http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/4231ac35/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/inchi/InChIGenerator.java ---------------------------------------------------------------------- diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/inchi/InChIGenerator.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/inchi/InChIGenerator.java new file mode 100644 index 0000000..145effe --- /dev/null +++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/inchi/InChIGenerator.java @@ -0,0 +1,95 @@ +/* +* +* Licensed to the Apache Software Foundation (ASF) under one +* or more contributor license agreements. See the NOTICE file +* distributed with this work for additional information +* regarding copyright ownership. The ASF licenses this file +* to you under the Apache License, Version 2.0 (the +* "License"); you may not use this file except in compliance +* with the License. You may obtain a copy of the License at +* +* http://www.apache.org/licenses/LICENSE-2.0 +* +* Unless required by applicable law or agreed to in writing, +* software distributed under the License is distributed on an +* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY +* KIND, either express or implied. See the License for the +* specific language governing permissions and limitations +* under the License. +* +*/ +package org.apache.airavata.datacat.parsers.gridchem.inchi; + +import org.apache.airavata.datacat.parsers.gridchem.util.Constants; +import org.apache.airavata.datacat.parsers.gridchem.util.GridChemProperties; + +import java.io.BufferedReader; +import java.io.FileReader; +import java.io.IOException; +import java.io.InputStreamReader; + +public class InChIGenerator { + + private String filePrefix; + + public InChIGenerator(String filePrefix) { + this.filePrefix = filePrefix; + } + + private BufferedReader runInChI(String molfile) throws IOException { + String[] command = { + "/bin/sh", + "-c", + "echo \"" + molfile + "\" | ./inchi-1 -STDIO -AuxNone -NoLabels -Key 2>/dev/null" + }; + Process inchi = Runtime.getRuntime().exec(command); + try { + inchi.waitFor(); + } catch (InterruptedException e) { + e.printStackTrace(); + } + return new BufferedReader(new InputStreamReader(inchi.getInputStream())); + } + + public InChI getInChI() throws IOException { + convertGaussian2Mol(); + String molfile = readFile(GridChemProperties.getInstance().getProperty( + Constants.TMP_DIR,"") + "/" + filePrefix + ".mol"); + BufferedReader input = runInChI(molfile); + + String result = input.readLine(); + String inchiStr = result == null ? "" : result; + + result = input.readLine(); + String inchiKey = result == null ? "" : result.substring(9); + InChI inChI = new InChI(inchiStr, inchiKey); + input.close(); + + return inChI; + } + + private void convertGaussian2Mol() throws IOException { + Process inchi = Runtime.getRuntime().exec("babel -i g09 " + + GridChemProperties.getInstance().getProperty(Constants.TMP_DIR,"") + "/" + filePrefix + ".out -o mol " + + GridChemProperties.getInstance().getProperty(Constants.TMP_DIR,"") + "/" + filePrefix + ".mol\n"); + try { + inchi.waitFor(); + } catch (InterruptedException e) { + e.printStackTrace(); + } + } + + private String readFile(String filename) throws IOException { + BufferedReader in = new BufferedReader(new FileReader(filename)); + String str = ""; + String molfile = ""; + + while ((str = in.readLine()) != null) { + molfile = molfile + str + "\n"; + } + + in.close(); + + return molfile; + } +}
http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/4231ac35/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/input/InputLexer.java ---------------------------------------------------------------------- diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/input/InputLexer.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/input/InputLexer.java new file mode 100644 index 0000000..0fbf3ff --- /dev/null +++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/input/InputLexer.java @@ -0,0 +1,799 @@ +/* +* +* 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.input;/* The following code was generated by JFlex 1.4.3 on 9/11/14 6:37 PM */ + +import java_cup.runtime.Symbol; +import org.apache.airavata.datacat.parsers.gridchem.Settings; + + +/** + * This class is a scanner generated by + * <a href="http://www.jflex.de/";>JFlex</a> 1.4.3 + * on 9/11/14 6:37 PM from the specification file + * <tt>input.flex</tt> + */ +public class InputLexer implements java_cup.runtime.Scanner { + + /** This character denotes the end of file */ + public static final int YYEOF = -1; + + /** initial size of the lookahead buffer */ + private static final int ZZ_BUFFERSIZE = 16384; + + /** lexical states */ + public static final int INPUTF = 30; + public static final int ITER2 = 4; + public static final int INPUTE = 28; + public static final int INPUTD = 26; + public static final int INPUTC = 24; + public static final int INPUTB = 22; + public static final int INPUTA = 20; + public static final int INTVALUE = 8; + public static final int INPUT = 18; + public static final int IGNOREALL = 16; + public static final int ITER = 2; + public static final int YYINITIAL = 0; + public static final int FLOAT2 = 14; + public static final int FLOAT1 = 12; + public static final int FLOATVALUE = 10; + public static final int ITER3 = 6; + + /** + * ZZ_LEXSTATE[l] is the state in the DFA for the lexical state l + * ZZ_LEXSTATE[l+1] is the state in the DFA for the lexical state l + * at the beginning of a line + * l is of the form l = 2*k, k a non negative integer + */ + private static final int ZZ_LEXSTATE[] = { + 0, 0, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, + 2, 2, 3, 3, 4, 4, 5, 5, 6, 6, 7, 7, 8, 8, 9, 9 + }; + + /** + * Translates characters to character classes + */ + private static final char [] ZZ_CMAP = { + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 11, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 0, 31, 3, 0, + 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 27, 25, 4, 0, 24, 29, 0, 0, 30, 0, 5, 28, + 0, 0, 0, 0, 23, 0, 0, 0, 20, 21, 22, 0, 0, 0, 0, 26, + 0, 0, 8, 0, 0, 9, 13, 0, 19, 17, 0, 0, 0, 7, 18, 12, + 16, 0, 10, 14, 15, 6, 0, 0, 0, 0, 0, 0, 2, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 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 = + "\12\0\4\1\1\2\2\1\1\3\1\1\1\4\10\1"+ + "\17\0\1\5\1\6\1\7\72\0\1\10\47\0\1\11"+ + "\5\0\1\12\124\0\1\13\1\14"; + + private static int [] zzUnpackAction() { + int [] result = new int[237]; + 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\40\0\100\0\140\0\200\0\240\0\300\0\340"+ + "\0\u0100\0\u0120\0\u0140\0\u0160\0\u0180\0\u01a0\0\u01c0\0\u01c0"+ + "\0\u01e0\0\u0200\0\u0200\0\u0220\0\u0220\0\u0240\0\u0260\0\u0280"+ + "\0\u02a0\0\u02c0\0\u02e0\0\u0300\0\u0320\0\u0340\0\u0360\0\u0380"+ + "\0\u0240\0\u03a0\0\u0280\0\u03c0\0\u02c0\0\u03e0\0\u0400\0\u0420"+ + "\0\u0440\0\u0460\0\u0480\0\u03a0\0\u03c0\0\u03e0\0\u04a0\0\u04c0"+ + "\0\u04e0\0\u0500\0\u0520\0\u0540\0\u0560\0\u0580\0\u05a0\0\u05c0"+ + "\0\u05e0\0\u0600\0\u0620\0\u0640\0\u0660\0\u0680\0\u06a0\0\u06c0"+ + "\0\u06e0\0\u0700\0\u0720\0\u0740\0\u0760\0\u0780\0\u07a0\0\u07c0"+ + "\0\u07e0\0\u0800\0\u0820\0\u0840\0\u0860\0\u0880\0\u08a0\0\u08c0"+ + "\0\u08e0\0\u0900\0\u0920\0\u0940\0\u0960\0\u0980\0\u09a0\0\u09c0"+ + "\0\u09e0\0\u0a00\0\u0a20\0\u0a40\0\u0a60\0\u0a80\0\u0aa0\0\u0ac0"+ + "\0\u0ae0\0\u0b00\0\u0b20\0\u0b40\0\u0b60\0\u0b80\0\u0ba0\0\u0bc0"+ + "\0\u0140\0\u0be0\0\u0c00\0\u0c20\0\u0c40\0\u0c60\0\u0c80\0\u0ca0"+ + "\0\u0cc0\0\u0ce0\0\u0d00\0\u0d20\0\u0d40\0\u0d60\0\u0d80\0\u0da0"+ + "\0\u0dc0\0\u0de0\0\u0e00\0\u0e20\0\u0e40\0\u0e60\0\u0e80\0\u0ea0"+ + "\0\u0ec0\0\u0ee0\0\u0f00\0\u0f20\0\u0f40\0\u0f60\0\u0f80\0\u0fa0"+ + "\0\u0fc0\0\u0fe0\0\u1000\0\u1020\0\u1040\0\u1060\0\u1080\0\u10a0"+ + "\0\u0140\0\u10c0\0\u10e0\0\u1100\0\u1120\0\u1140\0\u0140\0\u1160"+ + "\0\u1180\0\u11a0\0\u11c0\0\u11e0\0\u1200\0\u1220\0\u1240\0\u1260"+ + "\0\u1280\0\u12a0\0\u12c0\0\u12e0\0\u1300\0\u1320\0\u1340\0\u1360"+ + "\0\u1380\0\u13a0\0\u13c0\0\u13e0\0\u1400\0\u1420\0\u1440\0\u1460"+ + "\0\u1480\0\u14a0\0\u14c0\0\u14e0\0\u1500\0\u1520\0\u1540\0\u1560"+ + "\0\u1580\0\u15a0\0\u15c0\0\u15e0\0\u1600\0\u1620\0\u1640\0\u1660"+ + "\0\u1680\0\u16a0\0\u16c0\0\u16e0\0\u1700\0\u1720\0\u1740\0\u1760"+ + "\0\u1780\0\u17a0\0\u17c0\0\u17e0\0\u1800\0\u1820\0\u1840\0\u1860"+ + "\0\u1880\0\u18a0\0\u18c0\0\u18e0\0\u1900\0\u1920\0\u1940\0\u1960"+ + "\0\u1980\0\u19a0\0\u19c0\0\u19e0\0\u1a00\0\u1a20\0\u1a40\0\u1a60"+ + "\0\u1a80\0\u1aa0\0\u1ac0\0\u1ae0\0\u1b00\0\u1b20\0\u1b40\0\u1b60"+ + "\0\u1b80\0\u1ba0\0\u1bc0\0\u0140\0\u0140"; + + private static int [] zzUnpackRowMap() { + int [] result = new int[237]; + int offset = 0; + offset = zzUnpackRowMap(ZZ_ROWMAP_PACKED_0, offset, result); + return result; + } + + private static int zzUnpackRowMap(String packed, int offset, int [] result) { + int i = 0; /* index in packed string */ + int j = offset; /* index in unpacked array */ + int l = packed.length(); + while (i < l) { + int high = packed.charAt(i++) << 16; + result[j++] = high | packed.charAt(i++); + } + return