+++ /dev/null
-/**
- * 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 occured 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)
-{
- 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())
- {
- 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 ((*_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())
- {
- 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 ((*_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 occured in the function GDEFileParser::getSecStructure()\n"
- << "Program needs to terminate.\nPlease contact the Clustal developers\n";
- exit(1);
- }
-}
-
-}
-
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