JIRA:RW-2375 CCleanup::WGSCleanup called with also_fix_location false, remove conditional around early SetBestFrame and SetCDSPartialsByFrameAndTranslation calls

git-svn-id: https://anonsvn.ncbi.nlm.nih.gov/repos/v1/trunk/c++@103512 78c7ea69-d796-4a43-9a09-de51944f1b03

Author: kans

src/app/table2asn/table2asn_validator.cpp

@@ -240,7 +240,7 @@ CTable2AsnValidator::~CTable2AsnValidator()
 void CTable2AsnValidator::Cleanup(CRef<CSeq_submit> submit, CSeq_entry_Handle& h_entry, const string& flags) const
 {
     if (flags.find('w') != string::npos) {
-        CCleanup::WGSCleanup(h_entry, true, CCleanup::eClean_NoNcbiUserObjects, false);
+        CCleanup::WGSCleanup(h_entry, true, CCleanup::eClean_NoNcbiUserObjects, false, false);
     }
 
     // ignore 'e' flag, run ExtendedCleanup() uncoditionally - but only after 'x'

src/objtools/cleanup/cleanup.cpp

@@ -2692,11 +2692,9 @@ bool CCleanup::WGSCleanup(CSeq_entry_Handle entry, bool instantiate_missing_prot
         } else {
             string current_name = GetProteinName(*new_cds, entry);
 
-            if (also_fix_location) {
-                change_this_cds |= SetBestFrame(*new_cds, entry.GetScope());
-
-                change_this_cds |= SetCDSPartialsByFrameAndTranslation(*new_cds, entry.GetScope());
-            }
+            // the next two lines should not be under the control of also_fix_location
+            change_this_cds |= SetBestFrame(*new_cds, entry.GetScope());
+            change_this_cds |= SetCDSPartialsByFrameAndTranslation(*new_cds, entry.GetScope());
 
             // retranslate
             if (new_cds->IsSetProduct() && entry.GetScope().GetBioseqHandleFromTSE(*(new_cds->GetProduct().GetId()), entry)) {