+++ /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 "MSFFileParser.h"
-
-namespace clustalw
-{
-
-/**
- * MSFFileParser contructor 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 occured 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->blankLine(_line))
- {
- _fileIn->close();
- return _numSeqs;
- }
- _numSeqs++;
- }
-
- return 0; // if you got to here-funny format/no seqs.
- }
- catch(...)
- {
- _fileIn->close();
- cerr << "An exception has occured 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;
-}
-
-
-}
-
git://source.jalview.org / jabaws.git / blobdiff