working on adding count file to mgcluster

diff --git a/mgclustercommand.cpp b/mgclustercommand.cpp
index 6ef968c2248de78e304291f3c781a2baa44ad8ea..a845e0bfe080782b2b12d2f1a634925781578d70 100644 (file)
--- a/mgclustercommand.cpp
+++ b/mgclustercommand.cpp
@@ -15,7 +15,6 @@ vector<string> MGClusterCommand::setParameters(){
                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 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);
@@ -178,10 +177,7 @@ 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"; }
+            temp = validParameter.validFile(parameters, "precision", false);           if (temp == "not found") { temp = "100"; }
                        precisionLength = temp.length();
                        m->mothurConvert(temp, precision); 
                        
@@ -274,13 +270,15 @@ int MGClusterCommand::execute(){
         string rabundFileName = fileroot+ tag + "." + getOutputFileNameTag("rabund");
         string listFileName = fileroot+ tag + "." + getOutputFileNameTag("list");
         
-               m->openOutputFile(sabundFileName,       sabundFile);
-               m->openOutputFile(rabundFileName,       rabundFile);
+        if (countfile == "") {
+            m->openOutputFile(sabundFileName,  sabundFile);
+            m->openOutputFile(rabundFileName,  rabundFile);
+        }
                m->openOutputFile(listFileName, listFile);
                
                if (m->control_pressed) { 
                        delete nameMap; delete read; delete list; delete rabund; 
-                       listFile.close(); rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".list")); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund"));
+                       listFile.close(); if (countfile == "") { rabundFile.close(); sabundFile.close();  m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund")); } m->mothurRemove((fileroot+ tag + ".list"));
                        outputTypes.clear();
                        return 0; 
                }
@@ -303,7 +301,7 @@ int MGClusterCommand::execute(){
                        
                        if (m->control_pressed) { 
                                delete nameMap; delete distMatrix; delete list; delete rabund; delete cluster;
-                               listFile.close(); rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".list")); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund"));
+                               listFile.close(); if (countfile == "") { rabundFile.close(); sabundFile.close();  m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund")); } m->mothurRemove((fileroot+ tag + ".list"));
                                outputTypes.clear();
                                return 0; 
                        }
@@ -315,7 +313,7 @@ int MGClusterCommand::execute(){
                                
                                if (m->control_pressed) { 
                                        delete nameMap; delete distMatrix; delete list; delete rabund; delete cluster;
-                                       listFile.close(); rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".list")); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund"));
+                                       listFile.close(); if (countfile == "") { rabundFile.close(); sabundFile.close();  m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund")); } m->mothurRemove((fileroot+ tag + ".list"));
                                        outputTypes.clear();
                                        return 0; 
                                }
@@ -338,7 +336,7 @@ int MGClusterCommand::execute(){
                                                
                                                if (m->control_pressed) { 
                                                        delete nameMap; delete distMatrix; delete list; delete rabund; delete cluster; delete temp;
-                                                       listFile.close(); rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".list")); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund"));
+                                                       listFile.close(); if (countfile == "") { rabundFile.close(); sabundFile.close();  m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund")); } m->mothurRemove((fileroot+ tag + ".list"));
                                                        outputTypes.clear();
                                                        return 0; 
                                                }
@@ -369,7 +367,7 @@ int MGClusterCommand::execute(){
                                        
                                        if (m->control_pressed) { 
                                                        delete nameMap; delete distMatrix; delete list; delete rabund; delete cluster; delete temp;
-                                                       listFile.close(); rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".list")); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund"));
+                                                       listFile.close(); if (countfile == "") { rabundFile.close(); sabundFile.close();  m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund")); } m->mothurRemove((fileroot+ tag + ".list"));
                                                        outputTypes.clear();
                                                        return 0; 
                                        }
@@ -399,7 +397,7 @@ int MGClusterCommand::execute(){
                        
                        if (m->control_pressed) { 
                                delete nameMap;  delete list; delete rabund; 
-                               listFile.close(); rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".list")); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund"));
+                               listFile.close(); if (countfile == "") { rabundFile.close(); sabundFile.close();  m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund")); } m->mothurRemove((fileroot+ tag + ".list"));
                                outputTypes.clear();
                                return 0; 
                        }
@@ -416,7 +414,7 @@ int MGClusterCommand::execute(){
                        
                        if (m->control_pressed) { 
                                delete nameMap;  delete list; delete rabund; delete hcluster;
-                               listFile.close(); rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".list")); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund"));
+                               listFile.close(); if (countfile == "") { rabundFile.close(); sabundFile.close();  m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund")); } m->mothurRemove((fileroot+ tag + ".list"));
                                outputTypes.clear();
                                return 0; 
                        }
@@ -432,7 +430,7 @@ int MGClusterCommand::execute(){
                                
                                if (m->control_pressed) { 
                                        delete nameMap;  delete list; delete rabund; delete hcluster;
-                                       listFile.close(); rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".list")); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund"));
+                                       listFile.close(); if (countfile == "") { rabundFile.close(); sabundFile.close();  m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund")); } m->mothurRemove((fileroot+ tag + ".list"));
                                        m->mothurRemove(distFile);
                                        m->mothurRemove(overlapFile);
                                        outputTypes.clear();
@@ -447,7 +445,7 @@ int MGClusterCommand::execute(){
                                                
