paralellized the indicator command

[mothur.git] / corraxescommand.cpp

diff --git a/corraxescommand.cpp b/corraxescommand.cpp
index ae91a24c108c16196fb67b508c62011c8cff1b63..20bdcbd11cb63408c5ab3fc55af1e07122b0f9ba 100644 (file)
--- a/corraxescommand.cpp
+++ b/corraxescommand.cpp
@@ -74,6 +74,7 @@ CorrAxesCommand::CorrAxesCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();
@@ -139,12 +140,12 @@ CorrAxesCommand::CorrAxesCommand(string option)  {
                        sharedfile = validParameter.validFile(parameters, "shared", true);
                        if (sharedfile == "not open") { abort = true; }
                        else if (sharedfile == "not found") { sharedfile = ""; }
-                       else { inputFileName = sharedfile; }
+                       else { inputFileName = sharedfile; m->setSharedFile(sharedfile); }
                        
                        relabundfile = validParameter.validFile(parameters, "relabund", true);
                        if (relabundfile == "not open") { abort = true; }
                        else if (relabundfile == "not found") { relabundfile = ""; }
-                       else { inputFileName = relabundfile; }
+                       else { inputFileName = relabundfile; m->setRelAbundFile(relabundfile); }
                        
                        metadatafile = validParameter.validFile(parameters, "metadata", true);
                        if (metadatafile == "not open") { abort = true; }
@@ -862,14 +863,14 @@ int CorrAxesCommand::getMetadata(){
                //read the first label, because it refers to the groups
                string columnLabel;
                iss >> columnLabel; m->gobble(iss); 
-
+               
                //save names of columns you are reading
                while (!iss.eof()) {
                        iss >> columnLabel; m->gobble(iss);
                        metadataLabels.push_back(columnLabel);
                }
                int count = metadataLabels.size();
-               
+                       
                //read rest of file
                while (!in.eof()) {
                        
@@ -878,7 +879,7 @@ int CorrAxesCommand::getMetadata(){
                        string group = "";
                        in >> group; m->gobble(in);
                        groupNames.push_back(group);
-                       
+                               
                        SharedRAbundFloatVector* tempLookup = new SharedRAbundFloatVector();
                        tempLookup->setGroup(group);
                        tempLookup->setLabel("1");
@@ -886,7 +887,6 @@ int CorrAxesCommand::getMetadata(){
                        for (int i = 0; i < count; i++) {
                                float temp = 0.0;
                                in >> temp; 
-                               
                                tempLookup->push_back(temp, group);
                        }