finishing the container classes, combining read.otu and read.list commands. some...

[mothur.git] / readotucommand.cpp

diff --git a/readotucommand.cpp b/readotucommand.cpp
index 130ecd0f08a540239e0cbbbf1862611528e1d8a8..c7e83e4db2e5a3048fcf9144db13c8044eada09c 100644 (file)
--- a/readotucommand.cpp
+++ b/readotucommand.cpp
@@ -15,6 +15,10 @@ ReadOtuCommand::ReadOtuCommand(){
                globaldata = GlobalData::getInstance();
                filename = globaldata->inputFileName;
                read = new ReadPhilFile(filename);
+               if (globaldata->getFormat() == "shared") {
+                       //read in group map info.
+                       groupMap = new GroupMap(globaldata->getGroupFile());
+               }
        }
        catch(exception& e) {
                cout << "Standard Error: " << e.what() << " has occurred in the ReadOtuCommand class Function ReadOtuCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -37,6 +41,15 @@ ReadOtuCommand::~ReadOtuCommand(){
 int ReadOtuCommand::execute(){
        try {
                read->read(&*globaldata); 
+               if (globaldata->getFormat() == "shared") {
+                       groupMap->readMap();
+                       globaldata->gGroupmap = groupMap;
+               
+                       shared = new SharedCommand();
+                       shared->execute();
+                       parselist = new ParseListCommand();
+                       parselist->execute();
+               }
                return 0;
        }
        catch(exception& e) {