+++ /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.
- *
- * 23-03-07,Nigel Brown(EMBL): added call to Alignment::testUniqueNames() to
- * test sequence names prior to appending; moved
- * Alignment::checkAllNamesDifferent() test into block handling loading of new
- * sequences.
- *
- * 02-04-07,Nigel Brown(EMBL): commented out the "No sequences in file..."
- * warnings in seqInput() and profileInput()and enabled the
- * higher-up-the-stack counterpart in MainWindow::errorHandler(), since the
- * former was causing a crash during the repaint after the user accepts the
- * message, because some state (what exactly?) is unstable at this depth after
- * a sequence load error, specifically when loading an empty file after
- * already loading some sequences.
- */
-
-#ifdef HAVE_CONFIG_H
- #include "config.h"
-#endif
-#include "FileReader.h"
-
-
-namespace clustalw
-{
-
-FileReader::FileReader()
-{
- fileIn = new InFileStream;
- structPenalties = NONE; // I think this should be ok.
-}
-
-FileReader::~FileReader()
-{
- delete fileIn;
-}
-
-
-/* check if we've read sequences without any information, i.e. header
- * but no sequence at all
- */
-bool FileReader::noEmptySequence(vector<Sequence> seqVector, string *offendingSeq)
-{
- vector<Sequence>::iterator si;
- for (si = seqVector.begin(); si != seqVector.end(); si++) {
- if (si->isEmpty()) {
- offendingSeq->assign(si->getName());
- return false;
- }
- }
- return true;
-}
-
-
-
-/*
- * The function seqInput is called from the interactive menu only. This is because it
- * allows us to append seqs. But this would not happen on command line.
- * It is called twice in the interactive menu, both times with append as false. It calls
- * the readseqs function to do the work.
- */
- int FileReader::seqInput(Alignment *alignPtr, bool append, string *offendingSeq)
-{
- int code;
-
- if(userParameters->getMenuFlag())
- {
- cout << "\n\nSequences should all be in 1 file.\n";
- cout << "\n7 formats accepted: \n";
- cout << "NBRF/PIR, EMBL/SwissProt, Pearson (Fasta), GDE, Clustal, GCG/MSF, \
- RSF.\n\n\n";
- }
-
- if (append)
- {
- int numSeqsAlready = alignPtr->getNumSeqs();
- code = readSeqs(alignPtr, numSeqsAlready + 1, offendingSeq);
- }
- else
- {
- code = readSeqs(alignPtr, 1, offendingSeq); // 1 is the first seq to be read
- }
-
- if(code == OK)
- {
- userParameters->setStructPenalties1(false);
- userParameters->setStructPenalties2(false);
-
- alignPtr->clearSecStruct1();
- alignPtr->clearSecStruct2();
-
- string typeOfAlign = userParameters->getDNAFlag() ? "DNA" : "PROTEIN";
- cout << "Sequences assumed to be "
- << typeOfAlign << endl;
-
- if (userParameters->getMenuFlag())
- {
- cout << "\n\n";
- alignPtr->printSequencesAddedInfo();
- }
- if(userParameters->getDNAFlag())
- {
- userParameters->setDNAMultiGap();
- }
- else
- {
- userParameters->setProtMultiGap();
- }
- userParameters->setEmpty(false);
- }
- else if(code == NOSEQUENCESINFILE) // no sequences
- {
- /* 02-04-07,nige: this causes a fatal repaint: let
- * MainWindow::errorHandler deal with it.
- */
- //utilityObject->error("No sequences in file! Bad format?\n");
- return code;
- }
- else
- {
- return code;
- }
- return code;
-}
-
-/*
- * The function readSeqs will create the FileParser that is needed and
- * it will read in all of the sequences. Depending on the filetype, it
- * will also check for secondary structure information.
- *
- * If there is a problem with one of the sequences its name will be
- * assigned to offendingSeq
- */
- int FileReader::readSeqs(Alignment *alignPtr, int firstSeq, string *offendingSeq)
-{
- string line;
- string fileName;
- string linuxFilePath = "file://";
- // static char *seq1, sname1[MAXNAMES + 1], title[MAXTITLES + 1];
- //int i, j;
- int noSeqs;
- //static int l1;
- static bool DNAFlag1;
- vector<Sequence> seqVector;
- vector<Sequence> seqRangeVector;
-
- auto_ptr<FileParser> fileParser; // Means we dont need to delete it!
