From: westcott <westcott>
Date: Mon, 10 May 2010 12:11:55 +0000 (+0000)
Subject: worked on trim.seqs
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=e21aedb9ffeabff18207d53e9cc5420d2e30a5b2

worked on trim.seqs
---

diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index 580dd9b..39f28d0 100644
--- a/classifyseqscommand.cpp
+++ b/classifyseqscommand.cpp
@@ -226,7 +226,7 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
 						}
 						
 					#endif
-					if (ableToOpen == 1) {  m->mothurOut("Unable to match group file with fasta file."); m->mothurOutEndLine(); abort = true;	}
+					if (ableToOpen == 1) {  m->mothurOut("Unable to match group file with fasta file, not using " + groupfileNames[i] + "."); m->mothurOutEndLine(); groupfileNames[i] = "";	}
 					
 				}
 			}
@@ -551,7 +551,10 @@ int ClassifySeqsCommand::execute(){
 			m->mothurOut("It took " + toString(time(NULL) - start) + " secs to classify " + toString(numFastaSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
 			start = time(NULL);
 			
-			PhyloSummary taxaSum(taxonomyFileName, groupfileNames[s]);
+			string group = "";
+			if (groupfile != "") {  group = groupfileNames[s]; }
+			
+			PhyloSummary taxaSum(taxonomyFileName, group);
 			
 			if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());	} delete classify; return 0; }
 			
diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 29fdc63..a544733 100644
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -604,7 +604,7 @@ void TrimSeqsCommand::getOligos(vector<string>& outFASTAVec){ //vector<ofstream*
 }
 //***************************************************************************************************************
 
-bool TrimSeqsCommand::stripBarcode(Sequence& seq, int& group){
+int TrimSeqsCommand::stripBarcode(Sequence& seq, int& group){
 	try {
 		string rawSequence = seq.getUnaligned();
 		bool success = bdiffs + 1;	//guilty until proven innocent
@@ -722,7 +722,7 @@ bool TrimSeqsCommand::stripBarcode(Sequence& seq, int& group){
 
 //***************************************************************************************************************
 
-bool TrimSeqsCommand::stripForward(Sequence& seq){
+int TrimSeqsCommand::stripForward(Sequence& seq){
 	try {
 		string rawSequence = seq.getUnaligned();
 		bool success = pdiffs + 1;	//guilty until proven innocent
diff --git a/trimseqscommand.h b/trimseqscommand.h
index e2b0687..a4a4215 100644
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -32,8 +32,8 @@ private:
 	void getOligos(vector<string>&);
 	bool stripQualThreshold(Sequence&, ifstream&);
 	bool cullQualAverage(Sequence&, ifstream&);
-	bool stripBarcode(Sequence&, int&);
-	bool stripForward(Sequence&);
+	int stripBarcode(Sequence&, int&);
+	int stripForward(Sequence&);
 	bool stripReverse(Sequence&);
 	bool cullLength(Sequence&);
 	bool cullHomoP(Sequence&);