broke up globaldata and moved error checking and help into commands

[mothur.git] / concensuscommand.cpp

diff --git a/concensuscommand.cpp b/concensuscommand.cpp
index 01df253a0dfbcbb18d37f9adb1cc241ad3ff78ce..09e0f324268332e0f691d42b00f003aab9f9c9c9 100644 (file)
--- a/concensuscommand.cpp
+++ b/concensuscommand.cpp
@@ -11,10 +11,21 @@
 
 //**********************************************************************************************************************
 
-ConcensusCommand::ConcensusCommand(){
+ConcensusCommand::ConcensusCommand(string option){
        try {
                globaldata = GlobalData::getInstance();
-               t = globaldata->gTree;
+               abort = false;
+               
+               //allow user to run help
+               if(option == "help") { help(); abort = true; }
+               
+               else {
+                       if (option != "") { cout << "There are no valid parameters for the concensus command." << endl; abort = true; }
+                       
+                       //no trees were read
+                       if (globaldata->gTree.size() == 0) {    cout << "You must execute the read.tree command, before you may use the concensus command." << endl; abort = true;  }
+                       else {  t = globaldata->gTree;  }
+               }
        }
        catch(exception& e) {
                cout << "Standard Error: " << e.what() << " has occurred in the ConcensusCommand class Function ConcensusCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -25,6 +36,30 @@ ConcensusCommand::ConcensusCommand(){
                exit(1);
        }       
 }
+
+//**********************************************************************************************************************
+
+void ConcensusCommand::help(){
+       try {
+               cout << "The concensus command can only be executed after a successful read.tree command." << "\n";
+               cout << "The concensus command has no parameters." << "\n";
+               cout << "The concensus command should be in the following format: concensus()." << "\n";
+               cout << "The concensus command output two files: .concensus.tre and .concensuspairs." << "\n";
+               cout << "The .concensus.tre file contains the concensus tree of the trees in your input file." << "\n";
+               cout << "The branch lengths are the percentage of trees in your input file that had the given pair." << "\n";
+               cout << "The .concensuspairs file contains a list of the internal nodes in your tree.  For each node, the pair that was used in the concensus tree " << "\n";
+               cout << "is reported with its percentage, as well as the other pairs that were seen for that node but not used and their percentages." << "\n" << "\n";         
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the ConcensusCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the ConcensusCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }       
+}
+
 //**********************************************************************************************************************
 
 ConcensusCommand::~ConcensusCommand(){}
@@ -34,7 +69,7 @@ ConcensusCommand::~ConcensusCommand(){}
 int ConcensusCommand::execute(){
        try {
                
-               if (t.size() == 0) { return 0; }
+               if (abort == true) { return 0; }
                else {  
                        numNodes = t[0]->getNumNodes();
                        numLeaves = t[0]->getNumLeaves();