-
- vector<int> _outputIndex; // Local version of outputIndex.
-
-
- if (userParameters->getMenuFlag())
- {
- utilityObject->getStr(string("Enter the name of the sequence file "), line);
- }
- else
- {
- line = userParameters->getSeqName();
- }
- if (line.length() == 0)
- {
- // We have no fileName, so return -1
- return -1;
- }
-
- // If we have file:// in the string, remove it!!
- string::size_type loc = line.find(linuxFilePath, 0);
- if(loc != string::npos)
- {
- fileName = line.substr(loc + linuxFilePath.length());
- line = fileName;
- }
- // Now we have the file name, we must open the file.
- fileIn->open(line.c_str()); //nige
- if (fileIn->fail())
- return CANNOTOPENFILE;
-
- sequenceFileName = line;
-
- // Check if the file exists!
- if (!fileIn->is_open())
- {
- utilityObject->error("Cannot open input file (%s)\n", line.c_str());
- return CANNOTOPENFILE;
- }
-
- userParameters->setSeqName(line);
-
-
- // NOTE I made a change here because the profile2Name was not stored!
- if(userParameters->getProfileNum() == 2 && userParameters->getProfile2Name().empty())
- {
- userParameters->setProfile2Name(line);
- }
- else if(userParameters->getProfileNum() == 1 && userParameters->getProfile1Name().empty())
- {
- userParameters->setProfile1Name(line);
- }
-
- noSeqs = 0;
-
- checkInfile(&noSeqs, fileParser);
-
- if (noSeqs == 0)
- {
- return NOSEQUENCESINFILE;
- }
-
-
- seqRangeVector = fileParser->getSeqRange(1, noSeqs, offendingSeq);
- if (seqRangeVector.size()==0)
- return fileParser->getParseExitCode();
- // FIXME Andreas Wilm (UCD): noEmptySequence check should be done
- // internally by FileParser instances
- if (noEmptySequence(seqRangeVector, offendingSeq) == false) {
- return EMPTYSEQUENCE; // Error there are same names.
- }
-
- for (int i=0; i < (int)seqRangeVector.size(); i++) {
- // Andreas Wilm (UCD): fixed wrong default output order
- // which is important when no alignment (convert!) is done
- // _outputIndex.push_back(i); // default output order
- _outputIndex.push_back(i+1); // default output order
-
- Sequence tempSeq = seqRangeVector[i];
-
- if (!userParameters->getExplicitDNAFlag())
- {
- DNAFlag1 = tempSeq.checkDNAFlag(); // check DNA/Prot
- if (i == 1)
- {
- userParameters->setDNAFlag(DNAFlag1);
- }
- } // type decided by first seq
- else
- {
- DNAFlag1 = userParameters->getDNAFlag();
- }
-
- seqVector.push_back(tempSeq);
-
- }
-
- if(firstSeq == 1) // New mulitple alignment, or else profile1
- {
- int prfNum = userParameters->getProfileNum();
- alignPtr->addSequences(&seqVector);
- //test names after saving
- if(alignPtr->checkAllNamesDifferent(offendingSeq) == false) { //nige moved
- return ALLNAMESNOTDIFFERENT; // Error there are same names.
- }
-
- userParameters->setProfileNum(prfNum);
- if(!alignPtr->addOutputIndex(&_outputIndex))
- {
- return OTHERERROR;
- }
- }
- else // profile2
- {
- //test names before appending
- if (! alignPtr->testUniqueNames(&seqVector, offendingSeq)) { //nige added
- return ALLNAMESNOTDIFFERENT;
- }
- alignPtr->appendSequences(&seqVector);
- if(!alignPtr->appendOutputIndex(&_outputIndex))
- {
- return OTHERERROR;
- }
- }
-
- // Then need to pass the length to the parser to get the secondary structure info.
-
- int maxAlnLength; // Get values from the Alignment object.