                                                if (m->control_pressed) { 
                                                        delete nameMap;  delete list; delete rabund; delete hcluster;
-                                                       listFile.close(); rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".list")); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund"));
+                                                       listFile.close(); if (countfile == "") { rabundFile.close(); sabundFile.close();  m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund")); } m->mothurRemove((fileroot+ tag + ".list"));
                                                        m->mothurRemove(distFile);
                                                        m->mothurRemove(overlapFile);
                                                        outputTypes.clear();
@@ -471,7 +469,7 @@ int MGClusterCommand::execute(){
                                                                
                                                                if (m->control_pressed) { 
                                                                        delete nameMap;  delete list; delete rabund; delete hcluster; delete temp;
-                                                                       listFile.close(); rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".list")); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund"));
+                                                                       listFile.close(); if (countfile == "") { rabundFile.close(); sabundFile.close();  m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund")); } m->mothurRemove((fileroot+ tag + ".list"));
                                                                        m->mothurRemove(distFile);
                                                                        m->mothurRemove(overlapFile);
                                                                        outputTypes.clear();
@@ -507,7 +505,7 @@ int MGClusterCommand::execute(){
                                        
                                        if (m->control_pressed) { 
                                                        delete nameMap; delete list; delete rabund; delete hcluster; delete temp;
-                                                       listFile.close(); rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".list")); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund"));
+                                                       listFile.close(); if (countfile == "") { rabundFile.close(); sabundFile.close();  m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund")); } m->mothurRemove((fileroot+ tag + ".list"));
                                                        m->mothurRemove(distFile);
                                                        m->mothurRemove(overlapFile);
                                                        outputTypes.clear();
@@ -529,14 +527,15 @@ int MGClusterCommand::execute(){
                }
                
                delete list;
-               if (!large) {delete rabund;}
+               delete rabund;
                listFile.close();
-               sabundFile.close();
-               rabundFile.close();
-       
+        if (countfile == "") {
+            sabundFile.close();
+            rabundFile.close();
+        }
                if (m->control_pressed) { 
                        delete nameMap; 
-                       listFile.close(); rabundFile.close(); sabundFile.close(); m->mothurRemove((fileroot+ tag + ".list")); m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund"));
+                       listFile.close(); if (countfile == "") { rabundFile.close(); sabundFile.close();  m->mothurRemove((fileroot+ tag + ".rabund")); m->mothurRemove((fileroot+ tag + ".sabund")); } m->mothurRemove((fileroot+ tag + ".list"));
                        outputTypes.clear();
                        return 0; 
                }
@@ -544,8 +543,10 @@ int MGClusterCommand::execute(){
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
                m->mothurOut(listFileName); m->mothurOutEndLine();      outputNames.push_back(listFileName); outputTypes["list"].push_back(listFileName);
-               m->mothurOut(rabundFileName); m->mothurOutEndLine();    outputNames.push_back(rabundFileName); outputTypes["rabund"].push_back(rabundFileName);
-               m->mothurOut(sabundFileName); m->mothurOutEndLine();    outputNames.push_back(sabundFileName); outputTypes["sabund"].push_back(sabundFileName);
+               if (countfile == "") {
+            m->mothurOut(rabundFileName); m->mothurOutEndLine();       outputNames.push_back(rabundFileName); outputTypes["rabund"].push_back(rabundFileName);
+            m->mothurOut(sabundFileName); m->mothurOutEndLine();       outputNames.push_back(sabundFileName); outputTypes["sabund"].push_back(sabundFileName);
+        }
                m->mothurOutEndLine();
                
                if (saveCutoff != cutoff) { 
@@ -588,12 +589,14 @@ int MGClusterCommand::execute(){
 void MGClusterCommand::printData(ListVector* mergedList){
        try {
                mergedList->print(listFile);
-               mergedList->getRAbundVector().print(rabundFile);
-               
-               SAbundVector sabund = mergedList->getSAbundVector();
+        SAbundVector sabund = mergedList->getSAbundVector();
+        
+        if (countfile == "") {
+            mergedList->getRAbundVector().print(rabundFile);
+            sabund.print(sabundFile);
+        }
 
                sabund.print(cout);
-               sabund.print(sabundFile);
        }
        catch(exception& e) {
                m->errorOut(e, "MGClusterCommand", "printData");

diff --git a/mgclustercommand.h b/mgclustercommand.h
index 6c75d6c606f90d33d2d67b687fa567309012dd3e..c9c23c80f88d0ab0c98ae058748c544a561b76d3 100644 (file)
--- a/mgclustercommand.h
+++ b/mgclustercommand.h
@@ -58,7 +58,7 @@ private:
        double cutoff;
        float penalty;
        int precision, length, precisionLength;
-       bool abort, minWanted, hclusterWanted, merge, hard, large;
+       bool abort, minWanted, hclusterWanted, merge, hard;
        
        void printData(ListVector*);
        ListVector* mergeOPFs(map<string, int>, float);