--- /dev/null
+/**
+ * Author: Mark Larkin
+ *
+ * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
+ */
+/**
+ * Changes:
+ *
+ * Mark 24-1-2007. I am now using the char "delimiter" for the delimiter when using
+ * getline. This is to get around the problem of some files having '\r'.
+ *
+ * 10-02-07,Nigel Brown(EMBL): Changed ifstream to InFileStream to handle
+ * cross-platform end-of-lines and removed delimiter member.
+ *
+ * 28-12-07,Paul McGettigan : replaced array processing with string processing this fixes bug #72
+ *
+ * 9-2-2008, Paul McGettigan : fixed problem where space after '>' but before sequence name was causing
+ * alignment to fail due to no sequence name being read in
+ * 15-2-2008, Paul McGettigan : fixed bug 91 where Pseudo -FASTA format files were not being processed as
+ * previously in v1.83
+ */
+
+#ifdef HAVE_CONFIG_H
+ #include "config.h"
+#endif
+#include "PearsonFileParser.h"
+
+namespace clustalw
+{
+
+/**
+ * Constructor for the Pearson file parser.
+ * @param filePath
+ * @return
+ */
+PearsonFileParser::PearsonFileParser(string filePath)
+{
+ fileName = filePath;
+ fillCharTab();
+}
+
+
+/**
+ * reads fasta/pearson file in one go instead of calling getSeq for
+ * each single sequence.
+ *
+ * FIXME AW: only PearsonFileParser::getSeqRange is special, rest is the
+ * same. should be defined in FileParser and then overloaded in special
+ * cases like here
+ */
+vector<Sequence>
+PearsonFileParser::getSeqRange(int firstSeq, int nSeqsToRead, string *offendingSeq)
+{
+ string characterSeq = "";
+ string name = "";
+ string title = "";
+ string blank = "";
+ string greater = ">";
+ //_line[0] = EOS;
+ vector<Sequence> seqRangeVector;
+
+ string line;
+
+
+ //int i, j;
+ int nSeqsRead = 0;
+ unsigned char c;
+ char delim;
+ int _currentSeqNum = 0; // Not at any sequence yet!
+
+ try
+ {
+ delim=FileParser::getDelimiter(fileName);
+ //cout << "delim = " << delim << endl;
+ ifstream _fileIn;
+ _fileIn.open(fileName.c_str(),ios::in);
+
+ // Read in lines until we get to the begining of sequence firstSeq.
+ string line="";
+
+ do {
+ std::getline(_fileIn,line,delim);
+ if(line.substr(0,1) == greater){
+ _currentSeqNum++;
+ }
+ } while(_currentSeqNum <firstSeq);
+
+
+ while (nSeqsRead < nSeqsToRead)
+ {
+ // get sequence name from current line (excluded '>' and read up to first ' ' or MAXNAMES
+ // remove the first char i.e. '>'
+ name=line.substr(1,MAXNAMES);
+ //if(name.find(">") != string::npos){
+ // andreas wilm: exit if angle bracket within header?
+ //}
+
+ while(name.substr(0,1)==" "){
+ name=name.substr(1,MAXNAMES);
+ }
+ //int i;
+ //i = name.find(" ");
+ if(name.find(" ") != string::npos){
+ name=name.substr(0,name.find(" "));
+ }
+ utilityObject->rTrim(&name); // also replaces linef
+
+ name=utilityObject->blankToUnderscore(name); // replace blanks with '_'
+
+
+ // Read in lines until we get to the begining of next sequence.
