+++ /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 "RSFFileParser.h"
-
-namespace clustalw
-{
-
-/**
- * Constructor sets up the chartab array.
- * @param filePath
- */
-RSFFileParser::RSFFileParser(string filePath)
-{
- fileName = filePath;
- fillCharTab();
-}
-
- vector<Sequence> RSFFileParser::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;
-}
-
-
-/**
- * get the sequence seqNum from the file.
- * @param seqNum The number of the sequence to get.
- * @return The sequence seqNum.
- */
- Sequence RSFFileParser::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); // start at the beginning
-
- // Need to get the cursor to the begining of the correct sequence.
- // This will be the case when we get to the seqNum {
- while (_currentSeqNum != seqNum)
- {
- while(*_line != '{')
- {
- if(!_fileIn->getline(_line, MAXLINE + 1)) // If we cannot get anymore!
- {
- _fileIn->close();
- return Sequence(blank, blank, blank);
- }
- }
- ++_currentSeqNum;
- if(_currentSeqNum == seqNum) // Found the sequence
- {
- break;
- }
- // Get next line so that we are past the '{' line
- _fileIn->getline(_line, MAXLINE + 1);
- }
-
- while (!keyword(_line, "name"))
- {
- if (!_fileIn->getline(_line, MAXLINE + 1))
- {
- _fileIn->close();
- return Sequence(blank, blank, blank);
- }
- }
- for (i = 5; i <= (int)strlen(_line); i++)
- {
- if (_line[i] != ' ')
- {
- break;
- }
- }
- strncpy(_sname, _line + i, MAXNAMES); // remember entryname
- for (i = 0; i <= (int)strlen(_sname); i++)
- {
- if (_sname[i] == ' ')
- {
- _sname[i] = EOS;
- break;
- }
- }
-
- _sname[MAXNAMES] = EOS;
- utilityObject->rTrim(_sname);
- utilityObject->blankToUnderscore(_sname); // replace blanks with '_'
- name = string(_sname);
-
-
- while (!keyword(_line, "sequence"))
- {
- if (!_fileIn->getline(_line, MAXLINE + 1))
- {
- _fileIn->close();
- return Sequence(blank, blank, blank);
- }
- }
-
- while (_fileIn->getline(_line, MAXLINE + 1))
- {
- for (i = 0; i <= MAXLINE; i++)
- {
- c = _line[i];
- if (c == EOS || c == '}')
- {
- break;
- }
- // EOL
- if (c == '.')
- {
- characterSeq += '-';
- }
- c = chartab[c];
- if (c)
- {
- characterSeq += c;
- }
- }
- if (c == '}')
- {
- 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 << "There was an exception in the RSFFileParser::getSeq function.\n"
- << "Need to end program\n";
- exit(1);
- }
-}
-
-/**
- * count the number of sequences in a GCG RSF alignment file
- * @return The number of sequences in the file.
- */
-int RSFFileParser::countSeqs()
-{
- char _line[MAXLINE + 1];
- int numSeqs;
-
- try
- {
- numSeqs = 0;
- _fileIn = new InFileStream; //nige
- _fileIn->open(fileName.c_str()); //nige
- _fileIn->seekg(0, std::ios::beg); // start at the beginning
-
- if(!_fileIn->is_open())
- {
- return 0; // No sequences found!
- }
-
- // skip the comments
- while (_fileIn->getline(_line, MAXLINE + 1))
- {
- // NOTE needed to change to -1 and -2 (it was -2 and -3)
- // This is because getline does not put the \n in!
- if (_line[strlen(_line) - 1] == '.' && _line[strlen(_line) - 2] == '.')
- {
- break;
- }
- }
-
- while (_fileIn->getline(_line, MAXLINE + 1))
- {
- if (*_line == '{')
- {
- numSeqs++;
- }
- }
- _fileIn->close();
- return numSeqs;
- }
- catch(...)
- {
- _fileIn->close();
- cerr << "An exception has occured in the function RSFFileParser::countSeqs()\n"
- << "Program needs to terminate.\nPlease contact the Clustal developers\n";
- exit(1);
- }
-}
-
-/**
- * Get the secondary structure information from the file.
