--- /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);
+}
+
+}
+
+
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