fixed bug with dist.shared subsampling. added mode parameter to dist.shared so...

[mothur.git] / listseqscommand.cpp

diff --git a/listseqscommand.cpp b/listseqscommand.cpp
index d60470cdebcc70114afcb79cc08edbb333816292..afbacc00aaaec2b92c5d81278d16b463c0f43ffe 100644 (file)
--- a/listseqscommand.cpp
+++ b/listseqscommand.cpp
@@ -71,7 +71,7 @@ ListSeqsCommand::ListSeqsCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
-               
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                else {
                        vector<string> myArray = setParameters();
                        
@@ -150,15 +150,18 @@ ListSeqsCommand::ListSeqsCommand(string option)  {
                        //check for required parameters
                        fastafile = validParameter.validFile(parameters, "fasta", true);
                        if (fastafile == "not open") { abort = true; }
-                       else if (fastafile == "not found") {  fastafile = "";  }        
+                       else if (fastafile == "not found") {  fastafile = "";  }
+                       else { m->setFastaFile(fastafile); }
                        
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { abort = true; }
                        else if (namefile == "not found") {  namefile = "";  }  
+                       else { m->setNameFile(namefile); }
                        
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { abort = true; }
                        else if (groupfile == "not found") {  groupfile = "";  }        
+                       else { m->setGroupFile(groupfile); }
                        
                        alignfile = validParameter.validFile(parameters, "alignreport", true);
                        if (alignfile == "not open") { abort = true; }
@@ -167,10 +170,12 @@ ListSeqsCommand::ListSeqsCommand(string option)  {
                        listfile = validParameter.validFile(parameters, "list", true);
                        if (listfile == "not open") { abort = true; }
                        else if (listfile == "not found") {  listfile = "";  }
-
+                       else { m->setListFile(listfile); }
+                       
                        taxfile = validParameter.validFile(parameters, "taxonomy", true);
                        if (taxfile == "not open") { abort = true; }
                        else if (taxfile == "not found") {  taxfile = "";  }
+                       else { m->setTaxonomyFile(taxfile); }
                        
                        if ((fastafile == "") && (namefile == "") && (listfile == "") && (groupfile == "") && (alignfile == "") && (taxfile == ""))  { m->mothurOut("You must provide a file."); m->mothurOutEndLine(); abort = true; }
                        
@@ -218,13 +223,13 @@ int ListSeqsCommand::execute(){
                //output to .accnos file
                for (int i = 0; i < names.size(); i++) {
                        
-                       if (m->control_pressed) { outputTypes.clear(); out.close(); remove(outputFileName.c_str()); return 0; }
+                       if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(outputFileName); return 0; }
                        
                        out << names[i] << endl;
                }
                out.close();
                
-               if (m->control_pressed) { outputTypes.clear();  remove(outputFileName.c_str()); return 0; }
+               if (m->control_pressed) { outputTypes.clear();  m->mothurRemove(outputFileName); return 0; }
                
                m->setAccnosFile(outputFileName);
                
@@ -308,13 +313,7 @@ int ListSeqsCommand::readList(){
                                
                                if (m->control_pressed) { in.close(); return 0; }
                                
-                               while (binnames.find_first_of(',') != -1) { 
-                                       string name = binnames.substr(0,binnames.find_first_of(','));
-                                       binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
-                                       names.push_back(name);
-                               }
-                       
-                               names.push_back(binnames);
+                               m->splitAtComma(binnames, names);
                        }
                }
                in.close();     
@@ -344,14 +343,7 @@ int ListSeqsCommand::readName(){
                        in >> secondCol;                        
                        
                        //parse second column saving each name
-                       while (secondCol.find_first_of(',') != -1) { 
-                               name = secondCol.substr(0,secondCol.find_first_of(','));
-                               secondCol = secondCol.substr(secondCol.find_first_of(',')+1, secondCol.length());
-                               names.push_back(name);
-                       }
-                       
-                       //get name after last ,
-                       names.push_back(secondCol);
+                       m->splitAtComma(secondCol, names);
                        
                        m->gobble(in);
                }
@@ -408,14 +400,14 @@ int ListSeqsCommand::readAlign(){
                        if (!in.eof())  {       in >> junk;             }
                        else                    {       break;                  }
                }
-               
+               //m->getline(in);
                
                while(!in.eof()){
                
                        if (m->control_pressed) { in.close(); return 0; }
 
                        in >> name;                             //read from first column
-                       
+                       //m->getline(in);
                        //read rest
                        for (int i = 0; i < 15; i++) {  
                                if (!in.eof())  {       in >> junk;             }