j; + } + + /** + * The transition table of the DFA + */ + private static final int [] ZZ_TRANS = zzUnpackTrans(); + + private static final String ZZ_TRANS_PACKED_0 = + "\5\13\1\14\56\13\1\15\2\13\1\16\51\13\1\17"+ + "\1\20\34\13\1\21\1\13\1\22\1\23\34\13\1\23"+ + "\1\13\1\24\1\25\34\13\1\25\1\13\1\26\1\27"+ + "\34\13\1\27\1\13\1\30\1\31\34\13\1\31\1\13"+ + "\1\32\1\33\34\13\1\33\37\13\1\34\46\0\1\35"+ + "\44\0\1\36\54\0\1\37\10\0\1\17\37\0\1\17"+ + "\35\0\1\40\1\0\1\22\37\0\1\24\37\0\1\41"+ + "\1\0\1\42\35\0\1\41\37\0\1\43\1\0\1\44"+ + "\35\0\1\43\37\0\1\45\1\0\1\46\35\0\1\45"+ + "\75\0\1\47\7\0\1\50\43\0\1\51\55\0\1\52"+ + "\45\0\1\53\1\0\1\54\37\0\1\55\37\0\1\56"+ + "\75\0\1\57\10\0\1\60\42\0\1\61\56\0\1\62"+ + "\44\0\1\63\37\0\1\64\11\0\1\65\41\0\1\66"+ + "\55\0\1\67\45\0\1\70\37\0\1\71\12\0\1\72"+ + "\40\0\1\73\31\0\1\74\71\0\1\75\37\0\1\76"+ + "\13\0\1\77\37\0\1\100\57\0\1\101\43\0\1\102"+ + "\37\0\1\103\14\0\1\104\36\0\1\105\56\0\1\106"+ + "\44\0\1\107\37\0\1\110\15\0\1\111\35\0\1\112"+ + "\60\0\1\113\42\0\1\114\37\0\1\115\13\0\1\116"+ + "\37\0\1\117\30\0\1\120\72\0\1\121\37\0\1\122"+ + "\16\0\1\123\34\0\1\124\56\0\1\125\44\0\1\126"+ + "\37\0\1\127\17\0\1\130\33\0\1\131\30\0\1\132"+ + "\72\0\1\133\37\0\1\134\11\0\1\135\53\0\1\136"+ + "\47\0\1\137\41\0\1\140\37\0\1\141\20\0\1\142"+ + "\32\0\1\143\62\0\1\144\40\0\1\145\37\0\1\146"+ + "\16\0\1\147\34\0\1\150\55\0\1\151\45\0\1\152"+ + "\37\0\1\153\13\0\1\154\37\0\1\155\63\0\1\156"+ + "\37\0\1\157\21\0\1\160\31\0\1\161\63\0\1\162"+ + "\37\0\1\163\22\0\1\164\30\0\1\165\63\0\1\166"+ + "\37\0\1\167\13\0\1\170\37\0\1\171\63\0\1\172"+ + "\37\0\1\173\17\0\1\174\33\0\1\175\63\0\1\176"+ + "\37\0\1\177\23\0\1\200\27\0\1\201\63\0\1\202"+ + "\37\0\1\203\21\0\1\204\31\0\1\205\63\0\1\206"+ + "\37\0\1\207\16\0\1\210\34\0\1\211\63\0\1\212"+ + "\37\0\1\213\13\0\1\214\37\0\1\215\63\0\1\216"+ + "\37\0\1\217\12\0\1\220\53\0\1\221\50\0\1\222"+ + "\37\0\1\223\6\0\1\224\70\0\1\225\37\0\1\226"+ + "\22\0\1\227\54\0\1\230\37\0\1\231\37\0\1\232"+ + "\37\0\1\233\37\0\1\234\37\0\1\235\37\0\1\236"+ + "\37\0\1\237\37\0\1\240\37\0\1\241\37\0\1\242"+ + "\37\0\1\243\37\0\1\244\37\0\1\245\37\0\1\246"+ + "\37\0\1\247\37\0\1\250\37\0\1\251\37\0\1\252"+ + "\37\0\1\253\37\0\1\254\37\0\1\255\37\0\1\256"+ + "\37\0\1\257\37\0\1\260\37\0\1\261\37\0\1\262"+ + "\37\0\1\263\37\0\1\264\37\0\1\265\37\0\1\266"+ + "\37\0\1\267\37\0\1\270\37\0\1\271\37\0\1\272"+ + "\37\0\1\273\37\0\1\274\37\0\1\275\37\0\1\276"+ + "\37\0\1\277\37\0\1\300\37\0\1\301\37\0\1\302"+ + "\37\0\1\303\37\0\1\304\37\0\1\305\37\0\1\306"+ + "\37\0\1\307\37\0\1\310\37\0\1\311\37\0\1\312"+ + "\37\0\1\313\37\0\1\314\37\0\1\315\37\0\1\316"+ + "\37\0\1\317\37\0\1\320\37\0\1\321\37\0\1\322"+ + "\37\0\1\323\37\0\1\324\37\0\1\325\37\0\1\326"+ + "\37\0\1\327\37\0\1\330\37\0\1\331\37\0\1\332"+ + "\37\0\1\333\37\0\1\334\37\0\1\335\37\0\1\336"+ + "\37\0\1\337\37\0\1\340\37\0\1\341\37\0\1\342"+ + "\37\0\1\343\37\0\1\344\37\0\1\345\37\0\1\346"+ + "\37\0\1\347\37\0\1\350\37\0\1\351\37\0\1\352"+ + "\37\0\1\353\37\0\1\354\37\0\1\355"; + + private static int [] zzUnpackTrans() { + int [] result = new int[7136]; + 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 = + "\12\0\1\11\21\1\17\0\3\1\72\0\1\11\47\0"+ + "\1\11\5\0\1\11\124\0\2\11"; + + private static int [] zzUnpackAttribute() { + int [] result = new int[237]; + 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 InputLexer(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 InputLexer(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 6: + { if (Settings.DEBUG) System.out.println("InputFlex: Found y coord. in input"); + yybegin (INPUTE); + return new Symbol(InputSym.INPUT6, new Float(yytext())); + } + case 13: break; + case 7: + { if (Settings.DEBUG) System.out.println("InputFlex: Found z coord. in input"); + yybegin (INPUT); + return new Symbol(InputSym.INPUT7, new Float(yytext())); + } + case 14: break; + case 4: + { if (Settings.DEBUG) System.out.println("InputFlex: Found integer3 in input"); + yybegin (INPUTC); + return new Symbol(InputSym.INPUT4, new Integer(yytext())); + } + case 15: break; + case 11: + { if (Settings.DEBUG) System.out.println("InputFlex: Found the second dash"); + yybegin (ITER); + return new Symbol(InputSym.DASH2); + } + case 16: break; + case 5: + { if (Settings.DEBUG) System.out.println("InputFlex: Found x coord. in input"); + yybegin (INPUTD); + return new Symbol(InputSym.INPUT5, new Float(yytext())); + } + case 17: break; + case 12: + { if (Settings.DEBUG) System.out.println("InputFlex: Found