X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=setcurrentcommand.cpp;h=9d59696ba2f47157dd059c066af108d6bb76e731;hp=9d277f3e71ae3635d5f14cf468822fa3e1181e8c;hb=a54ba6143022dc7294f4fdc468fc10b627c64b0e;hpb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e

diff --git a/setcurrentcommand.cpp b/setcurrentcommand.cpp
index 9d277f3..9d59696 100644
--- a/setcurrentcommand.cpp
+++ b/setcurrentcommand.cpp
@@ -18,6 +18,7 @@ vector<string> SetCurrentCommand::setParameters(){
         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 psummary("summary", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(psummary);
 		CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pfasta);
 		CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pname);
 		CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pgroup);
@@ -54,7 +55,7 @@ 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, biom, count and 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, count, summary 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";
@@ -290,6 +291,14 @@ SetCurrentCommand::SetCurrentCommand(string option)  {
 					//if the user has not given a path then, add inputdir. else leave path alone.
 					if (path == "") {	parameters["biom"] = inputDir + it->second;		}
 				}
+                
+                it = parameters.find("summary");
+				//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["summary"] = inputDir + it->second;		}
+				}
 			}
 			
 			//check for parameters
@@ -402,6 +411,12 @@ SetCurrentCommand::SetCurrentCommand(string option)  {
 			if (biomfile == "not open") { m->mothurOut("Ignoring: " + parameters["biom"]); m->mothurOutEndLine(); biomfile = ""; }
 			else if (biomfile == "not found") {  biomfile = "";  }	
 			if (biomfile != "") { m->setBiomFile(biomfile); }
+            
+            summaryfile = validParameter.validFile(parameters, "summary", true);
+			if (summaryfile == "not open") { m->mothurOut("Ignoring: " + parameters["summary"]); m->mothurOutEndLine(); summaryfile = ""; }
+			else if (summaryfile == "not found") {  summaryfile = "";  }
+			if (summaryfile != "") { m->setSummaryFile(summaryfile); }
+
 			
 			processors = validParameter.validFile(parameters, "processors", false);
 			if (processors == "not found") {  processors = "1";  }	
@@ -476,6 +491,8 @@ int SetCurrentCommand::execute(){
 					m->setBiomFile("");
                 }else if (types[i] == "count") {
 					m->setCountTableFile("");
+                }else if (types[i] == "summary") {
+					m->setSummaryFile("");
 				}else if (types[i] == "processors") {
 					m->setProcessors("1");
 				}else if (types[i] == "all") {