X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=clearcutcommand.cpp;h=1b0a532cace0792297ce3162a03c7a382b66b282;hp=d3c7fa48128246f8f4cb28ad53727329b3de856c;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=4e4d3cb3315fe25b40383c6f65cd6be23f58903d diff --git a/clearcutcommand.cpp b/clearcutcommand.cpp index d3c7fa4..1b0a532 100644 --- a/clearcutcommand.cpp +++ b/clearcutcommand.cpp @@ -19,26 +19,26 @@ extern "C" { //********************************************************************************************************************** vector ClearcutCommand::setParameters(){ try { - CommandParameter pphylip("phylip", "InputTypes", "", "", "FastaPhylip", "FastaPhylip", "none",false,false); parameters.push_back(pphylip); - CommandParameter pfasta("fasta", "InputTypes", "", "", "FastaPhylip", "FastaPhylip", "none",false,false); parameters.push_back(pfasta); - CommandParameter pverbose("verbose", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pverbose); - CommandParameter pquiet("quiet", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pquiet); - CommandParameter pversion("version", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pversion); - CommandParameter pseed("seed", "String", "", "", "*", "", "",false,false); parameters.push_back(pseed); - CommandParameter pnorandom("norandom", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pnorandom); - CommandParameter pshuffle("shuffle", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pshuffle); - CommandParameter pneighbor("neighbor", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pneighbor); - CommandParameter pexpblen("expblen", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pexpblen); - CommandParameter pexpdist("expdist", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pexpdist); - CommandParameter pDNA("DNA", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pDNA); - CommandParameter pprotein("protein", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pprotein); - CommandParameter pjukes("jukes", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pjukes); - CommandParameter pkimura("kimura", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pkimura); - CommandParameter pstdout("stdout", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pstdout); - CommandParameter pntrees("ntrees", "Number", "", "1", "", "", "",false,false); parameters.push_back(pntrees); - CommandParameter pmatrixout("matrixout", "String", "", "", "", "", "",false,false); parameters.push_back(pmatrixout); - CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); - CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); + CommandParameter pphylip("phylip", "InputTypes", "", "", "FastaPhylip", "FastaPhylip", "none","tree",false,false,true); parameters.push_back(pphylip); + CommandParameter pfasta("fasta", "InputTypes", "", "", "FastaPhylip", "FastaPhylip", "none","tree",false,false,true); parameters.push_back(pfasta); + CommandParameter pverbose("verbose", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pverbose); + CommandParameter pquiet("quiet", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pquiet); + CommandParameter pversion("version", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pversion); + CommandParameter pseed("seed", "String", "", "", "*", "", "","",false,false); parameters.push_back(pseed); + CommandParameter pnorandom("norandom", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pnorandom); + CommandParameter pshuffle("shuffle", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pshuffle); + CommandParameter pneighbor("neighbor", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pneighbor); + CommandParameter pexpblen("expblen", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pexpblen); + CommandParameter pexpdist("expdist", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pexpdist); + CommandParameter pDNA("DNA", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pDNA); + CommandParameter pprotein("protein", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pprotein); + CommandParameter pjukes("jukes", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pjukes); + CommandParameter pkimura("kimura", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pkimura); + CommandParameter pstdout("stdout", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pstdout); + CommandParameter pntrees("ntrees", "Number", "", "1", "", "", "","",false,false); parameters.push_back(pntrees); + CommandParameter pmatrixout("matrixout", "String", "", "", "", "", "","",false,false); parameters.push_back(pmatrixout); + CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir); + CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir); vector myArray; for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } @@ -86,7 +86,22 @@ string ClearcutCommand::getHelpString(){ exit(1); } } - +//********************************************************************************************************************** +string ClearcutCommand::getOutputPattern(string type) { + try { + string pattern = ""; + + if (type == "matrixout") { pattern = "[filename],"; } + else if (type == "tree") { pattern = "[filename],tre"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "ClearcutCommand", "getOutputPattern"); + exit(1); + } +} //********************************************************************************************************************** ClearcutCommand::ClearcutCommand(){ try { @@ -244,56 +259,57 @@ int ClearcutCommand::execute() { if (abort == true) { if (calledHelp) { return 0; } return 2; } //prepare filename - string outputName = outputDir + m->getRootName(m->getSimpleName(inputFile)) + "tre"; + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputFile)); + string outputName = getOutputFileName("tree", variables); outputNames.push_back(outputName); outputTypes["tree"].push_back(outputName); vector cPara; - char* tempClearcut = new char[8]; - strcpy(tempClearcut, "clearcut"); + char* tempClearcut = new char[9]; + *tempClearcut = '\0'; strncat(tempClearcut, "clearcut", 8); cPara.push_back(tempClearcut); //you gave us a distance matrix - if (phylipfile != "") { char* temp = new char[10]; strcpy(temp, "--distance"); cPara.push_back(temp); } + if (phylipfile != "") { char* temp = new char[11]; *temp = '\0'; strncat(temp, "--distance", 10); cPara.push_back(temp); } //you gave us a fastafile - if (fastafile != "") { char* temp = new char[11]; strcpy(temp, "--alignment"); cPara.push_back(temp); } + if (fastafile != "") { char* temp = new char[12]; *temp = '\0'; strncat(temp, "--alignment", 11); cPara.push_back(temp); } - if (version) { char* temp = new char[9]; strcpy(temp, "--version"); cPara.push_back(temp); } - if (verbose) { char* temp = new char[9]; strcpy(temp, "--verbose"); cPara.push_back(temp); } - if (quiet) { char* temp = new char[7]; strcpy(temp, "--quiet"); cPara.push_back(temp); } + if (version) { char* temp = new char[10]; *temp = '\0'; strncat(temp, "--version", 9); cPara.push_back(temp); } + if (verbose) { char* temp = new char[10]; *temp = '\0'; strncat(temp, "--verbose", 9); cPara.push_back(temp); } + if (quiet) { char* temp = new char[8]; *temp = '\0'; strncat(temp, "--quiet", 7); cPara.push_back(temp); } if (seed != "*") { string tempSeed = "--seed=" + seed; - char* temp = new char[tempSeed.length()]; - strcpy(temp, tempSeed.c_str()); + char* temp = new char[tempSeed.length()+1]; + *temp = '\0'; strncat(temp, tempSeed.c_str(), tempSeed.length()); cPara.push_back(temp); } - if (norandom) { char* temp = new char[10]; strcpy(temp, "--norandom"); cPara.push_back(temp); } - if (shuffle) { char* temp = new char[9]; strcpy(temp, "--shuffle"); cPara.push_back(temp); } - if (neighbor) { char* temp = new char[10]; strcpy(temp, "--neighbor"); cPara.push_back(temp); } + if (norandom) { char* temp = new char[11]; *temp = '\0'; strncat(temp, "--norandom", 10); cPara.push_back(temp); } + if (shuffle) { char* temp = new char[10]; *temp = '\0'; strncat(temp, "--shuffle", 9); cPara.push_back(temp); } + if (neighbor) { char* temp = new char[11]; *temp = '\0'; strncat(temp, "--neighbor", 10); cPara.push_back(temp); } string tempIn = "--in=" + inputFile; - char* tempI = new char[tempIn.length()]; - strcpy(tempI, tempIn.c_str()); + char* tempI = new char[tempIn.length()+1]; + *tempI = '\0'; strncat(tempI, tempIn.c_str(), tempIn.length()); cPara.push_back(tempI); - if (stdoutWanted) { char* temp = new char[8]; strcpy(temp, "--stdout"); cPara.push_back(temp); } + if (stdoutWanted) { char* temp = new char[9]; *temp = '\0'; strncat(temp, "--stdout", 8); cPara.push_back(temp); } else{ string tempOut = "--out=" + outputName; - - char* temp = new char[tempOut.length()]; - strcpy(temp, tempOut.c_str()); + char* temp = new char[tempOut.length()+1]; + *temp = '\0'; strncat(temp, tempOut.c_str(), tempOut.length()); cPara.push_back(temp); } - if (DNA) { char* temp = new char[5]; strcpy(temp, "--DNA"); cPara.push_back(temp); } - if (protein) { char* temp = new char[9]; strcpy(temp, "--protein"); cPara.push_back(temp); } - if (jukes) { char* temp = new char[7]; strcpy(temp, "--jukes"); cPara.push_back(temp); } - if (kimura) { char* temp = new char[8]; strcpy(temp, "--kimura"); cPara.push_back(temp); } + if (DNA) { char* temp = new char[6]; *temp = '\0'; strncat(temp, "--DNA", 5); cPara.push_back(temp); } + if (protein) { char* temp = new char[10]; *temp = '\0'; strncat(temp, "--protein", 9); cPara.push_back(temp); } + if (jukes) { char* temp = new char[8]; *temp = '\0'; strncat(temp, "--jukes", 7); cPara.push_back(temp); } + if (kimura) { char* temp = new char[9]; *temp = '\0'; strncat(temp, "--kimura", 8); cPara.push_back(temp); } if (matrixout != "") { string tempMatrix = "--matrixout=" + outputDir + matrixout; - char* temp = new char[tempMatrix.length()]; - strcpy(temp, tempMatrix.c_str()); + char* temp = new char[tempMatrix.length()+1]; + *temp = '\0'; strncat(temp, tempMatrix.c_str(), tempMatrix.length()); cPara.push_back(temp); outputNames.push_back((outputDir + matrixout)); outputTypes["matrixout"].push_back((outputDir + matrixout)); @@ -301,13 +317,13 @@ int ClearcutCommand::execute() { if (ntrees != "1") { string tempNtrees = "--ntrees=" + ntrees; - char* temp = new char[tempNtrees.length()]; - strcpy(temp, tempNtrees.c_str()); + char* temp = new char[tempNtrees.length()+1]; + *temp = '\0'; strncat(temp, tempNtrees.c_str(), tempNtrees.length()); cPara.push_back(temp); } - if (expblen) { char* temp = new char[9]; strcpy(temp, "--expblen"); cPara.push_back(temp); } - if (expdist) { char* temp = new char[9]; strcpy(temp, "--expdist"); cPara.push_back(temp); } + if (expblen) { char* temp = new char[10]; *temp = '\0'; strncat(temp, "--expblen", 9); cPara.push_back(temp); } + if (expdist) { char* temp = new char[10]; *temp = '\0'; strncat(temp, "--expdist", 9); cPara.push_back(temp); } char** clearcutParameters; clearcutParameters = new char*[cPara.size()];