the first dash"); + yybegin (INPUT); + return new Symbol(InputSym.DASH1); + } + case 18: break; + case 9: + { if (Settings.DEBUG) System.out.println("InputFlex: Found Input Orientation"); + yybegin(INPUTF); + return new Symbol(InputSym.INPUT1); + } + case 19: break; + case 8: + { yybegin(IGNOREALL); + return new Symbol(InputSym.SCFDONE); + } + case 20: break; + case 3: + { if (Settings.DEBUG) System.out.println("InputFlex: Found integer2 in input"); + yybegin (INPUTB); + return new Symbol(InputSym.INPUT3, new Integer(yytext())); + } + case 21: break; + case 10: + { if (Settings.DEBUG) System.out.println("InputFlex: Found Number of steps"); + yybegin(ITER); + return new Symbol(InputSym.FOUNDITER); + } + case 22: break; + case 1: + { + } + case 23: break; + case 2: + { if (Settings.DEBUG) System.out.println("InputFlex: Found integer1 in input"); + yybegin (INPUTA); + return new Symbol(InputSym.INPUT2, new Integer(yytext())); + } + case 24: break; + default: + if (zzInput == YYEOF && zzStartRead == zzCurrentPos) { + zzAtEOF = true; + zzDoEOF(); + { return new java_cup.runtime.Symbol(InputSym.EOF); } + } + else { + zzScanError(ZZ_NO_MATCH); + } + } + } + } + + /** + * Converts an int token code into the name of the + * token by reflection on the cup symbol class/interface sym + * + * This code was contributed by Karl Meissner <[email protected]> + */ + private String getTokenName(int token) { + try { + java.lang.reflect.Field [] classFields = InputSym.class.getFields(); + for (int i = 0; i < classFields.length; i++) { + if (classFields[i].getInt(null) == token) { + return classFields[i].getName(); + } + } + } catch (Exception e) { + e.printStackTrace(System.err); + } + + return "UNKNOWN TOKEN"; + } + + /** + * Same as next_token but also prints the token to standard out + * for debugging. + * + * This code was contributed by Karl Meissner <[email protected]> + */ + public java_cup.runtime.Symbol debug_next_token() throws java.io.IOException { + java_cup.runtime.Symbol s = next_token(); + System.out.println( " --"+ yytext() + "--" + getTokenName(s.sym) + "--"); + return s; + } + + /** + * Runs the scanner on input files. + * + * This is a standalone scanner, it will print any unmatched + * text to System.out unchanged. + * + * @param argv the command line, contains the filenames to run + * the scanner on. + */ + public static void main(String argv[]) { + if (argv.length == 0) { + System.out.println("Usage : java InputLexer <inputfile>"); + } + else { + for (int i = 0; i < argv.length; i++) { + InputLexer scanner = null; + try { + scanner = new InputLexer( 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/input/InputParser.java ---------------------------------------------------------------------- diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/input/InputParser.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/input/InputParser.java new file mode 100644 index 0000000..97a583a --- /dev/null +++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/input/InputParser.java @@ -0,0 +1,385 @@ +/* +* +* 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.input; + + +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 InputParser extends java_cup.runtime.lr_parser implements GridChemQueueParser { + + /** Default constructor. */ + public InputParser() {super();} + + /** Constructor which sets the default scanner. */ + public InputParser(java_cup.runtime.Scanner s) {super(s);} + + /** + * Constructor which uses a file reader. + */ + public InputParser(final FileReader fileReader) { + super(new InputLexer(fileReader)); + } + + + /** Production table. */ + protected static final short _production_table[][] = + lr_parser.unpackFromStrings(new String[]{ + "\000\015\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\016\004\000\002\016\003\000\002\017\010\000" + + "\002\012\003\000\002\013\003\000\002\014\003\000\002" + + "\015\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\031\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\024" + + "\001\002\000\006\010\ufffa\011\ufffa\001\002\000\006\010" + + "\021\011\016\001\002\000\006\004\ufffc\006\ufffc\001\002" + + "\000\006\010\ufffb\011\ufffb\001\002\000\004\013\025\001" + + "\002\000\004\013\ufff8\001\002\000\004\016\026\001\002" + + "\000\004\017\ufff7\001\002\000\004\017\030\001\002\000" + + "\004\020\ufff6\001\002\000\004\020\032\001\002\000\006" + + "\010\ufff5\011\ufff5\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\031\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\006\016\017\017\016\001\001\000\004\012\022\001" + + "\001\000\002\001\001\000\004\017\021\001\001\000\002" + + "\001\001\000\002\001\001\000\002\001\001\000\002\001" + + "\001\000\004\013\026\001\001\000\002\001\001\000\004" + + "\014\030\001\001\000\002\001\001\000\004\015\032\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 + // z_coord, y_coord, x_coord and atomic number + 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 atomCount=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("Z")){ + results.put("InputParser_z_coordinate_"+zCount,dataString); + zCount++; + }else if(keyString.equalsIgnoreCase("Y")){ + results.put("InputParser_y_coordinate_"+yCount,dataString); + yCount++; + }else if(keyString.equalsIgnoreCase("X")){ + results.put("InputParser_x_coordinate_"+xCount,dataString); + xCount++; + }else if(keyString.equalsIgnoreCase("AtomicNumber")){ + results.put("InputParser_atomic_number_"+atomCount,dataString); + atomCount++; + } + } + + } + 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 InputParser InputParser; + + /** Constructor */ + CUP$parser$actions(InputParser InputParser) { + this.InputParser = InputParser; + } + + /** 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 12: // 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); + InputParser.addToResult("Z "+in7); + + CUP$parser$result = new java_cup.runtime.Symbol(11/*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 11: // 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); + InputParser.addToResult("Y "+in6); + + CUP$parser$result = new java_cup.runtime.Symbol(10/*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 10: // 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); + InputParser.addToResult("X "+in5); + + CUP$parser$result = new java_cup.runtime.Symbol(9/*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 9: // 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); + InputParser.addToResult("AtomicNumber "+in3); + CUP$parser$result = new java_cup.runtime.Symbol(8/*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 8: // cycle2 ::= INPUT2 inp3 INPUT4 inp5 inp6 inp7 + { + Object RESULT = null; + + CUP$parser$result = new java_cup.runtime.Symbol(13/*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(12/*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(12/*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"); + + } + } +} + http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/4231ac35/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/input/InputSym.java ---------------------------------------------------------------------- diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/input/InputSym.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/input/InputSym.java new file mode 100644 index 0000000..5d52fa3 --- /dev/null +++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/input/InputSym.java @@ -0,0 +1,46 @@ +/* +* +* 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.input; +//---------------------------------------------------- +// The following code was generated by CUP v0.10k +// Thu Sep 11 18:37:51 IST 2014 +//---------------------------------------------------- + +/** CUP generated class containing symbol constants. */ +public class InputSym { + /* terminals */ + public static final int ENERGY = 11; + public static final int EOF = 0; + public static final int ITERATION = 10; + public static final int INPUT7 = 14; + public static final int error = 1; + public static final int INPUT6 = 13; + public static final int INPUT5 = 12; + public static final int INPUT4 = 9; + public static final int SCFDONE = 4; + public static final int INPUT3 = 8; + public static final int FOUNDITER = 3; + public static final int INPUT2 = 7; + public static final int DASH2 = 6; + public static final int INPUT1 = 2; + public static final int DASH1 = 5; +} + http://git-wip-us.apache.org/repos/asf/airavata-sandbox/blob/4231ac35/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/method/MethodLexer.java ---------------------------------------------------------------------- diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/method/MethodLexer.