added sorted parameter to get.oturep, added error checking to chimera classes in...

[mothur.git] / chimeraslayer.cpp

diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp
index 0b7c2211668ec950401dcd00f8533cd7f5af9404..9b85b5cd4da6dc6e4bc28fcc9d279bbd768da7c5 100644 (file)
--- a/chimeraslayer.cpp
+++ b/chimeraslayer.cpp
@@ -58,7 +58,7 @@ void ChimeraSlayer::print(ostream& out) {
 }
 
 //***************************************************************************************************************
-void ChimeraSlayer::getChimeras() {
+int ChimeraSlayer::getChimeras() {
        try {
                
                //read in query sequences and subject sequences
@@ -69,6 +69,8 @@ void ChimeraSlayer::getChimeras() {
                
                int numSeqs = querySeqs.size();
                
+               if (unaligned) { mothurOut("Your sequences need to be aligned when you use the chimeraslayer method."); mothurOutEndLine(); return 1;  }
+               
                chimeraResults.resize(numSeqs);
                chimeraFlags.resize(numSeqs, "no");
                spotMap.resize(numSeqs);
@@ -212,6 +214,8 @@ void ChimeraSlayer::getChimeras() {
                if (seqMask != "") {
                        delete decalc; 
                }
+               
+               return 0;
        }
        catch(exception& e) {
                errorOut(e, "ChimeraSlayer", "getChimeras");