temp[1];
+            if(firstElement.equals("e6")){
+                results.put("GFinalCoord_e6_"+e6Count,dataElement);
+                e6Count++;
+            }else if(firstElement.equals("e5")){
+                results.put("GFinalCoord_e5_"+e5Count,dataElement);
+                e5Count++;
+            }else if(firstElement.equals("e4")){
+                results.put("GFinalCoord_e4_"+e4Count,dataElement);
+                e4Count++;
+            }else if(firstElement.equals("e")){
+                results.put("GFinalCoord_e_"+e,dataElement);
+                e++;
+            }
+        }
+        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;
+  }
+
+
+  private final GFinalCoordParser GFinalCoordParser;
+
+  /** Constructor */
+  CUP$parser$actions(GFinalCoordParser GFinalCoordParser) {
+    this.GFinalCoordParser = GFinalCoordParser;
+  }
+
+  /** 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 9: // inp6 ::= INPUT6 
+            {
+              Object RESULT = null;
+		int e6left = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left;
+		int e6right = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right;
+		Float e6 = (Float)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value;
+        GFinalCoordParser.addToResult("e6 "+e6);
+
+              CUP$parser$result = new java_cup.runtime.Symbol(8/*inp6*/, ((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 8: // inp5 ::= INPUT5 
+            {
+              Object RESULT = null;
+		int e5left = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left;
+		int e5right = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right;
+		Float e5 = (Float)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value;
+        GFinalCoordParser.addToResult("e5 "+e5);
+
+              CUP$parser$result = new java_cup.runtime.Symbol(7/*inp5*/, ((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 7: // inp4 ::= INPUT4 
+            {
+              Object RESULT = null;
+		int e4left = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left;
+		int e4right = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right;
+		Float e4 = (Float)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value;
+        GFinalCoordParser.addToResult("e4 "+e4);
+
+              CUP$parser$result = new java_cup.runtime.Symbol(6/*inp4*/, ((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: // inp3 ::= INPUT3 
+            {
+              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;
+        GFinalCoordParser.addToResult("e "+e);
+
+              CUP$parser$result = new java_cup.runtime.Symbol(5/*inp3*/, ((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 5: // scfcycle ::= INPUT2 inp3 inp4 inp5 inp6 
+            {
+              Object RESULT = null;
+
+              CUP$parser$result = new java_cup.runtime.Symbol(4/*scfcycle*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-4)).left, ((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;
+
+              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 INPUT1 
+            {
+              Object RESULT = null;
+
+              CUP$parser$result = new java_cup.runtime.Symbol(2/*scfintro*/, ((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 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;
+
+              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/gfinalcoord/GFinalCoordSym.java
----------------------------------------------------------------------
diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gfinalcoord/GFinalCoordSym.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gfinalcoord/GFinalCoordSym.java
