added code to format fast files for uchime. started work on sff.multiple command

[mothur.git] / clusterfragmentscommand.cpp

diff --git a/clusterfragmentscommand.cpp b/clusterfragmentscommand.cpp
index ad1bd81b4a9d4554751cfbbc5eb836e107e7b53d..4a338419af8900f8b7ebd693225a7e9f4d193481 100644 (file)
--- a/clusterfragmentscommand.cpp
+++ b/clusterfragmentscommand.cpp
@@ -66,6 +66,28 @@ string ClusterFragmentsCommand::getHelpString(){
                exit(1);
        }
 }
+//**********************************************************************************************************************
+string ClusterFragmentsCommand::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 == "fasta") {  outputFileName =  "fragclust.fasta"; }
+            else if (type == "name") {  outputFileName =  "fragclust.names"; }
+            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, "ClusterFragmentsCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+
 //**********************************************************************************************************************
 ClusterFragmentsCommand::ClusterFragmentsCommand(){    
        try {
@@ -147,7 +169,7 @@ ClusterFragmentsCommand::ClusterFragmentsCommand(string option) {
                        // ...at some point should added some additional type checking...
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not found") { namefile =  "";  }
-                       else if (namefile == "not open") { abort = true; }      
+                       else if (namefile == "not open") { namefile = ""; abort = true; }       
                        else {  readNameFile(); m->setNameFile(namefile); }
                        
                        string temp;
@@ -157,6 +179,11 @@ ClusterFragmentsCommand::ClusterFragmentsCommand(string option) {
                        temp = validParameter.validFile(parameters, "percent", false);          if (temp == "not found"){       temp = "0";                             }
                        m->mothurConvert(temp, percent);
                        
+                       if (namefile == "") {
+                               vector<string> files; files.push_back(fastafile);
+                               parser.getNameFile(files);
+                       }
+                       
                }
                                
        }
@@ -225,8 +252,8 @@ int ClusterFragmentsCommand::execute(){
                
                string fileroot = outputDir + m->getRootName(m->getSimpleName(fastafile));
                
-               string newFastaFile = fileroot + "fragclust.fasta";
-               string newNamesFile = fileroot + "fragclust.names";
+               string newFastaFile = fileroot + getOutputFileNameTag("fasta");
+               string newNamesFile = fileroot + getOutputFileNameTag("name");
                
                if (m->control_pressed) { return 0; }