datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mfinalcoord/MFinalCoordParser.java - airavata-sandbox - Git at Google

 /*
 *
 * 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.mfinalcoord;


 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 MFinalCoordParser extends java_cup.runtime.lr_parser implements GridChemQueueParser {

   /** Default constructor. */
   public MFinalCoordParser() {super();}

   /** Constructor which sets the default scanner. */
   public MFinalCoordParser(java_cup.runtime.Scanner s) {super(s);}

     /**
      * Constructor which uses a file reader.
      */
     public MFinalCoordParser(final FileReader fileReader) {
         super(new MFinalCoordLexer(fileReader));
     }


     /** Production table. */
   protected static final short _production_table[][] =
     lr_parser.unpackFromStrings(new String[]{
             "\000\016\000\002\003\005\000\002\002\004\000\002\004" +
                     "\003\000\002\005\004\000\002\005\003\000\002\006\006" +
                     "\000\002\017\004\000\002\017\003\000\002\020\010\000" +
                     "\002\012\003\000\002\013\003\000\002\014\003\000\002" +
                     "\015\003\000\002\016\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\032\000\004\005\005\001\002\000\004\004\010\001" +
                     "\002\000\004\004\uffff\001\002\000\004\002\007\001\002" +
                     "\000\004\002\000\001\002\000\004\007\015\001\002\000" +
                     "\006\004\010\006\013\001\002\000\006\004\ufffd\006\ufffd" +
                     "\001\002\000\004\002\001\001\002\000\006\004\ufffe\006" +
                     "\ufffe\001\002\000\004\011\016\001\002\000\004\012\ufff8" +
                     "\001\002\000\004\012\025\001\002\000\006\010\ufffa\011" +
                     "\ufffa\001\002\000\006\010\022\011\016\001\002\000\006" +
                     "\004\ufffc\006\ufffc\001\002\000\006\010\ufffb\011\ufffb\001" +
                     "\002\000\004\013\026\001\002\000\004\013\ufff7\001\002" +
                     "\000\004\016\027\001\002\000\004\017\ufff6\001\002\000" +
                     "\004\017\031\001\002\000\004\020\ufff5\001\002\000\004" +
                     "\020\033\001\002\000\006\010\ufff4\011\ufff4\001\002\000" +
                     "\006\010\ufff9\011\ufff9\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\032\000\006\003\005\004\003\001\001\000\006\005" +
                     "\010\006\011\001\001\000\002\001\001\000\002\001\001" +
                     "\000\002\001\001\000\002\001\001\000\004\006\013\001" +
                     "\001\000\002\001\001\000\002\001\001\000\002\001\001" +
                     "\000\010\012\016\017\020\020\017\001\001\000\002\001" +
                     "\001\000\004\013\023\001\001\000\002\001\001\000\006" +
                     "\012\016\020\022\001\001\000\002\001\001\000\002\001" +
                     "\001\000\002\001\001\000\002\001\001\000\004\014\027" +
                     "\001\001\000\002\001\001\000\004\015\031\001\001\000" +
                     "\002\001\001\000\004\016\033\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();
         HashMap<String,String> results= new HashMap<String,String>();
         int zCount=0;
         int xCount=0;
         int yCount=0;
         int center=0;
         int atom=0;
         for(int i=0;i<result.size();i++) {
             String singleString = result.get(i);
             String[] temp = singleString.split(" ");
             if (temp.length > 1) {
                 String keyElement = temp[0];
                 String dataElement = temp[1];
                 if (keyElement.equals("Z")) {
                     results.put("FinalCoordParser_Z_coord_" + zCount, dataElement);
                     zCount++;
                 } else if (keyElement.equals("Y")) {
                     results.put("FinalCoordParser_Y_coord_" + yCount, dataElement);
                     yCount++;
                 } else if (keyElement.equals("X")) {
                     results.put("FinalCoordParser_X_coord_" + xCount, dataElement);
                     xCount++;
                 } else if (keyElement.equals("Atom")) {
                     results.put("FinalCoordParser_AtomicNumber_" + atom, dataElement);
                     atom++;
                 } else if (keyElement.equals("center")) {
                     results.put("FinalCoordParser_CenterNumber_" + center, dataElement);
                     center++;
                 }
             }
         }
 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 MFinalCoordParser MFinalCoordParser;

   /** Constructor */
   CUP$parser$actions(MFinalCoordParser MFinalCoordParser) {
     this.MFinalCoordParser = MFinalCoordParser;
   }

   /** 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 13: // inp7 ::= INPUT7
             {
               Object RESULT = null;
 		int in7left = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left;
 		int in7right = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right;
 		Float in7 = (Float)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value;
 		 //___________________________________________________________________
    if (DEBUG) System.out.println("CUP:Input:  z coordinate "+in7);
                 MFinalCoordParser.addToResult("Z "+in7);

