From c5c3ba0fa9d18707c9c9ce692cff061b6f882e44 Mon Sep 17 00:00:00 2001
From: westcott <westcott>
Date: Thu, 17 Sep 2009 13:48:20 +0000
Subject: [PATCH] added check for blank files in openInputFile, add check for
 groupfiles that contain more seqs than the list files in sharedcommand

---
 groupmap.h        |  3 ++-
 mothur.h          |  4 ++++
 pintail.cpp       | 11 ++++-------
 sharedcommand.cpp | 17 +++++++++++++++--
 4 files changed, 25 insertions(+), 10 deletions(-)

diff --git a/groupmap.h b/groupmap.h
index d69699d..54225e2 100644
--- a/groupmap.h
+++ b/groupmap.h
@@ -26,7 +26,8 @@ public:
 	void setGroup(string, string);
 	vector<string> namesOfGroups;
 	map<string, int> groupIndex;  //groupname, vectorIndex in namesOfGroups. - used by collectdisplays.
-		
+	int getNumSeqs()  {  return groupmap.size();  }
+			
 private:
 	ifstream fileHandle;
 	string groupFileName;
diff --git a/mothur.h b/mothur.h
index e3e2ef4..836e066 100644
--- a/mothur.h
+++ b/mothur.h
@@ -425,6 +425,10 @@ inline int openInputFile(string fileName, ifstream& fileHandle){
 		return 1;
 	}
 	else {
+		//check for blank file
+		gobble(fileHandle);
+		if (fileHandle.eof()) { mothurOut(fileName + " is blank. Please correct."); mothurOutEndLine();  return 1;  }
+		
 		return 0;
 	}
 	
diff --git a/pintail.cpp b/pintail.cpp
index 7b99cab..5f575f2 100644
--- a/pintail.cpp
+++ b/pintail.cpp
@@ -146,18 +146,15 @@ void Pintail::getChimeras() {
 			mothurOut("Done."); mothurOutEndLine();
 		}else {		createProcessesPairs();		}
 		
-/*string o = "foronlinepintailpairs-eachgap";
+string o = "closestmatch.eachgap.fasta";
 ofstream out7;
 openOutputFile(o, out7);
 
 for (int i = 0; i < bestfit.size(); i++) {
-	out7 << querySeqs[i]->getName() << endl;
-	out7 << querySeqs[i]->getUnaligned() << endl << endl;
-	
-	out7 << bestfit[i]->getName() << endl;
-	out7 << bestfit[i]->getUnaligned() << endl << endl << endl;
+	out7 << ">" << querySeqs[i]->getName() << "-"<< bestfit[i]->getName() << endl;
+	out7 << bestfit[i]->getAligned() << endl;
 }		
-out7.close();/*/	
+out7.close();	
 		//find P
 		mothurOut("Getting conservation... "); cout.flush();
 		if (consfile == "") { 
diff --git a/sharedcommand.cpp b/sharedcommand.cpp
index 4b35138..717d3aa 100644
--- a/sharedcommand.cpp
+++ b/sharedcommand.cpp
@@ -57,12 +57,26 @@ int SharedCommand::execute(){
 		//read in listfile
 		read = new ReadOTUFile(globaldata->inputFileName);	
 		read->read(&*globaldata); 
+		delete read;
 
 		input = globaldata->ginput;
 		SharedList = globaldata->gSharedList;
 		string lastLabel = SharedList->getLabel();
 		vector<SharedRAbundVector*> lookup; 
-				
+		
+		if (SharedList->getNumSeqs() != groupMap->getNumSeqs()) {  
+			mothurOut("Your group file contains " + toString(groupMap->getNumSeqs()) + " sequences and list file contains " + toString(SharedList->getNumSeqs()) + " sequences. Please correct."); mothurOutEndLine(); 
+			
+			//delete memory
+			for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
+				delete it3->second;
+			}
+			delete SharedList;
+			globaldata->gSharedList = NULL;
+			
+			return(0); 
+		}
+		
 		//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 		set<string> processedLabels;
 		set<string> userLabels = globaldata->labels;
@@ -131,7 +145,6 @@ int SharedCommand::execute(){
 		}
 		
 		globaldata->gSharedList = NULL;
-		delete read;
 		
 		out.close();
 		
-- 
2.39.2