// ========================================================================== // parse_lm // ========================================================================== // Copyright (c) 2006-2011, Knut Reinert, FU Berlin // All rights reserved. // // Redistribution and use in source and binary forms, with or without // modification, are permitted provided that the following conditions are met: // // * Redistributions of source code must retain the above copyright // notice, this list of conditions and the following disclaimer. // * Redistributions in binary form must reproduce the above copyright // notice, this list of conditions and the following disclaimer in the // documentation and/or other materials provided with the distribution. // * Neither the name of Knut Reinert or the FU Berlin nor the names of // its contributors may be used to endorse or promote products derived // from this software without specific prior written permission. // // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE // ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE // FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL // DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR // SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER // CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT // LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY // OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH // DAMAGE. // // ========================================================================== // Author: Manuel Holtgrewe // ========================================================================== // Parsing for the "general" format of lastz. // ========================================================================== // SEQAN_NO_GENERATED_FORWARDS #ifndef EXTRAS_INCLUDE_SEQAN_PARSE_LM_PARSE_LASTZ_GENERAL_H_ #define EXTRAS_INCLUDE_SEQAN_PARSE_LM_PARSE_LASTZ_GENERAL_H_ namespace seqan { // ============================================================================ // Forwards // ============================================================================ // ============================================================================ // Tags, Classes, Enums // ============================================================================ struct LastzGeneral_; typedef Tag LastzGeneral; // ============================================================================ // Metafunctions // ============================================================================ // ============================================================================ // Functions // ============================================================================ // ---------------------------------------------------------------------------- // Function readRecord() // ---------------------------------------------------------------------------- /** .Function.readRecord ..cat:Local Match Store ..signature:readRecord(store, stream, LastzGeneral()) ..summary:Read Lastz "general" format record. ..param.store:@Class.LocalMatchStore@ object to read into. ...type:Class.LocalMatchStore ..returns:$int$, 0 on success, non-0 on errors and EOF ..include:seqan/parse_lm.h */ template int readRecord(TLocalMatchStore & store, RecordReader > & recordReader, LastzGeneral const & /*tag*/) { typedef typename TLocalMatchStore::TPosition TPosition; typedef typename TLocalMatchStore::TPosition TId; if (atEnd(recordReader)) return 1; // Skip any comments. while (value(recordReader) == '#') { int res = skipLine(recordReader); if (res) return res; if (atEnd(recordReader)) return 1; } SEQAN_ASSERT_NEQ(value(recordReader), '#'); // Read line. CharString buffer; int res = 0; CharString subjectName; CharString queryName; char subjectStrand = 'X'; char queryStrand = 'X'; TPosition subjectBeginPos = 0; TPosition subjectEndPos = 0; TPosition queryBeginPos = 0; TPosition queryEndPos = 0; // Field: score res = readDigits(buffer, recordReader); if (res) return res; // Skip TAB. res = skipChar(recordReader, '\t'); if (res) return res; // Field: name1 readUntilChar(subjectName, recordReader, '\t'); if (res) return res; // Skip TAB. res = skipChar(recordReader, '\t'); if (res) return res; // Field: strand1 clear(buffer); res = readNChars(buffer, recordReader, 1); if (res) return res; subjectStrand = buffer[0]; if (subjectStrand != '+' && subjectStrand != '-') return 1; // FORMAT ERROR, should probably be a constant // Skip TAB. res = skipChar(recordReader, '\t'); if (res) return res; // Field: size1 clear(buffer); res = readDigits(buffer, recordReader); if (res) return res; // NOTE: Result is ignored. // Skip TAB. res = skipChar(recordReader, '\t'); if (res) return res; // Field: zstart1 clear(buffer); res = readDigits(buffer, recordReader); if (res) return res; subjectBeginPos = lexicalCast(buffer); // Skip TAB. res = skipChar(recordReader, '\t'); if (res) return res; // Field: end1 clear(buffer); res = readDigits(buffer, recordReader); if (res) return res; subjectEndPos = lexicalCast(buffer); // Skip TAB. res = skipChar(recordReader, '\t'); if (res) return res; // Field: name2 readUntilChar(queryName, recordReader, '\t'); if (res) return res; // Skip TAB. res = skipChar(recordReader, '\t'); if (res) return res; // Field: strand2 clear(buffer); res = readNChars(buffer, recordReader, 1); if (res) return res; queryStrand = buffer[0]; if (queryStrand != '+' && queryStrand != '-') return 1; // FORMAT ERROR, should probably be a constant // Skip TAB. res = skipChar(recordReader, '\t'); if (res) return res; // Field: size2 clear(buffer); res = readDigits(buffer, recordReader); if (res) return res; // NOTE: Result is ignored. // Skip TAB. res = skipChar(recordReader, '\t'); if (res) return res; // Field: zstart2 clear(buffer); res = readDigits(buffer, recordReader); if (res) return res; queryBeginPos = lexicalCast(buffer); // Skip TAB. res = skipChar(recordReader, '\t'); if (res) return res; // Field: end2 clear(buffer); res = readDigits(buffer, recordReader); if (res) return res; queryEndPos = lexicalCast(buffer); // Skip TAB. res = skipChar(recordReader, '\t'); if (res) return res; // Field: identity clear(buffer); res = readUntilWhitespace(buffer, recordReader); if (res) return res; // NOTE: Result is ignored. // Skip TAB. res = skipChar(recordReader, '\t'); if (res) return res; // Field: idPct clear(buffer); res = readUntilWhitespace(buffer, recordReader); if (res) return res; // NOTE: Result is ignored. // Skip TAB. res = skipChar(recordReader, '\t'); if (res) return res; // Field: coverage clear(buffer); res = readUntilWhitespace(buffer, recordReader); if (res) return res; // NOTE: Result is ignored. // Skip TAB. res = skipChar(recordReader, '\t'); if (res) return res; // Field: covPct clear(buffer); res = readUntilWhitespace(buffer, recordReader); if (res) return res; // NOTE: Result is ignored. // Skip to next line, ignore EOF here. skipLine(recordReader); // Finally, append the local match. if (subjectStrand == '-') ::std::swap(subjectBeginPos, subjectEndPos); if (queryStrand == '-') ::std::swap(queryBeginPos, queryEndPos); appendLocalMatch(store, subjectName, subjectBeginPos, subjectEndPos, queryName, queryBeginPos, queryEndPos); return 0; } } // namespace seqan #endif // EXTRAS_INCLUDE_SEQAN_PARSE_LM_PARSE_LASTZ_GENERAL_H_