fixed bugs for 1.8

[mothur.git] / secondarystructurecommand.cpp

diff --git a/secondarystructurecommand.cpp b/secondarystructurecommand.cpp
index e2302d38bf02f5c58daae759713deb28a1a75b6b..8acd696406c288303128a3c36aef3e6d816f2fbe 100644 (file)
--- a/secondarystructurecommand.cpp
+++ b/secondarystructurecommand.cpp
@@ -15,6 +15,7 @@
 AlignCheckCommand::AlignCheckCommand(string option){
        try {
                abort = false;
+               haderror = 0;
                
                //allow user to run help
                if(option == "help") { help(); abort = true; }
@@ -124,6 +125,8 @@ int AlignCheckCommand::execute(){
                        if (seq.getName() != "") {
                                statData data = getStats(seq.getAligned());
                                
+                               if (haderror == 1) { break; }
+                               
                                out << seq.getName() << '\t' << data.pound << '\t' << data.dash << '\t' << data.plus << '\t' << data.equal << '\t';
                                out << data.loop << '\t' << data.tilde << '\t' << data.total << endl;
                        }
@@ -184,8 +187,11 @@ statData AlignCheckCommand::getStats(string sequence){
                statData data;
                sequence = "*" + sequence; // need to pad the sequence so we can index it by 1
                
-               int seqLength = sequence.length();
-               for(int i=1;i<seqLength;i++){
+               int length = sequence.length();
+               
+               if (length != seqLength) { mothurOut("your sequences are " + toString(length) + " long, but your map file only contains " + toString(seqLength) + " entries. please correct."); mothurOutEndLine(); haderror = 1; return data;  }
+               
+               for(int i=1;i<length;i++){
                        if(structMap[i] != 0){
                                if(sequence[i] == 'A'){
                                        if(sequence[structMap[i]] == 'T')               {       data.tilde++;   }