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Posted to commits@airavata.apache.org by sc...@apache.org on 2015/08/24 21:28:54 UTC
[16/32] 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/mopta/MOptaParser.java
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diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mopta/MOptaParser.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mopta/MOptaParser.java
new file mode 100644
index 0000000..4fffdcb
--- /dev/null
+++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mopta/MOptaParser.java
@@ -0,0 +1,388 @@
+/*
+*
+* 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.mopta;
+
+
+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 MOptaParser extends java_cup.runtime.lr_parser implements GridChemQueueParser {
+
+ /**
+ * Constructor which uses a file reader.
+ */
+ public MOptaParser(final FileReader fileReader) {
+ super(new MOptaLexer(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\015\000\002\007\003"});
+ /**
+ * Parse-action table.
+ */
+ protected static final short[][] _action_table =
+ lr_parser.unpackFromStrings(new String[]{
+ "\000\025\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\026\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\017\021\001\002\000" +
+ "\004\020\022\001\002\000\004\021\023\001\002\000\004" +
+ "\022\024\001\002\000\004\023\025\001\002\000\006\005" +
+ "\ufffb\011\ufffb\001\002\000\004\002\001\001\002\000\006" +
+ "\005\ufffe\011\ufffe\001\002"});
+ /**
+ * <code>reduce_goto</code> table.
+ */
+ protected static final short[][] _reduce_table =
+ lr_parser.unpackFromStrings(new String[]{
+ "\000\025\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\026\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\000\002\001" +
+ "\001\000\002\001\001\000\002\001\001"});
+ /**
+ * Instance of action encapsulation class.
+ */
+ protected CUP$parser$actions action_obj;
+ //Each string is of the format
+ //energy and iteraction
+ private ArrayList<String> result = new ArrayList<String>();
+ private String tempStr = "";
+
+ /**
+ * Default constructor.
+ */
+ public MOptaParser() {
+ super();
+ }
+
+ /**
+ * Constructor which sets the default scanner.
+ */
+ public MOptaParser(java_cup.runtime.Scanner s) {
+ super(s);
+ }
+
+ /**
+ * Access to production table.
+ */
+ public short[][] production_table() {
+ return _production_table;
+ }
+
+ /**
+ * Access to parse-action table.
+ */
+ public short[][] action_table() {
+ return _action_table;
+ }
+
+ /**
+ * Access to <code>reduce_goto</code> table.
+ */
+ public short[][] reduce_table() {
+ return _reduce_table;
+ }
+
+ 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 energyCount=0;
+ int iterationCount=0;
+ for(int i=0;i<result.size();i++){
+ String singleString = result.get(i);
+ String[] temp= singleString.split(" ");
+ if(temp.length>1){
+ String keyString= temp[0];
+ String dataString=temp[1];
+ if(keyString.equalsIgnoreCase("ENERGY")){
+ results.put("MoptaParser_ENERGY_"+energyCount,dataString);
+ energyCount++;
+ }else if(keyString.equalsIgnoreCase("ITERATION")){
+ results.put("MoptaParser_ITERATION_"+iterationCount,dataString);
+ iterationCount++;
+ }
+
+ }
+
+ }
+ return results;
+ }
+
+ /**
+ * Action encapsulation object initializer.
+ */
+ protected void init_actions() {
+ action_obj = new CUP$parser$actions(this);
+ }
+
+ /**
+ * Invoke a user supplied parse action.
+ */
+ public java_cup.runtime.Symbol do_action(
+ int act_num,
+ java_cup.runtime.lr_parser parser,
+ java.util.Stack stack,
+ int top)
+ throws java.lang.Exception {
+ /* call code in generated class */
+ return action_obj.CUP$parser$do_action(act_num, parser, stack, top);
+ }
+
+ /**
+ * Indicates start state.
+ */
+ public int start_state() {
+ return 0;
+ }
+
+ /**
+ * Indicates start production.
+ */
+ public int start_production() {
+ return 1;
+ }
+
+ /**
+ * <code>EOF</code> Symbol index.
+ */
+ public int EOF_sym() {
+ return 0;
+ }
+
+ /**
+ * <code>error</code> Symbol index.
+ */
+ public int error_sym() {
+ return 1;
+ }
+
+
+}
+
+/**
+ * Cup generated class to encapsulate user supplied action code.
