root/trunk/dbbuilder/src/org/bridgedb/util/hmdb/ParseHmdb.java @ 321

// PathVisio,
// a tool for data visualization and analysis using Biological Pathways
// Copyright 2006-2009 BiGCaT Bioinformatics
//
// Licensed 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.bridgedb.util.hmdb;

import java.io.IOException;
import java.io.LineNumberReader;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

/**
 * Parse Metabocards from Hmdb
 */
public class ParseHmdb
{
        /**
         * represents some information from
         * a single HMDB metabocard
         */
        static class Compound
        {
                /** store a key, value field */
                void storeField (String key, String value)
                {
                        // check for "Not Available" lines
                        if (value.equals ("Not Available"))
                        {
                                value = null;
                        }
                        if (key.equals("name"))
                        {
                                symbol = value;
                        }
                        else if (key.equals("chemical_formula"))
                        {
                                formula = value;
                        }
                        else if (key.equals("kegg_compound_id"))
                        {
                                idKegg = value == null ? null : value.split("; ");
                        }
                        else if (key.equals("biocyc_id"))
                        {
                                idBioc = value == null ? null : value.split("; ");
                        }
                        else if (key.equals("pubchem_compound_id"))
                        {
                                idPubchem = value == null ? null : value.split("; ");
                        }
                        else if (key.equals("chebi_id"))
                        {
                                idChebi = value == null ? null : value.split("; ");
                        }
                        else if (key.equals("cas_number"))
                        {
                                idCas = value == null ? null : value.split("; ");
                        }
                        else if (key.equals("synonyms"))
                        {
                                synonyms = value == null ? null : value.split("; ");
                        }
                        else if (key.equals("wikipedia_link"))
                        {
                                idWikipedia = value == null ? null : value.split("; ");
                        }
                        else if (key.equals("smiles_canonical"))
                        {
                                smiles = value;
                        }
                }

                String idHmdb = null;
                String symbol = null;
                String formula = null;
                String[] idKegg = null;
                String[] idPubchem = null;
                String[] idChebi = null;
                String[] idCas = null;
                String[] idBioc = null;
                String[] idWikipedia = null;
                String smiles = null;
                String[] synonyms = null;
        }

        /**
         * Signals error while parsing a Metabocards-formatted file.
         * This exception means that either the file is corrupt,
         * not a valid metabocards file, or (possibly)
         * that the metabocards format has changed.
         */
        static class ParseException extends Exception
        {
                ParseException (String message)
                {
                        super(message);
                }

                ParseException (String message, int lineNo, String line)
                {
                        super("Parse error: " + message + " at " + lineNo + "\n" + line);
                }
        }

        /**
         * Reads a single metabocard from a text file.
         * returns null if there are no more records to read.
         */
        Compound readNext (LineNumberReader reader) throws IOException, ParseException
        {
                Compound result = new Compound();;

                int state = 0;
                String line;
                String key = null;
                String value = null;

                Pattern p1 = Pattern.compile ("#BEGIN_METABOCARD (HMDB\\d+)");
                Pattern p2 = Pattern.compile ("#END_METABOCARD (HMDB\\d+)");
                Pattern p3 = Pattern.compile ("# ([a-zA-Z0-9_]+):");

                while ((line = reader.readLine()) != null)
                {
                        int newState = state;

                        switch (state)
                        {
                        // state 0: expect begin
                        case 0:
                                Matcher m1 = p1.matcher(line);
                                if (m1.matches())
                                {
                                        newState = 1;
                                        result.idHmdb = m1.group(1);
                                }
                                else if (line.equals (""))
                                {
                                        // ignore
                                }
                                else
                                {
                                        throw new ParseException ("begin expected", reader.getLineNumber(), line);
                                }
                                break;
                        // state 1: expect key, end or empty
                        case 1:
                                Matcher m2 = p2.matcher (line);
                                Matcher m3 = p3.matcher (line);
                                if (m2.matches())
                                {
                                        // end
                                        return result;
                                }
                                else if (m3.matches())
                                {
                                        // store unless this is the first key
                                        if (key != null) result.storeField (key, value);

                                        key = m3.group(1);
                                        value = null;
                                        newState = 1;
                                }
                                else if (line.equals (""))
                                {
                                        // ignore
                                }
                                else
                                {
                                        if (value == null)
                                        {
                                                value = line;
                                        }
                                        else
                                        {
                                                value += "\n" + line;
                                        }
                                }
                                break;
                        }
                        state = newState;
                }
                if (state != 0)
                {
                        // The record was not properly terminated.
                        throw new ParseException ("Parse error: unexpected end of file");
                }
                else
                {
                        // end of file reached, no more records
                        return null;
                }
        }

}