X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=heatmapsimcommand.cpp;h=98739b68291fd42d83d1190a46313886126f02bf;hp=3de10e6a8cd9411d6829ac699ffd11991af81007;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=49d2b7459c5027557564b21e9487dadafbbbdc96 diff --git a/heatmapsimcommand.cpp b/heatmapsimcommand.cpp index 3de10e6..98739b6 100644 --- a/heatmapsimcommand.cpp +++ b/heatmapsimcommand.cpp @@ -23,16 +23,17 @@ //********************************************************************************************************************** vector HeatMapSimCommand::setParameters(){ try { - CommandParameter pshared("shared", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none",false,false); parameters.push_back(pshared); - CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none",false,false); parameters.push_back(pphylip); - CommandParameter pname("name", "InputTypes", "", "", "none", "none", "ColumnName",false,false); parameters.push_back(pname); - CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "ColumnName",false,false); parameters.push_back(pcolumn); - CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups); - CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel); - CommandParameter pcalc("calc", "Multiple", "jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-morisitahorn-braycurtis", "jest-thetayc", "", "", "",true,false); parameters.push_back(pcalc); - CommandParameter pfontsize("fontsize", "Number", "", "24", "", "", "",false,false); parameters.push_back(pfontsize); - CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); - CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); + CommandParameter pshared("shared", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none","svg",false,false,true); parameters.push_back(pshared); + CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none","svg",false,false); parameters.push_back(pphylip); + CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none","",false,false); parameters.push_back(pname); + CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none","",false,false); parameters.push_back(pcount); + CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "ColumnName","svg",false,false); parameters.push_back(pcolumn); + CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups); + CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel); + CommandParameter pcalc("calc", "Multiple", "jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-morisitahorn-braycurtis", "jest-thetayc", "", "", "","",true,false); parameters.push_back(pcalc); + CommandParameter pfontsize("fontsize", "Number", "", "24", "", "", "","",false,false); parameters.push_back(pfontsize); + 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); } @@ -48,9 +49,8 @@ string HeatMapSimCommand::getHelpString(){ try { string helpString = ""; ValidCalculators validCalculator; - helpString += "The heatmap.sim command parameters are shared, phylip, column, name, groups, calc, fontsize and label. shared or phylip or column and name are required unless valid current files exist.\n"; - helpString += "There are two ways to use the heatmap.sim command. The first is with the read.otu command. \n"; - helpString += "With the read.otu command you may use the groups, label and calc parameters. \n"; + helpString += "The heatmap.sim command parameters are shared, phylip, column, name, count, groups, calc, fontsize and label. shared or phylip or column and name are required unless valid current files exist.\n"; + helpString += "There are two ways to use the heatmap.sim command. The first is with a shared file, and you may use the groups, label and calc parameter. \n"; helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included in your heatmap.\n"; helpString += "The group names are separated by dashes. The label parameter allows you to select what distance levels you would like a heatmap created for, and is also separated by dashes.\n"; helpString += "The fontsize parameter allows you to adjust the font size of the picture created, default=24.