+ */
+class CUP$parser$actions {
+
+
+ private static final String tableLabel = "SCF Intermediate Results:";
+ //__________________________________
+ public static boolean DEBUG = true;
+ private static JTable table;
+// private static String cycle = "0";
+ private final MOptaParser MOptaParser;
+
+ /**
+ * Constructor
+ */
+ CUP$parser$actions(MOptaParser MOptaParser) {
+ this.MOptaParser = MOptaParser;
+ }
+
+/* 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!");
+ } */
+// }
+
+ public static JTable getTable() {
+ return table;
+ }
+
+ public static String getTableLabel() {
+ return tableLabel;
+ }
+
+ /**
+ * 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);
+ MOptaParser.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 FLOAT4 FLOAT5 FLOAT6 FLOAT7 FLOAT8
+ {
+ Object RESULT = null;
+ // propagate RESULT from NT$0
+ if (((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 9)).value != null)
+ RESULT = (Object) ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 9)).value;
+ int cleft = ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 10)).left;
+ int cright = ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 10)).right;
+ Integer c = (Integer) ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 10)).value;
+
+ CUP$parser$result = new java_cup.runtime.Symbol(4/*scfcycle*/, ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 10)).left, ((java_cup.runtime.Symbol) CUP$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$top - 0)).value;
+ //___________________________________________________________________
+ if (DEBUG) System.out.println("CUP:gscfa:scfcycle: ITERATION " + c);
+ MOptaParser.addToResult("ITERATION "+c);
+// temp2.print(c);
+// temp2.print(" ");
+// cycle = c;
+
+// parseSCF.putField("iteration "+cycle, cycle);
+
+ CUP$parser$result = new java_cup.runtime.Symbol(6/*NT$0*/, ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 0)).right, ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 0)).right, RESULT);
+ }
+ return CUP$parser$result;
+
+ /*. . . . . . . . . . . . . . . . . . . .*/
+ case 4: // scfpat ::= scfcycle
+ {
+ Object RESULT = null;
+
+ CUP$parser$result = new java_cup.runtime.Symbol(3/*scfpat*/, ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 0)).left, ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 0)).right, RESULT);
+ }
+ return CUP$parser$result;
+
+ /*. . . . . . . . . . . . . . . . . . . .*/
+ case 3: // scfpat ::= scfpat scfcycle
+ {
+ Object RESULT = null;
+ if (DEBUG) System.out.println("CUP:gscfa: in scfpat");
+ CUP$parser$result = new java_cup.runtime.Symbol(3/*scfpat*/, ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 1)).left, ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 0)).right, RESULT);
+ }
+ return CUP$parser$result;
+
+ /*. . . . . . . . . . . . . . . . . . . .*/
+ case 2: // scfintro ::= FOUNDITER
+ {
+ Object RESULT = null;
+ if (DEBUG) System.out.println("CUP:gscfa: found start of SCF Iteration");
+ CUP$parser$result = new java_cup.runtime.Symbol(2/*scfintro*/, ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 0)).left, ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 0)).right, RESULT);
+ }
+ return CUP$parser$result;
+
+ /*. . . . . . . . . . . . . . . . . . . .*/
+ case 1: // $START ::= startpt EOF
+ {
+ Object RESULT = null;
+ int start_valleft = ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 1)).left;
+ int start_valright = ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 1)).right;
+ Object start_val = (Object) ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 1)).value;
+ RESULT = start_val;
+ CUP$parser$result = new java_cup.runtime.Symbol(0/*$START*/, ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 1)).left, ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 0)).right, RESULT);
+ }
+ /* ACCEPT */
+ CUP$parser$parser.done_parsing();
+ return CUP$parser$result;
+
+ /*. . . . . . . . . . . . . . . . . . . .*/
+ case 0: // startpt ::= scfintro scfpat SCFDONE
+ {
+ Object RESULT = null;
+ if (DEBUG) System.out.println("CUP:gscfa: end of parse tree ");
+ table = new JTable();
+
+// table = parseSCF.getTable();
+
+ CUP$parser$result = new java_cup.runtime.Symbol(1/*startpt*/, ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 2)).left, ((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top - 0)).right, RESULT);
+ }
+ return CUP$parser$result;
+
+ /* . . . . . .*/
+ default:
+ throw new Exception(
+ "Invalid action number found in internal parse table");
+
+ }
+ }
+}
+
http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/4231ac35/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mopta/MOptaSym.java
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diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mopta/MOptaSym.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mopta/MOptaSym.java
new file mode 100644
index 0000000..664d448
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+++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mopta/MOptaSym.java
@@ -0,0 +1,51 @@
+/*
+*
+* 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.mopta;
+//----------------------------------------------------
+// The following code was generated by CUP v0.10k
+// Fri Sep 12 00:11:41 IST 2014
+//----------------------------------------------------
+
+/**
+ * CUP generated class containing symbol constants.
