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/**
* Author: Mark Larkin
*
* Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
*/
/**
* Changes:
*
* 10-02-07,Nigel Brown(EMBL): changed ifstream to InFileStream to handle
* cross-platform end-of-lines.
*/
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#include "MSFFileParser.h"
namespace clustalw
{
/**
* MSFFileParser constructor sets up the chartab array.
* @param filePath
* @return
*/
MSFFileParser::MSFFileParser(string filePath)
{
fileName = filePath;
fillCharTab();
}
vector<Sequence> MSFFileParser::getSeqRange(int firstSeq, int no, string *offendingSeq)
{
vector<Sequence> seqRangeVector;
int i;
for (i=0; i<no; i++)
{
Sequence tempSeq = getSeq(firstSeq + i);
if (parseExitCode!=OK) {
seqRangeVector.clear();
return seqRangeVector;
}
seqRangeVector.push_back(tempSeq);
}
return seqRangeVector;
}
/**
* The function getSeq finds the sequence seqNum in the file and returns it.
* @param seqNum The number of the sequence in the file to get.
* @return A sequence object containing the seqNum'th sequence from the file.
*/
Sequence MSFFileParser::getSeq(int seqNum, string *offendingSeq)
{
char _line[MAXLINE + 1];
char _sname[MAXNAMES + 1];
string characterSeq = "";
string name = "";
string title = "";
string blank = "";
_line[0] = EOS;
int i, j, k;
unsigned char c;
try
{
_fileIn = new InFileStream; //nige
_fileIn->open(fileName.c_str()); //nige
_fileIn->seekg(0, std::ios::beg);
for (i = 0;; i++)
{
if (!_fileIn->getline(_line, MAXLINE + 1))
{
_fileIn->close();
return Sequence(blank, blank, blank);
}
// read the title
if (utilityObject->lineType(_line, "//"))
{
break;
}
// lines...ignore
}
while (_fileIn->getline(_line, MAXLINE + 1))
{
if (!utilityObject->blankLine(_line))
{
for (i = 1; i < seqNum; i++)
{
_fileIn->getline(_line, MAXLINE + 1);
}
for (j = 0; j <= (int)strlen(_line); j++)
{
if (_line[j] != ' ')
{
break;
}
}
for (k = j; k <= (int)strlen(_line); k++)
{
if (_line[k] == ' ')
{
break;
}
}
// Get the name of the sequence
strncpy(_sname, _line + j, utilityObject->MIN(MAXNAMES, k - j));
_sname[utilityObject->MIN(MAXNAMES, k - j)] = EOS;
utilityObject->rTrim(_sname);
utilityObject->blankToUnderscore(_sname);
name = string(_sname);
for (i = k; i <= MAXLINE; i++)
{
c = _line[i];
if (c == '.' || c == '~')
{
c = '-';
}
if (c == '*')
{
c = 'X';
}
if (c == '\n' || c == EOS)
{
break;
}
// EOL
c = chartab[c];
if (c)
{
characterSeq += c;
}
}
for (i = 0;; i++)
{
if (!_fileIn->getline(_line, MAXLINE + 1))
{
_fileIn->close();
return Sequence(characterSeq, name, title);
}
if (utilityObject->blankLine(_line))
{
break;
}
}
}
}
_fileIn->close();
if ((int)characterSeq.length() > userParameters->getMaxAllowedSeqLength())
{
parseExitCode=SEQUENCETOOBIG;
if (offendingSeq!=NULL)
offendingSeq->assign(name);
// return empty seq
return Sequence(blank, blank, blank);
}
return Sequence(characterSeq, name, title);;
}
catch(...)
{
_fileIn->close();
cerr << "An exception has occurred in the function MSFFileParser::getSeq()\n"
<< "Program needs to terminate.\nPlease contact the Clustal developers\n";
exit(1);
}
}
/**
* The function countSeqs counts the number of sequences in the file.
* @return The number of sequences in the file.
*/
int MSFFileParser::countSeqs()
{
char _line[MAXLINE + 1];
int _numSeqs;
try
{
_fileIn = new InFileStream; //nige
_fileIn->open(fileName.c_str()); //nige
if(!_fileIn->is_open())
{
return 0; // No sequences found!
}
while (_fileIn->getline(_line, MAXLINE + 1))
{
if (utilityObject->lineType(_line, "//"))
{
break;
}
}
while (_fileIn->getline(_line, MAXLINE + 1))
{
if (!utilityObject->blankLine(_line))
{
break;
}
// Look for next non- blank line
}
_numSeqs = 1;
while (_fileIn->getline(_line, MAXLINE + 1))
{
if (utilityObject->blankLineNumericLabel(_line))
{
_fileIn->close();
return _numSeqs;
}
_numSeqs++;
}
return 0; // if you got to here-funny format/no seqs.
}
catch(...)
{
_fileIn->close();
cerr << "An exception has occurred in the function MSFFileParser::countSeqs()\n"
<< "Program needs to terminate.\nPlease contact the Clustal developers\n";
exit(1);
}
}
/**
* There is no secondary structure information in MSF files. Set structPenalties to NONE.
* @param gapPenaltyMask
* @param secStructMask
* @param secStructName
* @param structPenalties
* @param length
*/
void MSFFileParser::getSecStructure(vector<char>& gapPenaltyMask, vector<char>& secStructMask,
string& secStructName, int &structPenalties, int length)
{
structPenalties = NONE;
}
}
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