new file mode 100644
index 0000000..3e1203a
--- /dev/null
+++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gfinalcoord/GFinalCoordSym.java
@@ -0,0 +1,41 @@
+/*
+*
+* 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.gfinalcoord;
+//----------------------------------------------------
+// The following code was generated by CUP v0.10k
+// Wed Sep 10 09:08:56 IST 2014
+//----------------------------------------------------
+
+/** CUP generated class containing symbol constants. */
+public class GFinalCoordSym {
+  /* terminals */
+  public static final int EOF = 0;
+  public static final int error = 1;
+  public static final int INPUT6 = 9;
+  public static final int INPUT5 = 8;
+  public static final int INPUT4 = 7;
+  public static final int SCFDONE = 5;
+  public static final int INPUT3 = 6;
+  public static final int FOUNDITER = 4;
+  public static final int INPUT2 = 3;
+  public static final int INPUT1 = 2;
+}
+

http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/4231ac35/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gmcscfa/GMCSCFaLexer.java
----------------------------------------------------------------------
diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gmcscfa/GMCSCFaLexer.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gmcscfa/GMCSCFaLexer.java
new file mode 100644
index 0000000..05439b1
--- /dev/null
+++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gmcscfa/GMCSCFaLexer.java
@@ -0,0 +1,782 @@
+/*
+*
+* 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.gmcscfa;/* The following code was generated by JFlex 1.4.3 on 9/10/14 9:36 AM */
+
+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 9/10/14 9:36 AM from the specification file
+ * <tt>gmcscfa.flex</tt>
+ */
+public class GMCSCFaLexer 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, 
+    11,  0,  0,  0,  0,  0,  0,  0, 19,  6,  0,  3,  0, 25,  4,  0, 
+     1,  2,  2,  2,  2,  2,  2,  2,  2,  2,  0,  0,  0,  0,  0,  0, 
+     0, 13,  0, 23, 18,  9,  5, 16,  0,  7,  0,  0, 14, 21, 15, 12, 
+    24, 22, 10, 20,  8,  0, 26,  0,  0, 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\0\1\14\5\0\1\15\61\0"+
+    "\1\16";
+
+  private static int [] zzUnpackAction() {
+    int [] result = new int[168];
+    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\33\0\66\0\121\0\154\0\207\0\242\0\275"+
+    "\0\330\0\363\0\u010e\0\u0129\0\u0144\0\u0129\0\u015f\0\u017a"+
+    "\0\u0129\0\u0195\0\u01b0\0\u01cb\0\u01e6\0\u0129\0\u0201\0\u021c"+
+    "\0\u0237\0\u0252\0\u026d\0\u0288\0\u02a3\0\u02be\0\u02d9\0\u02f4"+
+    "\0\u030f\0\u032a\0\u01b0\0\u0345\0\u0360\0\u0201\0\u037b\0\u0237"+
+    "\0\u0396\0\u026d\0\u03b1\0\u02a3\0\u03cc\0\u02d9\0\u03e7\0\u0402"+
+    "\0\u041d\0\u0345\0\u0438\0\u0453\0\u0396\0\u03b1\0\u03cc\0\u03e7"+
+    "\0\u046e\0\u0489\0\u04a4\0\u04bf\0\u04da\0\u04f5\0\u0510\0\u052b"+
+    "\0\u0546\0\u0561\0\u057c\0\u0597\0\u05b2\0\u05cd\0\u05e8\0\u0603"+
+    "\0\u061e\0\u0639\0\u0654\0\u066f\0\u068a\0\u06a5\0\u06c0\0\u06db"+
+    "\0\u06f6\0\u0711\0\u072c\0\u0747\0\u0762\0\u077d\0\u0798\0\u07b3"+
+    "\0\u07ce\0\u07e9\0\u0804\0\u081f\0\u083a\0\u0855\0\u0870\0\u088b"+
+    "\0\u08a6\0\u08c1\0\u08dc\0\u08f7\0\u0912\0\u092d\0\u0948\0\u0963"+
+    "\0\u097e\0\u0999\0\u09b4\0\u09cf\0\u09ea\0\u0129\0\u0a05\0\u0129"+
+    "\0\u0a20\0\u0a3b\0\u0a56\0\u0a71\0\u0a8c\0\u0129\0\u0aa7\0\u0ac2"+
+    "\0\u0add\0\u0af8\0\u0b13\0\u0b2e\0\u0b49\0\u0b64\0\u0b7f\0\u0b9a"+
+    "\0\u0bb5\0\u0bd0\0\u0beb\0\u0c06\0\u0c21\0\u0c3c\0\u0c57\0\u0c72"+
