chimeracode

[mothur.git] / readdistcommand.cpp

diff --git a/readdistcommand.cpp b/readdistcommand.cpp
index f6b41951962b7ce6b85ae50a9958bc0408c13835..9cb2046139ba7d275aa31cb1e9024bf9a729cbf2 100644 (file)
--- a/readdistcommand.cpp
+++ b/readdistcommand.cpp
@@ -22,21 +22,63 @@ ReadDistCommand::ReadDistCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"phylip", "column", "name", "cutoff", "precision", "group"};
+                       string Array[] =  {"phylip", "column", "name", "cutoff", "precision", "group","outputdir","inputdir"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
                        map<string, string> parameters = parser.getParameters();
                        
                        ValidParameters validParameter;
+                       map<string,string>::iterator it;
                
                        //check to make sure all parameters are valid for command
-                       for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) { 
+                       for (it = parameters.begin(); it != parameters.end(); it++) { 
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
                        globaldata->newRead();
                        
+                       //if the user changes the input directory command factory will send this info to us in the output parameter 
+                       string inputDir = validParameter.validFile(parameters, "inputdir", false);              
+                       if (inputDir == "not found"){   inputDir = "";          }
+                       else {
+                               string path;
+                               it = parameters.find("phylip");
+                               //user has given a template file
+                               if(it != parameters.end()){ 
+                                       path = hasPath(it->second);
+                                       //if the user has not given a path then, add inputdir. else leave path alone.
+                                       if (path == "") {       parameters["phylip"] = inputDir + it->second;           }
+                               }
+                               
+                               it = parameters.find("column");
+                               //user has given a template file
+                               if(it != parameters.end()){ 
+                                       path = hasPath(it->second);
+                                       //if the user has not given a path then, add inputdir. else leave path alone.
+                                       if (path == "") {       parameters["column"] = inputDir + it->second;           }
+                               }
+                               
+                               it = parameters.find("name");
+                               //user has given a template file
+                               if(it != parameters.end()){ 
+                                       path = hasPath(it->second);
+                                       //if the user has not given a path then, add inputdir. else leave path alone.
+                                       if (path == "") {       parameters["name"] = inputDir + it->second;             }
+                               }
+                               
+                               it = parameters.find("group");
+                               //user has given a template file
+                               if(it != parameters.end()){ 
+                                       path = hasPath(it->second);
+                                       //if the user has not given a path then, add inputdir. else leave path alone.
+                                       if (path == "") {       parameters["group"] = inputDir + it->second;            }
+                               }
+                       }
+
+                       //if the user changes the output directory command factory will send this info to us in the output parameter 
+                       outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
+
                        //check for required parameters
                        phylipfile = validParameter.validFile(parameters, "phylip", true);
                        if (phylipfile == "not open") { abort = true; }
@@ -92,10 +134,12 @@ ReadDistCommand::ReadDistCommand(string option){
                                else if (format == "phylip") { read = new ReadPhylipMatrix(distFileName); }
                                else if (format == "matrix") { 
                                        groupMap = new GroupMap(groupfile);
-                                       groupMap->readMap();
-       
-                                       if (globaldata->gGroupmap != NULL) { delete globaldata->gGroupmap;  }
-                                       globaldata->gGroupmap = groupMap;
+                                       int error = groupMap->readMap();
+                                       if (error == 1) { delete groupMap; abort = true; }
+                                       else {
+                                               if (globaldata->gGroupmap != NULL) { delete globaldata->gGroupmap;  }
+                                               globaldata->gGroupmap = groupMap;
+                                       }
                                }
                
                                if (format != "matrix" ) {
@@ -164,6 +208,36 @@ int ReadDistCommand::execute(){
                        openInputFile(distFileName, in);
                        matrix = new FullMatrix(in); //reads the matrix file
                        in.close();
+                       
+                       //if files don't match...
+                       if (matrix->getNumSeqs() < groupMap->getNumSeqs()) {  
+                               mothurOut("Your distance file contains " + toString(matrix->getNumSeqs()) + " sequences, and your group file contains " + toString(groupMap->getNumSeqs()) + " sequences.");  mothurOutEndLine();                               
+                               //create new group file
+                               if(outputDir == "") { outputDir += hasPath(groupfile); }
+                               
+                               string newGroupFile = outputDir + getRootName(getSimpleName(groupfile)) + "editted.groups";
+                               ofstream outGroups;
+                               openOutputFile(newGroupFile, outGroups);
+                               
+                               for (int i = 0; i < matrix->getNumSeqs(); i++) {
+                                       Names temp = matrix->getRowInfo(i);
+                                       outGroups << temp.seqName << '\t' << temp.groupName << endl;
+                               }
+                               outGroups.close();
+                               
+                               mothurOut(newGroupFile + " is a new group file containing only the sequence that are in your distance file. I will read this file instead."); mothurOutEndLine();
+                               
+                               //read new groupfile
+                               delete groupMap; groupMap = NULL;
+                               groupfile = newGroupFile;
+                               globaldata->setGroupFile(groupfile); 
+                               
+                               groupMap = new GroupMap(groupfile);
+                               groupMap->readMap();
+                               
+                               globaldata->gGroupmap = groupMap;
+                       }
+                       
                        //memory leak prevention
                        if (globaldata->gMatrix != NULL) { delete globaldata->gMatrix;  }
                        globaldata->gMatrix = matrix; //save matrix for coverage commands
@@ -178,8 +252,9 @@ int ReadDistCommand::execute(){
                        if (globaldata->gSparseMatrix != NULL) { delete globaldata->gSparseMatrix;  }
                        globaldata->gSparseMatrix = read->getMatrix();
                        numDists = globaldata->gSparseMatrix->getNNodes();
+       //cout << "matrix contains " << numDists << " distances." << endl;
                        
-      int lines = cutoff / (1.0/precision);
+    /*  int lines = cutoff / (1.0/precision);
       vector<float> dist_cutoff(lines+1,0);
                        for (int i = 0; i <= lines;i++) {       
        dist_cutoff[i] = (i + 0.5) / precision; 
@@ -195,7 +270,7 @@ int ReadDistCommand::execute(){
           }
         }
                        }
-
+*/
      // string dist_string = "Dist:";
     //  string count_string = "Count: ";
                        //for (int i = 0; i <= lines;i++) {