\n"; @@ -73,27 +73,20 @@ string HeatMapSimCommand::getHelpString(){ } } //********************************************************************************************************************** - -string HeatMapSimCommand::getOutputFileNameTag(string type, string inputName=""){ - try { - string outputFileName = ""; - map >::iterator it; +string HeatMapSimCommand::getOutputPattern(string type) { + try { + string pattern = ""; - //is this a type this command creates - it = outputTypes.find(type); - if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); } - else { - if (type == "svg") { outputFileName = "svg"; } - else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; } - } - return outputFileName; - } - catch(exception& e) { - m->errorOut(e, "HeatMapSimCommand", "getOutputFileNameTag"); - exit(1); - } + if (type == "svg") { pattern = "[filename],svg"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "HeatMapCommand", "getOutputPattern"); + exit(1); + } } - //********************************************************************************************************************** HeatMapSimCommand::HeatMapSimCommand(){ try { @@ -174,6 +167,14 @@ HeatMapSimCommand::HeatMapSimCommand(string option) { //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { parameters["shared"] = inputDir + it->second; } } + + it = parameters.find("count"); + //user has given a template file + if(it != parameters.end()){ + path = m->hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["count"] = inputDir + it->second; } + } } //required parameters @@ -197,6 +198,12 @@ HeatMapSimCommand::HeatMapSimCommand(string option) { else if (namefile == "not found") { namefile = ""; } else { m->setNameFile(namefile); } + countfile = validParameter.validFile(parameters, "count", true); + if (countfile == "not open") { abort = true; countfile = ""; } + else if (countfile == "not found") { countfile = ""; } + else { m->setCountTableFile(countfile); } + + if ((countfile != "") && (namefile != "")) { m->mothurOut("You must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; } //error checking on files if ((sharedfile == "") && ((phylipfile == "") && (columnfile == ""))) { @@ -224,8 +231,12 @@ HeatMapSimCommand::HeatMapSimCommand(string option) { namefile = m->getNameFile(); if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); } else { - m->mothurOut("You need to provide a namefile if you are going to use the column format."); m->mothurOutEndLine(); - abort = true; + countfile = m->getCountTableFile(); + if (countfile != "") { m->mothurOut("Using " + countfile + " as input file for the count parameter."); m->mothurOutEndLine(); } + else { + m->mothurOut("You need to provide a name or count file if you are going to use the column format."); m->mothurOutEndLine(); + abort = true; + } } } } @@ -520,20 +531,28 @@ int HeatMapSimCommand::runCommandDist() { in.close(); }else { //read names file - NameAssignment* nameMap = new NameAssignment(namefile); - nameMap->readMap(); - - //put names in order in vector - for (int i = 0; i < nameMap->size(); i++) { - names.push_back(nameMap->get(i)); - } - - //resize matrix - matrix.resize(nameMap->size()); - for (int i = 0; i < nameMap->size(); i++) { - matrix[i].resize(nameMap->size(), 0.0); - } - + NameAssignment* nameMap; + CountTable ct; + if (namefile != "") { + nameMap = new NameAssignment(namefile); + nameMap->readMap(); + + //put names in order in vector + for (int i = 0; i < nameMap->size(); i++) { + names.push_back(nameMap->get(i)); + } + }else if (countfile != "") { + nameMap = NULL; + ct.readTable(countfile); + names = ct.getNamesOfSeqs(); + } + + //resize matrix + matrix.resize(names.size()); + for (int i = 0; i < names.size(); i++) { + matrix[i].resize(names.size(), 0.0); + } + //read column file string first, second; double dist; @@ -544,19 +563,26 @@ int HeatMapSimCommand::runCommandDist() { if (m->control_pressed) { return 0; } - map::iterator itA = nameMap->find(first); - map::iterator itB = nameMap->find(second); - - if(itA == nameMap->end()){ m->mothurOut("AAError: Sequence '" + first + "' was not found in the names file, please correct\n"); exit(1); } - if(itB == nameMap->end()){ m->mothurOut("ABError: Sequence '" + second + "' was not found in the names file, please correct\n"); exit(1); } - - //save distance - matrix[itA->second][itB->second] = dist; - matrix[itB->second][itA->second] = dist; + if (namefile != "") { + map::iterator itA = nameMap->find(first); + map::iterator itB = nameMap->find(second); + + if(itA == nameMap->end()){ m->mothurOut("AAError: Sequence '" + first + "' was not found in the names file, please correct\n"); exit(1); } + if(itB == nameMap->end()){ m->mothurOut("ABError: Sequence '" + second + "' was not found in the names file, please correct\n"); exit(1); } + + //save distance + matrix[itA->second][itB->second] = dist; + matrix[itB->second][itA->second] = dist; + }else if (countfile != "") { + int itA = ct.get(first); + int itB = ct.get(second); + matrix[itA][itB] = dist; + matrix[itB][itA] = dist; + } } in.close(); - delete nameMap; + if (namefile != "") { delete nameMap; } }