+
+ title = ""; // No title information
+
+ while(std::getline(_fileIn,line,delim) ){
+
+ string::const_iterator iterator1 = line.begin();
+ while(iterator1 != line.end()){
+
+ // Andreas Wilm (UCD): exit if angle brackets within sequence
+ if(*iterator1=='>' && iterator1!=line.begin()) {
+ /* error output handled in Clustal.cpp
+ cerr << "\nMultiple angle brackets inside sequence found:"
+ << " invalid format.\n"
+ << "Maybe you forgot a linebreak between sequences?\n";
+ */
+
+ parseExitCode=BADFORMAT;
+ _fileIn.close();
+ seqRangeVector.clear();
+ return seqRangeVector;
+ }
+
+ if(*iterator1 =='\n' || *iterator1 =='\r' || *iterator1 == EOS || *iterator1 =='>'){
+ break;
+ }
+ c = *iterator1;
+
+ c = chartab[c];
+ if(c){
+ characterSeq.append(1,c);
+ }
+ iterator1++;
+ }
+ if(*iterator1 == '>'){
+ break;
+ }
+ }
+
+ // check sequence
+ if ((int)characterSeq.length() > userParameters->getMaxAllowedSeqLength())
+ {
+ /* error output handled in Clustal.cpp */
+ parseExitCode=SEQUENCETOOBIG;
+ if (offendingSeq!=NULL)
+ offendingSeq->assign(name);
+ _fileIn.close();
+ seqRangeVector.clear();
+ return seqRangeVector;
+ }
+ else if (characterSeq.length() == 0)
+ {
+ parseExitCode=EMPTYSEQUENCE;
+ if (offendingSeq!=NULL)
+ offendingSeq->assign(name);
+ _fileIn.close();
+ seqRangeVector.clear();
+ return seqRangeVector;
+ }
+
+ seqRangeVector.push_back(Sequence(characterSeq, name, title));
+ characterSeq = "";
+ nSeqsRead++;
+ } // while (nSeqsRead < nSeqsToRead)
+
+ _fileIn.close();
+
+ return seqRangeVector;
+ }
+
+ catch(...)
+ {
+ cerr << "There was an exception in the PearsonFileParser::getSeqRange function.\n"
+ << "Need to end program\n";
+ exit(1);
+ }
+}
+
+
+
+/**
+ * The function getSeq is used to get the sequence 'seqNum' in the file. It returns a
+ * sequence object containing the sequence.
+ * Deprecated: where possible use faster getSeqRange which reads
+ * sequences in one go
+ * @param seqNum The number of the sequence to get.
+ * @return
+ */
+ Sequence PearsonFileParser::getSeq(int seqNum, string *offendingSeq)
+{
+ //char _line[MAXLINE + 1];
+ //char tseq[MAXLINE + 1];
+ //char sname[MAXNAMES + 1];
+ //sname [MAXNAMES] = '\0';
+ string characterSeq = "";
+ string name = "";
+ string title = "";
+ string blank = "";
+ string greater = ">";
+ //_line[0] = EOS;
+
+ string line;
+
+ cerr << "Use of PearsonFileParser::getSeq is deprecated!\n";
+ //int i, j;
+ unsigned char c;
+ char delim;
+ 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
+ */
+ delim=FileParser::getDelimiter(fileName);
+ //cout << "delim = " << delim << endl;
+ ifstream _fileIn;
+ _fileIn.open(fileName.c_str(),ios::in);
+
+ //////////////////////////////////////////////////
+ //PMcG replace char array with string processing
+ //////////////////////////////////////////////////
+
+ // Read in lines until we get to the begining of sequence seqNum.
+ string line="";
+
+ do {
+ std::getline(_fileIn,line,delim);
+ if(line.substr(0,1) == greater){
+ _currentSeqNum++;
+ }
+ } while(_currentSeqNum <seqNum);
+
+
+ // get sequence name from current line (excluded '>' and read up to first ' ' or MAXNAMES
+ // remove the first char i.e. '>'
+ name=line.substr(1,MAXNAMES);
+
+ //////////////////////////////////////
+ // PMcG 9-2-2008 need to handle spaces at start of sequence name to conform to 1.83 handling
+ //////////////////////////////////////
+ while(name.substr(0,1)==" "){
+ name=name.substr(1,MAXNAMES);
+ }
+ //int i;
+ //i = name.find(" ");
+ if(name.find(" ") != string::npos){
+ name=name.substr(0,name.find(" "));
+ }
+ name=utilityObject->blankToUnderscore(name); // replace blanks with '_'
+
+
+ // Read in lines until we get to the begining of sequence seqNum.
