Spelling fixes

Gbp-Pq: Name spelling

diff --git a/c++/include/objtools/alnmgr/seqids_extractor.hpp b/c++/include/objtools/alnmgr/seqids_extractor.hpp
index d38e3769bb62cadeec973f0dba7c2e9bbf20923c..359f02ef29da93a1f9c411c9d8a531c930168012 100644 (file)
--- a/c++/include/objtools/alnmgr/seqids_extractor.hpp
+++ b/c++/include/objtools/alnmgr/seqids_extractor.hpp
@@ -232,7 +232,7 @@ public:
                         else if (*id_vec[i] != *id) {
                             string err("Inconsistent Seq-ids found in seg ");
                             err += NStr::NumericToString(i) +
-                                ".  Excpected " + id_vec[i]->AsString() +
+                                ".  Expected " + id_vec[i]->AsString() +
                                 ", encountered " + id->AsString() + ".";
                             NCBI_THROW(CAlnException, eInvalidSeqId, err);
                         }

diff --git a/c++/src/algo/winmask/seq_masker_ostat_factory.cpp b/c++/src/algo/winmask/seq_masker_ostat_factory.cpp
index 74263c516db0877241b7d15fb98a7c0c1acb888d..eeaba1a0770bf2acfd0ef581a8206376609443fb 100644 (file)
--- a/c++/src/algo/winmask/seq_masker_ostat_factory.cpp
+++ b/c++/src/algo/winmask/seq_masker_ostat_factory.cpp
@@ -75,7 +75,7 @@ CSeqMaskerOstat * CSeqMaskerOstatFactory::create(
         }
         else NCBI_THROW( CSeqMaskerOstatFactoryException,
                          eBadName,
-                         "unkown unit counts format" );
+                         "unknown unit counts format" );
     }
     catch( CException & e ) {
         NCBI_RETHROW( e, CSeqMaskerOstatFactoryException, eCreateFail,
@@ -113,7 +113,7 @@ CSeqMaskerOstat * CSeqMaskerOstatFactory::create(
         }
         else NCBI_THROW( CSeqMaskerOstatFactoryException,
                          eBadName,
-                         "unkown unit counts format" );
+                         "unknown unit counts format" );
     }
     catch( CException & e ) {
         NCBI_RETHROW( e, CSeqMaskerOstatFactoryException, eCreateFail,

diff --git a/c++/src/app/blastdb/blastdbcheck.cpp b/c++/src/app/blastdb/blastdbcheck.cpp
index 8084fec5cbb4b0d156548936ca91e2ba64814079..9484176464f13b494d9327779c8773f7c83e0707 100644 (file)
--- a/c++/src/app/blastdb/blastdbcheck.cpp
+++ b/c++/src/app/blastdb/blastdbcheck.cpp
@@ -245,7 +245,7 @@ void CBlastDbCheckApplication::Init(void)
          "Require that all sequences in the database have taxid set.");
 
     arg_desc->AddFlag
-        ("cdd_delta", "Do aditional tests for a CDD database for DELTA-BLAST");
+        ("cdd_delta", "Do additional tests for a CDD database for DELTA-BLAST");
 
     // Setup arg.descriptions for this application
     SetupArgDescriptions(arg_desc.release());

diff --git a/c++/src/app/blastdb/makeprofiledb.cpp b/c++/src/app/blastdb/makeprofiledb.cpp
index 1ca659493c797f31c7cac6aa922ab4773ddd3a09..7998727df7e53e1a2b35c613582ad15c53eca8d1 100644 (file)
--- a/c++/src/app/blastdb/makeprofiledb.cpp
+++ b/c++/src/app/blastdb/makeprofiledb.cpp
@@ -1811,7 +1811,7 @@ bool CMakeProfileDBApp::x_CheckDelta( const CPssm  & pssm, Int4 seq_size, const
     if( !x_ValidateCd(freqs, obsr, BLASTAA_SIZE) && m_ExcludeInvalid)
     {
        *m_LogFile << filename +
-                       " was excluded: it conatins an invalid CD \n";
+                       " was excluded: it contains an invalid CD \n";
        return false;
     }
     return true;

