added set.dir command and modified commands to redirect input and output, removed...

[mothur.git] / getgroupcommand.cpp

diff --git a/getgroupcommand.cpp b/getgroupcommand.cpp
index 59987a33e6f169c589f608168a12d9e11747c2b7..c754f8eb1bb2ba79daf77c3a060a0ebf770252dd 100644 (file)
--- a/getgroupcommand.cpp
+++ b/getgroupcommand.cpp
@@ -3,27 +3,74 @@
  *  Mothur
  *
  *  Created by Thomas Ryabin on 2/2/09.
- *  Copyright 2009 __MyCompanyName__. All rights reserved.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  *
  */
 
 #include "getgroupcommand.h"
 
-
-GetgroupCommand::GetgroupCommand(){
+//**********************************************************************************************************************
+GetgroupCommand::GetgroupCommand(string option){
        try {
                globaldata = GlobalData::getInstance();
-               groupMap = globaldata->gGroupmap;
+               abort = false;
+               
+               //allow user to run help
+               if(option == "help") { help(); abort = true; }
+               
+               else {
+                       //valid paramters for this command
+                       string Array[] =  {"outputdir","inputdir"};
+                       vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+                       
+                       OptionParser parser(option);
+                       map<string,string> parameters = parser.getParameters();
+                       
+                       ValidParameters validParameter;
+                       //check to make sure all parameters are valid for command
+                       for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) { 
+                               if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
+                       }
+                       
+                       //if the user changes the output directory command factory will send this info to us in the output parameter 
+                       string outputDir = validParameter.validFile(parameters, "outputdir", false);            if (outputDir == "not found"){  outputDir = "";         }
+                       
+                       if ((globaldata->getSharedFile() == "")) { mothurOut("You must use the read.otu command to read a groupfile or a sharedfile before you can use the get.group command."); mothurOutEndLine(); abort = true; }
+                               
+                       if (abort == false) {
+                               //open shared file
+                               sharedfile = globaldata->getSharedFile();
+                               openInputFile(sharedfile, in);
+               
+                               //open output file
+                               if (outputDir == "") { outputDir += hasPath(sharedfile); }
+                               outputFile = outputDir + getRootName(getSimpleName(sharedfile)) + "bootGroups";
+                               openOutputFile(outputFile, out);
+
+                       }
+               }
        }
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the GetgroupCommand class Function GetgroupCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "GetgroupCommand", "GetgroupCommand");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the GetgroupCommand class function GetgroupCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+//**********************************************************************************************************************
+
+void GetgroupCommand::help(){
+       try {
+               mothurOut("The get.group command can only be executed after a successful read.otu command.\n");
+               //mothurOut("The get.group command outputs a .bootGroups file to you can use in addition to the tree file generated by the bootstrap.shared command to run the consensus command.\n");
+               mothurOut("You may not use any parameters with the get.group command.\n");
+               mothurOut("The get.group command should be in the following format: \n");
+               mothurOut("get.group()\n");
+               mothurOut("Example get.group().\n");
+               
+       }
+       catch(exception& e) {
+               errorOut(e, "GetgroupCommand", "help");
                exit(1);
-       }       
-                       
+       }
 }
 
 //**********************************************************************************************************************
@@ -35,20 +82,54 @@ GetgroupCommand::~GetgroupCommand(){
 
 int GetgroupCommand::execute(){
        try {
-               vector<string> groupNames = groupMap->namesOfGroups;    
-               for(int i = 0; i < groupNames.size(); i++)
-                       cout << groupNames[i] << "\n";
+       
+               if (abort == true) { return 0; }
+       
+               int num, inputData, count;
+               count = 0;  
+               string holdLabel, nextLabel, groupN, label;
+               
+               //read in first row since you know there is at least 1 group.
+               in >> label >> groupN >> num;
+               holdLabel = label;
+               
+               //output first group
+               mothurOut(groupN); mothurOutEndLine();
+               out << groupN << '\t' << groupN << endl;        
+                       
+               //get rest of line
+               for(int i=0;i<num;i++){
+                       in >> inputData;
+               }
+               
+               if (in.eof() != true) { in >> nextLabel; }
+               
+               //read the rest of the groups info in
+               while ((nextLabel == holdLabel) && (in.eof() != true)) {
+                       in >> groupN >> num;
+                       count++;
+                       
+                       //output next group
+                       mothurOut(groupN); mothurOutEndLine();
+                       out << groupN << '\t' << groupN << endl;                                
+                       
+                       //fill vector.  
+                       for(int i=0;i<num;i++){
+                               in >> inputData;
+                       }
+                       
+                       if (in.eof() != true) { in >> nextLabel; }
+               }
+               
+               in.close();
+               out.close();
                return 0;       
        }
 
        catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the GetgroupCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               errorOut(e, "GetgroupCommand", "execute");
                exit(1);
        }
-       catch(...) {
-               cout << "An unknown error has occurred in the GetgroupCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }       
 }