added deunique.tree command

[mothur.git] / chimeraccodecommand.cpp

diff --git a/chimeraccodecommand.cpp b/chimeraccodecommand.cpp
index 0b6117a98efba24d95da9df73aa15062141a8cad..df4e67db118462e1115857331c7adcc4551a272c 100644 (file)
--- a/chimeraccodecommand.cpp
+++ b/chimeraccodecommand.cpp
@@ -52,7 +52,7 @@ string ChimeraCcodeCommand::getHelpString(){
                helpString += "The chimera.ccode command should be in the following format: \n";
                helpString += "chimera.ccode(fasta=yourFastaFile, reference=yourTemplate) \n";
                helpString += "Example: chimera.ccode(fasta=AD.align, reference=core_set_aligned.imputed.fasta) \n";
-               helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n";     
+               helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n";       
                return helpString;
        }
        catch(exception& e) {
@@ -82,6 +82,7 @@ ChimeraCcodeCommand::ChimeraCcodeCommand(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();
@@ -127,48 +128,64 @@ ChimeraCcodeCommand::ChimeraCcodeCommand(string option)  {
                                
                                //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 = 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];               }
-                                       }
-       
-                                       int ableToOpen;
-                                       ifstream in;
                                        
-                                       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() + m->getSimpleName(fastaFileNames[i]);
-                                                       m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
-                                                       ifstream in2;
-                                                       ableToOpen = m->openInputFile(tryPath, in2, "noerror");
-                                                       in2.close();
-                                                       fastaFileNames[i] = tryPath;
+                                       bool ignore = false;
+                                       if (fastaFileNames[i] == "current") { 
+                                               fastaFileNames[i] = m->getFastaFile(); 
+                                               if (fastaFileNames[i] != "") {  m->mothurOut("Using " + fastaFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
+                                               else {  
+                                                       m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true; 
+                                                       //erase from file list
+                                                       fastaFileNames.erase(fastaFileNames.begin()+i);
+                                                       i--;
                                                }
                                        }
                                        
-                                       //if you can't open it, try default location
-                                       if (ableToOpen == 1) {
-                                               if (m->getOutputDir() != "") { //default path is set
-                                                       string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
-                                                       m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
-                                                       ifstream in2;
-                                                       ableToOpen = m->openInputFile(tryPath, in2, "noerror");
-                                                       in2.close();
-                                                       fastaFileNames[i] = tryPath;
-                                               }
-                                       }
+                                       if (!ignore) {
                                        
-                                       in.close();
+                                               if (inputDir != "") {
+                                                       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];               }
+                                               }
+               
+                                               int ableToOpen;
+                                               ifstream in;
+                                               
+                                               ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
                                        
-                                       if (ableToOpen == 1) { 
-                                               m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); 
-                                               //erase from file list
-                                               fastaFileNames.erase(fastaFileNames.begin()+i);
-                                               i--;
+                                               //if you can't open it, try default location
+                                               if (ableToOpen == 1) {
+                                                       if (m->getDefaultPath() != "") { //default path is set
+                                                               string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
+                                                               m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+                                                               ifstream in2;
+                                                               ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+                                                               in2.close();
+                                                               fastaFileNames[i] = tryPath;
+                                                       }
+                                               }
+                                               
+                                               //if you can't open it, try default location
+                                               if (ableToOpen == 1) {
+                                                       if (m->getOutputDir() != "") { //default path is set
+                                                               string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
+                                                               m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+                                                               ifstream in2;
+                                                               ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+                                                               in2.close();
+                                                               fastaFileNames[i] = tryPath;
+                                                       }
+                                               }
+                                               
+                                               in.close();
+                                               
+                                               if (ableToOpen == 1) { 
+                                                       m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); 
+                                                       //erase from file list
+                                                       fastaFileNames.erase(fastaFileNames.begin()+i);
+                                                       i--;
+                                               }
                                        }
                                }
                                
@@ -287,7 +304,7 @@ int ChimeraCcodeCommand::execute(){
                                if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   MPI_File_close(&outMPIAccnos);  for (int j = 0; j < outputNames.size(); j++) {   remove(outputNames[j].c_str()); } outputTypes.clear();  delete chimera; return 0;  }
                        
                                if (pid == 0) { //you are the root process 
-                                       string outTemp = "For full window mapping info refer to " + mapInfo + "\n\n";
+                                       string outTemp = "For full window mapping info refer to " + mapInfo + "\n";
                                        
                                        //print header
                                        int length = outTemp.length();