X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=collectsharedcommand.cpp;h=dd1ec270334e09f1d316ce060c2ab8c185e0d313;hp=3b43a40f4cd33c4f006776ba764c04fa3866d96b;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=19fcbbdba99658f5eca244803280f9ee7f9f6607 diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp index 3b43a40..dd1ec27 100644 --- a/collectsharedcommand.cpp +++ b/collectsharedcommand.cpp @@ -54,14 +54,14 @@ //********************************************************************************************************************** vector CollectSharedCommand::setParameters(){ try { - CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared); - CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel); - CommandParameter pfreq("freq", "Number", "", "100", "", "", "",false,false); parameters.push_back(pfreq); - CommandParameter pcalc("calc", "Multiple", "sharedchao-sharedsobs-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-whittaker-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-structchi2-hamming-gower-memchi2-memchord-memeuclidean-mempearson", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan", "", "", "",true,false); parameters.push_back(pcalc); - CommandParameter pall("all", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pall); - CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups); - CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); - CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); + CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pshared); + CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel); + CommandParameter pfreq("freq", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pfreq); + CommandParameter pcalc("calc", "Multiple", "sharedchao-sharedsobs-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-whittaker-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-structchi2-hamming-gower-memchi2-memchord-memeuclidean-mempearson", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan", "", "", "","",true,false,true); parameters.push_back(pcalc); + CommandParameter pall("all", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pall); + CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups); + 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); } @@ -97,6 +97,60 @@ string CollectSharedCommand::getHelpString(){ exit(1); } } +//********************************************************************************************************************** +string CollectSharedCommand::getOutputPattern(string type) { + try { + string pattern = ""; + + if (type == "sharedchao") { pattern = "[filename],shared.chao"; } + else if (type == "sharedsobs") { pattern = "[filename],shared.sobs"; } + else if (type == "sharedace") { pattern = "[filename],shared.ace"; } + else if (type == "jabund") { pattern = "[filename],jabund"; } + else if (type == "sorabund") { pattern = "[filename],sorabund"; } + else if (type == "jclass") { pattern = "[filename],jclass"; } + else if (type == "sorclass") { pattern = "[filename],sorclass"; } + else if (type == "jest") { pattern = "[filename],jest"; } + else if (type == "sorest") { pattern = "[filename],sorest"; } + else if (type == "thetayc") { pattern = "[filename],thetayc"; } + else if (type == "thetan") { pattern = "[filename],thetan"; } + else if (type == "kstest") { pattern = "[filename],kstest"; } + else if (type == "whittaker") { pattern = "[filename],whittaker"; } + else if (type == "sharednseqs") { pattern = "[filename],shared.nseqs"; } + else if (type == "ochiai") { pattern = "[filename],ochiai"; } + else if (type == "anderberg") { pattern = "[filename],anderberg"; } + else if (type == "kulczynski") { pattern = "[filename],kulczynski"; } + else if (type == "kulczynskicody") { pattern = "[filename],kulczynskicody"; } + else if (type == "lennon") { pattern = "[filename],lennon"; } + else if (type == "morisitahorn") { pattern = "[filename],morisitahorn"; } + else if (type == "braycurtis") { pattern = "[filename],braycurtis"; } + else if (type == "odum") { pattern = "[filename],odum"; } + else if (type == "canberra") { pattern = "[filename],canberra"; } + else if (type == "structeuclidean") { pattern = "[filename],structeuclidean"; } + else if (type == "structchord") { pattern = "[filename],structchord"; } + else if (type == "hellinger") { pattern = "[filename],hellinger"; } + else if (type == "manhattan") { pattern = "[filename],manhattan"; } + else if (type == "structpearson") { pattern = "[filename],structpearson"; } + else if (type == "soergel") { pattern = "[filename],soergel"; } + else if (type == "spearman") { pattern = "[filename],spearman"; } + else if (type == "structkulczynski") { pattern = "[filename],structkulczynski";} + else if (type == "structchi2") { pattern = "[filename],structchi2"; } + else if (type == "speciesprofile") { pattern = "[filename],speciesprofile"; } + else if (type == "hamming") { pattern = "[filename],hamming"; } + else if (type == "gower") { pattern = "[filename],gower"; } + else if (type == "memchi2") { pattern = "[filename],memchi2"; } + else if (type == "memchord") { pattern = "[filename],memchord"; } + else if (type == "memeuclidean") { pattern = "[filename],memeuclidean"; } + else if (type == "mempearson") { pattern = "[filename],mempearson"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "CollectSharedCommand", "getOutputPattern"); + exit(1); + } +} + //********************************************************************************************************************** CollectSharedCommand::CollectSharedCommand(){ try { @@ -270,11 +324,11 @@ CollectSharedCommand::CollectSharedCommand(string option) { else { m->splitAtDash(groups, Groups); } - m->Groups = Groups; + m->setGroups(Groups); string temp; temp = validParameter.validFile(parameters, "freq", false); if (temp == "not found") { temp = "100"; } - convert(temp, freq); + m->mothurConvert(temp, freq); temp = validParameter.validFile(parameters, "all", false); if (temp == "not found") { temp = "false"; } all = m->isTrue(temp); @@ -282,128 +336,130 @@ CollectSharedCommand::CollectSharedCommand(string option) { if (abort == false) { string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(sharedfile)); - + map variables; + variables["[filename]"] = fileNameRoot; + ValidCalculators validCalculator; for (int i=0; isetGroups(m->Groups, m->namesOfGroups, "collect"); + Groups = m->getGroups(); + vector allGroups = m->getAllGroups(); + util->setGroups(Groups, allGroups, "collect"); + m->setGroups(Groups); + m->setAllGroups(allGroups); delete util; while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { @@ -448,7 +508,7 @@ int CollectSharedCommand::execute(){ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); for(int i=0;iGroups.clear(); + m->clearGroups(); return 0; } @@ -495,7 +555,7 @@ int CollectSharedCommand::execute(){ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); for(int i=0;iGroups.clear(); + m->clearGroups(); delete input; return 0; } @@ -528,7 +588,7 @@ int CollectSharedCommand::execute(){ for(int i=0;iGroups.clear(); + m->clearGroups(); return 0; } @@ -538,7 +598,7 @@ int CollectSharedCommand::execute(){ for(int i=0;iGroups.clear(); + m->clearGroups(); delete input; m->mothurOutEndLine();