X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=otuhierarchycommand.cpp;h=14138de30355151035a7ddca66f5bd928e534bc5;hb=1d5962b46d9e72a2b855b4176d1c47df9a163fac;hp=a8a3531a67e97dd8669bbc24b83d2e930356e98c;hpb=74844a60d80c6dd06e3fb02ee9b928424f9019b0;p=mothur.git diff --git a/otuhierarchycommand.cpp b/otuhierarchycommand.cpp index a8a3531..14138de 100644 --- a/otuhierarchycommand.cpp +++ b/otuhierarchycommand.cpp @@ -9,6 +9,54 @@ #include "otuhierarchycommand.h" +//********************************************************************************************************************** +vector OtuHierarchyCommand::getValidParameters(){ + try { + string Array[] = {"list","label","output","outputdir","inputdir"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "OtuHierarchyCommand", "getValidParameters"); + exit(1); + } +} +//********************************************************************************************************************** +OtuHierarchyCommand::OtuHierarchyCommand(){ + try { + abort = true; + //initialize outputTypes + vector tempOutNames; + outputTypes["otuheirarchy"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "OtuHierarchyCommand", "OtuHierarchyCommand"); + exit(1); + } +} +//********************************************************************************************************************** +vector OtuHierarchyCommand::getRequiredParameters(){ + try { + string Array[] = {"list","label"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "OtuHierarchyCommand", "getRequiredParameters"); + exit(1); + } +} +//********************************************************************************************************************** +vector OtuHierarchyCommand::getRequiredFiles(){ + try { + vector myArray; + return myArray; + } + catch(exception& e) { + m->errorOut(e, "OtuHierarchyCommand", "getRequiredFiles"); + exit(1); + } +} //********************************************************************************************************************** OtuHierarchyCommand::OtuHierarchyCommand(string option) { try { @@ -33,6 +81,10 @@ OtuHierarchyCommand::OtuHierarchyCommand(string option) { if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } } + //initialize outputTypes + vector tempOutNames; + outputTypes["otuheirarchy"] = tempOutNames; + //if the user changes the input directory command factory will send this info to us in the output parameter string inputDir = validParameter.validFile(parameters, "inputdir", false); if (inputDir == "not found"){ inputDir = ""; } @@ -41,7 +93,7 @@ OtuHierarchyCommand::OtuHierarchyCommand(string option) { it = parameters.find("list"); //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["list"] = inputDir + it->second; } } @@ -54,7 +106,7 @@ OtuHierarchyCommand::OtuHierarchyCommand(string option) { //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(listFile); //if user entered a file with a path then preserve it + outputDir += m->hasPath(listFile); //if user entered a file with a path then preserve it } //check for optional parameter and set defaults @@ -62,7 +114,7 @@ OtuHierarchyCommand::OtuHierarchyCommand(string option) { label = validParameter.validFile(parameters, "label", false); if (label == "not found") { m->mothurOut("label is a required parameter for the otu.hierarchy command."); m->mothurOutEndLine(); abort = true; } else { - splitAtDash(label, labels); + m->splitAtDash(label, labels); if (labels.size() != 2) { m->mothurOut("You must provide 2 labels."); m->mothurOutEndLine(); abort = true; } } @@ -110,6 +162,8 @@ int OtuHierarchyCommand::execute(){ //get listvectors that correspond to labels requested, (or use smart distancing to get closest listvector) vector lists = getListVectors(); + if (m->control_pressed) { outputTypes.clear(); return 0; } + //determine which is little and which is big, putting little first if (lists.size() == 2) { //if big is first swap them @@ -123,6 +177,9 @@ int OtuHierarchyCommand::execute(){ //map sequences to bin number in the "little" otu map littleBins; for (int i = 0; i < lists[0].getNumBins(); i++) { + + if (m->control_pressed) { return 0; } + string names = lists[0].get(i); //parse bin @@ -137,12 +194,14 @@ int OtuHierarchyCommand::execute(){ } ofstream out; - string outputFileName = outputDir + getRootName(getSimpleName(listFile)) + lists[0].getLabel() + "-" + lists[1].getLabel() + ".otu.hierarchy"; - openOutputFile(outputFileName, out); + string outputFileName = outputDir + m->getRootName(m->getSimpleName(listFile)) + lists[0].getLabel() + "-" + lists[1].getLabel() + ".otu.hierarchy"; + m->openOutputFile(outputFileName, out); //go through each bin in "big" otu and output the bins in "little" otu which created it for (int i = 0; i < lists[1].getNumBins(); i++) { + if (m->control_pressed) { outputTypes.clear(); out.close(); remove(outputFileName.c_str()); return 0; } + string names = lists[1].get(i); //output column 1 @@ -174,9 +233,11 @@ int OtuHierarchyCommand::execute(){ out.close(); + if (m->control_pressed) { outputTypes.clear(); remove(outputFileName.c_str()); return 0; } + m->mothurOutEndLine(); m->mothurOut("Output File Name: "); m->mothurOutEndLine(); - m->mothurOut(outputFileName); m->mothurOutEndLine(); + m->mothurOut(outputFileName); m->mothurOutEndLine(); outputNames.push_back(outputFileName); outputTypes["otuheirarchy"].push_back(outputFileName); m->mothurOutEndLine(); return 0; @@ -202,7 +263,7 @@ vector OtuHierarchyCommand::getListVectors() { //open file ifstream in; - openInputFile(listFile, in); + m->openInputFile(listFile, in); //get first list vector in file ListVector* list = NULL; @@ -211,11 +272,13 @@ vector OtuHierarchyCommand::getListVectors() { pos = in.tellg(); lastPos = pos; list = new ListVector(in); - gobble(in); + m->gobble(in); lastLabel = list->getLabel(); } while ((list != NULL) && (userLabels.size() != 0)) { + + if (m->control_pressed) { in.close(); delete list; return lists; } //is this a listvector that we want? if(labels.count(list->getLabel()) == 1){ @@ -229,7 +292,7 @@ vector OtuHierarchyCommand::getListVectors() { } //you have a label the user want that is smaller than this label and the last label has not already been processed - if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { string saveLabel = list->getLabel(); int savePos = in.tellg(); @@ -260,11 +323,11 @@ vector OtuHierarchyCommand::getListVectors() { if (!in.eof()) { pos = in.tellg(); list = new ListVector(in); - gobble(in); + m->gobble(in); }else { list = NULL; } } - + if (m->control_pressed) { in.close(); return lists; } //output error messages about any remaining user labels set::iterator it; @@ -279,6 +342,8 @@ vector OtuHierarchyCommand::getListVectors() { } } + if (m->control_pressed) { in.close(); return lists; } + //run last label if you need to if (needToRun == true) { if (list != NULL) { delete list; } @@ -295,7 +360,7 @@ vector OtuHierarchyCommand::getListVectors() { } } - + in.close(); return lists; } catch(exception& e) {