added otu.association command. added calcSpearman, calcKendall and calcPearson functi...

[mothur.git] / seqerrorcommand.cpp

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index 5c80047681c15640c5926d771536a42ea60a8c9d..d8ebe50fb11859367256a28286dec9789cc70d36 100644 (file)
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -176,9 +176,13 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
                                if (queryFileName != "") { m->mothurOut("Using " + queryFileName + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current fasta file and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
                        }
-                       else if (queryFileName == "not open") { abort = true; } 
+                       else if (queryFileName == "not open") { queryFileName = ""; abort = true; }     
                        else { m->setFastaFile(queryFileName); }
-
+                       
+                       referenceFileName = validParameter.validFile(parameters, "reference", true);
+                       if (referenceFileName == "not found") { m->mothurOut("reference is a required parameter for the seq.error command."); m->mothurOutEndLine(); abort = true; }
+                       else if (referenceFileName == "not open") { abort = true; }     
+                       
                        //check for optional parameters
                        namesFileName = validParameter.validFile(parameters, "name", true);
                        if(namesFileName == "not found"){       namesFileName = "";     }
@@ -209,7 +213,7 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
                        //check for optional parameter and set defaults
                        // ...at some point should added some additional type checking...
                        temp = validParameter.validFile(parameters, "threshold", false);        if (temp == "not found") { temp = "1.00"; }
-                       convert(temp, threshold);  
+                       m->mothurConvert(temp, threshold);  
                        
                        temp = validParameter.validFile(parameters, "save", false);                     if (temp == "not found"){       temp = "f";                             }
                        save = m->isTrue(temp); 
@@ -238,10 +242,15 @@ SeqErrorCommand::SeqErrorCommand(string option)  {
                        
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors); 
+                       m->mothurConvert(temp, processors); 
 
                        substitutionMatrix.resize(6);
                        for(int i=0;i<6;i++){   substitutionMatrix[i].resize(6,0);      }
+                       
+                       if ((namesFileName == "") && (queryFileName != "")){
+                               vector<string> files; files.push_back(queryFileName); 
+                               parser.getNameFile(files);
+                       }
                }
        }
        catch(exception& e) {
@@ -273,9 +282,9 @@ int SeqErrorCommand::execute(){
 
                if(namesFileName != ""){        weights = getWeights(); }
                
-               vector<unsigned long int> fastaFilePos;
-               vector<unsigned long int> qFilePos;
-               vector<unsigned long int> reportFilePos;
+               vector<unsigned long long> fastaFilePos;
+               vector<unsigned long long> qFilePos;
+               vector<unsigned long long> reportFilePos;
                
                setLines(queryFileName, qualFileName, reportFileName, fastaFilePos, qFilePos, reportFilePos);
                
@@ -731,7 +740,7 @@ int SeqErrorCommand::driver(string filename, string qFileName, string rFileName,
                        index++;
                        
                        #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-                               unsigned long int pos = queryFile.tellg();
+                               unsigned long long pos = queryFile.tellg();
                                if ((pos == -1) || (pos >= line.end)) { break; }
                        #else
                                if (queryFile.eof()) { break; }
@@ -1204,7 +1213,7 @@ void SeqErrorCommand::printQualityFR(vector<vector<int> > qualForwardMap, vector
 }
 /**************************************************************************************************/
 
-int SeqErrorCommand::setLines(string filename, string qfilename, string rfilename, vector<unsigned long int>& fastaFilePos, vector<unsigned long int>& qfileFilePos, vector<unsigned long int>& rfileFilePos) {
+int SeqErrorCommand::setLines(string filename, string qfilename, string rfilename, vector<unsigned long long>& fastaFilePos, vector<unsigned long long>& qfileFilePos, vector<unsigned long long>& rfileFilePos) {
        try {
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
                //set file positions for fasta file
@@ -1246,7 +1255,7 @@ int SeqErrorCommand::setLines(string filename, string qfilename, string rfilenam
                                        map<string, int>::iterator it = firstSeqNames.find(sname);
                                        
                                        if(it != firstSeqNames.end()) { //this is the start of a new chunk
-                                               unsigned long int pos = inQual.tellg(); 
+                                               unsigned long long pos = inQual.tellg(); 
                                                qfileFilePos.push_back(pos - input.length() - 1);       
                                                firstSeqNames.erase(it);
                                        }
@@ -1267,7 +1276,7 @@ int SeqErrorCommand::setLines(string filename, string qfilename, string rfilenam
                
                //get last file position of qfile
                FILE * pFile;
-               unsigned long int size;
+               unsigned long long size;
                
                //get num bytes in file
                pFile = fopen (qfilename.c_str(),"rb");
@@ -1305,7 +1314,7 @@ int SeqErrorCommand::setLines(string filename, string qfilename, string rfilenam
                                map<string, int>::iterator it = firstSeqNamesReport.find(sname);
                        
                                if(it != firstSeqNamesReport.end()) { //this is the start of a new chunk
-                                       unsigned long int pos = inR.tellg(); 
+                                       unsigned long long pos = inR.tellg(); 
                                        rfileFilePos.push_back(pos - input.length() - 1);       
                                        firstSeqNamesReport.erase(it);
                                }
@@ -1326,7 +1335,7 @@ int SeqErrorCommand::setLines(string filename, string qfilename, string rfilenam
                
                //get last file position of qfile
                FILE * rFile;
-               unsigned long int sizeR;
+               unsigned long long sizeR;
                
                //get num bytes in file
                rFile = fopen (rfilename.c_str(),"rb");
@@ -1346,7 +1355,7 @@ int SeqErrorCommand::setLines(string filename, string qfilename, string rfilenam
                fastaFilePos.push_back(0); qfileFilePos.push_back(0);
                //get last file position of fastafile
                FILE * pFile;
-               unsigned long int size;
+               unsigned long long size;
                
                //get num bytes in file
                pFile = fopen (filename.c_str(),"rb");