moved utilities out of mothur.h and into mothurOut class.

[mothur.git] / sffinfocommand.cpp

diff --git a/sffinfocommand.cpp b/sffinfocommand.cpp
index 4e53f69cb3e7dd51c3d4b30c10a09d76339b6f2c..a691a405ddb31fb022ebf37c98b40deb8e54c6a5 100644 (file)
--- a/sffinfocommand.cpp
+++ b/sffinfocommand.cpp
@@ -43,25 +43,25 @@ SffInfoCommand::SffInfoCommand(string option)  {
                        sffFilename = validParameter.validFile(parameters, "sff", false);
                        if (sffFilename == "not found") { m->mothurOut("sff is a required parameter for the sffinfo command."); m->mothurOutEndLine(); abort = true;  }
                        else { 
-                               splitAtDash(sffFilename, filenames);
+                               m->splitAtDash(sffFilename, filenames);
                                
                                //go through files and make sure they are good, if not, then disregard them
                                for (int i = 0; i < filenames.size(); i++) {
                                        if (inputDir != "") {
-                                               string path = hasPath(filenames[i]);
+                                               string path = m->hasPath(filenames[i]);
                                                //if the user has not given a path then, add inputdir. else leave path alone.
                                                if (path == "") {       filenames[i] = inputDir + filenames[i];         }
                                        }
        
                                        ifstream in;
-                                       int ableToOpen = openInputFile(filenames[i], in, "noerror");
+                                       int ableToOpen = m->openInputFile(filenames[i], in, "noerror");
                                
                                        //if you can't open it, try default location
                                        if (ableToOpen == 1) {
                                                if (m->getDefaultPath() != "") { //default path is set
-                                                       string tryPath = m->getDefaultPath() + getSimpleName(filenames[i]);
+                                                       string tryPath = m->getDefaultPath() + m->getSimpleName(filenames[i]);
                                                        m->mothurOut("Unable to open " + filenames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
-                                                       ableToOpen = openInputFile(tryPath, in, "noerror");
+                                                       ableToOpen = m->openInputFile(tryPath, in, "noerror");
                                                        filenames[i] = tryPath;
                                                }
                                        }
@@ -83,25 +83,25 @@ SffInfoCommand::SffInfoCommand(string option)  {
                        if (accnosName == "not found") { accnosName = "";  }
                        else { 
                                hasAccnos = true;
-                               splitAtDash(accnosName, accnosFileNames);
+                               m->splitAtDash(accnosName, accnosFileNames);
                                
                                //go through files and make sure they are good, if not, then disregard them
                                for (int i = 0; i < accnosFileNames.size(); i++) {
                                        if (inputDir != "") {
-                                               string path = hasPath(accnosFileNames[i]);
+                                               string path = m->hasPath(accnosFileNames[i]);
                                                //if the user has not given a path then, add inputdir. else leave path alone.
                                                if (path == "") {       accnosFileNames[i] = inputDir + accnosFileNames[i];             }
                                        }
        
                                        ifstream in;
-                                       int ableToOpen = openInputFile(accnosFileNames[i], in, "noerror");
+                                       int ableToOpen = m->openInputFile(accnosFileNames[i], in, "noerror");
                                
                                        //if you can't open it, try default location
                                        if (ableToOpen == 1) {
                                                if (m->getDefaultPath() != "") { //default path is set
-                                                       string tryPath = m->getDefaultPath() + getSimpleName(accnosFileNames[i]);
+                                                       string tryPath = m->getDefaultPath() + m->getSimpleName(accnosFileNames[i]);
                                                        m->mothurOut("Unable to open " + accnosFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
-                                                       ableToOpen = openInputFile(tryPath, in, "noerror");
+                                                       ableToOpen = m->openInputFile(tryPath, in, "noerror");
                                                        accnosFileNames[i] = tryPath;
                                                }
                                        }
@@ -124,19 +124,19 @@ SffInfoCommand::SffInfoCommand(string option)  {
                        }
                        
                        string temp = validParameter.validFile(parameters, "qfile", false);                     if (temp == "not found"){       temp = "T";                             }
-                       qual = isTrue(temp); 
+                       qual = m->isTrue(temp); 
                        
