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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 "GDEFileParser.h"
namespace clustalw
{
/*
* Constructor sets up the chartab array.
*
*/
GDEFileParser::GDEFileParser(string filePath)
{
fileName = filePath;
fillCharTab();
}
/*
* Nothing to do in destruction of object.
*/
GDEFileParser::~GDEFileParser()
{
}
vector<Sequence> GDEFileParser::getSeqRange(int firstSeq, int no, string *offendingSeq)
{
vector<Sequence> seqRangeVector;
int i;
for (i=0; i<no; i++)
{
Sequence tempSeq = getSeq(firstSeq + i, offendingSeq);
if (parseExitCode!=OK) {
seqRangeVector.clear();
return seqRangeVector;
}
seqRangeVector.push_back(tempSeq);
}
return seqRangeVector;
}
/*
* The getSeq function is used to get sequence number seqNum from the file.
*/
Sequence GDEFileParser::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;
unsigned char c;
int _currentSeqNum = 0; // Not at any sequence yet!
try
{
_fileIn = new InFileStream; //nige
_fileIn->open(fileName.c_str()); //nige
_fileIn->seekg(0, std::ios::beg);
bool dnaFlagSet = userParameters->getDNAFlag();
while (_currentSeqNum != seqNum)
{
while((*_line != '#' && dnaFlagSet) ||
(*_line != '%' && !dnaFlagSet))
{
if(!_fileIn->getline(_line, MAXLINE + 1))
{
_fileIn->close();
return Sequence(blank, blank, blank);
}
}
++_currentSeqNum;
if(_currentSeqNum == seqNum) // Found the sequence
{
break;
}
// Get next line so that we are past the '#' or '%' line
_fileIn->getline(_line, MAXLINE + 1); //nige
}
for (i = 1; i <= MAXNAMES; i++)
{
if (_line[i] == '(' || _line[i] == '\n' || _line[i] == '\r')
{
break;
}
_sname[i - 1] = _line[i];
}
i--;
_sname[i] = EOS;
for (i--; i > 0; i--)
{
if (isspace(_sname[i]))
{
_sname[i] = EOS;
}
else
{
break;
}
}
utilityObject->blankToUnderscore(_sname);
name = string(_sname);
title = "";
while (_fileIn->getline(_line, MAXLINE + 1))
{
if (*_line == '%' || *_line == '#' || *_line == '"')
{
break;
}
for (i = 0; i <= MAXLINE; i++)
{
c = _line[i];
if (c == '\n' || c == EOS)
{
break;
}
c = chartab[c];
if (c)
{
characterSeq += c;
}
}
}
_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 << "There was an exception in the GDEnFileParser::getSeq function.\n"
<< "Need to end program\n";
exit(1);
}
}
/*
* The countSeqs function returns the number of sequences in the file.
*/
int GDEFileParser::countSeqs()
{
char line[MAXLINE + 1];
int _nseqs = 0;
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 ((*line == '%') && (userParameters->getDNAFlag() == false))
{
_nseqs++;
}
else if ((*line == '#') && (userParameters->getDNAFlag() == true))
{
_nseqs++;
}
}
_fileIn->close();
return _nseqs;
}
catch(...)
{
_fileIn->close();
cerr << "An exception has occurred in the function GDEFileParser::countSeqs()\n"
<< "Program needs to terminate.\nPlease contact the Clustal developers\n";
exit(1);
}
}
/*
* getSecStructure gets the secondary structure from the file.
*/
void GDEFileParser::getSecStructure(vector<char>& gapPenaltyMask, vector<char>& secStructMask,
string& secStructName, int &structPenalties, int length)
{
bool guigetss = false;
if(userParameters->getProfileNum() == 1 && userParameters->getStructPenalties1())
guigetss = true;
if(userParameters->getProfileNum() == 2 && userParameters->getStructPenalties2())
guigetss = true;
char _title[MAXLINE + 1];
char _line[MAXLINE + 1];
char _lin2[MAXLINE + 1];
char _sname[MAXNAMES + 1];
int i, len, offset = 0;
unsigned char c;
try
{
_fileIn = new InFileStream; //nige
_fileIn->open(fileName.c_str()); //nige
_fileIn->seekg(0, std::ios::beg);
// NOTE I think I should empty the masks before pushing onto them!
