Merge remote-tracking branch 'origin/master'

[mothur.git] / mgclustercommand.cpp

diff --git a/mgclustercommand.cpp b/mgclustercommand.cpp
index 42f6d0ad72b7fcc35674b3734664f4c48b2e0fab..cffb80f9e8f2963d4983c6637d8eef2b33566de4 100644 (file)
--- a/mgclustercommand.cpp
+++ b/mgclustercommand.cpp
@@ -14,7 +14,8 @@ 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 pcount("count", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pcount);
+        //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);
@@ -165,6 +166,13 @@ MGClusterCommand::MGClusterCommand(string option) {
                        if (namefile == "not open") { abort = true; }   
                        else if (namefile == "not found") { namefile = ""; }
                        else { m->setNameFile(namefile); }
+            
+            countfile = validParameter.validFile(parameters, "count", true);
+                       if (countfile == "not open") { abort = true; }  
+                       else if (countfile == "not found") { countfile = ""; }
+            else { m->setCountTableFile(countfile); }
+            
+            if (countfile != "" && namefile != "") { m->mothurOut("Cannot have both a name file and count file. Please use one or the other."); m->mothurOutEndLine(); abort = true; }
                        
                        if ((blastfile == "")) { m->mothurOut("When executing a mgcluster command you must provide a blastfile."); m->mothurOutEndLine(); abort = true; }
                        
@@ -215,7 +223,6 @@ MGClusterCommand::MGClusterCommand(string option) {
 //**********************************************************************************************************************
 int MGClusterCommand::execute(){
        try {
-               cout << "1" << endl;
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                //read names file
@@ -235,20 +242,22 @@ int MGClusterCommand::execute(){
                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);
-//            createRabund(nameMapCounts);
-//            rabund = &rav;
-//        }else {
-//            rabund = new RAbundVector(list->getRAbundVector());
-//        }
+        list = new ListVector(nameMap->getListVector());
+        RAbundVector* rabund = NULL;
+        
+        if(countfile != "") {
+            //map<string, int> nameMapCounts = m->readNames(namefile);
+            ct = new CountTable();
+            ct->readTable(countfile);
+            createRabund(ct, list);
+            rabund = &rav;
+        }else {
+            rabund = new RAbundVector(list->getRAbundVector());
+        }
         
                 
-               list = new ListVector(nameMap->getListVector());
-               RAbundVector* rabund = new RAbundVector(list->getRAbundVector());
+               //list = new ListVector(nameMap->getListVector());
+               //rabund = new RAbundVector(list->getRAbundVector());
                
                if (m->control_pressed) { outputTypes.clear(); delete nameMap; delete read; delete list; delete rabund; return 0; }
                
@@ -519,8 +528,8 @@ int MGClusterCommand::execute(){
                        m->mothurRemove(overlapFile);
                }
                
-               delete list; 
-               delete rabund;
+               delete list;
+               if (!large) {delete rabund;}
                listFile.close();
                sabundFile.close();
                rabundFile.close();
@@ -714,22 +723,33 @@ void MGClusterCommand::sortHclusterFiles(string unsortedDist, string unsortedOve
 }
 
 //**********************************************************************************************************************
-//
-//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);
-//     }
-//    
-//}
+
+void MGClusterCommand::createRabund(CountTable* ct, ListVector* list){
+    try {
+        //vector<string> names = ct.getNamesOfSeqs();
+
+        //for ( int i; i < ct.getNumGroups(); i++ ) {    rav.push_back( ct.getNumSeqs(names[i]) );    }
+        //return rav;
+        
+        for(int i = 0; i < list->getNumBins(); i++) { 
+           vector<string> binNames;
+           string bin = list->get(i);
+           m->splitAtComma(bin, binNames);
+           int total = 0;
+           for (int j = 0; j < binNames.size(); j++) { 
+               total += ct->getNumSeqs(binNames[j]);
+           }
+           rav.push_back(total);   
+       }
+        
+        
+    }
+    catch(exception& e) {
+               m->errorOut(e, "MGClusterCommand", "createRabund");
+               exit(1);
+       }
+    
+}
 
 //**********************************************************************************************************************