+ */
+public class MOptaSym {
+ /* terminals */
+ public static final int FLOAT5 = 14;
+ public static final int FLOAT4 = 13;
+ public static final int FLOAT3 = 11;
+ public static final int FLOAT2 = 10;
+ public static final int FLOAT1 = 9;
+ public static final int INTCycle = 7;
+ public static final int INT3 = 6;
+ public static final int FLOAT = 8;
+ public static final int INT2 = 5;
+ public static final int INT1 = 4;
+ public static final int EOF = 0;
+ public static final int FOUNDITER = 2;
+ public static final int error = 1;
+ public static final int SCFDONE = 3;
+ public static final int ENERGY = 12;
+ public static final int FLOAT8 = 17;
+ public static final int FLOAT7 = 16;
+ public static final int FLOAT6 = 15;
+}
+
http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/4231ac35/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mp2to5a/MP2to5aLexer.java
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diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mp2to5a/MP2to5aLexer.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mp2to5a/MP2to5aLexer.java
new file mode 100644
index 0000000..54c0221
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+++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mp2to5a/MP2to5aLexer.java
@@ -0,0 +1,681 @@
+/*
+*
+* 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.mp2to5a;/* The following code was generated by JFlex 1.4.3 on 9/14/14 11:25 AM */
+
+/* MP2 to MP5 Keywords
+ Last Update: 12/31/2000
+ http://www.gaussian.com/00000456.htm
+*/
+
+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 9/14/14 11:25 AM from the specification file
+ * <tt>mp2to5a.flex</tt>
+ */
+public class MP2to5aLexer 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 IGNOREALL = 4;
+ public static final int FLOATVAL = 2;
+ public static final int YYINITIAL = 0;
+
+ /**
+ * 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
+ };
+
+ /**
+ * 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,
+ 0, 0, 0, 0, 0, 0, 0, 0, 6, 7, 0, 2, 0, 2, 3, 0,
+ 1, 1, 1, 1, 10, 15, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 11, 4, 0, 0, 0, 0, 0, 0, 0, 8, 0, 0,
+ 9, 12, 0, 13, 14, 16, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 4, 4, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 5, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 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 =
+ "\3\0\5\1\3\0\1\2\1\0\1\3\3\0\1\4"+
+ "\1\2\5\0\1\5\2\0\1\6\1\0\1\7";
+
+ private static int [] zzUnpackAction() {
+ int [] result = new int[30];
+ 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\21\0\42\0\63\0\104\0\125\0\146\0\167"+
+ "\0\210\0\231\0\146\0\252\0\273\0\63\0\314\0\335"+
+ "\0\356\0\63\0\377\0\377\0\u0110\0\u0121\0\u0132\0\u0143"+
+ "\0\63\0\u0154\0\u0165\0\63\0\u0176\0\63";
+
+ private static int [] zzUnpackRowMap() {
+ int [] result = new int[30];
+ 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 =
+ "\10\4\1\5\7\4\1\6\1\4\1\7\1\10\2\4"+
+ "\1\10\4\4\1\7\4\4\1\7\22\4\32\0\1\11"+
+ "\17\0\1\12\11\0\1\13\1\0\1\14\6\0\1\13"+
+ "\4\0\1\13\2\0\1\13\10\0\1\13\4\0\1\13"+
+ "\13\0\1\15\4\0\1\16\12\0\1\17\10\0\1\14"+
+ "\2\0\2\20\4\0\1\14\1\20\3\0\1\14\7\0"+
