--- /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.
+ *
+ * 27-4-2007, Mark Larkin (UCD): Made 2 small changes to getSecStructure function. There
+ * was a problem with the secondary structure info in windows.
+ */
+
+#ifdef HAVE_CONFIG_H
+ #include "config.h"
+#endif
+#include "ClustalFileParser.h"
+
+namespace clustalw
+{
+
+ClustalFileParser::ClustalFileParser(string filePath)
+{
+ fileName = filePath;
+ fillCharTab();
+ _fileIn = 0;
+}
+
+ClustalFileParser::~ClustalFileParser()
+{
+
+}
+
+
+ vector<Sequence> ClustalFileParser::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;
+}
+
+
+ Sequence ClustalFileParser::getSeq(int seqNum, string *offendingSeq)
+{
+ char line[MAXLINE + 1];
+ line[0] = EOS;
+ char tseq[MAXLINE + 1];
+ tseq[0] = '\0';
+ char sname[MAXNAMES + 150];
+
+ for(int i = 1; i < MAXNAMES + 1; i++)
+ {
+ line[i] = tseq[i] = sname[i] = '0';
+ }
+ string characterSeq = "";
+ string name = "";
+ string title = ""; // Nothing happens it here!!!
+
+ int i, j;
+ unsigned char c;
+ string blank = "";
+
+ try
+ {
+ _fileIn = new InFileStream; //nige
+ _fileIn->open(fileName.c_str()); //nige
+ _fileIn->seekg(0, std::ios::beg); // start at the beginning
+
+ _fileIn->getline(line, MAXLINE + 1); // read the title line...ignore it
+
+ while (_fileIn->getline(line, MAXLINE + 1)) //nige
+ {
+ if (!clustalBlankline(line))
+ {
+
+ for (i = 1; i < seqNum; i++)
+ {
+ _fileIn->getline(line, MAXLINE + 1); //nige
+ }
+ for (j = 0; j <= (int)strlen(line); j++)
+ if (line[j] != ' ')
+ {
+ break;
+ }
+ string _tempStr = string(line);
+
+ sscanf(_tempStr.c_str(), "%s%s", sname, tseq);
+ for (j = 0; j < MAXNAMES; j++)
+ {
+ if (sname[j] == ' ')
+ {
+ break;
+ }
+ }
+ sname[j] = EOS;
+ utilityObject->rTrim(sname);
+ utilityObject->blankToUnderscore(sname); // replace blanks with '_'
+ name = string(sname);
+
+ for (i = 0; i <= MAXLINE; i++)
+ {
+ c = tseq[i];
+ if (isspace(c) || c == EOS)
+ {
+ break;
+ }
+ // EOL
+ c = chartab[c];
+ if (c)
+ {
+ characterSeq += c; // Add the character to the sequence
+ }
+ }
+
+ for (i = 0;; i++)
+ {
+ if (!_fileIn->getline(line, MAXLINE + 1)) // If we cant get another line!
+ {
+ freeFileResources(_fileIn);
+ 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);
+ }
+ if (clustalBlankline(line))
+ {
+ break;
+ }
+ }
+ }
+ }
+ freeFileResources(_fileIn);
+
+ 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(...)
+ {
+ freeFileResources(_fileIn);
+ cerr << "An exception has occured in the function ClustalFileParser::getSeq()\n"
+ << "Program needs to terminate.\nPlease contact the Clustal developers\n";
+ exit(1);
+ }
+}
+
+/*
+ * The function countSeqs tells us how many sequences are in a clustal format file.
+ * Need to check if the file is open!
+ */
+int ClustalFileParser::countSeqs()
+{
+ char line[MAXLINE + 1];
+ int _nseqs;
+
+ try
+ {
+ _fileIn = new InFileStream; //nige
+ _fileIn->open(fileName.c_str()); //nige
+
+ if(!_fileIn->is_open())
+ {
+ freeFileResources(_fileIn);
+ return 0; // No sequences found!
+ }
+
+
+ while (_fileIn->getline(line, MAXLINE + 1))
+ {
+ if (!utilityObject->blankLine(line))
+ {
+ break;
+ }
+ }
+
+ // This gets us to the begining of the sequence lines!
+ while (_fileIn->getline(line, MAXLINE + 1))
+ {
+ if (!clustalBlankline(line))
+ {
+ break;
+ }
+ }
+ _nseqs = 1;
+
+ while (_fileIn->getline(line, MAXLINE + 1))
+ {
+ if (clustalBlankline(line))
+ {
+ freeFileResources(_fileIn);
+ return _nseqs;
+ }
+ _nseqs++;
+ }
+ freeFileResources(_fileIn);
+ return (int)0; // if you got to here-funny format/no seqs.