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/method/MethodLexer.java new file mode 100644 index 0000000..d9f9d08 --- /dev/null +++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/method/MethodLexer.java @@ -0,0 +1,752 @@ +/* +* +* 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.method;/* The following code was generated by JFlex 1.4.3 on 9/11/14 11:51 PM */ + +import java_cup.runtime.Symbol; +import java_cup.sym; +import org.apache.airavata.datacat.parsers.gridchem.Settings; + +import java.io.FileOutputStream; +import java.io.IOException; +import java.io.PrintStream; + + +/** + * This class is a scanner generated by + * <a href="http://www.jflex.de/";>JFlex</a> 1.4.3 + * on 9/11/14 11:51 PM from the specification file + * <tt>method.flex</tt> + */ +public class MethodLexer 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 = 6; + public static final int ITER1 = 4; + public static final int YYINITIAL = 0; + public static final int ITER = 2; + + /** + * ZZ_LEXSTATE[l] is the state in the DFA for the lexical state l + * ZZ_LEXSTATE[l+1] is the state in the DFA for the lexical state l + * at the beginning of a line + * l is of the form l = 2*k, k a non negative integer + */ + private static final int ZZ_LEXSTATE[] = { + 0, 0, 1, 1, 2, 2, 2, 2 + }; + + /** + * 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, 0, 0, 2, 0, 0, + 0, 7, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, + 0, 20, 10, 9, 21, 19, 0, 6, 0, 22, 0, 0, 0, 24, 15, 23, + 18, 12, 13, 11, 16, 14, 0, 0, 0, 17, 25, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 3, + 4, 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, 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\6\1\2\0\1\2\1\3\3\0\1\4\6\0"+ + "\1\5\33\0\1\6\5\0\1\7\1\10\6\0\1\11"; + + private static int [] zzUnpackAction() { + int [] result = new int[66]; + int offset = 0; + offset = zzUnpackAction(ZZ_ACTION_PACKED_0, offset, result); + return result; + } + + private static int zzUnpackAction(String packed, int offset, int [] result) { + int i = 0; /* index in packed string */ + int j = offset; /* index in unpacked array */ + int l = packed.length(); + while (i < l) { + int count = packed.charAt(i++); + int value = packed.charAt(i++); + do result[j++] = value; while (--count > 0); + } + return j; + } + + + /** + * Translates a state to a row index in the transition table + */ + private static final int [] ZZ_ROWMAP = zzUnpackRowMap(); + + private static final String ZZ_ROWMAP_PACKED_0 = + "\0\0\0\32\0\64\0\116\0\150\0\202\0\234\0\266"+ + "\0\320\0\352\0\u0104\0\116\0\116\0\u011e\0\u0138\0\u0152"+ + "\0\116\0\u016c\0\u0186\0\u01a0\0\u01ba\0\u01d4\0\u01ee\0\116"+ + "\0\u0208\0\u0222\0\u023c\0\u0256\0\u0270\0\u028a\0\u02a4\0\u02be"+ + "\0\u02d8\0\u02f2\0\u030c\0\u0326\0\u0340\0\u035a\0\u0374\0\u038e"+ + "\0\u03a8\0\u03c2\0\u03dc\0\u03f6\0\u0410\0\u042a\0\u0444\0\u045e"+ + "\0\u0478\0\u0492\0\u04ac\0\116\0\u04c6\0\u04e0\0\u04fa\0\u0514"+ + "\0\u052e\0\116\0\116\0\u0548\0\u0562\0\u057c\0\u0596\0\u05b0"+ + "\0\u05ca\0\116"; + + private static int [] zzUnpackRowMap() { + int [] result = new int[66]; + 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 = + "\2\4\1\5\32\4\1\6\2\4\1\7\2\4\1\10"+ + "\3\4\1\11\46\4\34\0\1\12\33\0\1\13\34\0"+ + "\1\14\1\15\33\0\1\16\35\0\1\17\15\0\1\20"+ + "\34\0\1\21\37\0\1\22\35\0\1\23\14\0\1\24"+ + "\31\0\1\25\47\0\1\26\13\0\1\27\43\0\1\30"+ + "\36\0\1\31\12\0\1\32\51\0\1\33\11\0\1\34"+ + "\30\0\1\35\32\0\1\36\35\0\1\37\14\0\1\40"+ + "\3\0\1\41\4\0\1\42\44\0\1\43\33\0\1\44"+ + "\34\0\1\45\11\0\1\46\53\0\1\47\30\0\1\50"+ + "\26\0\1\51\13\0\1\52\54\0\1\53\21\0\1\54"+ + "\42\0\1\55\5\0\1\56\55\0\1\57\11\0\1\60"+ + "\53\0\1\61\3\0\1\62\52\0\1\63\27\0\1\64"+ + "\36\0\1\65\5\0\1\66\46\0\1\67\43\0\1\70"+ + "\2\0\1\71\47\0\1\72\34\0\1\73\10\0\1\74"+ + "\31\0\1\75\31\0\1\76\31\0\1\77\31\0\1\100"+ + "\31\0\1\101\31\0\1\102\27\0"; + + private static int [] zzUnpackTrans() { + int [] result = new int[1508]; + 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\5\1\2\0\2\11\3\0\1\11\6\0"+ + "\1\11\33\0\1\11\5\0\2\11\6\0\1\11"; + + private static int [] zzUnpackAttribute() { + int [] result = new int[66]; + 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 MethodLexer(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 MethodLexer(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: + { System.out.println("MethodFlex: Found opt "); + System.out.println(yytext()); + try{ + PrintStream temp = new PrintStream(new FileOutputStream("runtype1")); + temp.print(yytext()); + System.out.println(yytext());} + catch (IOException ie){ System.out.println("Error in Gaussian Lexer");} + + yybegin(IGNOREALL); + return new Symbol(MethodSym.RUNTYP); + } + case 10: break; + case 7: + { if (Settings.DEBUG) System.out.println("MethodFlex: RUNTYP=GRADIENT"); + if (Settings.DEBUG) System.out.println(yytext()); + try{ + PrintStream temp = new PrintStream(new FileOutputStream("runtype1")); + temp.print("gradient"); + System.out.println(yytext());} + catch (IOException ie){ System.out.println("Error in Gaussian Lexer");} + yybegin(IGNOREALL); + return new Symbol(MethodSym.RUNTYP); + } + case 11: break; + case 8: + { if (Settings.DEBUG) System.out.println("MethodFlex: RUNTYP=ENERGY"); + if (Settings.DEBUG) System.out.println(yytext()); + try{ + PrintStream temp = new PrintStream(new FileOutputStream("runtype1")); + temp.print("optimize"); + System.out.println(yytext());} + catch (IOException ie){ System.out.println("Error in Gaussian Lexer");} + yybegin(IGNOREALL); + return new Symbol(MethodSym.RUNTYP); + } + case 12: break; + case 9: + { if (Settings.DEBUG) System.out.println("MethodFlex: Found Gaussian 98"); + yybegin(ITER); + return new Symbol(MethodSym.FOUNDITER); + } + case 13: break; + case 2: + { if (Settings.DEBUG) System.out.println("MethodFlex: Found G1"); + if (Settings.DEBUG) System.out.println(yytext()); + try{ + PrintStream temp = new PrintStream(new FileOutputStream("runtype1")); + temp.print(yytext()); + System.out.println(yytext());} + catch (IOException ie){ System.out.println("Error in Gaussian Lexer");} + yybegin(IGNOREALL); + return new Symbol(MethodSym.RUNTYP); + } + case 14: break; + case 6: + { if (Settings.DEBUG) System.out.println("MethodFlex: RUNTYP=ENERGY"); + if (Settings.DEBUG) System.out.println(yytext()); + try{ + PrintStream temp = new PrintStream(new FileOutputStream("runtype1")); + temp.print("energy"); + System.out.println(yytext());} + catch (IOException ie){ System.out.println("Error in Gaussian Lexer");} + yybegin(IGNOREALL); + return new Symbol(MethodSym.RUNTYP); + } + case 15: break; + case 3: + { if (Settings.DEBUG) System.out.println("MethodFlex: Found G2"); + if (Settings.DEBUG) System.out.println(yytext()); + try{ + PrintStream temp = new PrintStream(new FileOutputStream("runtype1")); + temp.print(yytext()); + System.out.println(yytext());} + catch (IOException ie){ System.out.println("Error in Gaussian Lexer");} + yybegin(IGNOREALL); + return new Symbol(MethodSym.RUNTYP); + } + case 16: break; + case 1: + { + } + case 17: break; + case 5: + { if (Settings.DEBUG) System.out.println("MethodFlex: Found CBS-Q"); + if (Settings.DEBUG) System.out.println(yytext()); + try{ + PrintStream temp = new PrintStream(new FileOutputStream("runtype1")); + temp.print(yytext()); + System.out.println(yytext());} + catch (IOException ie){ System.out.println("Error in Gaussian Lexer");} + yybegin(IGNOREALL); + return new Symbol(MethodSym.RUNTYP); + } + case 18: break; + default: + if (zzInput == YYEOF && zzStartRead == zzCurrentPos) { + zzAtEOF = true; + zzDoEOF(); + { return new java_cup.runtime.Symbol(sym.EOF); } + } + else { + zzScanError(ZZ_NO_MATCH); + } + } + } + } + + /** + * Converts an int token code into the name of the + * token by reflection on the cup symbol class/interface sym + * + * This code was contributed by Karl Meissner <[email protected]> + */ + private String getTokenName(int token) { + try { + java.lang.reflect.Field [] classFields = sym.class.getFields(); + for (int i = 0; i < classFields.length; i++) { + if (classFields[i].getInt(null) == token) { + return classFields[i].getName(); + } + } + } catch (Exception e) { + e.printStackTrace(System.err); + } + + return "UNKNOWN TOKEN"; + } + + /** + * Same as next_token but also prints the token to standard out + * for debugging. + * + * This code was contributed by Karl Meissner <[email protected]> + */ + public java_cup.runtime.Symbol debug_next_token() throws java.io.IOException { + java_cup.runtime.Symbol s = next_token(); + System.out.println( " --"+ yytext() + "--" + getTokenName(s.sym) + "--"); + return s; + } + + /** + * Runs the scanner on input files. + * + * This is a standalone scanner, it will print any unmatched + * text to System.out unchanged. + * + * @param argv the command line, contains the filenames to run + * the scanner on. + */ + public static void main(String argv[]) { + if (argv.length == 0) { + System.out.println("Usage : java MethodLexer <inputfile>"); + } + else { + for (int i = 0; i < argv.length; i++) { + MethodLexer scanner = null; + try { + scanner = new MethodLexer( 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/method/MethodParser.java ---------------------------------------------------------------------- diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/method/MethodParser.