fixed valid parameters to include shared parameter for read.shared command.

[mothur.git] / readdistcommand.cpp

diff --git a/readdistcommand.cpp b/readdistcommand.cpp
index 4cf5c4e368067510ea7462dcd27eff9ac59d47ed..116e670a6e36f20df403cabf0610f7d60b4bbb5a 100644 (file)
--- a/readdistcommand.cpp
+++ b/readdistcommand.cpp
@@ -17,24 +17,31 @@ ReadDistCommand::ReadDistCommand(){
                format = globaldata->getFormat();       
                
                if (format == "column") { read = new ReadColumnMatrix(filename); }      
-               else if (format == "phylip") { read = new ReadPhylipMatrix(filename); } 
-                       
-               if(globaldata->getPrecision() != ""){
-                       convert(globaldata->getPrecision(), precision); 
+               else if (format == "phylip") { read = new ReadPhylipMatrix(filename); }
+               else if (format == "matrix") { 
+                               groupMap = new GroupMap(globaldata->getGroupFile());
+                               groupMap->readMap();
+                               globaldata->gGroupmap = groupMap;
                }
                
-               if(globaldata->getCutOff() != ""){
-                       convert(globaldata->getCutOff(), cutoff);       
-                       cutoff += (5 / (precision * 10.0));
-               }
-               read->setCutoff(cutoff);
+               if (format != "matrix" ) {
+                       if(globaldata->getPrecision() != ""){
+                               convert(globaldata->getPrecision(), precision); 
+                       }
+               
+                       if(globaldata->getCutOff() != ""){
+                               convert(globaldata->getCutOff(), cutoff);       
+                               cutoff += (5 / (precision * 10.0));
+                       }
+                       read->setCutoff(cutoff);
        
-               if(globaldata->getNameFile() != ""){    
-                       nameMap = new NameAssignment(globaldata->getNameFile());
-                       nameMap->readMap(1,2);
-               }
-               else{
-                       nameMap = NULL;
+                       if(globaldata->getNameFile() != ""){    
+                               nameMap = new NameAssignment(globaldata->getNameFile());
+                               nameMap->readMap(1,2);
+                       }
+                       else{
+                               nameMap = NULL;
+                       }
                }
                        
        }
@@ -57,9 +64,17 @@ ReadDistCommand::~ReadDistCommand(){
 //**********************************************************************************************************************
 int ReadDistCommand::execute(){
        try {
-               read->read(nameMap);
-               globaldata->setListVector(read->getListVector());
-               globaldata->setSparseMatrix(read->getMatrix());
+               
+               if (format == "matrix") {
+                       ifstream in;
+                       openInputFile(filename, in);
+                       matrix = new FullMatrix(in); //reads the matrix file
+                       globaldata->gMatrix = matrix; //save matrix for coverage commands
+               }else {
+                       read->read(nameMap);
+                       globaldata->setListVector(read->getListVector());
+                       globaldata->setSparseMatrix(read->getMatrix());
+               }
                return 0;
        }
        catch(exception& e) {