#include "inputdata.h"
//**********************************************************************************************************************
-vector<string> PCACommand::getValidParameters(){
+vector<string> PCACommand::setParameters(){
try {
- string Array[] = {"label", "groups","metric","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(pshared);
+ CommandParameter prelabund("relabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prelabund);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
+ CommandParameter pmetric("metric", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pmetric);
+ CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+ 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, "PCACommand", "getValidParameters");
+ m->errorOut(e, "PCACommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-PCACommand::PCACommand(){
+string PCACommand::getHelpString(){
try {
- abort = true; calledHelp = true;
- vector<string> tempOutNames;
- outputTypes["pca"] = tempOutNames;
- outputTypes["loadings"] = tempOutNames;
+ string helpString = "";
+ helpString += "The pca command parameters are shared, relabund, label, groups and metric. shared or relabund is required unless you have a valid current file.";
+ helpString += "The label parameter is used to analyze specific labels in your input. Default is the first label in your shared or relabund file. Multiple labels may be separated by dashes.\n";
+ helpString += "The groups parameter allows you to specify which groups you would like analyzed. Groupnames are separated by dashes.\n";
+ helpString += "The metric parameter allows indicate you if would like the pearson correlation coefficient calculated. Default=True";
+ helpString += "Example pca(groups=yourGroups).\n";
+ helpString += "Example pca(groups=A-B-C).\n";
+ helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n";
+ return helpString;
}
catch(exception& e) {
- m->errorOut(e, "PCACommand", "PCACommand");
+ m->errorOut(e, "PCACommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> PCACommand::getRequiredParameters(){
- try {
- vector<string> myArray;
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "PCACommand", "getRequiredParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-vector<string> PCACommand::getRequiredFiles(){
+PCACommand::PCACommand(){
try {
- string Array[] = {"shared","relabund","or"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["pca"] = tempOutNames;
+ outputTypes["loadings"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "PCACommand", "getRequiredFiles");
+ m->errorOut(e, "PCACommand", "PCACommand");
exit(1);
}
}
try {
abort = false; calledHelp = false;
- globaldata = GlobalData::getInstance();
-
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
else {
- //valid paramters for this command
- string Array[] = {"label","groups","metric","outputdir", "inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string, string> parameters = parser. getParameters();
for (it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
- //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 = ""; }
-
+
//initialize outputTypes
vector<string> tempOutNames;
outputTypes["pca"] = tempOutNames;
outputTypes["loadings"] = tempOutNames;
- //make sure the user has already run the read.otu command
- if ((globaldata->getSharedFile() == "") && (globaldata->getRelAbundFile() == "")) {
- m->mothurOut("You must read a list and a group, shared or relabund file before you can use the pca command."); m->mothurOutEndLine(); abort = true;
+ //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("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("relabund");
+ //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["relabund"] = inputDir + it->second; }
+ }
}
- if (globaldata->getSharedFile() != "") { mode = "shared"; inputFile = globaldata->getSharedFile(); }
- if (globaldata->getRelAbundFile() != "") { mode = "relabund"; inputFile = globaldata->getRelAbundFile(); }
+ //check for required parameters
+ sharedfile = validParameter.validFile(parameters, "shared", true);
+ if (sharedfile == "not open") { sharedfile = ""; abort = true; }
+ else if (sharedfile == "not found") { sharedfile = ""; }
+ else { mode = "sharedfile"; inputFile = sharedfile; }
+
+ relabundfile = validParameter.validFile(parameters, "relabund", true);
+ if (relabundfile == "not open") { relabundfile = ""; abort = true; }
+ else if (relabundfile == "not found") { relabundfile = ""; }
+ else { mode = "relabund"; inputFile = relabundfile; }
+
+ if ((sharedfile == "") && (relabundfile == "")) {
+ //is there are current file available for any of these?
+ //give priority to shared, then list, then rabund, then sabund
+ //if there is a current shared file, use it
+ sharedfile = m->getSharedFile();
+ if (sharedfile != "") { inputFile = sharedfile; mode = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
+ else {
+ relabundfile = m->getRelAbundFile();
+ if (relabundfile != "") { inputFile = relabundfile; mode = "relabund"; m->mothurOut("Using " + relabundfile + " as input file for the relabund parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("No valid current files. You must provide a relabund or shared file."); 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 = "";
metric = m->isTrue(temp);
label = validParameter.validFile(parameters, "label", false);
- if (label == "not found") { label = ""; labels = globaldata->labels; if(labels.size() == 0) { m->mothurOut("You did not provide a label, I will use the first label in your inputfile."); m->mothurOutEndLine(); } }
+ if (label == "not found") { label = ""; if(labels.size() == 0) { m->mothurOut("You did not provide a label, I will use the first label in your inputfile."); m->mothurOutEndLine(); } }
else { m->splitAtDash(label, labels); }
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = ""; }
else { m->splitAtDash(groups, Groups); }
- globaldata->Groups = Groups;
+ m->Groups = Groups;
}
}
}
//**********************************************************************************************************************
-void PCACommand::help(){
- try {
- m->mothurOut("The pca command can only be run after a successful read.otu command of a shared or relabund file."); m->mothurOutEndLine();
- m->mothurOut("The pca command parameters are label, groups and metric. No parameters are required."); m->mothurOutEndLine();
- m->mothurOut("The label parameter is used to analyze specific labels in your input. Default is the first label in your shared or relabund file. Multiple labels may be separated by dashes.\n");
- m->mothurOut("The groups parameter allows you to specify which groups you would like analyzed. Groupnames are separated by dashes.\n");
- m->mothurOut("The metric parameter allows indicate you if would like the pearson correlation coefficient calculated. Default=True"); m->mothurOutEndLine();
- m->mothurOut("Example pca(groups=yourGroups).\n");
- m->mothurOut("Example pca(groups=A-B-C).\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, "PCACommand", "help");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-PCACommand::~PCACommand(){}
-//**********************************************************************************************************************
int PCACommand::execute(){
try {
string fbase = outputDir + m->getRootName(m->getSimpleName(inputFile));
string outputFileName = fbase + lookupFloat[0]->getLabel();
- output(outputFileName, globaldata->Groups, G, d);
+ output(outputFileName, m->Groups, G, d);
if (metric) {
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