X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=heatmapsimcommand.cpp;h=98739b68291fd42d83d1190a46313886126f02bf;hp=3b0d7984bc1d0be02cb66c9d816f72df94e48f36;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=49b8297d25caae7ad4cf1e5208a4a66fdfe071fe diff --git a/heatmapsimcommand.cpp b/heatmapsimcommand.cpp index 3b0d798..98739b6 100644 --- a/heatmapsimcommand.cpp +++ b/heatmapsimcommand.cpp @@ -20,87 +20,269 @@ #include "sharedbraycurtis.h" +//********************************************************************************************************************** +vector HeatMapSimCommand::setParameters(){ + try { + 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); } + return myArray; + } + catch(exception& e) { + m->errorOut(e, "HeatMapSimCommand", "setParameters"); + exit(1); + } +} +//********************************************************************************************************************** +string HeatMapSimCommand::getHelpString(){ + try { + string helpString = ""; + ValidCalculators validCalculator; + 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"; + helpString += "The heatmap.sim command should be in the following format: heatmap.sim(groups=yourGroups, calc=yourCalc, label=yourLabels).\n"; + helpString += "Example heatmap.sim(groups=A-B-C, calc=jabund).\n"; + helpString += "The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n"; + helpString += validCalculator.printCalc("heat"); + helpString += "The default value for calc is jclass-thetayc.\n"; + helpString += "The heatmap.sim command outputs a .svg file for each calculator you choose at each label you specify.\n"; + helpString += "The second way to use the heatmap.sim command is with a distance file representing the distance bewteen your groups. \n"; + helpString += "Using the command this way, the phylip or column parameter are required, and only one may be used. If you use a column file the name filename is required. \n"; + helpString += "The heatmap.sim command should be in the following format: heatmap.sim(phylip=yourDistanceFile).\n"; + helpString += "Example heatmap.sim(phylip=amazonGroups.dist).\n"; + helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n"; + return helpString; + } + catch(exception& e) { + m->errorOut(e, "HeatMapSimCommand", "getHelpString"); + exit(1); + } +} +//********************************************************************************************************************** +string HeatMapSimCommand::getOutputPattern(string type) { + try { + string pattern = ""; + + 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 { + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["svg"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "HeatMapSimCommand", "HeatMapSimCommand"); + exit(1); + } +} //********************************************************************************************************************** -HeatMapSimCommand::HeatMapSimCommand(string option){ +HeatMapSimCommand::HeatMapSimCommand(string option) { try { - globaldata = GlobalData::getInstance(); - abort = false; + abort = false; calledHelp = false; allLines = 1; - lines.clear(); - labels.clear(); - Groups.clear(); - Estimators.clear(); - + //allow user to run help - if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; } + if(option == "help") { help(); abort = true; calledHelp = true; } + else if(option == "citation") { citation(); abort = true; calledHelp = true;} else { - //valid paramters for this command - string AlignArray[] = {"groups","line","label", "calc"}; - vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); ValidParameters validParameter; + map::iterator it; //check to make sure all parameters are valid for command - for (map::iterator it = parameters.begin(); it != parameters.end(); it++) { + for (it = parameters.begin(); it != parameters.end(); it++) { if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } } - //make sure the user has already run the read.otu command - if (globaldata->getSharedFile() == "") { - cout << "You must read a list and a group, or a shared before you can use the heatmap.sim command." << endl; abort = true; + //initialize outputTypes + vector tempOutNames; + outputTypes["svg"] = tempOutNames; + + format = ""; + + //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 = ""; } + else { + string path; + it = parameters.find("phylip"); + //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["phylip"] = inputDir + it->second; } + } + + it = parameters.find("column"); + //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["column"] = inputDir + it->second; } + } + + it = parameters.find("name"); + //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["name"] = inputDir + it->second; } + } + + it = parameters.find("shared"); + //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["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; } + } } - //check for optional parameter and set defaults - // ...at some point should added some additional type checking... - line = validParameter.validFile(parameters, "line", false); - if (line == "not found") { line = ""; } - else { - if(line != "all") { splitAtDash(line, lines); allLines = 0; } - else { allLines = 1; } + //required parameters + phylipfile = validParameter.validFile(parameters, "phylip", true); + if (phylipfile == "not open") { abort = true; } + else if (phylipfile == "not found") { phylipfile = ""; } + else { format = "phylip"; inputfile = phylipfile; m-> setPhylipFile(phylipfile); if (outputDir == "") { outputDir += m->hasPath(phylipfile); } } + + columnfile = validParameter.validFile(parameters, "column", true); + if (columnfile == "not open") { abort = true; } + else if (columnfile == "not found") { columnfile = ""; } + else { format = "column"; inputfile = columnfile; m->setColumnFile(columnfile); if (outputDir == "") { outputDir += m->hasPath(columnfile); } } + + sharedfile = validParameter.validFile(parameters, "shared", true); + if (sharedfile == "not open") { abort = true; } + else if (sharedfile == "not found") { sharedfile = ""; } + else { format = "shared"; inputfile = sharedfile; m->setSharedFile(sharedfile); if (outputDir == "") { outputDir += m->hasPath(sharedfile); } } + + namefile = validParameter.validFile(parameters, "name", true); + if (namefile == "not open") { abort = true; } + 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 == ""))) { + sharedfile = m->getSharedFile(); + if (sharedfile != "") { format = "shared"; inputfile = sharedfile; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); } + else { + //is there are current file available for either of these? + //give priority to column, then phylip + columnfile = m->getColumnFile(); + if (columnfile != "") { format = "column"; inputfile = columnfile; m->mothurOut("Using " + columnfile + " as input file for the column parameter."); m->mothurOutEndLine(); } + else { + phylipfile = m->getPhylipFile(); + if (phylipfile != "") { format = "phylip"; inputfile = phylipfile; m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); } + else { + m->mothurOut("No valid current files. You must provide a shared or phylip or column file."); m->mothurOutEndLine(); + abort = true; + } + } + } } + else if ((phylipfile != "") && (columnfile != "")) { m->mothurOut("When running the heatmap.sim command with a distance file you may not use both the column and the phylip parameters."); m->mothurOutEndLine(); abort = true; } + if (columnfile != "") { + if (namefile == "") { + namefile = m->getNameFile(); + if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); } + else { + 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; + } + } + } + } + + + //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 = m->hasPath(inputfile); } + + //check for optional parameter and set defaults + // ...at some point should added some additional type checking... + label = validParameter.validFile(parameters, "label", false); if (label == "not found") { label = ""; } else { - if(label != "all") { splitAtDash(label, labels); allLines = 0; } + if(label != "all") { m->splitAtDash(label, labels); allLines = 0; } else { allLines = 1; } } - - //make sure user did not use both the line and label parameters - if ((line != "") && (label != "")) { cout << "You cannot use both the line and label parameters at the same time. " << endl; abort = true; } - //if the user has not specified any line or labels use the ones from read.otu - else if ((line == "") && (label == "")) { - allLines = globaldata->allLines; - labels = globaldata->labels; - lines = globaldata->lines; - } - + calc = validParameter.validFile(parameters, "calc", false); if (calc == "not found") { calc = "jest-thetayc"; } else { - if (calc == "default") { calc = "jest-thetayc"; } + if (calc == "default") { calc = "jest-thetayc"; } } - splitAtDash(calc, Estimators); - + m->splitAtDash(calc, Estimators); + if (m->inUsersGroups("citation", Estimators)) { + ValidCalculators validCalc; validCalc.printCitations(Estimators); + //remove citation from list of calcs + for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") { Estimators.erase(Estimators.begin()+i); break; } } + } + groups = validParameter.validFile(parameters, "groups", false); if (groups == "not found") { groups = ""; } else { - splitAtDash(groups, Groups); - globaldata->Groups = Groups; + m->splitAtDash(groups, Groups); + m->setGroups(Groups); } + string temp = validParameter.validFile(parameters, "fontsize", false); if (temp == "not found") { temp = "24"; } + m->mothurConvert(temp, fontsize); + if (abort == false) { - validCalculator = new ValidCalculators(); - heatmap = new HeatMapSim(); + ValidCalculators validCalculator; int i; for (i=0; iisValidCalculator("heat", Estimators[i]) == true) { + if (validCalculator.isValidCalculator("heat", Estimators[i]) == true) { if (Estimators[i] == "jabund") { heatCalculators.push_back(new JAbund()); }else if (Estimators[i] == "sorabund") { @@ -132,143 +314,293 @@ HeatMapSimCommand::HeatMapSimCommand(string option){ } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the HeatMapSimCommand class Function HeatMapSimCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "HeatMapSimCommand", "HeatMapSimCommand"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the HeatMapSimCommand class function HeatMapSimCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } - //********************************************************************************************************************** -void HeatMapSimCommand::help(){ +int HeatMapSimCommand::execute(){ try { - cout << "The heatmap.sim command can only be executed after a successful read.otu command." << "\n"; - cout << "The heatmap.sim command parameters are groups, calc, line and label. No parameters are required, but you may not use line and label at the same time." << "\n"; - cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like included in your heatmap." << "\n"; - cout << "The group names are separated by dashes. The line and label allow you to select what distance levels you would like a heatmap created for, and are also separated by dashes." << "\n"; - cout << "The heatmap.sim command should be in the following format: heatmap.sim(groups=yourGroups, calc=yourCalc, line=yourLines, label=yourLabels)." << "\n"; - cout << "Example heatmap.sim(groups=A-B-C, line=1-3-5, calc=jabund)." << "\n"; - cout << "The default value for groups is all the groups in your groupfile, and all lines in your inputfile will be used." << "\n"; - validCalculator->printCalc("heat", cout); - cout << "The default value for calc is jclass-thetayc." << "\n"; - cout << "The heatmap.sim command outputs a .svg file for each calculator you choose at each line or label you specify." << "\n"; - cout << "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups)." << "\n" << "\n"; - + + if (abort == true) { if (calledHelp) { return 0; } return 2; } + + heatmap = new HeatMapSim(outputDir, inputfile, fontsize); + + if (format == "shared") { + runCommandShared(); + }else{ runCommandDist(); } + + delete heatmap; + + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0; } + + m->mothurOutEndLine(); + m->mothurOut("Output File Names: "); m->mothurOutEndLine(); + for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); } + m->mothurOutEndLine(); + + return 0; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the HeatMapSimCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "HeatMapSimCommand", "execute"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the HeatMapSimCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } //********************************************************************************************************************** - -HeatMapSimCommand::~HeatMapSimCommand(){ - delete input; - delete read; - delete heatmap; - delete validCalculator; -} - -//********************************************************************************************************************** - -int HeatMapSimCommand::execute(){ +int HeatMapSimCommand::runCommandShared() { try { - - if (abort == true) { return 0; } - - int count = 1; - //if the users entered no valid calculators don't execute command - if (heatCalculators.size() == 0) { cout << "No valid calculators." << endl; return 0; } + if (heatCalculators.size() == 0) { m->mothurOut("No valid calculators."); m->mothurOutEndLine(); return 0; } - //you have groups - read = new ReadOTUFile(globaldata->inputFileName); - read->read(&*globaldata); - - input = globaldata->ginput; + input = new InputData(sharedfile, "sharedfile"); lookup = input->getSharedRAbundVectors(); - vector lastLookup = lookup; - - if (lookup.size() < 2) { cout << "You have not provided enough valid groups. I cannot run the command." << endl; return 0;} + string lastLabel = lookup[0]->getLabel(); + + if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups. I cannot run the command."); m->mothurOutEndLine(); return 0;} //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label. set processedLabels; set userLabels = labels; - set userLines = lines; - - //as long as you are not at the end of the file or done wih the lines you want - while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) { + if (m->control_pressed) { delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->clearGroups(); return 0; } - if(allLines == 1 || lines.count(count) == 1 || labels.count(lookup[0]->getLabel()) == 1){ + //as long as you are not at the end of the file or done wih the lines you want + while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { + + if (m->control_pressed) { delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->clearGroups(); return 0; } + + if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){ - cout << lookup[0]->getLabel() << '\t' << count << endl; - heatmap->getPic(lookup, heatCalculators); + m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); + vector outfilenames = heatmap->getPic(lookup, heatCalculators); + for(int i = 0; i < outfilenames.size(); i++) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } processedLabels.insert(lookup[0]->getLabel()); userLabels.erase(lookup[0]->getLabel()); - userLines.erase(count); } - if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) { - cout << lastLookup[0]->getLabel() << '\t' << count << endl; - heatmap->getPic(lastLookup, heatCalculators); + if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + string saveLabel = lookup[0]->getLabel(); + + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + lookup = input->getSharedRAbundVectors(lastLabel); + + m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); + vector outfilenames = heatmap->getPic(lookup, heatCalculators); + for(int i = 0; i < outfilenames.size(); i++) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } - processedLabels.insert(lastLookup[0]->getLabel()); - userLabels.erase(lastLookup[0]->getLabel()); + processedLabels.insert(lookup[0]->getLabel()); + userLabels.erase(lookup[0]->getLabel()); + + //restore real lastlabel to save below + lookup[0]->setLabel(saveLabel); } //prevent memory leak - if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; } } - lastLookup = lookup; + + lastLabel = lookup[0]->getLabel(); //get next line to process - lookup = input->getSharedRAbundVectors(); - count++; + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + lookup = input->getSharedRAbundVectors(); + } + + if (m->control_pressed) { delete input; m->clearGroups(); return 0; } + //output error messages about any remaining user labels set::iterator it; bool needToRun = false; for (it = userLabels.begin(); it != userLabels.end(); it++) { - cout << "Your file does not include the label "<< *it; - if (processedLabels.count(lastLookup[0]->getLabel()) != 1) { - cout << ". I will use " << lastLookup[0]->getLabel() << "." << endl; + m->mothurOut("Your file does not include the label " + *it); + if (processedLabels.count(lastLabel) != 1) { + m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine(); needToRun = true; }else { - cout << ". Please refer to " << lastLookup[0]->getLabel() << "." << endl; + m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine(); } } - //run last line if you need to + if (m->control_pressed) { delete input; m->clearGroups(); return 0; } + + //run last label if you need to if (needToRun == true) { - cout << lastLookup[0]->getLabel() << '\t' << count << endl; - heatmap->getPic(lastLookup, heatCalculators); + for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } } + lookup = input->getSharedRAbundVectors(lastLabel); + + m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); + vector outfilenames = heatmap->getPic(lookup, heatCalculators); + for(int i = 0; i < outfilenames.size(); i++) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } + + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } } - for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; } + if (m->control_pressed) { delete input; m->clearGroups(); return 0; } //reset groups parameter - globaldata->Groups.clear(); - + m->clearGroups(); + + delete input; + return 0; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the HeatMapSimCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "HeatMapSimCommand", "runCommandShared"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the HeatMapSimCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; +} +//********************************************************************************************************************** +int HeatMapSimCommand::runCommandDist() { + try { + + vector< vector > matrix; + vector names; + ifstream in; + + //read distance file and create distance vector and names vector + if (format == "phylip") { + //read phylip file + m->openInputFile(phylipfile, in); + + string name; + int numSeqs; + in >> numSeqs >> name; + + //save name + names.push_back(name); + + //resize the matrix and fill with zeros + matrix.resize(numSeqs); + for(int i = 0; i < numSeqs; i++) { + matrix[i].resize(numSeqs, 0.0); + } + + //determine if matrix is square or lower triangle + //if it is square read the distances for the first sequence + char d; + bool square; + while((d=in.get()) != EOF){ + + //is d a number meaning its square + if(isalnum(d)){ + square = true; + in.putback(d); + + for(int i=0;i> matrix[0][i]; + } + break; + } + + //is d a line return meaning its lower triangle + if(d == '\n'){ + square = false; + break; + } + } + + //read rest of matrix + if (square == true) { + for(int i=1;i> name; + names.push_back(name); + + if (m->control_pressed) { return 0; } + + for(int j=0;j> matrix[i][j]; } + m->gobble(in); + } + }else { + double dist; + for(int i=1;i> name; + names.push_back(name); + + if (m->control_pressed) { return 0; } + + for(int j=0;j> dist; + matrix[i][j] = dist; matrix[j][i] = dist; + } + m->gobble(in); + } + } + in.close(); + }else { + //read names file + 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; + m->openInputFile(columnfile, in); + + while (!in.eof()) { + in >> first >> second >> dist; m->gobble(in); + + if (m->control_pressed) { return 0; } + + 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(); + + if (namefile != "") { delete nameMap; } + } + + + string outputFileName = heatmap->getPic(matrix, names); + outputNames.push_back(outputFileName); //vector>, vector + outputTypes["svg"].push_back(outputFileName); + + return 0; + } + catch(exception& e) { + m->errorOut(e, "HeatMapSimCommand", "runCommandDist"); exit(1); - } + } } - //********************************************************************************************************************** + + + + + +