added sequence name to error string in fastq.info. Changed np_shannon to npshannon.

[mothur.git] / consensuscommand.cpp

diff --git a/consensuscommand.cpp b/consensuscommand.cpp
index a7469902d44cb9f16b4a109f8e0bc7a0182f7f86..e522b098f0703d6909f1906c3039fb4459e99854 100644 (file)
--- a/consensuscommand.cpp
+++ b/consensuscommand.cpp
@@ -10,43 +10,41 @@
 #include "consensuscommand.h"
 
 //**********************************************************************************************************************
-vector<string> ConcensusCommand::getValidParameters(){ 
+vector<string> ConcensusCommand::setParameters(){      
        try {
-               vector<string> myArray; 
+               vector<string> myArray;
+               for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
                return myArray;
        }
        catch(exception& e) {
-               m->errorOut(e, "ConcensusCommand", "getValidParameters");
+               m->errorOut(e, "ConcensusCommand", "setParameters");
                exit(1);
        }
 }
 //**********************************************************************************************************************
-vector<string> ConcensusCommand::getRequiredParameters(){      
+string ConcensusCommand::getHelpString(){      
        try {
-               vector<string> myArray; 
-               return myArray;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "ConcensusCommand", "getRequiredParameters");
-               exit(1);
-       }
-}
-//**********************************************************************************************************************
-vector<string> ConcensusCommand::getRequiredFiles(){   
-       try {
-               string AlignArray[] =  {"tree","group"};
-               vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
-               return myArray;
+               string helpString = "";
+               helpString += "The consensus command can only be executed after a successful read.tree command.\n";
+               helpString += "The consensus command has no parameters.\n";
+               helpString += "The consensus command should be in the following format: consensus().\n";
+               helpString += "The consensus command output two files: .consensus.tre and .consensuspairs.\n";
+               helpString += "The .consensus.tre file contains the consensus tree of the trees in your input file.\n";
+               helpString += "The branch lengths are the percentage of trees in your input file that had the given pair.\n";
+               helpString += "The .consensuspairs file contains a list of the internal nodes in your tree.  For each node, the pair that was used in the consensus tree \n";
+               helpString += "is reported with its percentage, as well as the other pairs that were seen for that node but not used and their percentages.\n";         
+               return helpString;
        }
        catch(exception& e) {
-               m->errorOut(e, "ConcensusCommand", "getRequiredFiles");
+               m->errorOut(e, "ConcensusCommand", "getHelpString");
                exit(1);
        }
 }
 //**********************************************************************************************************************
 ConcensusCommand::ConcensusCommand(){  
        try {
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
+               setParameters();
                vector<string> tempOutNames;
                outputTypes["tree"] = tempOutNames;
                outputTypes["nodepairs"] = tempOutNames;
@@ -60,8 +58,9 @@ ConcensusCommand::ConcensusCommand(){
 
 ConcensusCommand::ConcensusCommand(string fileroot)  {
        try {
-               globaldata = GlobalData::getInstance();
-               abort = false;
+               abort = false; calledHelp = false;   
+               
+               setParameters();
                
                //initialize outputTypes
                vector<string> tempOutNames;
@@ -69,8 +68,6 @@ ConcensusCommand::ConcensusCommand(string fileroot)  {
                outputTypes["nodepairs"] = tempOutNames;
                
                filename = fileroot;
-               
-               t = globaldata->gTree;
        
        }
        catch(exception& e) {
@@ -78,40 +75,20 @@ ConcensusCommand::ConcensusCommand(string fileroot)  {
                exit(1);
        }
 }
-
-//**********************************************************************************************************************
-
-void ConcensusCommand::help(){
-       try {
-               m->mothurOut("The consensus command can only be executed after a successful read.tree command.\n");
-               m->mothurOut("The consensus command has no parameters.\n");
-               m->mothurOut("The consensus command should be in the following format: consensus().\n");
-               m->mothurOut("The consensus command output two files: .consensus.tre and .consensuspairs.\n");
-               m->mothurOut("The .consensus.tre file contains the consensus tree of the trees in your input file.\n");
-               m->mothurOut("The branch lengths are the percentage of trees in your input file that had the given pair.\n");
-               m->mothurOut("The .consensuspairs file contains a list of the internal nodes in your tree.  For each node, the pair that was used in the consensus tree \n");
-               m->mothurOut("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) {
-               m->errorOut(e, "ConcensusCommand", "help");
-               exit(1);
-       }
-}
-
-//**********************************************************************************************************************
-
-ConcensusCommand::~ConcensusCommand(){}
-
 //**********************************************************************************************************************
 
 int ConcensusCommand::execute(){
        try {
                
-               if (abort == true) { return 0; }
-               else {  
-                       numNodes = t[0]->getNumNodes();
-                       numLeaves = t[0]->getNumLeaves();
-               }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
+               
+               
+               m->mothurOut("This command is not currently in use."); m->mothurOutEndLine();
+       /*      
+               t = globaldata->gTree;
+               numNodes = t[0]->getNumNodes();
+               numLeaves = t[0]->getNumLeaves();
+               
                
                //get the possible pairings
                getSets();      
@@ -205,12 +182,19 @@ int ConcensusCommand::execute(){
                outputFile = filename + ".cons.tre";  outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
                m->openOutputFile(outputFile, out);
                
-               consensusTree->printForBoot(out);
+               consensusTree->print(out, "boot");
                
                out.close(); out2.close();
                
                delete consensusTree; 
                
+               //set first tree file as new current treefile
+               string currentTree = "";
+               itTypes = outputTypes.find("tree");
+               if (itTypes != outputTypes.end()) {
+                       if ((itTypes->second).size() != 0) { currentTree = (itTypes->second)[0]; m->setTreeFile(currentTree); }
+               }
+               */
                return 0;
        }
        catch(exception& e) {