X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pairwiseseqscommand.cpp;h=db032516e69e631147dbe3f2179a99a53ea2a1e2;hb=b553a5240d60e4e2b267fa26e4ba6c55acaba795;hp=0c9bcc5f8a5961de5054fbb0b2412f3df10c4506;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/pairwiseseqscommand.cpp b/pairwiseseqscommand.cpp
index 0c9bcc5..db03251 100644
--- a/pairwiseseqscommand.cpp
+++ b/pairwiseseqscommand.cpp
@@ -69,7 +69,7 @@ string PairwiseSeqsCommand::getHelpString(){
 		helpString += "The pairwise.seqs command should be in the following format: \n";
 		helpString += "pairwise.seqs(fasta=yourfastaFile, align=yourAlignmentMethod) \n";
 		helpString += "Example pairwise.seqs(fasta=candidate.fasta, align=blast)\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) {
@@ -99,6 +99,7 @@ PairwiseSeqsCommand::PairwiseSeqsCommand(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();
@@ -141,48 +142,63 @@ PairwiseSeqsCommand::PairwiseSeqsCommand(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 output 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) {
+					
+						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");
 					
-					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(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 output 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--;
+						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--;
+						}
 					}
 				}