From 54a6cb0ef32b761ebd7ae35f1e60947edf44d699 Mon Sep 17 00:00:00 2001
From: westcott <westcott>
Date: Tue, 15 Jun 2010 12:05:46 +0000
Subject: [PATCH] final commit before testing 1.11

---
 removeseqscommand.cpp |  6 +++---
 seqsummarycommand.cpp |  3 ++-
 sequence.cpp          | 46 ++++++++++++++++++++++++-------------------
 3 files changed, 31 insertions(+), 24 deletions(-)

diff --git a/removeseqscommand.cpp b/removeseqscommand.cpp
index 35d9bea..5816cfd 100644
--- a/removeseqscommand.cpp
+++ b/removeseqscommand.cpp
@@ -334,7 +334,7 @@ int RemoveSeqsCommand::readName(){
 		string name, firstCol, secondCol;
 		
 		bool wroteSomething = false;
-	int numSeqsInNames = 0;	
+		
 		while(!in.eof()){
 			if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 
@@ -359,7 +359,7 @@ int RemoveSeqsCommand::readName(){
 					validSecond.push_back(parsedNames[i]);
 				}
 			}
-		numSeqsInNames += parsedNames.size();	
+			
 			if ((dups) && (validSecond.size() != parsedNames.size())) {  //if dups is true and we want to get rid of anyone, get rid of everyone
 				for (int i = 0; i < parsedNames.size(); i++) {  names.insert(parsedNames[i]);  }
 			}else {
@@ -394,7 +394,7 @@ int RemoveSeqsCommand::readName(){
 		}
 		in.close();
 		out.close();
-cout << "your names file contains " << numSeqsInNames << endl;		
+
 		if (wroteSomething == false) {
 			m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine();
 			remove(outputFileName.c_str()); 
diff --git a/seqsummarycommand.cpp b/seqsummarycommand.cpp
index f225d50..d613391 100644
--- a/seqsummarycommand.cpp
+++ b/seqsummarycommand.cpp
@@ -230,7 +230,7 @@ int SeqSummaryCommand::execute(){
 					openInputFile(fastafile, inFASTA);
 					numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 					inFASTA.close();
-					
+			cout << numSeqs << endl;		
 					lines.push_back(new linePair(0, numSeqs));
 					
 					driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, summaryFile, lines[0]);
@@ -334,6 +334,7 @@ int SeqSummaryCommand::driverCreateSummary(vector<int>& startPosition, vector<in
 			if (m->control_pressed) { in.close(); outSummary.close(); return 1; }
 					
 			Sequence current(in);
+	
 			if (current.getName() != "") {
 				startPosition.push_back(current.getStartPos());
 				endPosition.push_back(current.getEndPos());
diff --git a/sequence.cpp b/sequence.cpp
index 71dd3a9..0afe3a9 100644
--- a/sequence.cpp
+++ b/sequence.cpp
@@ -129,31 +129,37 @@ Sequence::Sequence(ifstream& fastaFile){
 		m = MothurOut::getInstance();
 		initialize();
 		fastaFile >> name;
-		name = name.substr(1);
-		string sequence;
+
+		if (name.length() != 0) { 
 		
-		//read comments
-		while ((name[0] == '#') && fastaFile) { 
-			while (!fastaFile.eof())	{	char c = fastaFile.get(); if (c == 10 || c == 13){	break;	}	} // get rest of line if there's any crap there
-			sequence = getCommentString(fastaFile);
+			name = name.substr(1); 
 			
-			if (fastaFile) {  
-				fastaFile >> name;  
-				name = name.substr(1);	
-			}else { 
-				name = "";
-				break;
-			}
-		}
+			string sequence;
 		
-		//read real sequence
-		while (!fastaFile.eof())	{	char c = fastaFile.get(); if (c == 10 || c == 13){	break;	}	} // get rest of line if there's any crap there
+			//read comments
+			while ((name[0] == '#') && fastaFile) { 
+				while (!fastaFile.eof())	{	char c = fastaFile.get(); if (c == 10 || c == 13){	break;	}	} // get rest of line if there's any crap there
+				sequence = getCommentString(fastaFile);
+				
+				if (fastaFile) {  
+					fastaFile >> name;  
+					name = name.substr(1);	
+				}else { 
+					name = "";
+					break;
+				}
+			}
+			
+			//read real sequence
+			while (!fastaFile.eof())	{	char c = fastaFile.get(); if (c == 10 || c == 13){	break;	}	} // get rest of line if there's any crap there
+			
+			sequence = getSequenceString(fastaFile);		
 		
-		sequence = getSequenceString(fastaFile);		
+			setAligned(sequence);	
+			//setUnaligned removes any gap characters for us						
+			setUnaligned(sequence);	
+		}
 		
-		setAligned(sequence);	
-		//setUnaligned removes any gap characters for us						
-		setUnaligned(sequence);	
 	}
 	catch(exception& e) {
 		m->errorOut(e, "Sequence", "Sequence");
-- 
2.39.2