#include "sharedmorisitahorn.h"
#include "sharedbraycurtis.h"
+
//**********************************************************************************************************************
-vector<string> HeatMapSimCommand::getValidParameters(){
+vector<string> HeatMapSimCommand::setParameters(){
try {
- string Array[] = {"groups","label", "calc","phylip","column","name","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ 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<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
- m->errorOut(e, "HeatMapSimCommand", "getValidParameters");
+ m->errorOut(e, "HeatMapSimCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-HeatMapSimCommand::HeatMapSimCommand(){
+string HeatMapSimCommand::getHelpString(){
try {
- //initialize outputTypes
- vector<string> tempOutNames;
- outputTypes["svg"] = tempOutNames;
+ 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", "HeatMapSimCommand");
+ m->errorOut(e, "HeatMapSimCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> HeatMapSimCommand::getRequiredParameters(){
- try {
- vector<string> myArray;
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "HeatMapSimCommand", "getRequiredParameters");
- 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);
+ }
}
//**********************************************************************************************************************
-vector<string> HeatMapSimCommand::getRequiredFiles(){
+HeatMapSimCommand::HeatMapSimCommand(){
try {
- vector<string> myArray;
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["svg"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "HeatMapSimCommand", "getRequiredFiles");
+ m->errorOut(e, "HeatMapSimCommand", "HeatMapSimCommand");
exit(1);
}
}
HeatMapSimCommand::HeatMapSimCommand(string option) {
try {
- globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
- 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","label", "calc","phylip","column","name","outputdir","inputdir"};
- vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
outputTypes["svg"] = tempOutNames;
format = "";
- //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 = ""; }
-
+
//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 = ""; }
//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; }
+ }
}
//required parameters
phylipfile = validParameter.validFile(parameters, "phylip", true);
if (phylipfile == "not open") { abort = true; }
else if (phylipfile == "not found") { phylipfile = ""; }
- else { format = "phylip"; if (outputDir == "") { outputDir += m->hasPath(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"; if (outputDir == "") { outputDir += m->hasPath(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 ((globaldata->getSharedFile() == "") && ((phylipfile == "") && (columnfile == ""))) { m->mothurOut("You must run the read.otu command or provide a distance file before running the heatmap.sim command."); m->mothurOutEndLine(); abort = true; }
+ 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 == "") { m->mothurOut("You need to provide a namefile if you are going to use the column format."); m->mothurOutEndLine(); abort = true; }
+ 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 (format == "") { format = "shared"; }
+ //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...
- if (format == "shared") {
- if (outputDir == "") { outputDir += m->hasPath(globaldata->getSharedFile()); }
-
- label = validParameter.validFile(parameters, "label", false);
- if (label == "not found") { label = ""; }
- else {
- if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
- else { allLines = 1; }
- }
-
- //if the user has not specified any labels use the ones from read.otu
- if (label == "") {
- allLines = globaldata->allLines;
- labels = globaldata->labels;
- }
+
+ label = validParameter.validFile(parameters, "label", false);
+ if (label == "not found") { label = ""; }
+ else {
+ if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
+ else { allLines = 1; }
+ }
- calc = validParameter.validFile(parameters, "calc", false);
- if (calc == "not found") { calc = "jest-thetayc"; }
- else {
- if (calc == "default") { calc = "jest-thetayc"; }
- }
- m->splitAtDash(calc, Estimators);
+ calc = validParameter.validFile(parameters, "calc", false);
+ if (calc == "not found") { calc = "jest-thetayc"; }
+ else {
+ if (calc == "default") { calc = "jest-thetayc"; }
+ }
+ 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 {
- m->splitAtDash(groups, Groups);
- globaldata->Groups = Groups;
- }
+ groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; }
+ else {
+ 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();
+ ValidCalculators validCalculator;
int i;
for (i=0; i<Estimators.size(); i++) {
- if (validCalculator->isValidCalculator("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") {
exit(1);
}
}
-
-//**********************************************************************************************************************
