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

[mothur.git] / getsharedotucommand.cpp

diff --git a/getsharedotucommand.cpp b/getsharedotucommand.cpp
index 1b69a25d4af7e638dbf48a64baec2390f37dcfec..5ae8da588ba4a6d36b6658527d8cd12e208c50c4 100644 (file)
--- a/getsharedotucommand.cpp
+++ b/getsharedotucommand.cpp
@@ -13,15 +13,15 @@
 //**********************************************************************************************************************
 vector<string> GetSharedOTUCommand::setParameters(){   
        try {
-               CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pfasta);
-               CommandParameter pgroup("group", "InputTypes", "", "", "none", "FNGLT", "none",false,true); parameters.push_back(pgroup);
-               CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none",false,true); parameters.push_back(plist);
-               CommandParameter poutput("output", "Multiple", "accnos-default", "default", "", "", "",false,false); parameters.push_back(poutput);
-               CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
-               CommandParameter punique("unique", "String", "", "", "", "", "",false,false); parameters.push_back(punique);
-               CommandParameter pshared("shared", "String", "", "", "", "", "",false,false); parameters.push_back(pshared);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none","fasta",false,false); parameters.push_back(pfasta);
+               CommandParameter pgroup("group", "InputTypes", "", "", "none", "FNGLT", "none","sharedseq",false,true,true); parameters.push_back(pgroup);
+               CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none","sharedseq",false,true,true); parameters.push_back(plist);
+               CommandParameter poutput("output", "Multiple", "accnos-default", "default", "", "", "","",false,false); parameters.push_back(poutput);
+               CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+               CommandParameter punique("unique", "String", "", "", "", "", "","",false,false,true); parameters.push_back(punique);
+               CommandParameter pshared("shared", "String", "", "", "", "", "","",false,false,true); parameters.push_back(pshared);
+               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);          }
@@ -59,28 +59,22 @@ string GetSharedOTUCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
-string GetSharedOTUCommand::getOutputFileNameTag(string type, string inputName=""){    
-       try {
-        string outputFileName = "";
-               map<string, vector<string> >::iterator it;
+string GetSharedOTUCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+
+        if (type == "fasta")            {   pattern =  "[filename],[distance],[group],shared.fasta";   }
+        else if (type == "accnos")      {   pattern =  "[filename],[distance],[group],accnos";         }
+        else if (type == "sharedseqs")  {   pattern =  "[filename],[distance],[group],shared.seqs";    }
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
         
-        //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 == "fasta")            {   outputFileName =  "shared.fasta";   }
-            else if (type == "accnos")      {   outputFileName =  "accnos";         }
-            else if (type == "sharedseqs")  {   outputFileName =  "shared.seqs";    }
-            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, "GetSharedOTUCommand", "getOutputFileNameTag");
-               exit(1);
-       }
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "GetSharedOTUCommand", "getOutputPattern");
+        exit(1);
+    }
 }
-
 //**********************************************************************************************************************
 GetSharedOTUCommand::GetSharedOTUCommand(){    
        try {
@@ -394,11 +388,13 @@ int GetSharedOTUCommand::process(ListVector* shared) {
                string outputFileNames;
                
                if (outputDir == "") { outputDir += m->hasPath(listfile); }
-               if (output != "accnos") {
-                       outputFileNames = outputDir + m->getRootName(m->getSimpleName(listfile)) + shared->getLabel() + userGroups + "." + getOutputFileNameTag("sharedseqs");
-               }else {
-                       outputFileNames = outputDir + m->getRootName(m->getSimpleName(listfile)) + shared->getLabel() + userGroups + "." + getOutputFileNameTag("accnos");
-               }
+        map<string, string> variables;
+        variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile));
+        variables["[distance]"] = shared->getLabel();
+        variables["[group]"] = userGroups;
+               if (output != "accnos") { outputFileNames = getOutputFileName("sharedseqs", variables); }
+               else { outputFileNames = getOutputFileName("accnos", variables); }
+        
                m->openOutputFile(outputFileNames, outNames);
                
                bool wroteSomething = false;
@@ -491,7 +487,8 @@ int GetSharedOTUCommand::process(ListVector* shared) {
                //if fasta file provided output new fasta file
                if ((fastafile != "") && wroteSomething) {
                        if (outputDir == "") { outputDir += m->hasPath(fastafile); }
-                       string outputFileFasta = outputDir + m->getRootName(m->getSimpleName(fastafile)) + shared->getLabel() + userGroups + "." + getOutputFileNameTag("fasta");
+            variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile));
+                       string outputFileFasta = getOutputFileName("fasta", variables);
                        ofstream outFasta;
                        m->openOutputFile(outputFileFasta, outFasta);
                        outputNames.push_back(outputFileFasta); outputTypes["fasta"].push_back(outputFileFasta);