+ }
+ catch(...)
+ {
+ freeFileResources(_fileIn);
+ cerr << "An exception has occured in the function ClustalFileParser::countSeqs()\n"
+ << "Program needs to terminate.\nPlease contact the Clustal developers\n";
+ exit(1);
+ }
+}
+
+/*
+ * This function is to get the secondary structure for a Clustal format file.
+ * I am aware that I am using some C and some C++ here, and this may seem like
+ * bad style, but I think it is better to use the C functions for processing the
+ * strings as they are already working.
+ */
+void ClustalFileParser::getSecStructure(vector<char>& gapPenaltyMask,
+ vector<char>& secStructMask, string& secStructName, int &structPenalties, int length)
+{
+ char title[MAXLINE + 1];
+ title[0] = '\0';
+ char line[MAXLINE + 1];
+ line[0] = '\0';
+ char lin2[MAXLINE + 1];
+ lin2[0] = '\0';
+ char tseq[MAXLINE + 1];
+ tseq[0] = '\0';
+ char sname[MAXNAMES + 1];
+ sname[0] = '\0';
+
+ for(int i = 1; i < MAXNAMES + 1; i++)
+ {
+ title[i] = line[i] = lin2[i] = tseq[i] = sname[i] ='0';
+ }
+
+ int i, j, len, ix, struct_index = 0;
+ char c;
+
+ try
+ {
+ _fileIn = new InFileStream; //nige
+ _fileIn->open(fileName.c_str()); //nige
+ _fileIn->seekg(0, std::ios::beg);
+
+ // NOTE clear out the masks
+ gapPenaltyMask.clear();
+ secStructMask.clear();
+
+ len = 0; // initialise length to zero
+
+ if (!_fileIn->getline(line, MAXLINE + 1))
+ {
+ freeFileResources(_fileIn);
+ return ;
+ }
+ // read the title line...ignore it
+
+ if (!_fileIn->getline(line, MAXLINE + 1))
+ {
+ freeFileResources(_fileIn);
+ return ;
+ }
+ // read the next line...
+ // skip any blank lines
+ for (;;)
+ {
+ if (!_fileIn->getline(line, MAXLINE + 1))
+ {
+ freeFileResources(_fileIn);
+ return ;
+ }
+ if (!utilityObject->blankLine(line))
+ {
+ break;
+ }
+ }
+
+ // look for structure table lines
+ ix = -1;
+ for (;;)
+ {
+ if (line[0] != '!')
+ {
+ break;
+ }
+ if (strncmp(line, "!SS", 3) == 0)
+ {
+ ix++;
+ sscanf(line + 4, "%s%s", sname, tseq);
+ for (j = 0; j < MAXNAMES; j++)
+ {
+ if (sname[j] == ' ')
+ {
+ break;
+ }
+ }
+ sname[j] = EOS;
+ utilityObject->rTrim(sname);
+ utilityObject->blankToUnderscore(sname);
+
+ 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;
+ struct_index = ix;
+ for (i = 0; i < length; i++)
+ {
+ secStructMask.push_back('.');
+ gapPenaltyMask.push_back('.');
+ }
+
+ secStructName = string(sname);
+
+ for (i = 0; len < length; i++)
+ {
+ c = tseq[i];
+ if (c == '\n' || c == EOS)
+ {
+ break;
+ }
+ // EOL
+ if (!isspace(c))
+ {
+ if(len < (int)secStructMask.size())
+ {
+ secStructMask[len++] = c; // NOTE array notation = BAD
+ }
+ }
+ }
+ }
+ }
+ else if (strncmp(line, "!GM", 3) == 0)
+ {
+ ix++;
+ sscanf(line + 4, "%s%s", sname, tseq);
+ for (j = 0; j < MAXNAMES; j++)
+ {
+ if (sname[j] == ' ')
+ {
+ break;
+ }
+ }
+ sname[j] = EOS;
+ utilityObject->rTrim(sname);
+ utilityObject->blankToUnderscore(sname);
+
+ 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;
+ struct_index = ix;
+ for (i = 0; i < length; i++)
+ {
+ gapPenaltyMask.push_back('1');
+ }
+
+ secStructName = string(sname);
+
+ for (i = 0; len < length; i++)
+ {
+ c = tseq[i];
+ if (c == '\n' || c == EOS)
+ {
+ break;
+ }
+ // EOL
+ if (!isspace(c))
+ {
+ if(len < (int)gapPenaltyMask.size())
+ {
+ gapPenaltyMask[len++] = c;
+ }
+ }
+ }
+ }
+ }
+ if (structPenalties != NONE)
+ {
+ break;
+ }
+ if (!_fileIn->getline(line, MAXLINE + 1))
+ {
+ freeFileResources(_fileIn);
+ return ;
+ }
+ }
+ if (structPenalties == NONE)
+ {
+ freeFileResources(_fileIn);
+ return ;
+ }
+
+ // skip any more comment lines
+ while (line[0] == '!')