- maxAlnLength = alignPtr->getMaxAlnLength();
-
- // look for a feature table / gap penalty mask (only if this is a profile)
- if (userParameters->getProfileNum() > 0)
- {
- structPenalties = NONE;
- secStructMask.clear();
- gapPenaltyMask.clear();
- secStructName = "";
-
- fileParser->getSecStructure(gapPenaltyMask, secStructMask, secStructName,
- structPenalties, maxAlnLength);
-
- // Andreas Wilm (UCD): bug 114
- // after calling getSecStructure gapPenaltyMask needs to be
- // allocated (it's copied/linked to later)
- if (gapPenaltyMask.empty())
- {
- gapPenaltyMask.resize(secStructMask.size());
- }
- }
-
- if (fileIn->is_open())
- {
- fileIn->close();
- }
- return OK; // return the number of seqs. read in this call
-}
-
-/*
- * The function profileInput is used to read profiles into the Alignment. If the first
- * profile is already there it will read in the second profile. It returns the number
- * of seqs. If it returns -1, couldnt open file.
- */
-int FileReader::profileInput(Alignment *alignPtr)
-{
- int code;
- //int i, totalNumOfSeqs = 0;
- string offendingSeq;
-
- if(userParameters->getProfileNum() == 2 && userParameters->getProfile1Empty())
- {
- utilityObject->error("You must read in profile number 1 first\n");
- return MUSTREADINPROFILE1FIRST;
- }
-
- if(userParameters->getProfileNum() == 1) // for the 1st profile
- {
- code = readSeqs(alignPtr, 1, &offendingSeq);
-
- if (code == OK)
- {
- // success; found some seqs.
- userParameters->setStructPenalties1(NONE);
- alignPtr->clearSecStruct1(); // Clear old info
-
- if (structPenalties != NONE) // feature table / mask in alignment
- {
- userParameters->setStructPenalties1(structPenalties);
- if (structPenalties == SECST)
- {
-
- alignPtr->addSecStructMask1(&secStructMask);
- }
- alignPtr->addGapPenaltyMask1(&gapPenaltyMask);
- alignPtr->addSecStructName1(secStructName);
-
- }
-
- alignPtr->setProfile1NumSeqs(alignPtr->getNumSeqs());
-
- userParameters->setProfile1Empty(false);
- userParameters->setProfile2Empty(true);
- cout << "No. of seqs = " << alignPtr->getNumSeqs() << endl;
- }
- else
- {
- return code; // FIXME and offendingSeq?
- }
- }
- else
- {
- // first seq to be read = profile1_nseqs + 1
- int profile1NumOfSeqs = alignPtr->getNumSeqs();
- code = readSeqs(alignPtr, profile1NumOfSeqs + 1, &offendingSeq);
- if(code == OK)
- {
- userParameters->setStructPenalties2(NONE);
- alignPtr->clearSecStruct2(); // Clear old info
-
- if (structPenalties != NONE) // feature table / mask in alignment
- {
- userParameters->setStructPenalties2(structPenalties);
- if (structPenalties == SECST)
- {
- alignPtr->addSecStructMask2(&secStructMask);
- }
- alignPtr->addGapPenaltyMask2(&gapPenaltyMask);
- alignPtr->addSecStructName2(secStructName);
- }
- cout << "No. of seqs in profile=" << alignPtr->getNumSeqs() - profile1NumOfSeqs
- << endl;
- cout << "Total no. of seqs =" << alignPtr->getNumSeqs() << endl;
- userParameters->setProfile2Empty(false);
- userParameters->setEmpty(false);
- }
- else
- {
- return code; // FIXME and offendingSeq?
- }
- }
- // Clear out the masks used in this class. This is important!!!!
- secStructMask.clear();
- gapPenaltyMask.clear();
- secStructName = "";
-
- string typeOfAlign = userParameters->getDNAFlag() ? "DNA" : "PROTEIN";
- cout << "Sequences assumed to be "
- << typeOfAlign << endl;
-
- if (userParameters->getMenuFlag())
- {
- cout<< "\n\n";
- }
-
- alignPtr->printSequencesAddedInfo();
-
- if(userParameters->getDNAFlag())
- {
- userParameters->setDNAMultiGap();
- }
- else
- {
- userParameters->setProtMultiGap();
- }
- return OK;
-}
-
-
-/*
- * The function checkInfile is used to find out which format the file is in, and it
- * also calls the appropriate function to count the seqences.
