sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / normalizesharedcommand.cpp

diff --git a/normalizesharedcommand.cpp b/normalizesharedcommand.cpp
index 43c8e2260c4e678bbd2e7718a6313b15d97eed8b..acd8208ea7ebb20a3d3810d254d0b24f5386d4d3 100644 (file)
--- a/normalizesharedcommand.cpp
+++ b/normalizesharedcommand.cpp
@@ -12,15 +12,15 @@
 //**********************************************************************************************************************
 vector<string> NormalizeSharedCommand::setParameters(){        
        try {
-               CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(pshared);    
-               CommandParameter prelabund("relabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prelabund);
-               CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
-               CommandParameter pmethod("method", "Multiple", "totalgroup-zscore", "totalgroup", "", "", "",false,false); parameters.push_back(pmethod);
-               CommandParameter pnorm("norm", "Number", "", "0", "", "", "",false,false); parameters.push_back(pnorm);
-               CommandParameter pmakerelabund("makerelabund", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pmakerelabund);
-               CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none","shared",false,false,true); parameters.push_back(pshared);      
+               CommandParameter prelabund("relabund", "InputTypes", "", "", "LRSS", "LRSS", "none","shared",false,false,true); parameters.push_back(prelabund);
+               CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+               CommandParameter pmethod("method", "Multiple", "totalgroup-zscore", "totalgroup", "", "", "","",false,false,true); parameters.push_back(pmethod);
+               CommandParameter pnorm("norm", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pnorm);
+               CommandParameter pmakerelabund("makerelabund", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pmakerelabund);
+               CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
                
                vector<string> myArray;
                for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
@@ -53,8 +53,21 @@ string NormalizeSharedCommand::getHelpString(){
                exit(1);
        }
 }
-
-
+//**********************************************************************************************************************
+string NormalizeSharedCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "shared") {  pattern = "[filename],[distance],norm.shared"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "NormalizeSharedCommand", "getOutputPattern");
+        exit(1);
+    }
+}
 //**********************************************************************************************************************
 NormalizeSharedCommand::NormalizeSharedCommand(){      
        try {
@@ -176,7 +189,7 @@ NormalizeSharedCommand::NormalizeSharedCommand(string option) {
                        if (temp == "not found") {  
                                norm = 0;  //once you have read, set norm to smallest group number
                        }else { 
-                               convert(temp, norm);
+                               m->mothurConvert(temp, norm);
                                if (norm < 0) { m->mothurOut("norm must be positive."); m->mothurOutEndLine(); abort=true; }
                        }
                        
@@ -449,7 +462,11 @@ int NormalizeSharedCommand::normalize(vector<SharedRAbundVector*>& thisLookUp){
                
                if (pickedGroups) { eliminateZeroOTUS(thisLookUp); }
                
-               string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputfile)) + thisLookUp[0]->getLabel() + ".norm.shared";
+        map<string, string> variables; 
+        variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputfile));
+        variables["[distance]"] = thisLookUp[0]->getLabel();
+               string outputFileName = getOutputFileName("shared",variables);
+        
                ofstream out;
                m->openOutputFile(outputFileName, out);
                outputNames.push_back(outputFileName); outputTypes["shared"].push_back(outputFileName);
@@ -540,7 +557,10 @@ int NormalizeSharedCommand::normalize(vector<SharedRAbundFloatVector*>& thisLook
                //save mothurOut's binLabels to restore for next label
                vector<string> saveBinLabels = m->currentBinLabels;
                
-               string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputfile)) + thisLookUp[0]->getLabel() + ".norm.shared";
+        map<string, string> variables; 
+        variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputfile));
+        variables["[distance]"] = thisLookUp[0]->getLabel();
+               string outputFileName = getOutputFileName("shared",variables);
                ofstream out;
                m->openOutputFile(outputFileName, out);
                outputNames.push_back(outputFileName); outputTypes["shared"].push_back(outputFileName);