               CUP$parser$result = new java_cup.runtime.Symbol(12/*inp7*/, ((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 12: // inp6 ::= INPUT6
             {
               Object RESULT = null;
 		int in6left = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left;
 		int in6right = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right;
 		Float in6 = (Float)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value;
 		 //___________________________________________________________________
    if (DEBUG) System.out.println("CUP:Input:  y coordinate "+in6);
                 MFinalCoordParser.addToResult("Y "+in6);

               CUP$parser$result = new java_cup.runtime.Symbol(11/*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 11: // inp5 ::= INPUT5
             {
               Object RESULT = null;
 		int in5left = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left;
 		int in5right = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right;
 		Float in5 = (Float)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value;
 		 //___________________________________________________________________
    if (DEBUG) System.out.println("CUP:Input:  x coordinate "+in5);
                 MFinalCoordParser.addToResult("X "+in5);

               CUP$parser$result = new java_cup.runtime.Symbol(10/*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 10: // inp3 ::= INPUT3
             {
               Object RESULT = null;
 		int in3left = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left;
 		int in3right = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right;
 		Integer in3 = (Integer)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value;
 		 //___________________________________________________________________
    if (DEBUG) System.out.println("CUP:Input:  atomic number "+in3);
                 MFinalCoordParser.addToResult("Atom "+in3);

               CUP$parser$result = new java_cup.runtime.Symbol(9/*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 9: // inp2 ::= INPUT2
             {
               Object RESULT = null;
 		int in2left = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left;
 		int in2right = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right;
 		Integer in2 = (Integer)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value;
 		 //___________________________________________________________________
    if (DEBUG) System.out.println("CUP:Input:  center number "+in2);
                 MFinalCoordParser.addToResult("center "+in2);

               CUP$parser$result = new java_cup.runtime.Symbol(8/*inp2*/, ((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: // cycle2 ::= inp2 inp3 INPUT4 inp5 inp6 inp7
             {
               Object RESULT = null;

               CUP$parser$result = new java_cup.runtime.Symbol(14/*cycle2*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-5)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT);
             }
           return CUP$parser$result;

           /*. . . . . . . . . . . . . . . . . . . .*/
           case 7: // cycle1 ::= cycle2
             {
               Object RESULT = null;

               CUP$parser$result = new java_cup.runtime.Symbol(13/*cycle1*/, ((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: // cycle1 ::= cycle1 cycle2
             {
               Object RESULT = null;

               CUP$parser$result = new java_cup.runtime.Symbol(13/*cycle1*/, ((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 5: // scfcycle ::= INPUT1 DASH1 cycle1 DASH2
             {
               Object RESULT = null;

               CUP$parser$result = new java_cup.runtime.Symbol(4/*scfcycle*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-3)).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;
 		 if (DEBUG) System.out.println("CUP:Input: 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:Input:  found the start of 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;

               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");

         }
     }
 }
	/*
	*
	* 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.mfinalcoord;


	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 MFinalCoordParser extends java_cup.runtime.lr_parser implements GridChemQueueParser {

	/** Default constructor. */
	public MFinalCoordParser() {super();}

	/** Constructor which sets the default scanner. */
	public MFinalCoordParser(java_cup.runtime.Scanner s) {super(s);}

	/**
	* Constructor which uses a file reader.
	*/
	public MFinalCoordParser(final FileReader fileReader) {
	super(new MFinalCoordLexer(fileReader));
	}


	/** Production table. */
	protected static final short _production_table[][] =
	lr_parser.unpackFromStrings(new String[]{
	"\000\016\000\002\003\005\000\002\002\004\000\002\004" +
	"\003\000\002\005\004\000\002\005\003\000\002\006\006" +
	"\000\002\017\004\000\002\017\003\000\002\020\010\000" +
	"\002\012\003\000\002\013\003\000\002\014\003\000\002" +
	"\015\003\000\002\016\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\032\000\004\005\005\001\002\000\004\004\010\001" +
	"\002\000\004\004\uffff\001\002\000\004\002\007\001\002" +
	"\000\004\002\000\001\002\000\004\007\015\001\002\000" +
	"\006\004\010\006\013\001\002\000\006\004\ufffd\006\ufffd" +
	"\001\002\000\004\002\001\001\002\000\006\004\ufffe\006" +
	"\ufffe\001\002\000\004\011\016\001\002\000\004\012\ufff8" +
	"\001\002\000\004\012\025\001\002\000\006\010\ufffa\011" +
	"\ufffa\001\002\000\006\010\022\011\016\001\002\000\006" +
	"\004\ufffc\006\ufffc\001\002\000\006\010\ufffb\011\ufffb\001" +
	"\002\000\004\013\026\001\002\000\004\013\ufff7\001\002" +
	"\000\004\016\027\001\002\000\004\017\ufff6\001\002\000" +
	"\004\017\031\001\002\000\004\020\ufff5\001\002\000\004" +
	"\020\033\001\002\000\006\010\ufff4\011\ufff4\001\002\000" +
	"\006\010\ufff9\011\ufff9\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\032\000\006\003\005\004\003\001\001\000\006\005" +
	"\010\006\011\001\001\000\002\001\001\000\002\001\001" +
	"\000\002\001\001\000\002\001\001\000\004\006\013\001" +
	"\001\000\002\001\001\000\002\001\001\000\002\001\001" +
	"\000\010\012\016\017\020\020\017\001\001\000\002\001" +
	"\001\000\004\013\023\001\001\000\002\001\001\000\006" +
	"\012\016\020\022\001\001\000\002\001\001\000\002\001" +
	"\001\000\002\001\001\000\002\001\001\000\004\014\027" +
	"\001\001\000\002\001\001\000\004\015\031\001\001\000" +
	"\002\001\001\000\004\016\033\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();
	HashMap<String,String> results= new HashMap<String,String>();
	int zCount=0;
	int xCount=0;
	int yCount=0;
	int center=0;
	int atom=0;
	for(int i=0;i<result.size();i++) {
	String singleString = result.get(i);
	String[] temp = singleString.split(" ");
	if (temp.length > 1) {
	String keyElement = temp[0];
	String dataElement = temp[1];
	if (keyElement.equals("Z")) {
	results.put("FinalCoordParser_Z_coord_" + zCount, dataElement);
	zCount++;
	} else if (keyElement.equals("Y")) {
	results.put("FinalCoordParser_Y_coord_" + yCount, dataElement);
	yCount++;
	} else if (keyElement.equals("X")) {
	results.put("FinalCoordParser_X_coord_" + xCount, dataElement);
	xCount++;
	} else if (keyElement.equals("Atom")) {
	results.put("FinalCoordParser_AtomicNumber_" + atom, dataElement);
	atom++;
	} else if (keyElement.equals("center")) {
	results.put("FinalCoordParser_CenterNumber_" + center, dataElement);
	center++;
	}
	}
	}
	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 MFinalCoordParser MFinalCoordParser;