- */
-void FileReader::checkInfile(int *nseqs, auto_ptr<FileParser>& fileParser)
-{
- char _lineIn[MAXLINE + 1];
- int i;
- int lengthLine = 0;
- *nseqs = 0;
-
- while (fileIn->getline(_lineIn, MAXLINE + 1))
- {
- if (!utilityObject->blankLine(_lineIn))
- {
- break;
- }
- }
- lengthLine = strlen(_lineIn) - 1; // Mark Change 20-6-07
-
- for (i = lengthLine; i >= 0; i--)
- {
- if (isgraph(_lineIn[i]))
- {
- break;
- }
- }
- _lineIn[i + 1] = EOS;
-
- // Put first 7 characters into upper case!
- for (i = 0; i <= 6 && i <= lengthLine; i++)
- {
- _lineIn[i] = toupper(_lineIn[i]);
- }
-
- // Create the parser to read the file.
- if (utilityObject->lineType(_lineIn, "ID"))
- {
- // EMBL/Swiss-Prot format ?
- fileParser.reset(new EMBLFileParser(sequenceFileName));
- if(userParameters->getDisplayInfo())
- cout << "Sequence format is EMBL\n";
- }
- else if (utilityObject->lineType(_lineIn, "CLUSTAL"))
- {
- fileParser.reset(new ClustalFileParser(sequenceFileName));
- if(userParameters->getDisplayInfo())
- cout << "Sequence format is CLUSTAL\n";
- }
- else if (utilityObject->lineType(_lineIn, "PILEUP")) // MSF
- {
- fileParser.reset(new MSFFileParser(sequenceFileName));
- if(userParameters->getDisplayInfo())
- cout << "Sequence format is MSF\n";
- }
- else if (utilityObject->lineType(_lineIn, "!!AA_MULTIPLE_ALIGNMENT")) // MSF
- {
- fileParser.reset(new MSFFileParser(sequenceFileName));
- userParameters->setDNAFlag(false);
- if(userParameters->getDisplayInfo())
- cout << "Sequence format is MSF\n";
- }
- else if (utilityObject->lineType(_lineIn, "!!NA_MULTIPLE_ALIGNMENT")) // MSF
- {
- fileParser.reset(new MSFFileParser(sequenceFileName));
- userParameters->setDNAFlag(true);
- if(userParameters->getDisplayInfo())
- cout << "Sequence format is MSF\n";
- }
- else if (strstr(_lineIn, "MSF") && _lineIn[strlen(_lineIn) - 1] == '.' &&
- _lineIn[strlen(_lineIn) - 2] == '.') // MSF
- {
- fileParser.reset(new MSFFileParser(sequenceFileName));
- if(userParameters->getDisplayInfo())
- cout << "Sequence format is MSF\n";
- }
- else if (utilityObject->lineType(_lineIn, "!!RICH_SEQUENCE")) // RSF
- {
- fileParser.reset(new RSFFileParser(sequenceFileName));
- if(userParameters->getDisplayInfo())
- cout << "Sequence format is RSF\n";
- }
- else if (utilityObject->lineType(_lineIn, "#NEXUS"))
- {
- //utilityObject->error("Cannot read NEXUS format\n");
- return;
- }
- else if (*_lineIn == '>')
- {
- if ((lengthLine>=3) && _lineIn[3] == ';') {
- //if(_lineIn[3] == ';') // distinguish PIR and Pearson
- {
- // PIR
- fileParser.reset(new PIRFileParser(sequenceFileName));
- if(userParameters->getDisplayInfo())
- cout << "Sequence format is PIR\n";
- }
- }
- else
- {
- // PEARSON
- fileParser.reset(new PearsonFileParser(sequenceFileName));
- if(userParameters->getDisplayInfo())
- cout << "Sequence format is Pearson\n";
- }
- }
- else if ((*_lineIn == '"') || (*_lineIn == '%') || (*_lineIn == '#'))
- {
- // GDE format
- fileParser.reset(new GDEFileParser(sequenceFileName));
- if(userParameters->getDisplayInfo())
- cout << "Sequence format is GDE\n";
-
- if (*_lineIn == '%')
- {
- userParameters->setDNAFlag(false);
- }
- else if (*_lineIn == '#')
- {
- userParameters->setDNAFlag(true);
- }
- }
- else
- {
- return ;
- }
-
- try
- {
- // Get the number of sequences. This is passed back as a pointer!
- *nseqs = fileParser->countSeqs();
- // no output in 1.83: cout << "number of seqs is: " << *nseqs << "\n";
- }
- catch(exception ex)
- {
- *nseqs = 0;
- }
-}
-
-
-}
-
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