+++ /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 "EMBLFileParser.h"
-
-namespace clustalw
-{
-
-/*
- * constructor sets up chartab array.
- */
-EMBLFileParser::EMBLFileParser(string filePath)
-{
- fileName = filePath;
- fillCharTab();
-}
-
-/*
- * dont need to destruct anything.
- */
-EMBLFileParser::~EMBLFileParser()
-{
-
-}
-
-
-/*
- * get range of sequences
- */
- vector<Sequence> EMBLFileParser::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 in the file.
- */
- Sequence EMBLFileParser::getSeq(int seqNum, string *offendingSeq)
-{
- char _line[MAXLINE + 1];
- //char _tseq[MAXLINE + 1];
- char _sname[MAXNAMES + 1];
- //char _title[MAXTITLES + 1];
- string characterSeq = "";
- string name = "";
- string title = "";
-
- _line[0] = EOS;
- int i;
- //int j;
- bool gotSeq = false;
- unsigned char c;
- int _currentSeqNum = 0;
- string blank = "";
-
- try
- {
- _fileIn = new InFileStream; //nige
- _fileIn->open(fileName.c_str()); //nige
- _fileIn->seekg(0, std::ios::beg); // start at the beginning
-
- // Read in lines until we get to the begining of sequence seqNum.
- while (_currentSeqNum != seqNum)
- {
- while(!utilityObject->lineType(_line, "ID"))
- {
- 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);
- }
-
- 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);
- name = string(_sname);
- // Andreas Wilm (UCD): why cout here? cout << name << "\n";
-
- while (!utilityObject->lineType(_line, "SQ"))
- {
- if(!_fileIn->getline(_line, MAXLINE + 1)) // If we cannot get anymore!
- {
- _fileIn->close();
- // FIXME AW: why return with a name but otherwise empty seq?
- return Sequence(blank, name, blank);
- }
- }
-
- while (_fileIn->getline(_line, MAXLINE + 1))
- {
- if (gotSeq && utilityObject->blankLine(_line))
- {
- break;
- }
-
- // NOTE I changed this to -1 and -2 because the getline doesnt return the \n
- if (strlen(_line) > 2 && _line[strlen(_line) - 1] == '.' &&
- _line[strlen(_line) - 2] == '.')
- {
- continue;
- }
-
- for (i = 0; i <= MAXLINE; i++)
- {
- c = _line[i];
- if (c == '\n' || c == EOS || c == '/')
- {
- break;
- }
- // EOL
- c = chartab[c];
- if (c)
- {
- gotSeq = true;
- 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 EMBLFileParser::getSeq function.\n"
- << "Need to end program\n";
- exit(1);
- }
-}
-
-/*
- * count the number of sequences in the file and return the number
- */
-int EMBLFileParser::countSeqs()
-{
- char line[MAXLINE + 1];
- // char c;
- line[0] = EOS;
- int numSeqs;
- // int i;
- //bool seqOk;
- numSeqs = 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 (utilityObject->lineType(line, "ID"))
- {
- numSeqs++;
- }
- }
-
- _fileIn->close();
- return numSeqs;
- }
- catch(...)
- {
- _fileIn->close();
- cerr << "An exception has occured in the function EMBLFileParser::countSeqs()\n"
- << "Program needs to terminate.\nPlease contact the Clustal developers\n";
- exit(1);
- }
-}
-
-/*
- * get secondary structure information from the file.
- */
-void EMBLFileParser::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];
- char _feature[MAXLINE + 1];
- int i;
- _line[0] = '\0';
-
- try
- {
- _fileIn = new InFileStream; //nige
- _fileIn->open(fileName.c_str()); //nige
- _fileIn->seekg(0, std::ios::beg);
-
- // clear out the masks
- gapPenaltyMask.clear();
- secStructMask.clear();
-
- // find the start of the sequence entry
- for (;;)
- {
- while (!utilityObject->lineType(_line, "ID"))
- {
- 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);
-
- // look for secondary structure feature table / gap penalty mask
- while (_fileIn->getline(_line, MAXLINE + 1))
- {
- if (utilityObject->lineType(_line, "FT"))
- {
- sscanf(_line + 2, "%s", _feature);
- if (strcmp(_feature, "HELIX") == 0 || strcmp(_feature, "STRAND") == 0)
- {
- 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('.');
- }
- do
- {
- getSwissFeature(&_line[2], secStructMask, length);
- _fileIn->getline(_line, MAXLINE + 1);
- }
- while (utilityObject->lineType(_line, "FT"));
- }
- else
- {
- do
- {
- _fileIn->getline(_line, MAXLINE + 1);
- }
- while (utilityObject->lineType(_line, "FT"));
- }
- secStructName = string(_sname);
- }
- }
- else if (utilityObject->lineType(_line, "GM"))
- {
- 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');
- }
- do
- {
- getSwissMask(&_line[2], gapPenaltyMask, length);
- _fileIn->getline(_line, MAXLINE + 1);
- }
- while (utilityObject->lineType(_line, "GM"));
- }
- else
- {
- do
- {
- _fileIn->getline(_line, MAXLINE + 1);
- }
- while (utilityObject->lineType(_line, "GM"));
- }
- secStructName = string(_sname);
- }
- if (utilityObject->lineType(_line, "SQ"))
- {
- break;
- }
-
- if (structPenalties != NONE)
- {
- break;
- }
- }
- }
- _fileIn->close();
- }
- catch(...)
- {
- _fileIn->close();
- cerr << "An exception has occured in the function EMBLFileParser::getSecStructure()\n"
- << "Program needs to terminate.\nPlease contact the Clustal developers\n";
- exit(1);
- }
-
-}
-
-/*
- * get the sec structure mask
- */
-void EMBLFileParser::getSwissFeature(char* line, vector<char>& secStructMask, int length)
-{
- char c, s, feature[MAXLINE + 1];
- int i, startPos, endPos;
-
- try
- {
- if (sscanf(line, "%s%d%d", feature, &startPos, &endPos) != 3)
- {
- 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 EMBLFileParser::getSwissFeature()\n"
- << "Program needs to terminate.\nPlease contact the Clustal developers\n";
- exit(1);
- }
-}
-
-/*
- * get the gap penalty mask.
- */
-void EMBLFileParser::getSwissMask(char* line, vector<char>& gapPenaltyMask, int length)
-{
- int i, value, startPos, endPos;
-
- try
- {
- if (sscanf(line, "%d%d%d", &value, &startPos, &endPos) != 3)
- {
- return;
- }
-
- if (value < 1 || value > 9)
- {
- return ;
- }
-
- if (startPos >= length || endPos >= length)
- {
- return ;
- }
- for (i = startPos - 1; i < endPos; i++)
- {
- gapPenaltyMask[i] = value + '0';
- }
- }
- catch(...)
- {
- cerr << "An exception has occured in the function EMBLFileParser::getSwissMask()\n"
- << "Program needs to terminate.\nPlease contact the Clustal developers\n";
- exit(1);
- }
-}
-
-
-}
git://source.jalview.org / jabaws.git / blobdiff