fixed bug with dist.shared subsampling. added mode parameter to dist.shared so...

[mothur.git] / sequenceparser.cpp

diff --git a/sequenceparser.cpp b/sequenceparser.cpp
index fd94b246a43217cc9cbfa131bfe4cd672955e001..3eb508dd737e15d4f06cb04c202608b5d5e1fe7c 100644 (file)
--- a/sequenceparser.cpp
+++ b/sequenceparser.cpp
@@ -37,13 +37,16 @@ SequenceParser::SequenceParser(string groupFile, string fastaFile, string nameFi
                m->openInputFile(fastaFile, in);
                
                map<string, string> seqName; //stores name -> sequence string so we can make new "unique" sequences when we parse the name file
+        int fastaCount = 0;
                while (!in.eof()) {
                        
                        if (m->control_pressed) { break; }
                        
                        Sequence seq(in); m->gobble(in);
+            fastaCount++;
+            if (m->debug) { if((fastaCount) % 1000 == 0){      m->mothurOut("[DEBUG]: reading seq " + toString(fastaCount) + "\n.");   } }
                        
-                       if (seq.getName() != "") {
+        if (seq.getName() != "") {
                                
                                 string group = groupMap->getGroup(seq.getName());
                                 if (group == "not found") {  error = 1; m->mothurOut("[ERROR]: " + seq.getName() + " is in your fasta file and not in your groupfile, please correct."); m->mothurOutEndLine();  }
@@ -133,7 +136,7 @@ SequenceParser::SequenceParser(string groupFile, string fastaFile, string nameFi
                inName.close();
                
                if (error == 1) { m->control_pressed = true; }
-               
+                       
                if (countName != (groupMap->getNumSeqs())) {
                        vector<string> groupseqsnames = groupMap->getNamesSeqs();
                        
@@ -253,6 +256,7 @@ vector<Sequence> SequenceParser::getSeqs(string g){
                        m->mothurOut("[ERROR]: No sequences available for group " + g + ", please correct."); m->mothurOutEndLine();
                }else {
                        seqForThisGroup = it->second;
+            if (m->debug) {  m->mothurOut("[DEBUG]: group " + g + " fasta file has " + toString(seqForThisGroup.size()) + " sequences.");  }
                }
                
                return seqForThisGroup; 
@@ -346,6 +350,7 @@ map<string, string> SequenceParser::getNameMap(string g){
                        m->mothurOut("[ERROR]: No nameMap available for group " + g + ", please correct."); m->mothurOutEndLine();
                }else {
                        nameMapForThisGroup = it->second;
+            if (m->debug) {  m->mothurOut("[DEBUG]: group " + g + " name file has " + toString(nameMapForThisGroup.size()) + " unique sequences.");  }
                }
                
                return nameMapForThisGroup;