captured stdout from system command, fixed bug in trim.seqs added error checks for...

[mothur.git] / chimeraslayer.cpp

diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp
index 70208607a00373eac0e13cfa4eb639d9025be99d..3f45e17ed5aad1e5007b530b5cb7025688b3b164 100644 (file)
--- a/chimeraslayer.cpp
+++ b/chimeraslayer.cpp
@@ -218,6 +218,8 @@ int ChimeraSlayer::doPrep() {
                
                        //generate blastdb
                        databaseLeft = new BlastDB(m->getRootName(m->getSimpleName(fastafile)), -1.0, -1.0, 1, -3);
+                       
+                       if (m->control_pressed) { return 0; }
 
                        for (int i = 0; i < templateSeqs.size(); i++) {         databaseLeft->addSequence(*templateSeqs[i]);    }
                        databaseLeft->generateDB();
@@ -325,6 +327,8 @@ vector<Sequence*> ChimeraSlayer::getTemplate(Sequence* q, vector<Sequence*>& use
                        
                        //generate blastdb
                        databaseLeft = new BlastDB(m->getRootName(m->getSimpleName(templateFileName)), -1.0, -1.0, 1, -3);
+                       
+                       if (m->control_pressed) { return userTemplate; }
 
                        for (int i = 0; i < userTemplate.size(); i++) { if (m->control_pressed) { return userTemplate; }   databaseLeft->addSequence(*userTemplate[i]); }
                        databaseLeft->generateDB();