+ "\1\21\31\0\1\22\2\0\1\23\1\24\2\0\1\24"+
+ "\4\0\1\23\4\0\1\23\14\0\1\25\1\0\1\26"+
+ "\4\0\1\23\10\0\1\23\4\0\1\23\15\0\1\27"+
+ "\17\0\1\30\14\0\1\31\25\0\1\32\1\0\1\33"+
+ "\11\0\1\34\25\0\1\35\13\0\1\36\11\0";
+
+ private static int [] zzUnpackTrans() {
+ int [] result = new int[391];
+ 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 =
+ "\3\0\1\11\4\1\3\0\1\1\1\0\1\11\3\0"+
+ "\1\11\1\1\5\0\1\11\2\0\1\11\1\0\1\11";
+
+ private static int [] zzUnpackAttribute() {
+ int [] result = new int[30];
+ 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 MP2to5aLexer(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 MP2to5aLexer(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("JFlex:mp2to5: "+yytext());
+ return new Symbol(MP2to5aSym.LIM, yytext());
+ }
+ case 8: break;
+ case 7:
+ { if(Settings.DEBUG) System.out.println("JFlex:mp2to5: "+yytext());
+ return new Symbol(MP2to5aSym.VAR, yytext());
+ }
+ case 9: break;
+ case 2:
+ { if(Settings.DEBUG) System.out.println("JFlex:mp2to5: "+yytext());
+ yybegin(YYINITIAL);
+ return new Symbol(MP2to5aSym.FLOAT, yytext());
+ }
+ case 10: break;
+ case 3:
+ { if(Settings.DEBUG) System.out.println("JFlex:mp2to5: "+yytext());
+ return new Symbol(MP2to5aSym.LIM, yytext());
+ }
+ case 11: break;
+ case 5:
+ { if(Settings.DEBUG) System.out.println("JFlex:mp2to5: "+yytext());
+ return new Symbol(MP2to5aSym.VAR, yytext());
+ }
+ case 12: break;
+ case 6:
+ { if(Settings.DEBUG) System.out.println("JFlex:mp2to5: "+yytext());
+ return new Symbol(MP2to5aSym.VAR, yytext());
+ }
+ case 13: break;
+ case 1:
+ {
+ }
+ case 14: break;
+ default:
+ if (zzInput == YYEOF && zzStartRead == zzCurrentPos) {
+ zzAtEOF = true;
+ zzDoEOF();
+ { return new java_cup.runtime.Symbol(MP2to5aSym.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 = MP2to5aSym.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 MP2to5aLexer <inputfile>");
+ }
+ else {
+ for (int i = 0; i < argv.length; i++) {
+ MP2to5aLexer scanner = null;
+ try {
+ scanner = new MP2to5aLexer( 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/mp2to5a/MP2to5aParser.java
----------------------------------------------------------------------
diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mp2to5a/MP2to5aParser.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mp2to5a/MP2to5aParser.java
new file mode 100644
index 0000000..1ae4db3
--- /dev/null
+++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mp2to5a/MP2to5aParser.java
@@ -0,0 +1,261 @@
+/*
+*
+* 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.mp2to5a;
+
+
+import java_cup.runtime.lr_parser;
+import org.apache.airavata.datacat.parsers.gridchem.GridChemQueueParser;
+import org.apache.airavata.datacat.parsers.gridchem.Settings;
+
+import java.io.FileReader;
+import java.util.ArrayList;
+import java.util.HashMap;
+
+public class MP2to5aParser extends java_cup.runtime.lr_parser implements GridChemQueueParser {
+
+ /** Default constructor. */
+ public MP2to5aParser() {super();}
+
+ /** Constructor which sets the default scanner. */
+ public MP2to5aParser(java_cup.runtime.Scanner s) {super(s);}
+
+ /**
+ * Constructor which uses a file reader.
