added uchime_src folder. added biom parameter to make.shared. added biom as a current...

[mothur.git] / setcurrentcommand.cpp

diff --git a/setcurrentcommand.cpp b/setcurrentcommand.cpp
index 5582abd03d6220da752943278cad50f4bceb1a76..96735405c5e148159ab762a720a93f88ec2354ee 100644 (file)
--- a/setcurrentcommand.cpp
+++ b/setcurrentcommand.cpp
@@ -15,6 +15,7 @@ vector<string> SetCurrentCommand::setParameters(){
                
                CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
                CommandParameter pflow("flow", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pflow);
+        CommandParameter pbiom("biom", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pbiom);
                CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pphylip);
                CommandParameter pcolumn("column", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pcolumn);
                CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pfasta);
@@ -52,7 +53,7 @@ string SetCurrentCommand::getHelpString(){
        try {
                string helpString = "";
                helpString += "The set.current command allows you to set the current files saved by mothur.\n";
-               helpString += "The set.current command parameters are: clear, phylip, column, list, rabund, sabund, name, group, design, order, tree, shared, ordergroup, relabund, fasta, qfile, sff, oligos, accnos, taxonomy.\n";
+               helpString += "The set.current command parameters are: clear, phylip, column, list, rabund, sabund, name, group, design, order, tree, shared, ordergroup, relabund, fasta, qfile, sff, oligos, accnos, biom and taxonomy.\n";
                helpString += "The clear paramter is used to indicate which file types you would like to clear values for, multiple types can be separated by dashes.\n";
                helpString += "The set.current command should be in the following format: \n";
                helpString += "set.current(fasta=yourFastaFile) or set.current(fasta=amazon.fasta, clear=name-accnos)\n";
@@ -272,6 +273,14 @@ SetCurrentCommand::SetCurrentCommand(string option)  {
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["flow"] = inputDir + it->second;             }
                                }
+                
+                it = parameters.find("biom");
+                               //user has given a template file
+                               if(it != parameters.end()){ 
+                                       path = m->hasPath(it->second);
+                                       //if the user has not given a path then, add inputdir. else leave path alone.
+                                       if (path == "") {       parameters["biom"] = inputDir + it->second;             }
+                               }
                        }
                        
                        //check for parameters
@@ -374,6 +383,11 @@ SetCurrentCommand::SetCurrentCommand(string option)  {
                        if (flowfile == "not open") { m->mothurOut("Ignoring: " + parameters["flow"]); m->mothurOutEndLine(); flowfile = ""; }
                        else if (flowfile == "not found") {  flowfile = "";  }  
                        if (flowfile != "") { m->setFlowFile(flowfile); }
+            
+            biomfile = validParameter.validFile(parameters, "biom", true);
+                       if (biomfile == "not open") { m->mothurOut("Ignoring: " + parameters["biom"]); m->mothurOutEndLine(); biomfile = ""; }
+                       else if (biomfile == "not found") {  biomfile = "";  }  
+                       if (biomfile != "") { m->setBiomFile(biomfile); }
                        
                        processors = validParameter.validFile(parameters, "processors", false);
                        if (processors == "not found") {  processors = "1";  }  
@@ -444,6 +458,8 @@ int SetCurrentCommand::execute(){
                                        m->setTaxonomyFile("");
                                }else if (types[i] == "flow") {
                                        m->setFlowFile("");
+                }else if (types[i] == "biom") {
+                                       m->setBiomFile("");
                                }else if (types[i] == "processors") {
                                        m->setProcessors("1");
                                }else if (types[i] == "all") {