changed normalize.shared and sub.sample commands to fix bug in normalize.shared and...

[mothur.git] / metastatscommand.cpp

diff --git a/metastatscommand.cpp b/metastatscommand.cpp
index 4bb50ab107bb4fdde1d97b790cd15f3cb42d8599..7942bfcce548030951e3c5157438d13eb88c17d6 100644 (file)
--- a/metastatscommand.cpp
+++ b/metastatscommand.cpp
@@ -10,6 +10,7 @@
 #include "metastatscommand.h"
 #include "metastats.h"
 #include "sharedutilities.h"
+#include "mothurmetastats.h"
 
 //**********************************************************************************************************************
 vector<string> MetaStatsCommand::setParameters(){      
@@ -52,7 +53,7 @@ string MetaStatsCommand::getHelpString(){
                helpString += "The metastats command should be in the following format: metastats(design=yourDesignFile).\n";
                helpString += "Example metastats(design=temp.design, groups=A-B-C).\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 += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n";
+               helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
                return helpString;
        }
        catch(exception& e) {
@@ -83,6 +84,7 @@ MetaStatsCommand::MetaStatsCommand(string option) {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();
@@ -133,7 +135,7 @@ MetaStatsCommand::MetaStatsCommand(string option) {
                                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; }
-                       }
+                       }else { m->setSharedFile(sharedfile); }
                        
                        //check for required parameters
                        designfile = validParameter.validFile(parameters, "design", true);
@@ -143,7 +145,7 @@ MetaStatsCommand::MetaStatsCommand(string option) {
                                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; }
-                       }
+                       }else { m->setDesignFile(designfile); }
                        
                        //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"){  
@@ -248,7 +250,7 @@ int MetaStatsCommand::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) {  outputTypes.clear(); for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } m->Groups.clear(); delete input; delete designMap;  for (int i = 0; i < outputNames.size(); i++) {      remove(outputNames[i].c_str()); } return 0; }
+                       if (m->control_pressed) {  outputTypes.clear(); for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } m->Groups.clear(); delete input; delete designMap;  for (int i = 0; i < outputNames.size(); i++) {      m->mothurRemove(outputNames[i]); } return 0; }
        
                        if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){                  
 
@@ -279,13 +281,13 @@ int MetaStatsCommand::execute(){
                        //prevent memory leak
                        for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
                        
-                       if (m->control_pressed) {  outputTypes.clear(); m->Groups.clear(); delete input;  delete designMap;  for (int i = 0; i < outputNames.size(); i++) {     remove(outputNames[i].c_str()); } return 0; }
+                       if (m->control_pressed) {  outputTypes.clear(); m->Groups.clear(); delete input;  delete designMap;  for (int i = 0; i < outputNames.size(); i++) {     m->mothurRemove(outputNames[i]); } return 0; }
 
                        //get next line to process
                        lookup = input->getSharedRAbundVectors();                               
                }
                
-               if (m->control_pressed) { outputTypes.clear(); m->Groups.clear(); delete input; delete designMap;  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str()); }  return 0; }
+               if (m->control_pressed) { outputTypes.clear(); m->Groups.clear(); delete input; delete designMap;  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]); }  return 0; }
 
                //output error messages about any remaining user labels
                set<string>::iterator it;
@@ -317,7 +319,7 @@ int MetaStatsCommand::execute(){
                delete input; 
                delete designMap;
                
-               if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {   remove(outputNames[i].c_str()); } return 0;}
+               if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {   m->mothurRemove(outputNames[i]); } return 0;}
                
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
@@ -395,13 +397,15 @@ int MetaStatsCommand::driver(int start, int num, vector<SharedRAbundVector*>& th
                        //get filename
                        string outputFileName = outputDir +  m->getRootName(m->getSimpleName(sharedfile)) + thisLookUp[0]->getLabel() + "." + setA + "-" + setB + ".metastats";
                        outputNames.push_back(outputFileName); outputTypes["metastats"].push_back(outputFileName);
-                       int nameLength = outputFileName.length();
-                       char * output = new char[nameLength];
-                       strcpy(output, outputFileName.c_str());
+                       //int nameLength = outputFileName.length();
+                       //char * output = new char[nameLength];
+                       //strcpy(output, outputFileName.c_str());
        
                        //build matrix from shared rabunds
-                       double** data;
-                       data = new double*[thisLookUp[0]->getNumBins()];
+                       //double** data;
+                       //data = new double*[thisLookUp[0]->getNumBins()];
+                       
+                       vector< vector<double> > data2; data2.resize(thisLookUp[0]->getNumBins());
                        
                        vector<SharedRAbundVector*> subset;
                        int setACount = 0;
@@ -426,22 +430,29 @@ int MetaStatsCommand::driver(int start, int num, vector<SharedRAbundVector*>& th
                        }else {
                                //fill data
                                for (int j = 0; j < thisLookUp[0]->getNumBins(); j++) {
-                                       data[j] = new double[subset.size()];
+                                       //data[j] = new double[subset.size()];
+                                       data2[j].resize(subset.size(), 0.0);
                                        for (int i = 0; i < subset.size(); i++) {
-                                               data[j][i] = (subset[i]->getAbundance(j));
+                                               //data[j][i] = (subset[i]->getAbundance(j));
+                                               data2[j][i] = (subset[i]->getAbundance(j));
                                        }
                                }
                                
                                m->mothurOut("Comparing " + setA + " and " + setB + "..."); m->mothurOutEndLine(); 
-                               metastat_main(output, thisLookUp[0]->getNumBins(), subset.size(), threshold, iters, data, setACount);
+                               //metastat_main(output, thisLookUp[0]->getNumBins(), subset.size(), threshold, iters, data, setACount);
+                               
+                               m->mothurOutEndLine();
+                               MothurMetastats mothurMeta(threshold, iters);
+                               mothurMeta.runMetastats(outputFileName , data2, setACount);
+                               m->mothurOutEndLine();
                                
                                m->mothurOutEndLine(); 
                        }
                        
                        //free memory
-                       delete output;
-                       for(int i = 0; i < thisLookUp[0]->getNumBins(); i++)  {  delete[] data[i];  }
-                       delete[] data; 
+                       //delete output;
+                       //for(int i = 0; i < thisLookUp[0]->getNumBins(); i++)  {  delete[] data[i];  }
+                       //delete[] data; 
                }
                
                return 0;