added pca command

[mothur.git] / getoturepcommand.cpp

diff --git a/getoturepcommand.cpp b/getoturepcommand.cpp
index ed26cbecb3f0b4aa67da540ba26ddfaf500602ce..41cc6b5eefca511b4137ecf635a841ca24159f1a 100644 (file)
--- a/getoturepcommand.cpp
+++ b/getoturepcommand.cpp
@@ -42,7 +42,7 @@ GetOTURepCommand::GetOTURepCommand(string option){
                        help(); abort = true;
                } else {
                        //valid paramters for this command
-                       string Array[] =  {"fasta","list","label","name", "group", "sorted"};
+                       string Array[] =  {"fasta","list","label","name", "group", "sorted", "phylip","column"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -69,6 +69,19 @@ GetOTURepCommand::GetOTURepCommand(string option){
                        listfile = validParameter.validFile(parameters, "list", true);
                        if (listfile == "not found") { mothurOut("list is a required parameter for the get.oturep command."); mothurOutEndLine(); abort = true; }
                        else if (listfile == "not open") { abort = true; }      
+                       
+                       phylipfile = validParameter.validFile(parameters, "phylip", true);
+                       if (phylipfile == "not found") { phylipfile = "";  }
+                       else if (phylipfile == "not open") { abort = true; }    
+                       
+                       columnfile = validParameter.validFile(parameters, "column", true);
+                       if (columnfile == "not found") { columnfile = ""; }
+                       else if (columnfile == "not open") { abort = true; }    
+                       
+                       if ((phylipfile == "") && (columnfile == "")) { mothurOut("When executing a get.oturep command you must enter a phylip or a column."); mothurOutEndLine(); abort = true; }
+                       else if ((phylipfile != "") && (columnfile != "")) { mothurOut("When executing a get.oturep command you must enter ONLY ONE of the following: phylip or column."); mothurOutEndLine(); abort = true; }
+               
+                       if (columnfile != "") {  if (namefile == "") {  cout << "You need to provide a namefile if you are going to use the column format." << endl; abort = true; }  }
 
                        //check for optional parameter and set defaults
                        // ...at some point should added some additional type checking...
@@ -110,10 +123,6 @@ GetOTURepCommand::GetOTURepCommand(string option){
                        }
                        
                        if (abort == false) {
-                       
-                               if(globaldata->gSparseMatrix != NULL)   {
-                                       matrix = globaldata->gSparseMatrix;
-                               }
 
                                //globaldata->gListVector bin 0 = first name read in distance matrix, globaldata->gListVector bin 1 = second name read in distance matrix
                                if (globaldata->gListVector != NULL) {
@@ -132,15 +141,6 @@ GetOTURepCommand::GetOTURepCommand(string option){
                                        }
                                } else { mothurOut("error, no listvector."); mothurOutEndLine(); }
 
-                               // Create a data structure to quickly access the distance information.
-                               // It consists of a vector of distance maps, where each map contains
-                               // all distances of a certain sequence. Vector and maps are accessed
-                               // via the index of a sequence in the distance matrix
-                               seqVec = vector<SeqMap>(globaldata->gListVector->size()); 
-                               for (MatData currentCell = matrix->begin(); currentCell != matrix->end(); currentCell++) {
-                                       seqVec[currentCell->row][currentCell->column] = currentCell->dist;
-                               }
-
                                fasta = new FastaMap();
                        }
                }
@@ -191,22 +191,21 @@ int GetOTURepCommand::execute(){
        try {
        
                if (abort == true) { return 0; }
-
                int error;
                
                //read fastafile
                fasta->readFastaFile(fastafile);
                
-               in.close();
-               
-               //set format to list so input can get listvector
-               globaldata->setFormat("list");
+               //in.close();
+               //read distance file and generate indexed distance file that can be used by findrep function
+//....new reading class....//
                
                //if user gave a namesfile then use it
-               if (namesfile != "") {
-                       readNamesFile();
-               }
+               if (namesfile != "") {  readNamesFile();        }
                
+               //set format to list so input can get listvector
+               globaldata->setFormat("list");
+
                //read list file
                read = new ReadOTUFile(listfile);
                read->read(&*globaldata); 
@@ -274,8 +273,6 @@ int GetOTURepCommand::execute(){
                        if (error == 1) { return 0; } //there is an error in hte input files, abort command
                }
                
-               delete matrix;
-               globaldata->gSparseMatrix = NULL;
                delete list;
                globaldata->gListVector = NULL;
 
@@ -371,7 +368,7 @@ string GetOTURepCommand::findRep(int bin, string& group, ListVector* thisList, i
                        SeqMap::iterator it;
                        SeqMap currMap;
                        for (size_t i=0; i < seqIndex.size(); i++) {
-                               currMap = seqVec[seqIndex[i]];
+       //currMap = seqVec[seqIndex[i]];
                                for (size_t j=0; j < seqIndex.size(); j++) {
                                        it = currMap.find(seqIndex[j]);         
                                        if (it != currMap.end()) {