+ */
+ public MP2to5aParser(final FileReader fileReader) {
+ super(new MP2to5aLexer(fileReader));
+ }
+
+ /** Production table. */
+ protected static final short _production_table[][] =
+ lr_parser.unpackFromStrings(new String[]{
+ "\000\005\000\002\003\004\000\002\002\004\000\002\003" +
+ "\003\000\002\004\003\000\002\004\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\007\000\006\023\004\024\006\001\002\000\010\002" +
+ "\ufffe\023\ufffe\024\ufffe\001\002\000\010\002\uffff\023\uffff" +
+ "\024\uffff\001\002\000\010\002\ufffd\023\ufffd\024\ufffd\001" +
+ "\002\000\010\002\011\023\004\024\006\001\002\000\010" +
+ "\002\001\023\001\024\001\001\002\000\004\002\000\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\007\000\006\003\006\004\004\001\001\000\002\001" +
+ "\001\000\002\001\001\000\002\001\001\000\004\004\007" +
+ "\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
+ //mp2SpecificOption
+ 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 count=0;
+ for(int i=0;i<result.size();i++){
+ String singleString= result.get(i);
+ String[] temp= singleString.split(" ");
+ if(temp.length>1){
+ String keyString=temp[0];
+ String dataString=temp[1];
+ if(keyString.equalsIgnoreCase("SpecificOption")){
+ results.put("MP2to5aParser_MP2_Specific_Option_"+count,dataString);
+ count++;
+ }
+ }
+
+ }
+ 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;}
+
+
+ /** User initialization code. */
+ public void user_init() throws java.lang.Exception
+ {
+ if(Settings.DEBUG) System.out.println("CUP:mp2to5a: entry");
+ }
+
+
+
+ ///public static boolean DEBUG = false;
+}
+
+/** Cup generated class to encapsulate user supplied action code.*/
+class CUP$parser$actions {
+ private final MP2to5aParser MP2to5aParser;
+
+ /** Constructor */
+ CUP$parser$actions(MP2to5aParser MP2to5aParser) {
+ this.MP2to5aParser = MP2to5aParser;
+ }
+
+ /** 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 4: // element ::= LIM
+ {
+ Object RESULT = null;
+ int sleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left;
+ int sright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right;
+ String s = (String)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value;
+ if(Settings.DEBUG) System.out.println("CUP:mp2to5a: MP2-Specific Option: "+s);
+ MP2to5aParser.addToResult("SpecificOption "+s);
+ // ParseMP2to5.put("Limitations to MP5: ", s);
+ CUP$parser$result = new java_cup.runtime.Symbol(2/*element*/, ((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: // element ::= VAR
+ {
+ Object RESULT = null;
+ int sleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left;
+ int sright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right;
+ String s = (String)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value;
+ if(Settings.DEBUG) System.out.println("CUP:mp2to5a: MP2-Specific Option: "+s);
+ MP2to5aParser.addToResult("SpecificOption "+s);
+ //ParseMP2to5.put("Variations of MP4: ", s);
+ CUP$parser$result = new java_cup.runtime.Symbol(2/*element*/, ((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 2: // startpt ::= element
+ {
+ Object RESULT = null;
+
+ CUP$parser$result = new java_cup.runtime.Symbol(1/*startpt*/, ((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 ::= startpt element
+ {
+ Object RESULT = null;
+
+ CUP$parser$result = new java_cup.runtime.Symbol(1/*startpt*/, ((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;
+
+ /* . . . . . .*/
+ 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/mp2to5a/MP2to5aSym.java
----------------------------------------------------------------------
diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mp2to5a/MP2to5aSym.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mp2to5a/MP2to5aSym.java
new file mode 100644
index 0000000..709154a
--- /dev/null
+++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mp2to5a/MP2to5aSym.java
