fixed bug in phylo.diversity rooting. added filename patterns and create filename...

[mothur.git] / removeotulabelscommand.cpp

diff --git a/removeotulabelscommand.cpp b/removeotulabelscommand.cpp
index a05e08154b10c6c0123a5f3f93847db520ee7959..5359db8de28e3bfb6a0aa1611e6407e830ddd68b 100644 (file)
--- a/removeotulabelscommand.cpp
+++ b/removeotulabelscommand.cpp
@@ -11,12 +11,12 @@
 //**********************************************************************************************************************
 vector<string> RemoveOtuLabelsCommand::setParameters(){        
        try {
-        CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(paccnos);
-        CommandParameter pconstaxonomy("constaxonomy", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pconstaxonomy);
-               CommandParameter potucorr("otucorr", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(potucorr);
-        CommandParameter pcorraxes("corraxes", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pcorraxes);
-        CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+        CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(paccnos);
+        CommandParameter pconstaxonomy("constaxonomy", "InputTypes", "", "", "none", "FNGLT", "none","constaxonomy",false,false); parameters.push_back(pconstaxonomy);
+               CommandParameter potucorr("otucorr", "InputTypes", "", "", "none", "FNGLT", "none","otucorr",false,false); parameters.push_back(potucorr);
+        CommandParameter pcorraxes("corraxes", "InputTypes", "", "", "none", "FNGLT", "none","corraxes",false,false); parameters.push_back(pcorraxes);
+        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);          }
@@ -46,26 +46,21 @@ string RemoveOtuLabelsCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
-string RemoveOtuLabelsCommand::getOutputFileNameTag(string type, string inputName=""){ 
-       try {
-        string outputFileName = "";
-               map<string, vector<string> >::iterator it;
+string RemoveOtuLabelsCommand::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 == "constaxonomy") {  outputFileName =  "pick.taxonomy"; }
-            else if (type == "otucorr") {  outputFileName =  "pick.corr"; }
-            else if (type == "corraxes") {  outputFileName =  "pick.axes"; }
-            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, "RemoveOtuLabelsCommand", "getOutputFileNameTag");
-               exit(1);
-       }
+        if (type == "constaxonomy")            {   pattern = "[filename],pick,[extension]";    }
+        else if (type == "otucorr")    {   pattern = "[filename],pick,[extension]";    }
+        else if (type == "corraxes")        {   pattern = "[filename],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, "RemoveOtuLabelsCommand", "getOutputPattern");
+        exit(1);
+    }
 }
 //**********************************************************************************************************************
 RemoveOtuLabelsCommand::RemoveOtuLabelsCommand(){      
@@ -73,7 +68,7 @@ RemoveOtuLabelsCommand::RemoveOtuLabelsCommand(){
                abort = true; calledHelp = true;
                setParameters();
         vector<string> tempOutNames;
-               outputTypes["contaxonomy"] = tempOutNames; 
+               outputTypes["constaxonomy"] = tempOutNames; 
         outputTypes["otucorr"] = tempOutNames;
         outputTypes["corraxes"] = tempOutNames;
        }
@@ -226,7 +221,10 @@ int RemoveOtuLabelsCommand::readClassifyOtu(){
        try {
                string thisOutputDir = outputDir;
                if (outputDir == "") {  thisOutputDir += m->hasPath(constaxonomyfile);  }
-               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(constaxonomyfile)) + getOutputFileNameTag("constaxonomy");
+               map<string, string> variables; 
+        variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(constaxonomyfile));
+        variables["[extension]"] = m->getExtension(constaxonomyfile);
+               string outputFileName = getOutputFileName("constaxonomy", variables);
                ofstream out;
                m->openOutputFile(outputFileName, out);
                
@@ -275,7 +273,10 @@ int RemoveOtuLabelsCommand::readOtuAssociation(){
        try {
                string thisOutputDir = outputDir;
                if (outputDir == "") {  thisOutputDir += m->hasPath(otucorrfile);  }
-               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(otucorrfile)) + getOutputFileNameTag("otucorr");
+        map<string, string> variables; 
+        variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(otucorrfile));
+        variables["[extension]"] = m->getExtension(otucorrfile);
+               string outputFileName = getOutputFileName("otucorr", variables);
                ofstream out;
                m->openOutputFile(outputFileName, out);
                
@@ -325,7 +326,10 @@ int RemoveOtuLabelsCommand::readCorrAxes(){
        try {
                string thisOutputDir = outputDir;
                if (outputDir == "") {  thisOutputDir += m->hasPath(corraxesfile);  }
-               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(corraxesfile)) + getOutputFileNameTag("corraxes");
+        map<string, string> variables; 
+        variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(corraxesfile));
+        variables["[extension]"] = m->getExtension(corraxesfile);
+               string outputFileName = getOutputFileName("corraxes", variables);
                ofstream out;
                m->openOutputFile(outputFileName, out);