working on unifrac parallelization

[mothur.git] / collectcommand.cpp

diff --git a/collectcommand.cpp b/collectcommand.cpp
index 8c1565b901d5b885ad86b91d31cb7cc041138535..2d952fa9b9a60ea762a83f967dc7e6c125fff61d 100644 (file)
--- a/collectcommand.cpp
+++ b/collectcommand.cpp
@@ -14,8 +14,13 @@
 #include "chao1.h"
 #include "bootstrap.h"
 #include "simpson.h"
+#include "simpsoneven.h"
+#include "invsimpson.h"
 #include "npshannon.h"
 #include "shannon.h"
+#include "smithwilson.h"
+#include "heip.h"
+#include "shannoneven.h"
 #include "jackknife.h"
 #include "geom.h"
 #include "qstat.h"
@@ -68,7 +73,7 @@ CollectCommand::CollectCommand(string option)  {
                        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;  }
                        }
                        
@@ -83,7 +88,7 @@ CollectCommand::CollectCommand(string option)  {
                        else { 
                                 if (calc == "default")  {  calc = "sobs-chao-ace-jack-shannon-npshannon-simpson";  }
                        }
-                       splitAtDash(calc, Estimators);
+                       m->splitAtDash(calc, Estimators);
 
                        string temp;
                        temp = validParameter.validFile(parameters, "freq", false);                     if (temp == "not found") { temp = "100"; }
@@ -145,8 +150,8 @@ int CollectCommand::execute(){
                        
                        if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str());         }  globaldata->Groups.clear(); if (hadShared != "") {  globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile");  } return 0; }
                        
-                       if (outputDir == "") { outputDir += hasPath(inputFileNames[p]); }
-                       string fileNameRoot = outputDir + getRootName(getSimpleName(inputFileNames[p]));
+                       if (outputDir == "") { outputDir += m->hasPath(inputFileNames[p]); }
+                       string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p]));
                        globaldata->inputFileName = inputFileNames[p];
                
                        if (inputFileNames.size() > 1) {
@@ -178,12 +183,27 @@ int CollectCommand::execute(){
                                        }else if (Estimators[i] == "shannon") { 
                                                cDisplays.push_back(new CollectDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"shannon")));
                                                outputNames.push_back(fileNameRoot+"shannon");
+                                       }else if (Estimators[i] == "shannoneven") { 
+                                               cDisplays.push_back(new CollectDisplay(new ShannonEven(), new OneColumnFile(fileNameRoot+"shannoneven")));
+                                               outputNames.push_back(fileNameRoot+"shannoneven");
                                        }else if (Estimators[i] == "npshannon") { 
                                                cDisplays.push_back(new CollectDisplay(new NPShannon(), new OneColumnFile(fileNameRoot+"np_shannon")));
                                                outputNames.push_back(fileNameRoot+"np_shannon");
+                                       }else if (Estimators[i] == "heip") { 
+                                               cDisplays.push_back(new CollectDisplay(new Heip(), new OneColumnFile(fileNameRoot+"heip")));
+                                               outputNames.push_back(fileNameRoot+"heip");
+                                       }else if (Estimators[i] == "smithwilson") { 
+                                               cDisplays.push_back(new CollectDisplay(new SmithWilson(), new OneColumnFile(fileNameRoot+"smithwilson")));
+                                               outputNames.push_back(fileNameRoot+"smithwilson");
                                        }else if (Estimators[i] == "simpson") { 
                                                cDisplays.push_back(new CollectDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"simpson")));
                                                outputNames.push_back(fileNameRoot+"simpson");
+                                       }else if (Estimators[i] == "simpsoneven") { 
+                                               cDisplays.push_back(new CollectDisplay(new SimpsonEven(), new OneColumnFile(fileNameRoot+"simpsoneven")));
+                                               outputNames.push_back(fileNameRoot+"simpsoneven");
+                                       }else if (Estimators[i] == "invsimpson") { 
+                                               cDisplays.push_back(new CollectDisplay(new InvSimpson(), new ThreeColumnFile(fileNameRoot+"invsimpson")));
+                                               outputNames.push_back(fileNameRoot+"invsimpson");
                                        }else if (Estimators[i] == "bootstrap") { 
                                                cDisplays.push_back(new CollectDisplay(new Bootstrap(), new OneColumnFile(fileNameRoot+"bootstrap")));
                                                outputNames.push_back(fileNameRoot+"bootstrap");
@@ -276,7 +296,7 @@ int CollectCommand::execute(){
                                        
                                }
                                //you have a label the user want that is smaller than this label and the last label has not already been processed 
-                               if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+                               if ((m->anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
                                        string saveLabel = order->getLabel();
                                        
                                        delete order;
@@ -394,7 +414,7 @@ vector<string> CollectCommand::parseSharedFile(string filename) {
                input = globaldata->ginput;
                vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
                
-               string sharedFileRoot = getRootName(filename);
+               string sharedFileRoot = m->getRootName(filename);
                
                //clears file before we start to write to it below
                for (int i=0; i<lookup.size(); i++) {
@@ -413,7 +433,7 @@ vector<string> CollectCommand::parseSharedFile(string filename) {
                
                        for (int i = 0; i < lookup.size(); i++) {
                                RAbundVector rav = lookup[i]->getRAbundVector();
-                               openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".rabund", *(filehandles[lookup[i]->getGroup()]));
+                               m->openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".rabund", *(filehandles[lookup[i]->getGroup()]));
                                rav.print(*(filehandles[lookup[i]->getGroup()]));
                                (*(filehandles[lookup[i]->getGroup()])).close();
                        }