- * @param gapPenaltyMask
- * @param secStructMask
- * @param secStructName
- * @param structPenalties
- * @param length
- */
-void RSFFileParser::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;
- _line[0] = EOS;
-
- try
- {
- secStructMask.clear();
- secStructMask.assign(length, '.');
- _fileIn = new InFileStream; //nige
- _fileIn->open(fileName.c_str()); //nige
- _fileIn->seekg(0, std::ios::beg); // Need to start at begining
-
- // skip the comments
- while (_fileIn->getline(_line, MAXLINE + 1))
- {
- if (_line[strlen(_line) - 1] == '.' && _line[strlen(_line) - 2] == '.')
- {
- break;
- }
- }
-
- // find the start of the sequence entry
- for (;;)
- {
- while (_fileIn->getline(_line, MAXLINE + 1))
- if (*_line == '{')
- {
- break;
- }
-
- while (!keyword(_line, "name"))
- {
- if (!_fileIn->getline(_line, MAXLINE + 1))
- {
- _fileIn->close();
- return;
- }
- }
-
- for (i = 5; i <= (int)strlen(_line); i++)
- {
- if (_line[i] != ' ')
- {
- break;
- }
- }
- strncpy(_sname, _line + i, MAXNAMES); // remember entryname
- for (i = 0; i <= (int)strlen(_sname); i++)
- {
- if (_sname[i] == ' ')
- {
- _sname[i] = EOS;
- break;
- }
- }
- _sname[MAXNAMES] = EOS;
- utilityObject->rTrim(_sname);
- utilityObject->blankToUnderscore(_sname); // replace blanks with '_'
-
- // look for secondary structure feature table / gap penalty mask
- while (_fileIn->getline(_line, MAXLINE + 1))
- {
- if (keyword(_line, "feature"))
- {
- 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;
- secStructMask.assign(length, '.');
- do
- {
- if (keyword(_line, "feature"))
- {
- getRSFFeature(&_line[7], secStructMask, length);
- }
- _fileIn->getline(_line, MAXLINE + 1);
- }
- while (!keyword(_line, "sequence"));
- }
- else
- {
- do
- {
- _fileIn->getline(_line, MAXLINE + 1);
- }
- while (!keyword(_line, "sequence"));
- }
- secStructName = string(_sname);
- }
- else if (keyword(_line, "sequence"))
- {
- break;
- }
-
- if (structPenalties != NONE)
- {
- break;
- }
- }
- }
- _fileIn->close();
- }
- catch(...)
- {
- _fileIn->close();
- cerr << "An exception has occured in the function RSFFileParser::getSecStructure()\n"
- << "Program needs to terminate.\nPlease contact the Clustal developers\n";
- exit(1);
- }
-}
-
-/**
- * get a feature from the file. Called by getSecStructure
- * @param line
- * @param secStructMask
- * @param length
- */
-void RSFFileParser::getRSFFeature(char* line, vector<char>& secStructMask, int length)
-{
- char c, s;
- char str1[MAXLINE + 1], str2[MAXLINE + 1], feature[MAXLINE + 1];
- int i, tmp, startPos, endPos;
-
- try
- {
- if (sscanf(line, "%d%d%d%s%s%s", &startPos, &endPos, &tmp, str1, str2,
- feature) != 6)
- {
- return;
- }
-
- if (strcmp(feature, "HELIX") == 0)
- {
- c = 'A';
- s = '$';
- }
- else if (strcmp(feature, "STRAND") == 0)
- {
- c = 'B';
- s = '%';
- }
- else
- {
- return ;
- }
-
- if (startPos >= length || endPos >= length)
- {
- return ;
- }
- secStructMask[startPos - 1] = s;
- for (i = startPos; i < endPos - 1; i++)
- {
- secStructMask[i] = c;
- }
- secStructMask[endPos - 1] = s;
- }
- catch(...)
- {
- cerr << "An exception has occured in the function RSFFileParser::getRSFFeature()\n"
- << "Program needs to terminate.\nPlease contact the Clustal developers\n";
- exit(1);
- }
-}
-
-/**
- * keyword checks if code is on the line!
- * @param line
- * @param code
- * @return
- */
-bool RSFFileParser::keyword(char *line, const char *code)
-{
- int i;
- char key[MAXLINE];
-
- for (i = 0; !isspace(line[i]) && line[i] != EOS; i++)
- {
- key[i] = line[i];
- }
- key[i] = EOS;
- return (strcmp(key, code) == 0);
-}
-
-}
-
-
git://source.jalview.org / jabaws.git / blobdiff