added check to make sure shhh.flows child processes finish properly. added subsamplin...

[mothur.git] / consensusseqscommand.cpp

diff --git a/consensusseqscommand.cpp b/consensusseqscommand.cpp
index 323dd45a5690cd047742b16b9bdb9f9c08972a5a..223e5dbb86600907fafaafdf5af48ee665adfc5b 100644 (file)
--- a/consensusseqscommand.cpp
+++ b/consensusseqscommand.cpp
@@ -139,15 +139,17 @@ ConsensusSeqsCommand::ConsensusSeqsCommand(string option)  {
                                fastafile = m->getFastaFile(); 
                                if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }       
+                       }else { m->setFastaFile(fastafile); }   
                        
                        namefile = validParameter.validFile(parameters, "name", true);
-                       if (namefile == "not open") { abort = true; }
-                       else if (namefile == "not found") { namefile = ""; }    
+                       if (namefile == "not open") { namefile = ""; abort = true; }
+                       else if (namefile == "not found") { namefile = ""; }
+                       else { m->setNameFile(namefile); }
                        
                        listfile = validParameter.validFile(parameters, "list", true);
                        if (listfile == "not open") { abort = true; }
                        else if (listfile == "not found") { listfile = "";  }   
+                       else { m->setListFile(listfile); }
                        
                        label = validParameter.validFile(parameters, "label", false);                   
                        if (label == "not found") { label = ""; }
@@ -157,11 +159,15 @@ ConsensusSeqsCommand::ConsensusSeqsCommand(string option)  {
                        }
                        
                        string temp = validParameter.validFile(parameters, "cutoff", false);  if (temp == "not found") { temp = "100"; }
-                       convert(temp, cutoff); 
+                       m->mothurConvert(temp, cutoff); 
                        
                        //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 = m->hasPath(fastafile);      }
-
+                       
+                       if (namefile == ""){
+                               vector<string> files; files.push_back(fastafile); 
+                               parser.getNameFile(files);
+                       }
                }
        }
        catch(exception& e) {
@@ -204,7 +210,7 @@ int ConsensusSeqsCommand::execute(){
                        int seqLength = 0;
                        for (map<string, string>::iterator it = nameMap.begin(); it != nameMap.end(); it++) {
                                
-                               if (m->control_pressed) { outSummary.close(); outFasta.close(); for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } return 0; }
+                               if (m->control_pressed) { outSummary.close(); outFasta.close(); for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } return 0; }
                                
                                string seq = fastaMap[it->second];
                                seqs.push_back(seq);
@@ -221,7 +227,7 @@ int ConsensusSeqsCommand::execute(){
                        //get counts
                        for (int j = 0; j < seqLength; j++) {
                                
-                               if (m->control_pressed) { outSummary.close(); outFasta.close(); for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } return 0; }
+                               if (m->control_pressed) { outSummary.close(); outFasta.close(); for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } return 0; }
                                
                                vector<int> counts; counts.resize(5, 0); //A,T,G,C,Gap
                                int numDots = 0;
@@ -274,7 +280,7 @@ int ConsensusSeqsCommand::execute(){
                        //as long as you are not at the end of the file or done wih the lines you want
                        while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                                
-                               if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str()); } delete list; delete input;  return 0;  }
+                               if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]); } delete list; delete input;  return 0;  }
                                
                                if(allLines == 1 || labels.count(list->getLabel()) == 1){                       
                                        
@@ -312,7 +318,7 @@ int ConsensusSeqsCommand::execute(){
                        }
                        
                        
-                       if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str()); } if (list != NULL) { delete list; } delete input; return 0;  }
+                       if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]); } if (list != NULL) { delete list; } delete input; return 0;  }
                        
                        //output error messages about any remaining user labels
                        set<string>::iterator it;
@@ -536,7 +542,6 @@ char ConsensusSeqsCommand::getBase(vector<int> counts, int size){  //A,T,G,C,Gap
                        if (counts[i] < zeroCutoff) { counts[i] = 0; }
                }
                
-               
                //any
                if ((counts[0] != 0) && (counts[1] != 0) && (counts[2] != 0) && (counts[3] != 0) && (counts[4] != 0)) {  conBase = 'n'; }
                //any no gap
@@ -600,7 +605,7 @@ char ConsensusSeqsCommand::getBase(vector<int> counts, int size){  //A,T,G,C,Gap
                //only gap
                else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] != 0)) {  conBase = '-'; }
                //cutoff removed all counts
-               else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] == 0)) {  m->mothurOut("cutoff ...."); m->mothurOutEndLine(); }
+               else if ((counts[0] == 0) && (counts[1] == 0) && (counts[2] == 0) && (counts[3] == 0) && (counts[4] == 0)) {  conBase = 'N'; }
                else{ m->mothurOut("[ERROR]: cannot find consensus base."); m->mothurOutEndLine(); }
                
                return conBase;