@@ -0,0 +1,51 @@
+/*
+*
+* 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.mp2to5a;
+//----------------------------------------------------
+// The following code was generated by CUP v0.10k
+// Sun Sep 14 11:25:52 IST 2014
+//----------------------------------------------------
+
+/** CUP generated class containing symbol constants. */
+public class MP2to5aSym {
+ /* terminals */
+ public static final int E4_SDTQ = 8;
+ public static final int MP2OPT = 16;
+ public static final int LIM = 18;
+ public static final int UMP4_SDQ = 11;
+ public static final int UMP4_SDTQ = 12;
+ public static final int E4_DQ = 6;
+ public static final int FCOPT = 13;
+ public static final int UMP4_DQ = 10;
+ public static final int E4_SDQ = 7;
+ public static final int E3 = 5;
+ public static final int E2 = 2;
+ public static final int FLOAT = 19;
+ public static final int EOF = 0;
+ public static final int error = 1;
+ public static final int MP4_T = 4;
+ public static final int FCOPT2 = 14;
+ public static final int ALGOPT = 15;
+ public static final int VAR = 17;
+ public static final int EUMP3 = 9;
+ public static final int EUMP2 = 3;
+}
+
http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/4231ac35/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mp2to5b/MP2to5bLexer.java
----------------------------------------------------------------------
diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mp2to5b/MP2to5bLexer.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mp2to5b/MP2to5bLexer.java
new file mode 100644
index 0000000..fa065ff
--- /dev/null
+++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mp2to5b/MP2to5bLexer.java
@@ -0,0 +1,687 @@
+package org.apache.airavata.datacat.parsers.gridchem.mp2to5b;/* The following code was generated by JFlex 1.4.3 on 9/14/14 11:52 AM */
+
+/* MP2 to MP5 Keywords
+ Last Update: 12/31/2000
+ http://www.gaussian.com/00000456.htm
+*/
+
+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 9/14/14 11:52 AM from the specification file
+ * <tt>mp2to5b.flex</tt>
+ */
+public class MP2to5bLexer 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 IGNOREALL = 4;
+ public static final int FLOATVAL = 2;
+ public static final int YYINITIAL = 0;
+
+ /**
+ * 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
+ };
+
+ /**
+ * 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,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 3, 7, 15, 4, 0,
+ 1, 2, 18, 2, 16, 14, 17, 2, 2, 2, 0, 0, 0, 26, 0, 0,
+ 0, 27, 0, 9, 5, 5, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 12, 28, 0, 0, 0, 13, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 20, 0, 0, 21, 19, 0, 0, 0, 22, 0, 0, 11, 0, 23, 24,
+ 0, 0, 0, 0, 0, 10, 0, 25, 0, 0, 0, 0, 6, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ 0, 0, 0, 0, 0, 0, 0, 0, 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 =
+ "\3\0\13\1\1\0\1\2\5\0\1\3\2\0\1\4"+
+ "\1\5\7\0\1\6\3\0\1\7\1\4\4\0\1\10"+
+ "\3\0\1\11\2\0\1\12";
+
+ private static int [] zzUnpackAction() {
+ int [] result = new int[51];
+ 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\127"+
+ "\0\u01b3\0\u01d0\0\u01ed\0\u020a\0\u0227\0\127\0\u0244\0\u015c"+
+ "\0\u0261\0\127\0\u027e\0\u029b\0\u02b8\0\u02d5\0\u02f2\0\u030f"+
+ "\0\u032c\0\127\0\u0349\0\u0366\0\u0383\0\127\0\u03a0\0\u03a0"+
+ "\0\u03bd\0\u03da\0\u03f7\0\127\0\u0414\0\u0431\0\u044e\0\127"+
+ "\0\u046b\0\u0488\0\127";
+
+ private static int [] zzUnpackRowMap() {
+ int [] result = new int[51];
+ 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 =
+ "\1\4\1\5\6\4\1\6\1\7\2\4\1\10\1\11"+
+ "\1\12\1\13\1\4\1\14\14\4\2\15\1\16\2\4"+
+ "\1\16\7\4\1\15\1\16\3\15\47\4\44\0\1\17"+
+ "\36\0\1\20\1\21\55\0\1\22\16\0\1\20\5\0"+
+ "\1\23\37\0\1\24\15\0\1\25\46\0\1\26\22\0"+
+ "\1\27\26\0\2\30\1\0\1\31\11\0\1\30\1\0"+
+ "\3\30\13\0\2\30\13\0\1\30\1\0\3\30\13\0"+
