edited createRabund function

diff --git a/mgclustercommand.cpp b/mgclustercommand.cpp
index e5681efb220d1635382ea6b077a36ea4e0f50226..42f6d0ad72b7fcc35674b3734664f4c48b2e0fab 100644 (file)
--- a/mgclustercommand.cpp
+++ b/mgclustercommand.cpp
@@ -14,6 +14,7 @@ vector<string> MGClusterCommand::setParameters(){
        try {
                CommandParameter pblast("blast", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pblast);
                CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
+        CommandParameter plarge("large", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(plarge);
                CommandParameter plength("length", "Number", "", "5", "", "", "",false,false); parameters.push_back(plength);
                CommandParameter ppenalty("penalty", "Number", "", "0.10", "", "", "",false,false); parameters.push_back(ppenalty);
                CommandParameter pcutoff("cutoff", "Number", "", "0.70", "", "", "",false,false); parameters.push_back(pcutoff);
@@ -169,6 +170,9 @@ MGClusterCommand::MGClusterCommand(string option) {
                        
                        //check for optional parameter and set defaults
                        string temp;
+            temp = validParameter.validFile(parameters, "large", false);                       if (temp == "not found") { temp = "false"; }            
+                       large = m->isTrue(temp); 
+            
                        temp = validParameter.validFile(parameters, "precision", false);                if (temp == "not found") { temp = "100"; }
                        precisionLength = temp.length();
                        m->mothurConvert(temp, precision); 
@@ -199,7 +203,7 @@ MGClusterCommand::MGClusterCommand(string option) {
                        hclusterWanted = m->isTrue(temp); 
                        
                        temp = validParameter.validFile(parameters, "hard", false);                     if (temp == "not found") { temp = "T"; }
-                       hard = m->isTrue(temp);
+                       hard = m->isTrue(temp);            
                }
 
        }
@@ -211,7 +215,7 @@ MGClusterCommand::MGClusterCommand(string option) {
 //**********************************************************************************************************************
 int MGClusterCommand::execute(){
        try {
-               
+               cout << "1" << endl;
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                //read names file
@@ -225,24 +229,26 @@ int MGClusterCommand::execute(){
                time_t start;
                float previousDist = 0.00000;
                float rndPreviousDist = 0.00000; 
-               
+        
                //read blastfile - creates sparsematrices for the distances and overlaps as well as a listvector
                //must remember to delete those objects here since readBlast does not
                read = new ReadBlast(blastfile, cutoff, penalty, length, minWanted, hclusterWanted);
                read->read(nameMap);
         
-        list = new ListVector(nameMap->getListVector());
-        RAbundVector* rabund = NULL;
-        if(large) {
-            map<string, int> nameMapCounts = m->readNames(namefile);
-            RAbundVector* rabund = createRabund(list, nameMapCounts);
-        }else {
-            RAbundVector* rabund = new RAbundVector(list->getRAbundVector());
-        }
+//        list = new ListVector(nameMap->getListVector());
+//        RAbundVector* rabund = NULL;
+//        
+//        if(large) {
+//            map<string, int> nameMapCounts = m->readNames(namefile);
+//            createRabund(nameMapCounts);
+//            rabund = &rav;
+//        }else {
+//            rabund = new RAbundVector(list->getRAbundVector());
+//        }
         
                 
-               //list = new ListVector(nameMap->getListVector());
-               //RAbundVector* rabund = new RAbundVector(list->getRAbundVector());
+               list = new ListVector(nameMap->getListVector());
+               RAbundVector* rabund = new RAbundVector(list->getRAbundVector());
                
                if (m->control_pressed) { outputTypes.clear(); delete nameMap; delete read; delete list; delete rabund; return 0; }
                
@@ -708,19 +714,22 @@ void MGClusterCommand::sortHclusterFiles(string unsortedDist, string unsortedOve
 }
 
 //**********************************************************************************************************************
-
-RAbundVector MGClusterCommand::createRabund(ListVector list, map<string, int> nameMapCounts){
-    try {
-        RAbundVector rav;
-        for(int i = 0; i < list->getNumBins(); i++) {   rav.push_back(nameMapCounts[i]);    }
-        return rav;
-    }
-    catch(exception& e) {
-               m->errorOut(e, "MGClusterCommand", "createRabund");
-               exit(1);
-       }
-    
-}
+//
+//void MGClusterCommand::createRabund(map<string, int> nameMapCounts){
+//    try {
+//        //RAbundVector rav;
+//        map<string,int>::iterator it;
+//        //it = nameMapCounts.begin();
+//        //for(int i = 0; i < list->getNumBins(); i++) {   rav.push_back((*it).second); it++;    }
+//        for ( it=nameMapCounts.begin(); it!=nameMapCounts.end(); it++ ) {    rav.push_back( it->second );    }
+//        //return rav;
+//    }
+//    catch(exception& e) {
+//             m->errorOut(e, "MGClusterCommand", "createRabund");
+//             exit(1);
+//     }
+//    
+//}
 
 //**********************************************************************************************************************
 

diff --git a/mgclustercommand.h b/mgclustercommand.h
index 889586ae305ac47bdb0f2d15880507aa68655dff..a727c973c5954052f577479eed1046142e2cc49a 100644 (file)
--- a/mgclustercommand.h
+++ b/mgclustercommand.h
@@ -47,6 +47,7 @@ private:
        HCluster* hcluster;
        ListVector* list;
        ListVector oldList;
+//    RAbundVector rav;
        vector<seqDist> overlapMatrix;
        vector<string> outputNames;
        
@@ -55,13 +56,13 @@ private:
        double cutoff;
        float penalty;
        int precision, length, precisionLength;
-       bool abort, minWanted, hclusterWanted, merge, hard;
+       bool abort, minWanted, hclusterWanted, merge, hard, large;
        
        void printData(ListVector*);
        ListVector* mergeOPFs(map<string, int>, float);
        void sortHclusterFiles(string, string);
        vector<seqDist> getSeqs(ifstream&);
-    RAbundVector createRabund(ListVector, map<string, int>);
+//    void createRabund(map<string, int>);
 
 };