#include "sharedutilities.h"
//**********************************************************************************************************************
-vector<string> MergeGroupsCommand::getValidParameters(){
+vector<string> MergeGroupsCommand::setParameters(){
try {
- string Array[] = {"shared","label","outputdir","design","groups","processors","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared);
+ CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pdesign);
+ CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+ 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<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
- m->errorOut(e, "MergeGroupsCommand", "getValidParameters");
+ m->errorOut(e, "MergeGroupsCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-MergeGroupsCommand::MergeGroupsCommand(){
+string MergeGroupsCommand::getHelpString(){
try {
- abort = true; calledHelp = true;
- vector<string> tempOutNames;
- outputTypes["shared"] = tempOutNames;
+ string helpString = "";
+ helpString += "The merge.groups command reads a shared file and a design file and merges the groups in the shared file that are in the same grouping in the design file.\n";
+ helpString += "The merge.groups command outputs a .shared file. \n";
+ helpString += "The merge.groups command parameters are shared, groups, label and design. The design and shared parameter are required.\n";
+ helpString += "The design parameter allows you to assign your groups to sets. It is required. \n";
+ helpString += "The design file looks like the group file. It is a 2 column tab delimited file, where the first column is the group name and the second column is the set the group belongs to.\n";
+ helpString += "The groups parameter allows you to specify which of the groups in your shared you would like included. The group names are separated by dashes.\n";
+ helpString += "The label parameter allows you to select what distance levels you would like, and are also separated by dashes.\n";
+ helpString += "The merge.groups command should be in the following format: merge.groups(design=yourDesignFile, shared=yourSharedFile).\n";
+ helpString += "Example merge.groups(design=temp.design, groups=A-B-C, shared=temp.shared).\n";
+ helpString += "The default value for groups is all the groups in your sharedfile, and all labels in your inputfile will be used.\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, "MergeGroupsCommand", "MetaStatsCommand");
+ m->errorOut(e, "MergeGroupsCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> MergeGroupsCommand::getRequiredParameters(){
- try {
- string Array[] = {"design", "shared"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "MergeGroupsCommand", "getRequiredParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-vector<string> MergeGroupsCommand::getRequiredFiles(){
+MergeGroupsCommand::MergeGroupsCommand(){
try {
- string Array[] = {};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["shared"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "MergeGroupsCommand", "getRequiredFiles");
+ m->errorOut(e, "MergeGroupsCommand", "MetaStatsCommand");
exit(1);
}
}
MergeGroupsCommand::MergeGroupsCommand(string option) {
try {
- globaldata = GlobalData::getInstance();
abort = false; calledHelp = false;
allLines = 1;
- labels.clear();
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
else {
- //valid paramters for this command
- string AlignArray[] = {"groups","label","outputdir","shared","design","processors","inputdir"};
- vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
//check for required parameters
designfile = validParameter.validFile(parameters, "design", true);
if (designfile == "not open") { abort = true; }
- else if (designfile == "not found") { designfile = ""; m->mothurOut("You must provide a design file."); m->mothurOutEndLine(); abort = true; }
+ else if (designfile == "not found") {
+ //if there is a current shared file, use it
+ designfile = m->getDesignFile();
+ if (designfile != "") { m->mothurOut("Using " + designfile + " as input file for the design parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current designfile and the design parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }
//make sure the user has already run the read.otu command
sharedfile = validParameter.validFile(parameters, "shared", true);
if (sharedfile == "not open") { abort = true; }
- else if (sharedfile == "not found") { sharedfile = ""; m->mothurOut("You must provide a shared file."); m->mothurOutEndLine(); abort = true; }
+ else if (sharedfile == "not found") {
+ //if there is a current shared file, use it
+ sharedfile = m->getSharedFile();
+ if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = "all"; }
m->splitAtDash(groups, Groups);
- globaldata->Groups = Groups;
+ m->Groups = Groups;
}
}
exit(1);
}
}
-
-//**********************************************************************************************************************
-
-void MergeGroupsCommand::help(){
- try {
- m->mothurOut("The merge.groups command reads a shared file and a design file and merges the groups in the shared file that are in the same grouping in the design file.\n");
- m->mothurOut("The merge.groups command outputs a .shared file. \n");
- m->mothurOut("The merge.groups command parameters are shared, groups, label and design. The design and shared parameter are required.\n");
- m->mothurOut("The design parameter allows you to assign your groups to sets when you are running metastat. mothur will run all pairwise comparisons of the sets. It is required. \n");
- m->mothurOut("The design file looks like the group file. It is a 2 column tab delimited file, where the first column is the group name and the second column is the set the group belongs to.\n");
- m->mothurOut("The groups parameter allows you to specify which of the groups in your shared you would like included. The group names are separated by dashes.\n");
- m->mothurOut("The label parameter allows you to select what distance levels you would like, and are also separated by dashes.\n");
- m->mothurOut("The merge.groups command should be in the following format: merge.groups(design=yourDesignFile, shared=yourSharedFile).\n");
- m->mothurOut("Example merge.groups(design=temp.design, groups=A-B-C, shared=temp.shared).\n");
- m->mothurOut("The default value for groups is all the groups in your sharedfile, and all labels in your inputfile will be used.\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, "MergeGroupsCommand", "help");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-
-MergeGroupsCommand::~MergeGroupsCommand(){}
-
//**********************************************************************************************************************
int MergeGroupsCommand::execute(){
//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) { out.close(); for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } globaldata->Groups.clear(); delete designMap; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { out.close(); for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->Groups.clear(); delete designMap; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
//prevent memory leak
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; }
- if (m->control_pressed) { out.close(); globaldata->Groups.clear(); delete designMap; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { out.close(); m->Groups.clear(); delete designMap; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
//get next line to process
lookup = input.getSharedRAbundVectors();
}
- if (m->control_pressed) { out.close(); globaldata->Groups.clear(); delete designMap; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { out.close(); m->Groups.clear(); delete designMap; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
//output error messages about any remaining user labels
set<string>::iterator it;
out.close();
//reset groups parameter
- globaldata->Groups.clear();
+ m->Groups.clear();
delete designMap;
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0;}
projects / mothur.git / blobdiff