	/** Constructor */
	CUP$parser$actions(MFinalCoordParser MFinalCoordParser) {
	this.MFinalCoordParser = MFinalCoordParser;
	}

	/** 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 13: // inp7 ::= INPUT7
	{
	Object RESULT = null;
	int in7left = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left;
	int in7right = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right;
	Float in7 = (Float)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value;
	//___________________________________________________________________
	if (DEBUG) System.out.println("CUP:Input: z coordinate "+in7);
	MFinalCoordParser.addToResult("Z "+in7);

	CUP$parser$result = new java_cup.runtime.Symbol(12/inp7/, ((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 12: // inp6 ::= INPUT6
	{
	Object RESULT = null;
	int in6left = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left;
	int in6right = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right;
	Float in6 = (Float)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value;
	//___________________________________________________________________
	if (DEBUG) System.out.println("CUP:Input: y coordinate "+in6);
	MFinalCoordParser.addToResult("Y "+in6);

	CUP$parser$result = new java_cup.runtime.Symbol(11/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 11: // inp5 ::= INPUT5
	{
	Object RESULT = null;
	int in5left = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left;
	int in5right = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right;
	Float in5 = (Float)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value;
	//___________________________________________________________________
	if (DEBUG) System.out.println("CUP:Input: x coordinate "+in5);
	MFinalCoordParser.addToResult("X "+in5);

	CUP$parser$result = new java_cup.runtime.Symbol(10/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 10: // inp3 ::= INPUT3
	{
	Object RESULT = null;
	int in3left = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left;
	int in3right = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right;
	Integer in3 = (Integer)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value;
	//___________________________________________________________________
	if (DEBUG) System.out.println("CUP:Input: atomic number "+in3);
	MFinalCoordParser.addToResult("Atom "+in3);

	CUP$parser$result = new java_cup.runtime.Symbol(9/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 9: // inp2 ::= INPUT2
	{
	Object RESULT = null;
	int in2left = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left;
	int in2right = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right;
	Integer in2 = (Integer)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value;
	//___________________________________________________________________
	if (DEBUG) System.out.println("CUP:Input: center number "+in2);
	MFinalCoordParser.addToResult("center "+in2);

	CUP$parser$result = new java_cup.runtime.Symbol(8/inp2/, ((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: // cycle2 ::= inp2 inp3 INPUT4 inp5 inp6 inp7
	{
	Object RESULT = null;

	CUP$parser$result = new java_cup.runtime.Symbol(14/cycle2/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-5)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT);
	}
	return CUP$parser$result;

	/. . . . . . . . . . . . . . . . . . . ./
	case 7: // cycle1 ::= cycle2
	{
	Object RESULT = null;

	CUP$parser$result = new java_cup.runtime.Symbol(13/cycle1/, ((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: // cycle1 ::= cycle1 cycle2
	{
	Object RESULT = null;

	CUP$parser$result = new java_cup.runtime.Symbol(13/cycle1/, ((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 5: // scfcycle ::= INPUT1 DASH1 cycle1 DASH2
	{
	Object RESULT = null;

	CUP$parser$result = new java_cup.runtime.Symbol(4/scfcycle/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-3)).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;
	if (DEBUG) System.out.println("CUP:Input: 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:Input: found the start of 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;

	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");

	}
	}
	}