diff --git a/c++/src/objects/seqalign/Dense_seg.cpp b/c++/src/objects/seqalign/Dense_seg.cpp
index 038f7e46f06aeacb46fab3eec34b65e820f9ef6c..879582a0f143afe79edf895b226cc8018ae6bac8 100644 (file)
--- a/c++/src/objects/seqalign/Dense_seg.cpp
+++ b/c++/src/objects/seqalign/Dense_seg.cpp
@@ -1001,7 +1001,7 @@ void CDense_seg::RemapToLoc(TDim row, const CSeq_loc& loc,
             if (loc_plus != (seq_loc_i.GetStrand() != eNa_strand_minus)) {
                 NCBI_THROW(CSeqalignException, eInvalidInputData,
                            "CDense_seg::RemapToLoc():"
-                           " The strand should be the same accross"
+                           " The strand should be the same across"
                            " the input seq-loc");
             }
         }

diff --git a/c++/src/objects/seqalign/Seq_align.cpp b/c++/src/objects/seqalign/Seq_align.cpp
index 0fd3ec17ed6793051d68218b5018d0419259f3df..f28a338fb77aa0d060277f495fb4e7886c7dfb9f 100644 (file)
--- a/c++/src/objects/seqalign/Seq_align.cpp
+++ b/c++/src/objects/seqalign/Seq_align.cpp
@@ -872,7 +872,7 @@ CSeq_align::CreateDensegFromStdseg(SSeqIdChooser* SeqIdChooser) const
         if (dim != ss.GetDim()  ||  row != dim) {
             NCBI_THROW(CSeqalignException, eInvalidInputAlignment,
                        "CreateDensegFromStdseg(): "
-                       "Inconsistent dimentions!");
+                       "Inconsistent dimensions!");
         }
 
         if (widths_determined[seg]) {

diff --git a/c++/src/objects/seqfeat/institution_codes.inc b/c++/src/objects/seqfeat/institution_codes.inc
index 443db6795d8e48b8d0708783f19bbef512ac829c..773d62671e265ccaf0861ee49391444eaf0e64a9 100644 (file)
--- a/c++/src/objects/seqfeat/institution_codes.inc
+++ b/c++/src/objects/seqfeat/institution_codes.inc
@@ -832,7 +832,7 @@ static const char* const kInstitutionCollectionCodeList[] = {
 "BPPT-ESC\tc\tBPPT Ethanol-Single Cell Protein-Fructose Syrup Technical Unit\t\t\t",
 "BPU\ts\tEoetvoes Lorand University, Department of Plant Taxonomy and Ecology\t\t\t",
 "BR<BEL>\ts\tBotanic Garden Meise\t\t\t",
-"BR<BRA>\tc\tJohanna Dobereiner Biological Resouce Center (CRB-JD)\t\t\t",
+"BR<BRA>\tc\tJohanna Dobereiner Biological Resource Center (CRB-JD)\t\t\t",
 "BRA\ts\tSlovak National Museum, Botany Department\t\t\t",
 "BRAD\ts\tUniversity of Bradford, Biology Department\t\t\t",
 "BRB\ts\tBrassica Resource Bank\t\t\t",

diff --git a/c++/src/objects/seqfeat/institution_codes.txt b/c++/src/objects/seqfeat/institution_codes.txt
index e8db20e6c0c5d8e592dbcf1411b8fa314405d8bf..b9deaae94819fbec13070bb49c13e3d3800f78f7 100644 (file)
--- a/c++/src/objects/seqfeat/institution_codes.txt
+++ b/c++/src/objects/seqfeat/institution_codes.txt
@@ -796,7 +796,7 @@ BPM s       Beipiao Paleontological Museum
 BPPT-ESC       c       BPPT Ethanol-Single Cell Protein-Fructose Syrup Technical Unit                  
 BPU    s       Eoetvoes Lorand University, Department of Plant Taxonomy and Ecology                    
 BR<BEL>        s       Botanic Garden Meise                    
-BR<BRA>        c       Johanna Dobereiner Biological Resouce Center (CRB-JD)                   
+BR<BRA>        c       Johanna Dobereiner Biological Resource Center (CRB-JD)                  
 BRA    s       Slovak National Museum, Botany Department                       
 BRAD   s       University of Bradford, Biology Department                      
 BRB    s       Brassica Resource Bank                  

diff --git a/c++/src/objmgr/util/sequence.cpp b/c++/src/objmgr/util/sequence.cpp
index 20279d27b933242c596cf67d79f15ffc2778b3b9..7169f88b061bdb6bc0846e19a76c84f002880125 100644 (file)
--- a/c++/src/objmgr/util/sequence.cpp
+++ b/c++/src/objmgr/util/sequence.cpp
@@ -385,7 +385,7 @@ string GetProteinName(const CBioseq_Handle& seq)
     if ( best_feats.empty() ) {
         NCBI_THROW_FMT(CObjMgrException, eFindFailed,
                        "GetProteinName("<<GetId(seq, eGetId_Best)<<"): "
-                       "the sequence does't have prot feature");
+                       "the sequence doesn't have prot feature");
     }
     if ( best_feats.size() > 1 ) {
         NCBI_THROW_FMT(CObjMgrException, eFindConflict,