+    "\0\u0c8d\0\u0ca8\0\u0cc3\0\u0cde\0\u0cf9\0\u0d14\0\u0d2f\0\u0d4a"+
+    "\0\u0d65\0\u0d80\0\u0d9b\0\u0db6\0\u0dd1\0\u0dec\0\u0e07\0\u0e22"+
+    "\0\u0e3d\0\u0e58\0\u0e73\0\u0e8e\0\u0ea9\0\u0ec4\0\u0edf\0\u0efa"+
+    "\0\u0f15\0\u0f30\0\u0f4b\0\u0f66\0\u0f81\0\u0f9c\0\u0fb7\0\u0129";
+
+  private static int [] zzUnpackRowMap() {
+    int [] result = new int[168];
+    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 =
+    "\7\14\1\15\57\14\1\16\1\17\26\14\1\20\2\14"+
+    "\1\21\1\22\31\14\2\23\1\24\25\14\1\24\17\14"+
+    "\1\25\14\14\1\26\3\27\25\26\1\30\1\26\1\14"+
+    "\2\31\1\32\25\14\1\32\2\14\2\33\1\34\25\14"+
+    "\1\34\2\14\2\35\1\36\25\14\1\36\2\14\2\37"+
+    "\1\40\25\14\1\40\1\14\43\0\1\41\23\0\2\17"+
+    "\61\0\1\42\2\0\2\22\31\0\2\43\1\0\1\44"+
+    "\27\0\2\43\45\0\1\45\16\0\2\46\31\0\2\46"+
+    "\26\0\1\47\2\0\2\50\1\0\1\51\27\0\2\50"+
+    "\31\0\2\52\1\0\1\53\27\0\2\52\31\0\2\54"+
+    "\1\0\1\55\27\0\2\54\31\0\2\56\1\0\1\57"+
+    "\27\0\2\56\41\0\1\60\52\0\1\61\2\0\2\62"+
+    "\50\0\1\63\43\0\1\64\2\0\2\65\31\0\2\66"+
+    "\31\0\2\67\31\0\2\70\42\0\1\71\51\0\1\72"+
+    "\13\0\1\73\51\0\1\74\14\0\1\75\50\0\1\76"+
+    "\16\0\1\77\46\0\1\100\14\0\1\101\50\0\1\102"+
+    "\20\0\1\103\44\0\1\104\14\0\1\105\50\0\1\106"+
+    "\21\0\1\107\43\0\1\110\14\0\1\111\50\0\1\112"+
+    "\10\0\1\113\54\0\1\114\14\0\1\115\50\0\1\116"+
+    "\16\0\1\117\46\0\1\120\11\0\1\121\53\0\1\122"+
+    "\20\0\1\123\44\0\1\124\15\0\1\125\47\0\1\126"+
+    "\14\0\1\127\50\0\1\130\11\0\1\131\53\0\1\132"+
+    "\30\0\1\133\34\0\1\134\16\0\1\135\46\0\1\136"+
+    "\15\0\1\137\47\0\1\140\17\0\1\141\45\0\1\142"+
+    "\20\0\1\143\44\0\1\144\14\0\1\145\50\0\1\146"+
+    "\33\0\1\147\31\0\1\150\12\0\1\151\52\0\1\152"+
+    "\12\0\1\153\52\0\1\154\20\0\1\155\44\0\1\156"+
+    "\13\0\1\157\51\0\1\160\12\0\1\161\41\0\1\162"+
+    "\24\0\1\163\31\0\1\164\41\0\1\165\34\0\1\166"+
+    "\31\0\1\167\24\0\1\170\32\0\1\171\32\0\1\172"+
+    "\32\0\1\173\32\0\1\174\32\0\1\175\32\0\1\176"+
+    "\32\0\1\177\41\0\1\200\21\0\1\201\37\0\1\202"+
+    "\37\0\1\203\20\0\1\204\27\0\1\205\37\0\1\206"+
+    "\32\0\1\207\32\0\1\210\32\0\1\211\35\0\1\212"+
+    "\31\0\1\213\35\0\1\214\16\0\1\215\43\0\1\216"+
+    "\41\0\1\217\27\0\1\220\36\0\1\221\32\0\1\222"+
+    "\11\0\1\223\41\0\1\224\32\0\1\225\43\0\1\226"+
+    "\34\0\1\227\33\0\1\230\25\0\1\231\15\0\1\232"+
+    "\40\0\1\233\32\0\1\234\44\0\1\235\14\0\1\236"+
+    "\52\0\1\237\12\0\1\240\33\0\1\241\35\0\1\242"+
+    "\32\0\1\243\32\0\1\244\41\0\1\245\25\0\1\246"+
+    "\42\0\1\247\35\0\1\250\2\0";
+
+  private static int [] zzUnpackTrans() {
+    int [] result = new int[4050];
+    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"+
+    "\1\11\1\0\1\11\5\0\1\11\61\0\1\11";
+
+  private static int [] zzUnpackAttribute() {
+    int [] result = new int[168];
+    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 GMCSCFaLexer(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 GMCSCFaLexer(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 4: 
+          { if  (Settings.DEBUG) System.out.println("GMCSCFaFlex: Found new line");
+          }
+        case 15: break;
+        case 7: 
+          { if (Settings.DEBUG) System.out.println("GMCSCFaFlex: Found the energy");
+   if (Settings.DEBUG) System.out.println(yytext());
+   yybegin(ITER5);
+   return new Symbol(GMCSCFaSym.ENERGY, new Float(yytext()));
+          }
+        case 16: break;
+        case 10: 
+          { if  (Settings.DEBUG) System.out.println("GMCSCFaFlex: Found float3");