-
-void HeatMapSimCommand::help(){
- try {
- m->mothurOut("The heatmap.sim command can only be executed after a successful read.otu command, or by providing a distance file.\n");
- m->mothurOut("The heatmap.sim command parameters are phylip, column, name, groups, calc and label. No parameters are required.\n");
- m->mothurOut("There are two ways to use the heatmap.sim command. The first is with the read.otu command. \n");
- m->mothurOut("With the read.otu command you may use the groups, label and calc parameters. \n");
- m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included in your heatmap.\n");
- m->mothurOut("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");
- m->mothurOut("The heatmap.sim command should be in the following format: heatmap.sim(groups=yourGroups, calc=yourCalc, label=yourLabels).\n");
- m->mothurOut("Example heatmap.sim(groups=A-B-C, calc=jabund).\n");
- m->mothurOut("The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n");
- validCalculator->printCalc("heat", cout);
- m->mothurOut("The default value for calc is jclass-thetayc.\n");
- m->mothurOut("The heatmap.sim command outputs a .svg file for each calculator you choose at each label you specify.\n");
- m->mothurOut("The second way to use the heatmap.sim command is with a distance file representing the distance bewteen your groups. \n");
- m->mothurOut("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");
- m->mothurOut("The heatmap.sim command should be in the following format: heatmap.sim(phylip=yourDistanceFile).\n");
- m->mothurOut("Example heatmap.sim(phylip=amazonGroups.dist).\n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
-
- }
- catch(exception& e) {
- m->errorOut(e, "HeatMapSimCommand", "help");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-
-HeatMapSimCommand::~HeatMapSimCommand(){}
-
//**********************************************************************************************************************
int HeatMapSimCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
- heatmap = new HeatMapSim(outputDir);
+ heatmap = new HeatMapSim(outputDir, inputfile, fontsize);
if (format == "shared") {
runCommandShared();
- }else if (format == "phylip") {
- globaldata->inputFileName = phylipfile;
- runCommandDist();
- }else if (format == "column") {
- globaldata->inputFileName = columnfile;
- runCommandDist();
- }
+ }else{ runCommandDist(); }
delete heatmap;
- delete validCalculator;
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); return 0; }
+ 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();
//if the users entered no valid calculators don't execute command
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();
string lastLabel = lookup[0]->getLabel();
set<string> processedLabels;
set<string> userLabels = labels;
- if (m->control_pressed) { delete read; delete input; globaldata->ginput = NULL; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } globaldata->Groups.clear(); return 0; }
+ if (m->control_pressed) { delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->clearGroups(); return 0; }
//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 read; delete input; globaldata->ginput = NULL; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } globaldata->Groups.clear(); return 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){
}
- if (m->control_pressed) { delete read; delete input; globaldata->ginput = NULL; globaldata->Groups.clear(); return 0; }
+ if (m->control_pressed) { delete input; m->clearGroups(); return 0; }
//output error messages about any remaining user labels
set<string>::iterator it;
}
}
- if (m->control_pressed) { delete read; delete input; globaldata->ginput = NULL; globaldata->Groups.clear(); return 0; }
+ if (m->control_pressed) { delete input; m->clearGroups(); return 0; }
//run last label if you need to
if (needToRun == true) {
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
}
- if (m->control_pressed) { delete read; delete input; globaldata->ginput = NULL; globaldata->Groups.clear(); return 0; }
+ if (m->control_pressed) { delete input; m->clearGroups(); return 0; }
//reset groups parameter
- globaldata->Groups.clear();
+ m->clearGroups();
- delete input; globaldata->ginput = NULL;
- delete read;
+ delete input;
return 0;
}
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;
if (m->control_pressed) { return 0; }
- map<string, int>::iterator itA = nameMap->find(first);
- map<string, int>::iterator itB = nameMap->find(second);
-
- if(itA == nameMap->end()){ cerr << "AAError: Sequence '" << first << "' was not found in the names file, please correct\n"; exit(1); }
- if(itB == nameMap->end()){ cerr << "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<string, int>::iterator itA = nameMap->find(first);
+ map<string, int>::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; }
}
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