--- /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