+
+ /* PMcG replace char array with string processing
+ while (_currentSeqNum != seqNum)
+ {
+ while(*_line != '>')
+ {
+ if(!_fileIn->getline(_line, MAXLINE + 1))
+ {
+ freeFileResources(_fileIn);
+ 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 = 1; i <= strlen(_line); i++)
+ {
+ if (_line[i] != ' ')
+ {
+ break;
+ }
+ }
+ strncpy(sname, _line + i, MAXNAMES); // remember entryname
+ for (i = 1; i <= strlen(sname); i++)
+ {
+ if (sname[i] == ' ')
+ {
+ break;
+ }
+ }
+ sname[i] = EOS;
+ utilityObject->rTrim(sname);
+ utilityObject->blankToUnderscore(sname); // replace blanks with '_'
+ name = string(sname);
+ */
+
+ title = ""; // No title information
+
+ string seqLine = "";
+ while(std::getline(_fileIn,seqLine,delim) ){
+ string::const_iterator iterator1 = seqLine.begin();
+ while(iterator1 != seqLine.end()){
+ if(*iterator1 =='\n' || *iterator1 =='\r' || *iterator1 == EOS || *iterator1 =='>'){
+ break;
+ }
+ c = *iterator1;
+ c = chartab[c];
+ // PMcG 15-02-2008 bug 91
+ // strip out spaces and numbers from pseudo_fasta files
+ // but need to maintain gaps if present in sequence input
+ // to replicate behaviour of v1.83
+ //if(*iterator1 != ' ' && !isdigit(*iterator1)){
+ if(c){
+ characterSeq.append(1,c);
+ }
+ iterator1++;
+ }
+ if(*iterator1 == '>'){
+ break;
+ }
+ }
+ /*
+ 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;
+ // return empty seq
+ return Sequence(blank, blank, blank);
+ }
+ else if (characterSeq.length() == 0)
+ {
+ parseExitCode=EMPTYSEQUENCE;
+ // return empty seq
+ return Sequence(blank, blank, blank);
+ }
+
+ return Sequence(characterSeq, name, title);
+ }
+
+ catch(...)
+ {
+ cerr << "There was an exception in the PearsonFileParser::getSeq function.\n"
+ << "Need to end program\n";
+ exit(1);
+ }
+}
+
+/**
+ * The function countSeqs, counts the number of sequences in a file.
+ * @return The number of sequences in the file.
+ */
+int PearsonFileParser::countSeqs()
+{
+ //char line[1000 + 1];
+ int _nseqs = 0;
+ string line2;
+ char delim;
+
+ try
+ {
+ //_fileIn = new InFileStream; //nige
+ //_fileIn->open(fileName.c_str()); //nige
+ delim=FileParser::getDelimiter(fileName);
+ ifstream _fileIn;
+ _fileIn.open(fileName.c_str(),ios::in);
+
+
+ if(!_fileIn.is_open())
+ {
+ return 0; // No sequences found!
+ }
+
+ /* while ((*_fileIn) >> line2/@_fileIn->getline(line, 1000 + 1)@/)
+ {
+ /@if(_nseqs == 50)
+ {
+ cout << "\n\n" << line << "\n\n";
+ exit(1);
+ }@/
+ */
+ while (std::getline(_fileIn,line2,delim)) {
+ if (line2[0] == '>')
+ {
+ _nseqs++;
+ }
+ }
+ _fileIn.close();
+ return _nseqs;
+ }
+ catch(...)
+ {
+ freeFileResources(_fileIn);
+ cerr << "An exception has occured in the function PearsonFileParser::countSeqs()\n"
+ << "Program needs to terminate.\nPlease contact the Clustal developers\n";
+ exit(1);
+ }
+}
+
+/**
+ * There is no secondary structure information in the Pearson file. This is here to
+ * set the structPenalties to NONE.
+ * @param gapPenaltyMask
+ * @param secStructMask
+ * @param secStructName
+ * @param structPenalties
+ * @param length
+ */
+void PearsonFileParser::getSecStructure(vector<char>& gapPenaltyMask,
+ vector<char>& secStructMask, string& secStructName,
+ int &structPenalties, int length)
+{
+ structPenalties = NONE;
+}
+
+}
+
+
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