adding labels to list file.

[mothur.git] / otuhierarchycommand.cpp

diff --git a/otuhierarchycommand.cpp b/otuhierarchycommand.cpp
index 091bf9bb0659dd0895bf47a414fa4ea86692f026..07e3c1d0146ef521563697fe07deb38d7837b67d 100644 (file)
--- a/otuhierarchycommand.cpp
+++ b/otuhierarchycommand.cpp
@@ -12,11 +12,11 @@
 //**********************************************************************************************************************
 vector<string> OtuHierarchyCommand::setParameters(){   
        try {
-               CommandParameter poutput("output", "Multiple", "name-number", "name", "", "", "",false,false); parameters.push_back(poutput);
-               CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
-               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 poutput("output", "Multiple", "name-number", "name", "", "", "","",false,false); parameters.push_back(poutput);
+               CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","otuheirarchy",false,true,true); parameters.push_back(plist);
+               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);          }
@@ -47,24 +47,19 @@ string OtuHierarchyCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
-string OtuHierarchyCommand::getOutputFileNameTag(string type, string inputName=""){    
-       try {
-        string outputFileName = "";
-               map<string, vector<string> >::iterator it;
+string OtuHierarchyCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
         
-        //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 == "otuheirarchy") {  outputFileName =  "otu.hierarchy"; }
-            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, "OtuHierarchyCommand", "getOutputFileNameTag");
-               exit(1);
-       }
+        if (type == "otuheirarchy") {  pattern = "[filename],[distance1],[tag],[distance2],otu.hierarchy"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "OtuHierarchyCommand", "getOutputPattern");
+        exit(1);
+    }
 }
 //**********************************************************************************************************************
 OtuHierarchyCommand::OtuHierarchyCommand(){    
@@ -180,56 +175,48 @@ int OtuHierarchyCommand::execute(){
                }
                
                //map sequences to bin number in the "little" otu
-               map<string, int> littleBins; 
+               map<string, int> littleBins;
+        vector<string> binLabels0 = lists[0].getLabels();
                for (int i = 0; i < lists[0].getNumBins(); i++) {
                
                        if (m->control_pressed) {  return 0; }
-                       
-                       string names = lists[0].get(i); 
-                       
-                       //parse bin
-                       while (names.find_first_of(',') != -1) { 
-                               string name = names.substr(0,names.find_first_of(','));
-                               names = names.substr(names.find_first_of(',')+1, names.length());
-                               littleBins[name] = i;  
-                       }
-                       
-                       //get last name
-                       littleBins[names] = i;
-               }
+                       string bin = lists[0].get(i);
+            vector<string> names; m->splitAtComma(bin, names);
+                       for (int j = 0; j < names.size(); j++) { littleBins[names[j]] = i; }
+        }
                
                ofstream out;
-               string outputFileName = outputDir + m->getRootName(m->getSimpleName(listFile)) + lists[0].getLabel() + "-" + lists[1].getLabel() + "." + getOutputFileNameTag("otuheirarchy");
+        map<string, string> variables; 
+        variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listFile));
+        variables["[distance1]"] = lists[0].getLabel();
+        variables["[tag]"] = "-"; 
+        variables["[distance2]"] = lists[1].getLabel();
+               string outputFileName = getOutputFileName("otuheirarchy",variables);
                m->openOutputFile(outputFileName, out);
                
                //go through each bin in "big" otu and output the bins in "little" otu which created it
+        vector<string> binLabels1 = lists[1].getLabels();
                for (int i = 0; i < lists[1].getNumBins(); i++) {
                
                        if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(outputFileName); return 0; }
                        
-                       string names = lists[1].get(i);
+                       string binnames = lists[1].get(i);
+            vector<string> names; m->splitAtComma(binnames, names);
                        
                        //output column 1
-                       if (output == "name")   {   out << names << '\t';       }
-                       else                                    {       out << i << '\t';               }
+                       if (output == "name")   {   out << binnames << '\t';    }
+                       else                                    {       out << binLabels1[i] << '\t';           }
                        
                        map<int, int> bins; //bin numbers in little that are in this bin in big
                        map<int, int>::iterator it;
                        
                        //parse bin
-                       while (names.find_first_of(',') != -1) { 
-                               string name = names.substr(0,names.find_first_of(','));
-                               names = names.substr(names.find_first_of(',')+1, names.length());
-                               bins[littleBins[name]] = littleBins[name];  
-                       }
-                       
-                       //get last name
-                       bins[littleBins[names]] = littleBins[names]; 
+                       for (int j = 0; j < names.size(); j++) { bins[littleBins[names[j]]] = littleBins[names[j]];   }
                        
                        string col2 = "";
                        for (it = bins.begin(); it != bins.end(); it++) {
                                if (output == "name")   {   col2 += lists[0].get(it->first) + "\t";     }
-                               else                                    {       col2 += toString(it->first) + "\t";             }
+                               else                                    {       col2 += binLabels0[it->first] + "\t";           }
                        }
                        
                        //output column 2