changed reading of name file to use buffered reads. note the splitAtWhiteSpace functi...

[mothur.git] / collectcommand.cpp

diff --git a/collectcommand.cpp b/collectcommand.cpp
index 5bd9fd75c474aeafdf632d8800b9c184916ccc83..7ad41367f795abe7aeeda1052a8211daf72aeaf4 100644 (file)
--- a/collectcommand.cpp
+++ b/collectcommand.cpp
@@ -44,7 +44,7 @@ vector<string> CollectCommand::setParameters(){
                CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(pshared);
                CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
                CommandParameter pfreq("freq", "Number", "", "100", "", "", "",false,false); parameters.push_back(pfreq);
-               CommandParameter pcalc("calc", "Multiple", "sobs-chao-nseqs-coverage-ace-jack-shannon-shannoneven-np_shannon-heip-smithwilson-simpson-simpsoneven-invsimpson-bootstrap-geometric-qstat-logseries-bergerparker-bstick-goodscoverage-efron-boneh-solow-shen", "sobs-chao-ace-jack-shannon-npshannon-simpson", "", "", "",true,false); parameters.push_back(pcalc);
+               CommandParameter pcalc("calc", "Multiple", "sobs-chao-nseqs-coverage-ace-jack-shannon-shannoneven-npshannon-heip-smithwilson-simpson-simpsoneven-invsimpson-bootstrap-geometric-qstat-logseries-bergerparker-bstick-goodscoverage-efron-boneh-solow-shen", "sobs-chao-ace-jack-shannon-npshannon-simpson", "", "", "",true,false); parameters.push_back(pcalc);
                CommandParameter pabund("abund", "Number", "", "10", "", "", "",false,false); parameters.push_back(pabund);
                CommandParameter psize("size", "Number", "", "0", "", "", "",false,false); parameters.push_back(psize);
                CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
@@ -94,7 +94,7 @@ CollectCommand::CollectCommand(){
                outputTypes["jack"] = tempOutNames;
                outputTypes["shannon"] = tempOutNames;
                outputTypes["shannoneven"] = tempOutNames;
-               outputTypes["np_shannon"] = tempOutNames;
+               outputTypes["npshannon"] = tempOutNames;
                outputTypes["heip"] = tempOutNames;
                outputTypes["smithwilson"] = tempOutNames;
                outputTypes["simpson"] = tempOutNames;
@@ -151,7 +151,7 @@ CollectCommand::CollectCommand(string option)  {
                        outputTypes["jack"] = tempOutNames;
                        outputTypes["shannon"] = tempOutNames;
                        outputTypes["shannoneven"] = tempOutNames;
-                       outputTypes["np_shannon"] = tempOutNames;
+                       outputTypes["npshannon"] = tempOutNames;
                        outputTypes["heip"] = tempOutNames;
                        outputTypes["smithwilson"] = tempOutNames;
                        outputTypes["simpson"] = tempOutNames;
@@ -280,13 +280,13 @@ CollectCommand::CollectCommand(string option)  {
 
                        string temp;
                        temp = validParameter.validFile(parameters, "freq", false);                     if (temp == "not found") { temp = "100"; }
-                       convert(temp, freq); 
+                       m->mothurConvert(temp, freq); 
                        
                        temp = validParameter.validFile(parameters, "abund", false);            if (temp == "not found") { temp = "10"; }
-                       convert(temp, abund); 
+                       m->mothurConvert(temp, abund); 
                        
                        temp = validParameter.validFile(parameters, "size", false);                     if (temp == "not found") { temp = "0"; }
-                       convert(temp, size); 
+                       m->mothurConvert(temp, size); 
                }
                
        }
@@ -307,7 +307,7 @@ int CollectCommand::execute(){
        
                for (int p = 0; p < inputFileNames.size(); p++) {
                        
-                       if (m->control_pressed) {  outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());         }  m->Groups.clear();  return 0; }
+                       if (m->control_pressed) {  outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        }  m->clearGroups();  return 0; }
                        
                        if (outputDir == "") { outputDir += m->hasPath(inputFileNames[p]); }
                        string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p]));
@@ -346,8 +346,8 @@ int CollectCommand::execute(){
                                                cDisplays.push_back(new CollectDisplay(new ShannonEven(), new OneColumnFile(fileNameRoot+"shannoneven")));
                                                outputNames.push_back(fileNameRoot+"shannoneven"); outputTypes["shannoneven"].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"); outputTypes["np_shannon"].push_back(fileNameRoot+"np_shannon");
+                                               cDisplays.push_back(new CollectDisplay(new NPShannon(), new OneColumnFile(fileNameRoot+"npshannon")));
+                                               outputNames.push_back(fileNameRoot+"npshannon"); outputTypes["npshannon"].push_back(fileNameRoot+"npshannon");
                                        }else if (Estimators[i] == "heip") { 
                                                cDisplays.push_back(new CollectDisplay(new Heip(), new OneColumnFile(fileNameRoot+"heip")));
                                                outputNames.push_back(fileNameRoot+"heip"); outputTypes["heip"].push_back(fileNameRoot+"heip");
@@ -413,10 +413,10 @@ int CollectCommand::execute(){
                        
                        if (m->control_pressed) {  
                                for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
-                               for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());         } outputTypes.clear(); 
+                               for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        } outputTypes.clear(); 
                                delete input;  
                                delete order; 
-                               m->Groups.clear();
+                               m->clearGroups();
                                return 0;
                        }
 
@@ -425,10 +425,10 @@ int CollectCommand::execute(){
                        
                                if (m->control_pressed) { 
                                        for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
-                                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());         } outputTypes.clear(); 
+                                       for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        } outputTypes.clear(); 
                                        delete input;  
                                        delete order; 
-                                       m->Groups.clear();
+                                       m->clearGroups();
                                        return 0;
                                }
 
@@ -474,9 +474,9 @@ int CollectCommand::execute(){
                        
                        if (m->control_pressed) { 
                                        for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
-                                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());         } outputTypes.clear(); 
+                                       for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        } outputTypes.clear(); 
                                        delete input;  
-                                       m->Groups.clear();
+                                       m->clearGroups();
                                        return 0;
                        }
                                
@@ -506,10 +506,10 @@ int CollectCommand::execute(){
                                
                                if (m->control_pressed) { 
                                        for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
-                                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());         } outputTypes.clear(); 
+                                       for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        } outputTypes.clear(); 
                                        delete input;  
                                        delete order;
-                                       m->Groups.clear();
+                                       m->clearGroups();
                                        return 0;
                                }
                                delete order;
@@ -520,7 +520,7 @@ int CollectCommand::execute(){
                        delete input;  
                }
                
-               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());         } return 0; }
+               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);        } return 0; }
                                
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
@@ -551,7 +551,7 @@ vector<string> CollectCommand::parseSharedFile(string filename) {
                
                //clears file before we start to write to it below
                for (int i=0; i<lookup.size(); i++) {
-                       remove((sharedFileRoot + lookup[i]->getGroup() + ".rabund").c_str());
+                       m->mothurRemove((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
                        filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
                }