testing 1.13.0

[mothur.git] / chimerapintailcommand.cpp

diff --git a/chimerapintailcommand.cpp b/chimerapintailcommand.cpp
index a8a85eb07bd8df6639ee7a3db7122d588c889e34..398d37ac7d4a25d51c56a1ce4bfea3051c2c12eb 100644 (file)
--- a/chimerapintailcommand.cpp
+++ b/chimerapintailcommand.cpp
@@ -131,9 +131,21 @@ ChimeraPintailCommand::ChimeraPintailCommand(string option)  {
                                }
 
                                ifstream in;
-                               int     ableToOpen = m->openInputFile(maskfile, in);
-                               if (ableToOpen == 1) { abort = true; }
-                               in.close();
+                               int     ableToOpen = m->openInputFile(maskfile, in, "no error");
+                               if (ableToOpen == 1) { 
+                                       if (m->getDefaultPath() != "") { //default path is set
+                                                       string tryPath = m->getDefaultPath() + m->getSimpleName(maskfile);
+                                                       m->mothurOut("Unable to open " + maskfile + ". Trying default " + tryPath); m->mothurOutEndLine();
+                                                       ableToOpen = m->openInputFile(tryPath, in, "noerror");
+                                                       maskfile = tryPath;
+                                       }
+                               }
+                                       in.close();
+                                       
+                               if (ableToOpen == 1) { 
+                                               m->mothurOut("Unable to open " + maskfile + "."); m->mothurOutEndLine(); 
+                                               abort = true;
+                               }
                        }
 
                        
@@ -159,6 +171,15 @@ ChimeraPintailCommand::ChimeraPintailCommand(string option)  {
                                        if (GoodFile) {  
                                                m->mothurOut("I found " + tempConsFile + " in your input file directory. I will use it to save time."); m->mothurOutEndLine();  consfile = tempConsFile;  FileTest.close();     
                                        }
+                               }else {
+                                       string tempConsFile = m->getDefaultPath() + m->getRootName(m->getSimpleName(templatefile)) + "freq";
+                                       ifstream FileTest2(tempConsFile.c_str());
+                                       if(FileTest2){  
+                                               bool GoodFile = m->checkReleaseVersion(FileTest2, m->getVersion());
+                                               if (GoodFile) {  
+                                                       m->mothurOut("I found " + tempConsFile + " in your input file directory. I will use it to save time."); m->mothurOutEndLine();  consfile = tempConsFile;  FileTest2.close();    
+                                               }
+                                       }
                                }
                        }       
                        
@@ -242,14 +263,34 @@ int ChimeraPintailCommand::execute(){
                                if (GoodFile) {  
                                        m->mothurOut("I found " + tempQuan + " in your input file directory. I will use it to save time."); m->mothurOutEndLine();  quanfile = tempQuan;  FileTest.close();     
                                }
+                       }else {
+                               string tryPath = m->getDefaultPath();
+                               string tempQuan = "";
+                               if ((!filter) && (maskfile == "")) {
+                                       tempQuan = tryPath + m->getRootName(m->getSimpleName(templatefile)) + "pintail.quan";
+                               }else if ((!filter) && (maskfile != "")) { 
+                                       tempQuan = tryPath + m->getRootName(m->getSimpleName(templatefile)) + "pintail.masked.quan";
+                               }else if ((filter) && (maskfile != "")) { 
+                                       tempQuan = tryPath + m->getRootName(m->getSimpleName(templatefile)) + "pintail.filtered." + m->getSimpleName(m->getRootName(fastaFileNames[s])) + "masked.quan";
+                               }else if ((filter) && (maskfile == "")) { 
+                                       tempQuan = tryPath + m->getRootName(m->getSimpleName(templatefile)) + "pintail.filtered." + m->getSimpleName(m->getRootName(fastaFileNames[s])) + "quan";
+                               }
+                               
+                               ifstream FileTest2(tempQuan.c_str());
+                               if(FileTest2){  
+                                       bool GoodFile = m->checkReleaseVersion(FileTest2, m->getVersion());
+                                       if (GoodFile) {  
+                                               m->mothurOut("I found " + tempQuan + " in your input file directory. I will use it to save time."); m->mothurOutEndLine();  quanfile = tempQuan;  FileTest2.close();    
+                                       }
+                               }
                        }
                        
                        chimera = new Pintail(fastaFileNames[s], templatefile, filter, processors, maskfile, consfile, quanfile, window, increment, outputDir);
                        
                        string outputFileName, accnosFileName;
                        if (maskfile != "") {
-                               outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + maskfile + ".pintail.chimeras";
-                               accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + maskfile + ".pintail.accnos";
+                               outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + m->getSimpleName(m->getRootName(maskfile)) + ".pintail.chimeras";
+                               accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + m->getSimpleName(m->getRootName(maskfile)) + ".pintail.accnos";
                        }else {
                                outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]))  + "pintail.chimeras";
                                accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]))  + "pintail.accnos";