+++ /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 "PIRFileParser.h"
-
-namespace clustalw
-{
-
-/**
- * PIRFileParser contructor sets up the chartab array.
- * @param filePath
- */
-PIRFileParser::PIRFileParser(string filePath)
-{
- fileName = filePath;
- fillCharTab();
-}
-
-
-/*
- * get range of sequences
- */
- vector<Sequence> PIRFileParser::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 function getSeq finds the sequence 'seqNum' in the file and returns it.
- * @param seqNum The number of the sequence to get from the file.
- * @return The 'seqNum' sequence from the file.
- */
- Sequence PIRFileParser::getSeq(int seqNum, string *offendingSeq)
-{
- char _line[MAXLINE + 1];
- char _sname[MAXNAMES + 1];
- char _title[MAXTITLES + 1];
- string characterSeq = "";
- string name = "";
- string title = "";
- string blank = "";
-
- _line[0] = EOS;
- int i;
- unsigned char c;
- int _currentSeqNum = 0;
-
- try
- {
- _fileIn = new InFileStream; //nige
- _fileIn->open(fileName.c_str()); //nige
- _fileIn->seekg(0, std::ios::beg);
-
- // Read in lines until we get to the begining of sequence 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);
- }
-
- // line contains the name of the sequence
- for (i = 4; i <= (int)strlen(_line); i++)
- {
- if (_line[i] != ' ')
- {
- break;
- }
- }
-
- strncpy(_sname, _line + i, MAXNAMES); // remember entryname
- _sname[MAXNAMES] = EOS;
- utilityObject->rTrim(_sname);
- utilityObject->blankToUnderscore(_sname); // replace blanks with '_'
- name = string(_sname);
-
- _fileIn->getline(_line, MAXLINE + 1);
- strncpy(_title, _line, MAXTITLES);
- _title[MAXTITLES] = EOS;
- i = strlen(_title);
- if (_title[i - 1] == '\n')
- {
- _title[i - 1] = EOS;
- }
- title = string(_title);
-
- while (_fileIn->getline(_line, MAXLINE + 1))
- {
- for (i = 0; i <= MAXLINE; i++)
- {
- c = _line[i];
- if (c == '\n' || c == EOS || c == '*')
- {
- break;
- }
-
- 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 PIRFileParser::getSeq function.\n"
- << "Need to end program\n";
- exit(1);
- }
-}
-
-/**
- * The function countSeqs finds the number of sequences in the file and returns it.
- * @return The number of sequences in the file.
- */
-int PIRFileParser::countSeqs()
-{
- char line[MAXLINE + 1], c;
- line[0] = EOS;
- int numSeqs, i;
- bool seqOk;
-
- try
- {
- _fileIn = new InFileStream; //nige
- _fileIn->open(fileName.c_str()); //nige
-
- if(!_fileIn->is_open())
- {
- return 0; // No sequences found!
- }
-
- // Get to begining of sequences!
- while (_fileIn->getline(line, MAXLINE + 1))
- {
- if (!utilityObject->blankLine(line))
- {
- break;
- }
- }
-
- // Now check the 1st sequence to make sure it ends with *
- seqOk = false;
- while (_fileIn->getline(line, MAXLINE + 1))
- {
- // Look for end of first seq
- if (*line == '>')
- {
- break;
- }
- for (i = 0; seqOk == false; i++)
- {
- c = line[i];
- if (c == '*')
- {
- seqOk = true; // ok - end of sequence found
- break;
- } // EOL
- if (c == '\n' || c == EOS)
- {
- break;
- }
- // EOL
- }
- if (seqOk == true)
- {
- break;
- }
- }
- if (seqOk == false)
- {
- _fileIn->close();
- utilityObject->error("PIR format sequence end marker '*'\nmissing for one or more sequences.\n");
- return 0; // funny format
- }
-
- numSeqs = 1;
-
- while (_fileIn->getline(line, MAXLINE + 1))
- {
- if (*line == '>')
- {
- // Look for start of next seq
- seqOk = false;
- while (_fileIn->getline(line, MAXLINE + 1))
- {
- // Look for end of seq
- if (*line == '>')
- {
- _fileIn->close();
- utilityObject->error("PIR format sequence end marker '*'\nmissing for one or more sequences.\n");
- return 0; // funny format
- }
- for (i = 0; seqOk == false; i++)
- {
- c = line[i];
- if (c == '*')
- {
- seqOk = true; // ok - sequence found
- break;
- }
- if (c == '\n' || c == EOS)
- {
- break;
- }
- }
- if (seqOk == true)
- {
- numSeqs++;
- break;
- }
- }
- }
- }
-
- _fileIn->close();
-
- return numSeqs;
- }
- catch(...)
- {
- _fileIn->close();
- cerr << "An exception has occured in the function PIRFileParser::countSeqs()\n"
- << "Program needs to terminate.\nPlease contact the Clustal developers\n";
- exit(1);
- }
-}
-
-/**
- * There is no secondary structure information in PIR files!
- * @param gapPenaltyMask
- * @param secStructMask
- * @param secStructName
- * @param structPenalties
- * @param length
- */
-void PIRFileParser::getSecStructure(vector<char>& gapPenaltyMask, vector<char>& secStructMask,
- string& secStructName, int &structPenalties, int length)
-{
- structPenalties = NONE;
-}
-
-}
-
git://source.jalview.org / jabaws.git / blobdiff