added load.logfile command. changed summary.single output for subsample=t.

[mothur.git] / classifytreecommand.cpp

diff --git a/classifytreecommand.cpp b/classifytreecommand.cpp
index bcf27698ce2bf68bf3dc6a3909228a9d4ccd5cb2..7861a01bab3420f1598e351b30765dbd0ae5f124 100644 (file)
--- a/classifytreecommand.cpp
+++ b/classifytreecommand.cpp
@@ -49,7 +49,27 @@ string ClassifyTreeCommand::getHelpString(){
                exit(1);
        }
 }
-
+//**********************************************************************************************************************
+string ClassifyTreeCommand::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 == "tree") {  outputFileName =  "taxonomy.tre"; }
+            else if (type == "summary") {  outputFileName =  "taxonomy.summary"; }
+            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, "ClassifyTreeCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 ClassifyTreeCommand::ClassifyTreeCommand(){    
        try {
@@ -197,11 +217,11 @@ int ClassifyTreeCommand::execute(){
         Tree* outputTree = T[0];
         delete reader;
 
-        if (namefile != "") { readNamesFile(); }
+        if (namefile != "") { m->readNames(namefile, nameMap, nameCount); }
                         
         if (m->control_pressed) { delete tmap;  delete outputTree;  return 0; }
                
-        readTaxonomyFile();
+        m->readTax(taxonomyfile, taxMap);
         
         /***************************************************/
         //             get concensus taxonomies                    //
@@ -242,7 +262,7 @@ int ClassifyTreeCommand::getClassifications(Tree*& T){
                
                string thisOutputDir = outputDir;
                if (outputDir == "") {  thisOutputDir += m->hasPath(treefile);  }
-               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(treefile)) + "taxonomy.summary";
+               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(treefile)) + getOutputFileNameTag("summary");
                outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName);
                
                ofstream out;
@@ -256,7 +276,7 @@ int ClassifyTreeCommand::getClassifications(Tree*& T){
                
                string treeOutputDir = outputDir;
                if (outputDir == "") {  treeOutputDir += m->hasPath(treefile);  }
-               string outputTreeFileName = treeOutputDir + m->getRootName(m->getSimpleName(treefile)) + "taxonomy.tre";
+               string outputTreeFileName = treeOutputDir + m->getRootName(m->getSimpleName(treefile)) + getOutputFileNameTag("tree");
                
                //create a map from tree node index to names of descendants, save time later
                map<int, map<string, set<string> > > nodeToDescendants; //node# -> (groupName -> groupMembers)
@@ -453,68 +473,6 @@ map<string, set<string> > ClassifyTreeCommand::getDescendantList(Tree*& T, int i
                exit(1);
        }
 }
-//**********************************************************************************************************************
-int ClassifyTreeCommand::readTaxonomyFile() {
-       try {
-               
-               ifstream in;
-               m->openInputFile(taxonomyfile, in);
-               
-               string name, tax;
-        
-               while(!in.eof()){
-                       in >> name >> tax;              
-                       m->gobble(in);
-                       
-                       //are there confidence scores, if so remove them
-                       if (tax.find_first_of('(') != -1) {  m->removeConfidences(tax); }
-                       
-                       taxMap[name] = tax;
-                       
-                       if (m->control_pressed) { in.close(); taxMap.clear(); return 0; }
-               }
-               in.close();
-               
-               return 0;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "ClassifyTreeCommand", "readTaxonomyFile");
-               exit(1);
-       }
-}
-
-/*****************************************************************/
-int ClassifyTreeCommand::readNamesFile() {
-       try {
-               ifstream inNames;
-               m->openInputFile(namefile, inNames);
-               
-               string name, names;
-        
-               while(!inNames.eof()){
-                       inNames >> name;                        //read from first column  A
-                       inNames >> names;               //read from second column  A,B,C,D
-                       m->gobble(inNames);
-                       
-                       //parse names into vector
-                       vector<string> theseNames;
-                       m->splitAtComma(names, theseNames);
-            
-                       for (int i = 0; i < theseNames.size(); i++) {  nameMap[theseNames[i]] = name;  }
-            nameCount[name] = theseNames.size();
-                       
-                       if (m->control_pressed) { inNames.close(); nameMap.clear(); return 0; }
-               }
-               inNames.close();
-               
-               return 0;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "ClassifyTreeCommand", "readNamesFile");
-               exit(1);
-       }
-}
-
 /*****************************************************************/