+ "\1\32\46\0\1\33\55\0\1\34\24\0\1\35\37\0"+
+ "\1\36\6\0\1\32\15\0\1\37\37\0\1\40\13\0"+
+ "\2\31\2\0\2\41\7\0\1\31\1\0\3\31\1\41"+
+ "\1\0\1\41\22\0\1\42\55\0\1\43\25\0\1\44"+
+ "\34\0\1\45\27\0\1\46\36\0\1\46\13\0\2\47"+
+ "\1\50\2\0\1\50\7\0\1\47\1\50\3\47\23\0"+
+ "\1\51\40\0\1\52\47\0\1\53\5\0\2\47\13\0"+
+ "\1\47\1\0\3\47\22\0\1\54\52\0\1\55\37\0"+
+ "\1\56\32\0\1\57\37\0\1\60\27\0\1\61\37\0"+
+ "\1\62\35\0\1\63\3\0";
+
+ private static int [] zzUnpackTrans() {
+ int [] result = new int[1189];
+ 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 =
+ "\3\0\1\11\12\1\1\0\1\11\5\0\1\11\2\0"+
+ "\1\1\1\11\7\0\1\11\3\0\1\11\1\1\4\0"+
+ "\1\11\3\0\1\11\2\0\1\11";
+
+ private static int [] zzUnpackAttribute() {
+ int [] result = new int[51];
+ 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 MP2to5bLexer(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 MP2to5bLexer(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("JFlex:mp2to5: "+yytext());
+ yybegin(YYINITIAL);
+ return new Symbol(MP2to5bSym.FLOAT, yytext());
+ }
+ case 11: break;
+ case 8:
+ { if(Settings.DEBUG) System.out.println("JFlex:mp2to5: "+yytext());
+ return new Symbol(MP2to5bSym.FCOPT, yytext());
+ }
+ case 12: break;
+ case 10:
+ { if(Settings.DEBUG) System.out.println("JFlex:mp2to5: "+yytext());
+ return new Symbol(MP2to5bSym.FCOPT, yytext());
+ }
+ case 13: break;
+ case 9:
+ { if(Settings.DEBUG) System.out.println("JFlex:mp2to5: "+yytext());
+ return new Symbol(MP2to5bSym.FCOPT, yytext());
+ }
+ case 14: break;
+ case 5:
+ { if(Settings.DEBUG) System.out.println("JFlex:mp2to5: "+yytext());
+ return new Symbol(MP2to5bSym.FCOPT2, yytext());
+ }
+ case 15: break;
+ case 7:
+ { if(Settings.DEBUG) System.out.println("JFlex:mp2to5: "+yytext());
+ return new Symbol(MP2to5bSym.FCOPT2, yytext());
+ }
+ case 16: break;
+ case 6:
+ { if(Settings.DEBUG) System.out.println("JFlex:mp2to5: "+yytext());
+ return new Symbol(MP2to5bSym.FCOPT, yytext());
+ }
+ case 17: break;
+ case 3:
+ { if(Settings.DEBUG) System.out.println("JFlex:mp2to5: "+yytext());
+ return new Symbol(MP2to5bSym.FCOPT2, yytext());
+ }
+ case 18: break;
+ case 2:
+ { if(Settings.DEBUG) System.out.println("JFlex:mp2to5: "+yytext());
+ return new Symbol(MP2to5bSym.FCOPT, yytext());
+ }
+ case 19: break;
+ case 1:
+ {
+ }
+ case 20: break;
+ default:
+ if (zzInput == YYEOF && zzStartRead == zzCurrentPos) {
+ zzAtEOF = true;
+ zzDoEOF();
+ { return new java_cup.runtime.Symbol(MP2to5bSym.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 = MP2to5bSym.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 MP2to5bLexer <inputfile>");
+ }
+ else {
+ for (int i = 0; i < argv.length; i++) {
+ MP2to5bLexer scanner = null;
+ try {
+ scanner = new MP2to5bLexer( 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/mp2to5b/MP2to5bParser.java
----------------------------------------------------------------------
diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mp2to5b/MP2to5bParser.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mp2to5b/MP2to5bParser.java
new file mode 100644
index 0000000..ba61f5f
--- /dev/null
+++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mp2to5b/MP2to5bParser.java
@@ -0,0 +1,263 @@
+/*
+*
+* 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.mp2to5b;
+
+
+import java_cup.runtime.lr_parser;
+import org.apache.airavata.datacat.parsers.gridchem.GridChemQueueParser;
+import org.apache.airavata.datacat.parsers.gridchem.Settings;
+
+import java.io.FileReader;
+import java.util.ArrayList;
+import java.util.HashMap;
+
+
+public class MP2to5bParser extends java_cup.runtime.lr_parser implements GridChemQueueParser{
+
+ /** Default constructor. */
+ public MP2to5bParser() {super();}
+
+ /** Constructor which sets the default scanner. */
+ public MP2to5bParser(java_cup.runtime.Scanner s) {super(s);}
+
+ /**
+ * Constructor which uses a file reader.
