changes while testing 1.27

[mothur.git] / normalizesharedcommand.cpp

diff --git a/normalizesharedcommand.cpp b/normalizesharedcommand.cpp
index bcec00a0bc6dd47e15ddcf72000dc4a9dbec9469..e41cfd9355ce1e08157069e59880aa32066e1505 100644 (file)
--- a/normalizesharedcommand.cpp
+++ b/normalizesharedcommand.cpp
@@ -54,7 +54,26 @@ string NormalizeSharedCommand::getHelpString(){
        }
 }
 
-
+//**********************************************************************************************************************
+string NormalizeSharedCommand::getOutputFileNameTag(string type, string inputName=""){ 
+       try {
+        string outputFileName = "";
+               map<string, vector<string> >::iterator it;
+        
+        //is this a type this command creates
+        it = outputTypes.find(type);
+        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+        else {
+            if (type == "shared") {  outputFileName =  "norm.shared"; }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return outputFileName;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "NormalizeSharedCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 NormalizeSharedCommand::NormalizeSharedCommand(){      
        try {
@@ -176,7 +195,7 @@ 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 +468,7 @@ int NormalizeSharedCommand::normalize(vector<SharedRAbundVector*>& thisLookUp){
                
                if (pickedGroups) { eliminateZeroOTUS(thisLookUp); }
                
-               string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputfile)) + thisLookUp[0]->getLabel() + ".norm.shared";
+               string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputfile)) + thisLookUp[0]->getLabel() + "." + getOutputFileNameTag("shared");
                ofstream out;
                m->openOutputFile(outputFileName, out);
                outputNames.push_back(outputFileName); outputTypes["shared"].push_back(outputFileName);
@@ -540,7 +559,7 @@ 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";
+               string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputfile)) + thisLookUp[0]->getLabel() + "." + getOutputFileNameTag("shared");
                ofstream out;
                m->openOutputFile(outputFileName, out);
                outputNames.push_back(outputFileName); outputTypes["shared"].push_back(outputFileName);
@@ -632,6 +651,7 @@ int NormalizeSharedCommand::eliminateZeroOTUS(vector<SharedRAbundVector*>& thisl
                
                //for each bin
                vector<string> newBinLabels;
+               string snumBins = toString(thislookup[0]->getNumBins());
                for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
                        if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) {  delete newLookup[j];  } return 0; }
                
@@ -647,7 +667,13 @@ int NormalizeSharedCommand::eliminateZeroOTUS(vector<SharedRAbundVector*>& thisl
                                        newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup());
                                }
                                //if there is a bin label use it otherwise make one
-                               string binLabel = "Otu" + toString(i+1);
+                               string binLabel = "Otu";
+                               string sbinNumber = toString(i+1);
+                               if (sbinNumber.length() < snumBins.length()) { 
+                                       int diff = snumBins.length() - sbinNumber.length();
+                                       for (int h = 0; h < diff; h++) { binLabel += "0"; }
+                               }
+                               binLabel += sbinNumber; 
                                if (i < m->currentBinLabels.size()) {  binLabel = m->currentBinLabels[i]; }
                                
                                newBinLabels.push_back(binLabel);
@@ -681,6 +707,7 @@ int NormalizeSharedCommand::eliminateZeroOTUS(vector<SharedRAbundFloatVector*>&
                
                //for each bin
                vector<string> newBinLabels;
+               string snumBins = toString(thislookup[0]->getNumBins());
                for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
                        if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) {  delete newLookup[j];  } return 0; }
                        
@@ -696,7 +723,13 @@ int NormalizeSharedCommand::eliminateZeroOTUS(vector<SharedRAbundFloatVector*>&
                                        newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup());
                                }
                                //if there is a bin label use it otherwise make one
-                               string binLabel = "Otu" + toString(i+1);
+                               string binLabel = "Otu";
+                               string sbinNumber = toString(i+1);
+                               if (sbinNumber.length() < snumBins.length()) { 
+                                       int diff = snumBins.length() - sbinNumber.length();
+                                       for (int h = 0; h < diff; h++) { binLabel += "0"; }
+                               }
+                               binLabel += sbinNumber; 
                                if (i < m->currentBinLabels.size()) {  binLabel = m->currentBinLabels[i]; }
                                
                                newBinLabels.push_back(binLabel);