+ {
+ if (!_fileIn->getline(line, MAXLINE + 1))
+ {
+ freeFileResources(_fileIn);
+ return ;
+ }
+ }
+
+ // skip the sequence lines and any comments after the alignment
+ for (;;)
+ {
+ if (isspace(line[0]) || line[0] == '\0') // Mark change 27-4-2007
+ {
+ break;
+ }
+ if (!_fileIn->getline(line, MAXLINE + 1))
+ {
+ freeFileResources(_fileIn);
+ return ;
+ }
+ }
+
+
+ // read the rest of the alignment
+
+ for (;;)
+ {
+ // skip any blank lines
+ for (;;)
+ {
+ if (!utilityObject->blankLine(line))
+ {
+ break;
+ }
+ if (!_fileIn->getline(line, MAXLINE + 1))
+ {
+ freeFileResources(_fileIn);
+ return ;
+ }
+ }
+ // get structure table line
+ for (ix = 0; ix < struct_index; ix++)
+ {
+ if (line[0] != '!')
+ {
+ if (structPenalties == SECST)
+ {
+ utilityObject->error("bad secondary structure format\n");
+ }
+ else
+ {
+ utilityObject->error("bad gap penalty mask format\n");
+ }
+ structPenalties = NONE;
+ freeFileResources(_fileIn);
+ return ;
+ }
+ if (!_fileIn->getline(line, MAXLINE + 1))
+ {
+ freeFileResources(_fileIn);
+ return ;
+ }
+ }
+ if (structPenalties == SECST)
+ {
+ if (strncmp(line, "!SS", 3) != 0)
+ {
+ utilityObject->error("bad secondary structure format\n");
+ structPenalties = NONE;
+ freeFileResources(_fileIn);
+ return ;
+ }
+ sscanf(line + 4, "%s%s", sname, tseq);
+ for (i = 0; len < length; i++)
+ {
+ c = tseq[i];
+ if (c == '\n' || c == EOS)
+ {
+ break;
+ }
+ // EOL
+ if (!isspace(c))
+ {
+ secStructMask[len++] = c;
+ }
+ }
+ }
+ else if (structPenalties == GMASK)
+ {
+ if (strncmp(line, "!GM", 3) != 0)
+ {
+ utilityObject->error("bad gap penalty mask format\n");
+ structPenalties = NONE;
+ freeFileResources(_fileIn);
+ return ;
+ }
+ sscanf(line + 4, "%s%s", sname, tseq);
+ for (i = 0; len < length; i++)
+ {
+ c = tseq[i];
+ if (c == '\n' || c == EOS)
+ {
+ break;
+ }
+ // EOL
+ if (!isspace(c))
+ {
+ gapPenaltyMask[len++] = c;
+ }
+ }
+ }
+
+ // skip any more comment lines
+ while (line[0] == '!')
+ {
+ if (!_fileIn->getline(line, MAXLINE + 1))
+ {
+ freeFileResources(_fileIn);
+ return ;
+ }
+ }
+
+ // skip the sequence lines
+ for (;;)
+ {
+ if (isspace(line[0]) || line[0] == '\0') // Mark change 27-4-2007
+ {
+ break;
+ }
+ if (!_fileIn->getline(line, MAXLINE + 1))
+ {
+ freeFileResources(_fileIn);
+ return ;
+ }
+ }
+ }
+ freeFileResources(_fileIn);
+ }
+ catch(...)
+ {
+ freeFileResources(_fileIn);
+ cerr << "An exception has occured in the function ClustalFileParser::getSecStructure()\n"
+ << "Program needs to terminate.\nPlease contact the Clustal developers\n";
+ exit(1);
+ }
+}
+
+bool ClustalFileParser::clustalBlankline(char* line)
+{
+ int i;
+
+ if (line[0] == '!')
+ {
+ return true;
+ }
+
+ for (i = 0; line[i] != '\n' && line[i] != EOS; i++)
+ {
+ if (isdigit(line[i]) || isspace(line[i]) || (line[i] == '*') ||
+ (line[i] == ':') || (line[i] == '.'))
+ ;
+ else
+ {
+ return false;
+ }
+ }
+ return true;
+}
+
+}
git://source.jalview.org / jabaws.git / blobdiff