working on pam

[mothur.git] / getotuscommand.cpp

diff --git a/getotuscommand.cpp b/getotuscommand.cpp
index 8d20e63b65b9a99b6476608fe4a108ce233718f0..3ca7f5d575db0a7e3a065ebcf371128698d5056b 100644 (file)
--- a/getotuscommand.cpp
+++ b/getotuscommand.cpp
@@ -15,13 +15,13 @@
 //**********************************************************************************************************************
 vector<string> GetOtusCommand::setParameters(){        
        try {
-               CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pgroup);
-               CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
-               CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos);
-               CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
-               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 pgroup("group", "InputTypes", "", "", "none", "none", "none","group",false,true, true); parameters.push_back(pgroup);
+               CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","list",false,true, true); parameters.push_back(plist);
+               CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(paccnos);
+               CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+               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);          }
@@ -54,25 +54,20 @@ string GetOtusCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
-string GetOtusCommand::getOutputFileNameTag(string type, string inputName=""){ 
-       try {
-        string outputFileName = "";
-               map<string, vector<string> >::iterator it;
+string GetOtusCommand::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 == "group")            {   outputFileName = "pick" + m->getExtension(inputName);  }
-            else if (type == "list")        {   outputFileName = "pick" + m->getExtension(inputName);  }
-            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, "GetOtusCommand", "getOutputFileNameTag");
-               exit(1);
-       }
+        if (type == "group")       {   pattern = "[filename],[tag],pick,[extension]";    }
+        else if (type == "list")        {   pattern = "[filename],[tag],pick,[extension]";    }
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "GetOtusCommand", "getOutputPattern");
+        exit(1);
+    }
 }
 //**********************************************************************************************************************
 GetOtusCommand::GetOtusCommand(){      
@@ -249,26 +244,33 @@ int GetOtusCommand::execute(){
 //**********************************************************************************************************************
 int GetOtusCommand::readListGroup(){
        try {
-               string thisOutputDir = outputDir;
+               InputData* input = new InputData(listfile, "list");
+               ListVector* list = input->getListVector();
+               string lastLabel = list->getLabel();
+               
+               //using first label seen if none is provided
+               if (label == "") { label = lastLabel; }
+        
+        string thisOutputDir = outputDir;
                if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
-               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + label + "." + getOutputFileNameTag("list", listfile);
+        map<string, string> variables;
+        variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
+        variables["[tag]"] = label;
+        variables["[extension]"] = m->getExtension(listfile);
+               string outputFileName = getOutputFileName("list", variables);
                
                ofstream out;
                m->openOutputFile(outputFileName, out);
-               
-               string GroupOutputDir = outputDir;
+        
+        string GroupOutputDir = outputDir;
                if (outputDir == "") {  GroupOutputDir += m->hasPath(groupfile);  }
-               string outputGroupFileName = GroupOutputDir + m->getRootName(m->getSimpleName(groupfile)) + label + "." + getOutputFileNameTag("group", groupfile);
+        variables["[filename]"] = GroupOutputDir + m->getRootName(m->getSimpleName(groupfile));
+        variables["[extension]"] = m->getExtension(groupfile);
+               string outputGroupFileName = getOutputFileName("group", variables);
                
                ofstream outGroup;
                m->openOutputFile(outputGroupFileName, outGroup);
-                       
-               InputData* input = new InputData(listfile, "list");
-               ListVector* list = input->getListVector();
-               string lastLabel = list->getLabel();
-               
-               //using first label seen if none is provided
-               if (label == "") { label = lastLabel; }
+
                
                //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
                set<string> labels; labels.insert(label);
@@ -365,6 +367,8 @@ int GetOtusCommand::processList(ListVector*& list, GroupMap*& groupMap, ofstream
                
                int numOtus = 0;
                //for each bin
+        vector<string> binLabels = list->getLabels();
+        vector<string> newBinLabels;
                for (int i = 0; i < list->getNumBins(); i++) {
                        if (m->control_pressed) { return 0; }
                        
@@ -398,7 +402,8 @@ int GetOtusCommand::processList(ListVector*& list, GroupMap*& groupMap, ofstream
                        
                        //if there are sequences from the groups we want in this bin add to new list, output to groupfile
                        if (keepBin) {  
-                               newList.push_back(binnames);    
+                               newList.push_back(binnames);
+                newBinLabels.push_back(binLabels[i]);
                                outGroup << groupFileOutput;
                                numOtus++;
                        }
@@ -407,7 +412,9 @@ int GetOtusCommand::processList(ListVector*& list, GroupMap*& groupMap, ofstream
                //print new listvector
                if (newList.getNumBins() != 0) {
                        wroteSomething = true;
-                       newList.print(out);
+                       newList.setLabels(newBinLabels);
+            newList.printHeaders(out);
+            newList.print(out);
                }
                
                m->mothurOut(newList.getLabel() + " - selected " + toString(numOtus) + " of the " + toString(list->getNumBins()) + " OTUs."); m->mothurOutEndLine();