added current as option is lists of file names, processors now outputted with current...

[mothur.git] / aligncommand.cpp

diff --git a/aligncommand.cpp b/aligncommand.cpp
index 60a1dc2f7c93818450cc60e839e91fdd9aac3fa4..a75f9d0f944947f8d941731c0322444e68d40682 100644 (file)
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -167,50 +167,64 @@ AlignCommand::AlignCommand(string option)  {
                                for (int i = 0; i < candidateFileNames.size(); i++) {
                                        //candidateFileNames[i] = m->getFullPathName(candidateFileNames[i]);
                                        
-                                       if (inputDir != "") {
-                                               string path = m->hasPath(candidateFileNames[i]);
-                                               //if the user has not given a path then, add inputdir. else leave path alone.
-                                               if (path == "") {       candidateFileNames[i] = inputDir + candidateFileNames[i];               }
-                                       }
-       
-                                       int ableToOpen;
-                                       ifstream in;
-                                       ableToOpen = m->openInputFile(candidateFileNames[i], in, "noerror");
-                                       in.close();     
-                                       
-                                       //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(candidateFileNames[i]);
-                                                       m->mothurOut("Unable to open " + candidateFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
-                                                       ifstream in2;
-                                                       ableToOpen = m->openInputFile(tryPath, in2, "noerror");
-                                                       in2.close();
-                                                       candidateFileNames[i] = tryPath;
+                                       bool ignore = false;
+                                       if (candidateFileNames[i] == "current") { 
+                                               candidateFileNames[i] = m->getFastaFile(); 
+                                               if (candidateFileNames[i] != "") {  m->mothurOut("Using " + candidateFileNames[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
+                                                       candidateFileNames.erase(candidateFileNames.begin()+i);
+                                                       i--;
                                                }
                                        }
                                        
-                                       //if you can't open it, try output location
-                                       if (ableToOpen == 1) {
-                                               if (m->getOutputDir() != "") { //default path is set
-                                                       string tryPath = m->getOutputDir() + m->getSimpleName(candidateFileNames[i]);
-                                                       m->mothurOut("Unable to open " + candidateFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
-                                                       ifstream in2;
-                                                       ableToOpen = m->openInputFile(tryPath, in2, "noerror");
-                                                       in2.close();
-                                                       candidateFileNames[i] = tryPath;
-                                               }
-                                       }
+                                       if (!ignore) {
                                        
-                                                                       
+                                               if (inputDir != "") {
+                                                       string path = m->hasPath(candidateFileNames[i]);
+                                                       //if the user has not given a path then, add inputdir. else leave path alone.
+                                                       if (path == "") {       candidateFileNames[i] = inputDir + candidateFileNames[i];               }
+                                               }
+               
+                                               int ableToOpen;
+                                               ifstream in;
+                                               ableToOpen = m->openInputFile(candidateFileNames[i], in, "noerror");
+                                               in.close();     
+                                               
+                                               //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(candidateFileNames[i]);
+                                                               m->mothurOut("Unable to open " + candidateFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+                                                               ifstream in2;
+                                                               ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+                                                               in2.close();
+                                                               candidateFileNames[i] = tryPath;
+                                                       }
+                                               }
+                                               
+                                               //if you can't open it, try output location
+                                               if (ableToOpen == 1) {
+                                                       if (m->getOutputDir() != "") { //default path is set
+                                                               string tryPath = m->getOutputDir() + m->getSimpleName(candidateFileNames[i]);
+                                                               m->mothurOut("Unable to open " + candidateFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+                                                               ifstream in2;
+                                                               ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+                                                               in2.close();
+                                                               candidateFileNames[i] = tryPath;
+                                                       }
+                                               }
+                                               
+                                                                               
 
-                                       if (ableToOpen == 1) { 
-                                               m->mothurOut("Unable to open " + candidateFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); 
-                                               //erase from file list
-                                               candidateFileNames.erase(candidateFileNames.begin()+i);
-                                               i--;
+                                               if (ableToOpen == 1) { 
+                                                       m->mothurOut("Unable to open " + candidateFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); 
+                                                       //erase from file list
+                                                       candidateFileNames.erase(candidateFileNames.begin()+i);
+                                                       i--;
+                                               }
                                        }
-                                       
                                }
                                
                                //make sure there is at least one valid file left