gapPenaltyMask.clear();
secStructMask.clear();
for (;;)
{
_line[0] = '\0';
// search for the next comment line
while (*_line != '"')
{
if (!_fileIn->getline(_line, MAXLINE + 1))
{
_fileIn->close();
return;
}
}
// is it a secondary structure entry?
if (strncmp(&_line[1], "SS_", 3) == 0)
{
for (i = 1; i <= MAXNAMES - 3; i++)
{
if (_line[i + 3] == '(' || _line[i + 3] == '\n' || _line[i + 3] == '\r')
{
break;
}
_sname[i - 1] = _line[i + 3];
}
i--;
_sname[i] = EOS;
// NOTE NOTE NOTE
// Is it possible for this to be executed????????????????
// if _line contains ( then we break and dont put it into _sname
// So how can sname have it???????
if (_sname[i - 1] == '(')
{
sscanf(&_line[i + 3], "%d", &offset);
}
else
{
offset = 0;
}
for (i--; i > 0; i--)
{
if (isspace(_sname[i]))
{
_sname[i] = EOS;
}
else
{
break;
}
}
utilityObject->blankToUnderscore(_sname);
secStructName = string(_sname);
if (userParameters->getInteractive() && !userParameters->getGui())
{
strcpy(_title, "Found secondary structure in alignment file: ");
strcat(_title, _sname);
(*_lin2) = utilityObject->promptForYesNo(_title,
"Use it to set local gap penalties ");
}
else
{
(*_lin2) = 'y';
}
if (guigetss || ((*_lin2 != 'n') && (*_lin2 != 'N')))
{
structPenalties = SECST;
for (i = 0; i < length; i++)
{
secStructMask.push_back('.');
}
len = 0;
while (_fileIn->getline(_line, MAXLINE + 1))
{
if (*_line == '%' || *_line == '#' || *_line == '"')
{
break;
}
for (i = offset; i < length; i++)
{
c = _line[i];
if (c == '\n' || c == EOS)
{
break;
}
// EOL
secStructMask[len++] = c;
}
if (len >= length) // NOTE i put in >=
{
break;
}
}
}
}
// or is it a gap penalty mask entry?
else if (strncmp(&_line[1], "GM_", 3) == 0)
{
for (i = 1; i <= MAXNAMES - 3; i++)
{
if (_line[i + 3] == '(' || _line[i + 3] == '\n')
{
break;
}
_sname[i - 1] = _line[i + 3];
}
i--;
_sname[i] = EOS;
// NOTE NOTE
// Again I dont think it is possible for _sname to have ( !!!!
if (_sname[i - 1] == '(')
{
sscanf(&_line[i + 3], "%d", &offset);
}
else
{
offset = 0;
}
for (i--; i > 0; i--)
{
if (isspace(_sname[i]))
{
_sname[i] = EOS;
}
else
{
break;
}
}
utilityObject->blankToUnderscore(_sname);
secStructName = string(_sname);
if (userParameters->getInteractive() && !userParameters->getGui())
{
strcpy(_title, "Found gap penalty mask in alignment file: ");
strcat(_title, _sname);
(*_lin2) = utilityObject->promptForYesNo(_title,
"Use it to set local gap penalties ");
}
else
{
(*_lin2) = 'y';
}
if (guigetss || ((*_lin2 != 'n') && (*_lin2 != 'N')))
{
structPenalties = GMASK;
for (i = 0; i < length; i++)
{
gapPenaltyMask.push_back('1');
}
len = 0;
while (_fileIn->getline(_line, MAXLINE + 1))
{
if (*_line == '%' || *_line == '#' || *_line == '"')
{
break;
}
for (i = offset; i < length; i++)
{
c = _line[i];
if (c == '\n' || c == EOS)
{
break;
}
// EOL
gapPenaltyMask[len++] = c;
}
if (len >= length) // NOTE I put in >=
{
break;
}
}
}
}
if (structPenalties != NONE)
{
break;
}
}
_fileIn->close();
}
catch(...)
{
_fileIn->close();
cerr << "An exception has occurred in the function GDEFileParser::getSecStructure()\n"
<< "Program needs to terminate.\nPlease contact the Clustal developers\n";
exit(1);
}
}
}
|