+     yybegin(ITER2);
+      return new Symbol(GMCSCFaSym.FLOAT3);
+          }
+        case 17: break;
+        case 9: 
+          { if  (Settings.DEBUG) System.out.println("GMCSCFaFlex: Found float2");
+  yybegin (ITER7);
+   return new Symbol(GMCSCFaSym.FLOAT2);
+          }
+        case 18: break;
+        case 12: 
+          { yybegin(DASH);
+          }
+        case 19: break;
+        case 8: 
+          { if (Settings.DEBUG) System.out.println("GMCSCFaFlex: ITER5");
+   if (Settings.DEBUG) System.out.println("GMCSCFaFlex: Found float1");
+   yybegin (ITER6);
+    return new Symbol(GMCSCFaSym.FLOAT1);
+          }
+        case 20: break;
+        case 5: 
+          { if  (Settings.DEBUG) System.out.println("GMCSCFaFlex: Found float value");
+  yybegin(ITER);
+          }
+        case 21: break;
+        case 13: 
+          { yybegin(IGNOREALL);
+  return new Symbol(GMCSCFaSym.SCFDONE);
+          }
+        case 22: break;
+        case 11: 
+          { if (Settings.DEBUG) System.out.println("GMCSCFaFlex: Found the dash");
+               yybegin(DASH);
+          }
+        case 23: break;
+        case 6: 
+          { if  (Settings.DEBUG) System.out.println("GMCSCFaFlex: Found float4");
+     yybegin(ITER);
+      return new Symbol(GMCSCFaSym.FLOAT4);
+          }
+        case 24: break;
+        case 2: 
+          { if (Settings.DEBUG) System.out.println("GMCSCFaFlex: Found the first integer in the iteration");
+   if (Settings.DEBUG) System.out.println(yytext());
+   yybegin(ITER4);
+   return new Symbol(GMCSCFaSym.INTCycle, new Integer(yytext()));
+          }
+        case 25: break;
+        case 14: 
+          { if (Settings.DEBUG) System.out.println("GMCSCFaFlex: Found START OF");
+	   yybegin(ITER);
+	   return new Symbol(GMCSCFaSym.FOUNDITER);
+          }
+        case 26: break;
+        case 1: 
+          { 
+          }
+        case 27: break;
+        case 3: 
+          { if (Settings.DEBUG) System.out.println("GMCSCFaFlex: Found the second integer in the iteration");
+     if (Settings.DEBUG) System.out.println(yytext());
+     yybegin(ITER8); 
+      return new Symbol(GMCSCFaSym.INT1, new Integer(yytext()));
+          }
+        case 28: break;
+        default: 
+          if (zzInput == YYEOF && zzStartRead == zzCurrentPos) {
+            zzAtEOF = true;
+            zzDoEOF();
+              { return new java_cup.runtime.Symbol(GMCSCFaSym.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 <me...@yahoo.com>
+   */
+  private String getTokenName(int token) {
+    try {
+      java.lang.reflect.Field [] classFields = GMCSCFaSym.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 <me...@yahoo.com>
+   */
+  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 GMCSCFaLexer <inputfile>");
+    }
+    else {
+      for (int i = 0; i < argv.length; i++) {
+        GMCSCFaLexer scanner = null;
+        try {
+          scanner = new GMCSCFaLexer( 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/gmcscfa/GMCSCFaSym.java
----------------------------------------------------------------------
diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gmcscfa/GMCSCFaSym.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gmcscfa/GMCSCFaSym.java
new file mode 100644
index 0000000..bfdd7d9
--- /dev/null
+++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gmcscfa/GMCSCFaSym.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.gmcscfa;
+//----------------------------------------------------
+// The following code was generated by CUP v0.10k
+// Wed Sep 10 09:37:06 IST 2014
