X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=secondarystructurecommand.cpp;h=c08ee6ab2d512b56c6d39fa2a1290ab12da22bde;hb=dd173a49e37f6bae73a63c32dd7c98d317bb4a79;hp=8acd696406c288303128a3c36aef3e6d816f2fbe;hpb=f89b6501b7d80e705b6c50ff2c8bdd8bb5d2edf7;p=mothur.git diff --git a/secondarystructurecommand.cpp b/secondarystructurecommand.cpp index 8acd696..c08ee6a 100644 --- a/secondarystructurecommand.cpp +++ b/secondarystructurecommand.cpp @@ -12,11 +12,11 @@ //********************************************************************************************************************** -AlignCheckCommand::AlignCheckCommand(string option){ +AlignCheckCommand::AlignCheckCommand(string option) { try { abort = false; haderror = 0; - + //allow user to run help if(option == "help") { help(); abort = true; } @@ -44,7 +44,7 @@ AlignCheckCommand::AlignCheckCommand(string option){ it = parameters.find("fasta"); //user has given a template file if(it != parameters.end()){ - path = hasPath(it->second); + path = m->hasPath(it->second); //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { parameters["fasta"] = inputDir + it->second; } } @@ -52,7 +52,7 @@ AlignCheckCommand::AlignCheckCommand(string option){ it = parameters.find("map"); //user has given a template file if(it != parameters.end()){ - path = hasPath(it->second); + path = m->hasPath(it->second); //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { parameters["map"] = inputDir + it->second; } } @@ -61,23 +61,23 @@ AlignCheckCommand::AlignCheckCommand(string option){ //check for required parameters mapfile = validParameter.validFile(parameters, "map", true); if (mapfile == "not open") { abort = true; } - else if (mapfile == "not found") { mapfile = ""; mothurOut("You must provide an map file."); mothurOutEndLine(); abort = true; } + else if (mapfile == "not found") { mapfile = ""; m->mothurOut("You must provide an map file."); m->mothurOutEndLine(); abort = true; } fastafile = validParameter.validFile(parameters, "fasta", true); if (fastafile == "not open") { abort = true; } - else if (fastafile == "not found") { fastafile = ""; mothurOut("You must provide an fasta file."); mothurOutEndLine(); abort = true; } + else if (fastafile == "not found") { fastafile = ""; m->mothurOut("You must provide an fasta file."); m->mothurOutEndLine(); abort = true; } //if the user changes the output directory command factory will send this info to us in the output parameter outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; - outputDir += hasPath(fastafile); //if user entered a file with a path then preserve it + outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it } } } catch(exception& e) { - errorOut(e, "AlignCheckCommand", "RemoveSeqsCommand"); + m->errorOut(e, "AlignCheckCommand", "RemoveSeqsCommand"); exit(1); } } @@ -85,15 +85,15 @@ AlignCheckCommand::AlignCheckCommand(string option){ void AlignCheckCommand::help(){ try { - mothurOut("The align.check command reads a fasta file and map file.\n"); - mothurOut("It outputs a file containing the secondary structure matches in the .align.check file.\n"); - mothurOut("The align.check command parameters are fasta and map, both are required.\n"); - mothurOut("The align.check command should be in the following format: align.check(fasta=yourFasta, map=yourMap).\n"); - mothurOut("Example align.check(map=silva.ss.map, fasta=amazon.fasta).\n"); - mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n"); + m->mothurOut("The align.check command reads a fasta file and map file.\n"); + m->mothurOut("It outputs a file containing the secondary structure matches in the .align.check file.\n"); + m->mothurOut("The align.check command parameters are fasta and map, both are required.\n"); + m->mothurOut("The align.check command should be in the following format: align.check(fasta=yourFasta, map=yourMap).\n"); + m->mothurOut("Example align.check(map=silva.ss.map, fasta=amazon.fasta).\n"); + m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n"); } catch(exception& e) { - errorOut(e, "AlignCheckCommand", "help"); + m->errorOut(e, "AlignCheckCommand", "help"); exit(1); } } @@ -109,19 +109,20 @@ int AlignCheckCommand::execute(){ readMap(); ifstream in; - openInputFile(fastafile, in); + m->openInputFile(fastafile, in); ofstream out; - string outfile = outputDir + getRootName(getSimpleName(fastafile)) + "align.check"; - openOutputFile(outfile, out); + string outfile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "align.check"; + m->openOutputFile(outfile, out); out << "name" << '\t' << "pound" << '\t' << "dash" << '\t' << "plus" << '\t' << "equal" << '\t'; out << "loop" << '\t' << "tilde" << '\t' << "total" << endl; while(!in.eof()){ + if (m->control_pressed) { in.close(); out.close(); remove(outfile.c_str()); return 0; } - Sequence seq(in); gobble(in); + Sequence seq(in); m->gobble(in); if (seq.getName() != "") { statData data = getStats(seq.getAligned()); @@ -135,11 +136,18 @@ int AlignCheckCommand::execute(){ in.close(); out.close(); + if (m->control_pressed) { remove(outfile.c_str()); return 0; } + + m->mothurOutEndLine(); + m->mothurOut("Output File Name: "); m->mothurOutEndLine(); + m->mothurOut(outfile); m->mothurOutEndLine(); + m->mothurOutEndLine(); + return 0; } catch(exception& e) { - errorOut(e, "AlignCheckCommand", "execute"); + m->errorOut(e, "AlignCheckCommand", "execute"); exit(1); } } @@ -150,13 +158,13 @@ void AlignCheckCommand::readMap(){ structMap.resize(1, 0); ifstream in; - openInputFile(mapfile, in); + m->openInputFile(mapfile, in); while(!in.eof()){ int position; in >> position; structMap.push_back(position); - gobble(in); + m->gobble(in); } in.close(); @@ -167,7 +175,7 @@ void AlignCheckCommand::readMap(){ for(int i=0;imothurOut("Your map file contains an error: line " + toString(i) + " does not match line " + toString(structMap[i]) + "."); m->mothurOutEndLine(); } } } @@ -175,7 +183,7 @@ void AlignCheckCommand::readMap(){ } catch(exception& e) { - errorOut(e, "AlignCheckCommand", "readMap"); + m->errorOut(e, "AlignCheckCommand", "readMap"); exit(1); } } @@ -189,7 +197,7 @@ statData AlignCheckCommand::getStats(string sequence){ int length = sequence.length(); - if (length != seqLength) { mothurOut("your sequences are " + toString(length) + " long, but your map file only contains " + toString(seqLength) + " entries. please correct."); mothurOutEndLine(); haderror = 1; return data; } + if (length != seqLength) { m->mothurOut("your sequences are " + toString(length) + " long, but your map file only contains " + toString(seqLength) + " entries. please correct."); m->mothurOutEndLine(); haderror = 1; return data; } for(int i=1;ierrorOut(e, "AlignCheckCommand", "getStats"); exit(1); } }