JIRA:RW-2387 Added support for eErr_SEQ_DESCR_BadContigOrScaffoldChromosome

git-svn-id: https://anonsvn.ncbi.nlm.nih.gov/repos/v1/trunk/c++@103509 78c7ea69-d796-4a43-9a09-de51944f1b03

Author: kans

include/objects/valerr/ValidErrItem.hpp

@@ -365,6 +365,7 @@ enum EErrType {
     eErr_SEQ_DESCR_BadNullCountry,
     eErr_SEQ_DESCR_BadNullCollectionDate,
     eErr_SEQ_DESCR_UnculturedGenome,
+    eErr_SEQ_DESCR_BadContigOrScaffoldChromosome,
     ERR_CODE_END(SEQ_DESCR),
 
 

src/objects/valerr/ValidErrItem.cpp

@@ -1013,6 +1013,9 @@ static const TErrTypStrs sc_ErrStrs[] = {
     { eErr_SEQ_DESCR_UnculturedGenome,
     { "UnculturedGenome",
         "A genomic sequence should not have uncultured in its organism name"} },
+    { eErr_SEQ_DESCR_BadContigOrScaffoldChromosome,
+    { "BadContigOrScaffoldChromosome",
+        "Chromosome name should not contain contig or scaffold" }},
 
 
     /* SEQ_GENERIC */

src/objtools/validator/valid_biosource.cpp

@@ -1480,6 +1480,10 @@ const bool isInfluenzaOrSars2)
                 "Problematic plasmid/chromosome/linkage group name '" + sname + "'",
                 obj, ctx);
         }
+        if (NStr::FindNoCase(sname, "contig") != string::npos || NStr::FindNoCase(sname, "scaffold") != string::npos)
+            PostObjErr(eDiag_Error, eErr_SEQ_DESCR_BadContigOrScaffoldChromosome,
+                "Chromosome should not include contig or scaffold: '" + sname + "'",
+                obj, ctx);
         break;
     case CSubSource::eSubtype_linkage_group:
         if (!CSubSource::IsLinkageGroupNameValid(sname, taxname)) {