+//----------------------------------------------------
+
+/** CUP generated class containing symbol constants. */
+public class GMCSCFaSym {
+  /* 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/gmcscfa/GmcscfaParser.java
----------------------------------------------------------------------
diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gmcscfa/GmcscfaParser.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gmcscfa/GmcscfaParser.java
new file mode 100644
index 0000000..7fc4800
--- /dev/null
+++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/gmcscfa/GmcscfaParser.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.gmcscfa;
+
+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 GmcscfaParser extends java_cup.runtime.lr_parser implements GridChemQueueParser {
+
+  /** Default constructor. */
+  public GmcscfaParser() {super();}
+
+  /** Constructor which sets the default scanner. */
+  public GmcscfaParser(java_cup.runtime.Scanner s) {super(s);}
+
+    /**
+     * Constructor which uses a file reader.
+     */
+    public GmcscfaParser(final FileReader fileReader) {
+        super(new GMCSCFaLexer(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\016\ufffc" +
+                    "\001\002\000\004\016\015\001\002\000\004\013\016\001" +
+                    "\002\000\004\013\ufffa\001\002\000\004\014\017\001\002" +
+                    "\000\004\015\020\001\002\000\004\006\021\001\002\000" +
+                    "\004\017\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\004\007\013\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\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, iteration
+    private ArrayList<String> result = new ArrayList<String>();
+    private String tempStr = "";
+
+    public void addToResult(String value) {
+        result.add(value);
+    }
+
+
+    public ArrayList<String> getResult() {
+        return result;
+    }
+
+    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 energy=0;
+        int iteration=0;
+        for (int i=0;i<result.size();i++){
+            String singleResult=result.get(i);
+            String[] temp= singleResult.split(" ");
+            if(temp.length>1){
+                String keyElement=temp[0];
+                String dataEelement=temp[1];
+                if(keyElement.equals("ENERGY")){
+                    results.put("GmcscfaParser_ENERGY_"+energy,dataEelement);
+                    energy++;
+                }else if (keyElement.equals("ITERATION")){
+                    results.put("GmcscfaParser_ITERATION_"+iteration,dataEelement);
+                    iteration++;
+                }
+            }
+        }
+        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 GmcscfaParser GmcscfaParser;
+
+  /** Constructor */
+  CUP$parser$actions(GmcscfaParser GmcscfaParser) {
+    this.GmcscfaParser = GmcscfaParser;
+  }
+
+  /** 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);
+   GmcscfaParser.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 en FLOAT1 FLOAT2 FLOAT3 INT1 FLOAT4 
+            {
+              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$top-0)).value;
+ //___________________________________________________________________
+   if (DEBUG) System.out.println("CUP:gscfa:scfcycle:  ITERATION "+c);
+    GmcscfaParser.addToResult("ITERATION "+c);
+//  temp2.print(c);
+//   temp2.print(" "); 
+//  cycle = c;
+ 
+//  parseSCF.putField("iteration "+cycle, cycle);
+ 
+              CUP$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");
+
+        }
+    }
+}
+