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

[mothur.git] / degapseqscommand.cpp

diff --git a/degapseqscommand.cpp b/degapseqscommand.cpp
index 8f8a5c3901d845b27cdbeb5a3f0c34df0b587ce2..6a9c25eb74d240404b16f2677ec30b047781a159 100644 (file)
--- a/degapseqscommand.cpp
+++ b/degapseqscommand.cpp
@@ -43,25 +43,25 @@ DegapSeqsCommand::DegapSeqsCommand(string option)  {
                        fastafile = validParameter.validFile(parameters, "fasta", false);
                        if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the degap.seqs command."); m->mothurOutEndLine(); abort = true;  }
                        else { 
-                               splitAtDash(fastafile, fastaFileNames);
+                               m->splitAtDash(fastafile, fastaFileNames);
                                
                                //go through files and make sure they are good, if not, then disregard them
                                for (int i = 0; i < fastaFileNames.size(); i++) {
                                        if (inputDir != "") {
-                                               string path = hasPath(fastaFileNames[i]);
+                                               string path = m->hasPath(fastaFileNames[i]);
                                                //if the user has not given a path then, add inputdir. else leave path alone.
                                                if (path == "") {       fastaFileNames[i] = inputDir + fastaFileNames[i];               }
                                        }
        
                                        ifstream in;
-                                       int ableToOpen = openInputFile(fastaFileNames[i], in, "noerror");
+                                       int ableToOpen = m->openInputFile(fastaFileNames[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(fastaFileNames[i]);
+                                                       string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
                                                        m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
-                                                       ableToOpen = openInputFile(tryPath, in, "noerror");
+                                                       ableToOpen = m->openInputFile(tryPath, in, "noerror");
                                                        fastaFileNames[i] = tryPath;
                                                }
                                        }
@@ -83,7 +83,7 @@ DegapSeqsCommand::DegapSeqsCommand(string option)  {
                        //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 = ""; 
-                               outputDir += hasPath(fastafile); //if user entered a file with a path then preserve it  
+                               outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it       
                        }
 
                }
@@ -128,16 +128,16 @@ int DegapSeqsCommand::execute(){
                                
                        m->mothurOut("Degapping sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
                        ifstream inFASTA;
-                       openInputFile(fastaFileNames[s], inFASTA);
+                       m->openInputFile(fastaFileNames[s], inFASTA);
                        
                        ofstream outFASTA;
-                       string degapFile = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + "ng.fasta";
-                       openOutputFile(degapFile, outFASTA);
+                       string degapFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "ng.fasta";
+                       m->openOutputFile(degapFile, outFASTA);
                        
                        while(!inFASTA.eof()){
                                if (m->control_pressed) {  inFASTA.close();  outFASTA.close(); remove(degapFile.c_str()); for (int j = 0; j < outputNames.size(); j++) {        remove(outputNames[j].c_str()); } return 0; }
                                 
-                               Sequence currSeq(inFASTA);  gobble(inFASTA);
+                               Sequence currSeq(inFASTA);  m->gobble(inFASTA);
                                if (currSeq.getName() != "") {
                                        outFASTA << ">" << currSeq.getName() << endl;
                                        outFASTA << currSeq.getUnaligned() << endl;