                        temp = validParameter.validFile(parameters, "fasta", false);                            if (temp == "not found"){       temp = "T";                             }
-                       fasta = isTrue(temp); 
+                       fasta = m->isTrue(temp); 
                        
                        temp = validParameter.validFile(parameters, "flow", false);                                     if (temp == "not found"){       temp = "F";                             }
-                       flow = isTrue(temp); 
+                       flow = m->isTrue(temp); 
                        
                        temp = validParameter.validFile(parameters, "trim", false);                                     if (temp == "not found"){       temp = "T";                             }
-                       trim = isTrue(temp); 
+                       trim = m->isTrue(temp); 
                        
                        temp = validParameter.validFile(parameters, "sfftxt", false);                           if (temp == "not found"){       temp = "F";                             }
-                       sfftxt = isTrue(temp); 
+                       sfftxt = m->isTrue(temp); 
                }
        }
        catch(exception& e) {
@@ -210,27 +210,27 @@ int SffInfoCommand::execute(){
 int SffInfoCommand::extractSffInfo(string input, string accnos){
        try {
                
-               if (outputDir == "") {  outputDir += hasPath(input); }
+               if (outputDir == "") {  outputDir += m->hasPath(input); }
                
                if (accnos != "")       {  readAccnosFile(accnos);  }
                else                            {       seqNames.clear();               }
 
                ofstream outSfftxt, outFasta, outQual, outFlow;
                string outFastaFileName, outQualFileName;
-               string sfftxtFileName = outputDir + getRootName(getSimpleName(input)) + "sff.txt";
-               string outFlowFileName = outputDir + getRootName(getSimpleName(input)) + "flow";
+               string sfftxtFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "sff.txt";
+               string outFlowFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "flow";
                if (trim) {
-                       outFastaFileName = outputDir + getRootName(getSimpleName(input)) + "fasta";
-                       outQualFileName = outputDir + getRootName(getSimpleName(input)) + "qual";
+                       outFastaFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "fasta";
+                       outQualFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "qual";
                }else{
-                       outFastaFileName = outputDir + getRootName(getSimpleName(input)) + "raw.fasta";
-                       outQualFileName = outputDir + getRootName(getSimpleName(input)) + "raw.qual";
+                       outFastaFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "raw.fasta";
+                       outQualFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "raw.qual";
                }
                
-               if (sfftxt) { openOutputFile(sfftxtFileName, outSfftxt); outSfftxt.setf(ios::fixed, ios::floatfield); outSfftxt.setf(ios::showpoint);  outputNames.push_back(sfftxtFileName); }
-               if (fasta)      { openOutputFile(outFastaFileName, outFasta);   outputNames.push_back(outFastaFileName); }
-               if (qual)       { openOutputFile(outQualFileName, outQual);             outputNames.push_back(outQualFileName);  }
-               if (flow)       { openOutputFile(outFlowFileName, outFlow);             outputNames.push_back(outFlowFileName);  }
+               if (sfftxt) { m->openOutputFile(sfftxtFileName, outSfftxt); outSfftxt.setf(ios::fixed, ios::floatfield); outSfftxt.setf(ios::showpoint);  outputNames.push_back(sfftxtFileName); }
+               if (fasta)      { m->openOutputFile(outFastaFileName, outFasta);        outputNames.push_back(outFastaFileName); }
+               if (qual)       { m->openOutputFile(outQualFileName, outQual);          outputNames.push_back(outQualFileName);  }
+               if (flow)       { m->openOutputFile(outFlowFileName, outFlow);          outputNames.push_back(outFlowFileName);  }
                
                ifstream in;
                in.open(input.c_str(), ios::binary);
@@ -671,11 +671,11 @@ int SffInfoCommand::readAccnosFile(string filename) {
                seqNames.clear();
                
                ifstream in;
-               openInputFile(filename, in);
+               m->openInputFile(filename, in);
                string name;
                
                while(!in.eof()){
-                       in >> name; gobble(in);
+                       in >> name; m->gobble(in);
                                                
                        seqNames.insert(name);