From 397d514f4c693c8c3500972e0ca16a39283ee549 Mon Sep 17 00:00:00 2001
From: Henric Zazzi <hzazzi@csc.kth.se>
Date: Tue, 18 Mar 2014 15:21:17 +0100
Subject: [PATCH] corrected single filename use

---
 main.cpp  |  2 +-
 xmlio.cpp | 12 ++++++------
 xmlio.h   |  6 +++---
 3 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/main.cpp b/main.cpp
index 3628583..d55f23c 100644
--- a/main.cpp
+++ b/main.cpp
@@ -73,7 +73,7 @@ int main(int argc, char **argv) {
     if (percolator.noFilename())
       THROW_ERROR(PRINT_TEXT::PERCOLATOR_FILE_NOT_ENTERED);
     xercesc::XMLPlatformUtils::Initialize();
-    percolator.setUniqueMzIDFilename(mzid.getUniqueFilename());
+    percolator.setFirstMzIDFilename(mzid.getFirstFilename());
     if (!percolator.getPoutValues(pout_values))
       THROW_ERROR(PRINT_TEXT::CANNOT_LOAD_PERCOLATOR_FILE);
     if (!mzid.insertMZIDValues(pout_values))
diff --git a/xmlio.cpp b/xmlio.cpp
index 1c77806..da0bc8e 100644
--- a/xmlio.cpp
+++ b/xmlio.cpp
@@ -99,8 +99,8 @@ bool MzIDIO::checkFilenames() {
   return b1 || warning;
   }
 //------------------------------------------------------------------------------
-string MzIDIO::getUniqueFilename() {
-  return filename.size()==1?filename[0]:"";
+string MzIDIO::getFirstFilename() {
+  return filename[0];
   }
 //------------------------------------------------------------------------------
 string MzIDIO::setOutputFileName(int mzidfilenameid) {
@@ -204,7 +204,7 @@ MzIDIO::~MzIDIO() {
 //------------------------------------------------------------------------------
 PercolatorOutI::PercolatorOutI() {
   filename="";
-  uniquemzidfilename="";
+  firstmzidfilename="";
   decoy=false;
   }
 //------------------------------------------------------------------------------
@@ -213,8 +213,8 @@ bool PercolatorOutI::setFilename(string filename) {
   return boost::filesystem::exists(filename.c_str());
   }
 //------------------------------------------------------------------------------
-void PercolatorOutI::setUniqueMzIDFilename(string filename) {
-  uniquemzidfilename=filename;
+void PercolatorOutI::setFirstMzIDFilename(string filename) {
+  firstmzidfilename=filename;
   }
 //------------------------------------------------------------------------------
 bool PercolatorOutI::noFilename() {
@@ -288,7 +288,7 @@ string PercolatorOutI::convertPSMIDFileName(string percolatorid) {
   string psmidfile;
   int i1;
 
-  psmidfile=boost::lexical_cast<boost::filesystem::path>(uniquemzidfilename).stem().string();
+  psmidfile=boost::lexical_cast<boost::filesystem::path>(firstmzidfilename).stem().string();
   i1=percolatorid.find(PERCOLATOR_PARAM::PSMID_START);
   if (i1!=string::npos)
     psmidfile=percolatorid.substr(0,i1);
diff --git a/xmlio.h b/xmlio.h
index f25c8dc..4bd7921 100644
--- a/xmlio.h
+++ b/xmlio.h
@@ -100,7 +100,7 @@ class MzIDIO : public XMLIO {
   void setFilename(string filename);
   bool addFilenames(string filenamefile);
   bool checkFilenames();
-  string getUniqueFilename();
+  string getFirstFilename();
   string setOutputFileName(int mzidfilenameid);
   bool insertMZIDValues(boost::unordered_map<PercolatorOutFeatures, string, PercolatorOutFeatures> pout_values);
   bool saveMZIDFile(auto_ptr<mzidXML::MzIdentMLType> &pmzid, int mzidfilenameid);
@@ -109,13 +109,13 @@ class MzIDIO : public XMLIO {
 //------------------------------------------------------------------------------
 class PercolatorOutI : public XMLIO {
   private:
-  string filename,uniquemzidfilename;
+  string filename,firstmzidfilename;
   bool decoy;
 
   public:
   PercolatorOutI();
   bool setFilename(string filename);
-  void setUniqueMzIDFilename(string filename);
+  void setFirstMzIDFilename(string filename);
   bool noFilename();
   void setDecoy();
   bool getPoutValues(boost::unordered_map<PercolatorOutFeatures, string, PercolatorOutFeatures> &pout_values);