+ */
+ public MP2to5bParser(final FileReader fileReader) {
+ super(new MP2to5bLexer(fileReader));
+ }
+
+ /** Production table. */
+ protected static final short _production_table[][] =
+ lr_parser.unpackFromStrings(new String[]{
+ "\000\005\000\002\003\004\000\002\002\004\000\002\003" +
+ "\003\000\002\004\003\000\002\004\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\007\000\006\017\004\020\005\001\002\000\010\002" +
+ "\ufffe\017\ufffe\020\ufffe\001\002\000\010\002\ufffd\017\ufffd" +
+ "\020\ufffd\001\002\000\010\002\uffff\017\uffff\020\uffff\001" +
+ "\002\000\010\002\011\017\004\020\005\001\002\000\010" +
+ "\002\001\017\001\020\001\001\002\000\004\002\000\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\007\000\006\003\006\004\005\001\001\000\002\001" +
+ "\001\000\002\001\001\000\002\001\001\000\004\004\007" +
+ "\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
+ //mp2SpecificOption
+ 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 j=0;
+ for (int i=0; i<result.size();i++){
+ String resultString= result.get(i);
+ String[] temp=resultString.split(" ");
+ if(temp.length<3){
+ continue;
+ }
+ String element=temp[2]+" "+temp[3]+" "+temp[4];
+ if (element.equalsIgnoreCase("Frozen Core Option:")){
+ j++;
+ String tempString= "MP2to5b_Frozen Core Option_" + j;
+ results.put(tempString,temp[6]);
+ }else{
+ continue;
+ }
+ }
+ 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;}
+
+
+ /** User initialization code. */
+ public void user_init() throws java.lang.Exception
+ {
+ if(Settings.DEBUG) System.out.println("CUP:mp2to5b: entry");
+ }
+
+
+
+ ///public static boolean DEBUG = false;
+}
+
+/** Cup generated class to encapsulate user supplied action code.*/
+class CUP$parser$actions {
+ private final MP2to5bParser MP2to5bParser;
+
+ /** Constructor */
+ CUP$parser$actions(MP2to5bParser MP2to5bParser) {
+ this.MP2to5bParser = MP2to5bParser;
+ }
+
+ /** 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 4: // element ::= FCOPT2
+ {
+ Object RESULT = null;
+ int sleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left;
+ int sright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right;
+ String s = (String)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value;
+ if(Settings.DEBUG) System.out.println("CUP:mp2to5b: Frozen Core Option: "+s);
+ MP2to5bParser.addToResult("CUP:mp2to5b: Frozen Core Option: "+s);
+ // ParseMP2to5.put("Frozen Core Option? (Check raw output) ", s);
+ CUP$parser$result = new java_cup.runtime.Symbol(2/*element*/, ((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: // element ::= FCOPT
+ {
+ Object RESULT = null;
+ int sleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).left;
+ int sright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right;
+ String s = (String)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-0)).value;
+ if(Settings.DEBUG) System.out.println("CUP:mp2to5b: Frozen Core Option: "+s);
+ MP2to5bParser.addToResult("CUP:mp2to5b: Frozen Core Option: "+s);
+
+ // ParseMP2to5.put("Frozen Core Option: ", s);
+ CUP$parser$result = new java_cup.runtime.Symbol(2/*element*/, ((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 2: // startpt ::= element
+ {
+ Object RESULT = null;
+
+ CUP$parser$result = new java_cup.runtime.Symbol(1/*startpt*/, ((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 ::= startpt element
+ {
+ Object RESULT = null;
+
+ CUP$parser$result = new java_cup.runtime.Symbol(1/*startpt*/, ((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;
+
+ /* . . . . . .*/
+ 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/mp2to5b/MP2to5bSym.java
----------------------------------------------------------------------
diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mp2to5b/MP2to5bSym.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mp2to5b/MP2to5bSym.java
new file mode 100644
index 0000000..69f1e51
--- /dev/null
+++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/mp2to5b/MP2to5bSym.java
@@ -0,0 +1,51 @@
+/*
+*
+* 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.mp2to5b;
+//----------------------------------------------------
+// The following code was generated by CUP v0.10k
+// Sun Sep 14 11:52:08 IST 2014
+//----------------------------------------------------
+
+/** CUP generated class containing symbol constants. */
+public class MP2to5bSym {
+ /* terminals */
+ public static final int E4_SDTQ = 8;
+ public static final int MP2OPT = 16;
+ public static final int LIM = 18;
+ public static final int UMP4_SDQ = 11;
+ public static final int UMP4_SDTQ = 12;
+ public static final int E4_DQ = 6;
+ public static final int FCOPT = 13;
+ public static final int UMP4_DQ = 10;
+ public static final int E4_SDQ = 7;
+ public static final int E3 = 5;
+ public static final int E2 = 2;
+ public static final int FLOAT = 19;
+ public static final int EOF = 0;
+ public static final int error = 1;
+ public static final int MP4_T = 4;
+ public static final int FCOPT2 = 14;
+ public static final int ALGOPT = 15;
+ public static final int VAR = 17;
+ public static final int EUMP3 = 9;
+ public static final int EUMP2 = 3;
+}
+