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/method/MethodParser.java new file mode 100644 index 0000000..4ff27bb --- /dev/null +++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/method/MethodParser.java @@ -0,0 +1,185 @@ +/* +* +* 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.method; + + +import java_cup.runtime.lr_parser; +import org.apache.airavata.datacat.parsers.gridchem.GridChemQueueParser; + +import java.io.FileReader; +import java.util.HashMap; + + +public class MethodParser extends java_cup.runtime.lr_parser implements GridChemQueueParser{ + + /** Default constructor. */ + public MethodParser() {super();} + + /** Constructor which sets the default scanner. */ + public MethodParser(java_cup.runtime.Scanner s) {super(s);} + + /** + * Constructor which uses a file reader. + */ + public MethodParser(final FileReader fileReader) { + super(new MethodLexer(fileReader)); + } + + + /** Production table. */ + protected static final short _production_table[][] = + lr_parser.unpackFromStrings(new String[]{ + "\000\003\000\002\003\003\000\002\002\004\000\002\004" + + "\004"}); + + /** 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\006\000\004\004\005\001\002\000\004\002\001\001" + + "\002\000\004\006\010\001\002\000\004\002\007\001\002" + + "\000\004\002\000\001\002\000\004\002\uffff\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\006\000\006\003\005\004\003\001\001\000\002\001" + + "\001\000\002\001\001\000\002\001\001\000\002\001\001" + + "\000\002\001\001"}); + + /** Access to <code>reduce_goto</code> table. */ + public short[][] reduce_table() {return _reduce_table;} + + /** Instance of action encapsulation class. */ + protected CUP$parser$actions action_obj; + + /** 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;} + + @Override + public HashMap<String, String> getParsedData() throws Exception { + return null; + } +} + +/** Cup generated class to encapsulate user supplied action code.*/ +class CUP$parser$actions { + + + //__________________________________ + public static boolean DEBUG = true; + + + private final MethodParser MethodParser; + + /** Constructor */ + CUP$parser$actions(MethodParser MethodParser) { + this.MethodParser = MethodParser; + } + + /** 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 2: // scfintro ::= FOUNDITER RUNTYP + { + Object RESULT = null; + if (DEBUG) System.out.println("CUP:gaussian: found FOUNDITER "); + CUP$parser$result = new java_cup.runtime.Symbol(2/*scfintro*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-1)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT); + } + return CUP$parser$result; + + /*. . . . . . . . . . . . . . . . . . . .*/ + case 1: // $START ::= startpt EOF + { + Object RESULT = null; + int start_valleft = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-1)).left; + int start_valright = ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-1)).right; + Object start_val = (Object)((java_cup.runtime.Symbol) CUP$parser$stack.elementAt(CUP$parser$top-1)).value; + RESULT = start_val; + CUP$parser$result = new java_cup.runtime.Symbol(0/*$START*/, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-1)).left, ((java_cup.runtime.Symbol)CUP$parser$stack.elementAt(CUP$parser$top-0)).right, RESULT); + } + /* ACCEPT */ + CUP$parser$parser.done_parsing(); + return CUP$parser$result; + + /*. . . . . . . . . . . . . . . . . . . .*/ + case 0: // startpt ::= scfintro + { + Object RESULT = null; + if (DEBUG) System.out.println("CUP:gaussian: end of parse tree "); + + + 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; + + /* . . . . . .*/ + 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/method/MethodSym.java ---------------------------------------------------------------------- diff --git a/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/method/MethodSym.java b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/method/MethodSym.java new file mode 100644 index 0000000..b84f358 --- /dev/null +++ b/datacat/parsers/src/main/java/org/apache/airavata/datacat/parsers/gridchem/method/MethodSym.java @@ -0,0 +1,37 @@ +/* +* +* 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.method; +//---------------------------------------------------- +// The following code was generated by CUP v0.10k +// Thu Sep 11 23:51:20 IST 2014 +//---------------------------------------------------- + +/** CUP generated class containing symbol constants. */ +public class MethodSym { + /* terminals */ + public static final int RUNTYP = 4; + public static final int SCFDONE = 3; + public static final int error = 1; + public static final int FOUNDITER = 2; + public static final int RUNTYP1 = 5; + public static final int EOF = 0; +} +