diff --git a/c++/src/objtools/align_format/taxFormat.cpp b/c++/src/objtools/align_format/taxFormat.cpp
index 9a6a21341d2321fd9b888cf732b472c158180feb..7c90155086300e9f5af65ceb9f209686cd9294e3 100644 (file)
--- a/c++/src/objtools/align_format/taxFormat.cpp
+++ b/c++/src/objtools/align_format/taxFormat.cpp
@@ -689,7 +689,7 @@ void CTaxFormat::x_LoadTaxTree(void)
             }            
         }
         if (!tax_load_ok) {
-            NCBI_THROW(CException, eUnknown,"Taxonomic load was not successfull.");
+            NCBI_THROW(CException, eUnknown,"Taxonomic load was not successful.");
         }
         m_TaxTreeLoaded = true;
             

diff --git a/c++/src/objtools/format/flat_file_config.cpp b/c++/src/objtools/format/flat_file_config.cpp
index b78c8c01376bddd782a759b9a3df57c4057de15e..c3db4cc53b4a5cd481d6f59e32da64ec1a4ed1c2 100644 (file)
--- a/c++/src/objtools/format/flat_file_config.cpp
+++ b/c++/src/objtools/format/flat_file_config.cpp
@@ -656,7 +656,7 @@ void CFlatFileConfig::AddArgumentDescriptions(CArgDescriptions& args)
 
          // from
          arg_desc->AddOptionalKey("from", "From",
-                                  "Begining of shown range", CArgDescriptions::eInteger);
+                                  "Beginning of shown range", CArgDescriptions::eInteger);
 
          // to
          arg_desc->AddOptionalKey("to", "To",

diff --git a/c++/src/objtools/readers/agp_converter.cpp b/c++/src/objtools/readers/agp_converter.cpp
index 20084f3072d8e59178885a02e7a0f8becedf07de..ce844abd697bf1710e07dc879379ef4fb0f6fc4b 100644 (file)
--- a/c++/src/objtools/readers/agp_converter.cpp
+++ b/c++/src/objtools/readers/agp_converter.cpp
@@ -728,7 +728,7 @@ void CAgpConverter::x_SetUpObjectOpeningAndClosingStrings(
         submit_block_writer.WriteObject(m_pSubmitBlock.GetPointer(), m_pSubmitBlock->GetThisTypeInfo());
         submit_block_writer.Flush();
         seq_sub_header_strm << "," << endl;
-        seq_sub_header_strm << "data entrys {" << endl;
+        seq_sub_header_strm << "data entries {" << endl;
 
         out_sObjectOpeningString = seq_sub_header_strm.str();
         out_sObjectClosingString = "} }" + out_sObjectClosingString;

diff --git a/c++/src/objtools/readers/agp_util.cpp b/c++/src/objtools/readers/agp_util.cpp
index e3b38efd35512ced9068f79310a89623d8b0e7bc..ad9a8db86ba36720423f4b4e8e2df36f7c2636c2 100644 (file)
--- a/c++/src/objtools/readers/agp_util.cpp
+++ b/c++/src/objtools/readers/agp_util.cpp
@@ -174,7 +174,7 @@ const CAgpErr::TStr CAgpErr::s_msg[]= {
 
     "object_beg != previous object_end + 1",
     "no valid AGP lines",
-    "consequtive gaps lines with the same type and linkage",
+    "consecutive gaps lines with the same type and linkage",
     "in \"Scaffold from component\" file, invalid scaffold-breaking gap",
     "in \"Chromosome from scaffold\" file, invalid \"within-scaffold\" gap",
 
@@ -194,7 +194,7 @@ const CAgpErr::TStr CAgpErr::s_msg[]= {
     // Content Warnings
     "gap at the end of object (OK if X is the circular chromosome/plasmid)",
     "gap at the beginning of object ",
-    "two consequtive gap lines (e.g. a gap at the end of "
+    "two consecutive gap lines (e.g. a gap at the end of "
         "a scaffold, two non scaffold-breaking gaps, ...)",
     "no components in object",
     "the span overlaps a previous span for this component",

diff --git a/c++/src/objtools/readers/agp_validate_reader.cpp b/c++/src/objtools/readers/agp_validate_reader.cpp
index 78ee42240699e67478ec6896f6e54021fa663f37..ba0efca022764e32e9303025723583579ff68c54 100644 (file)
--- a/c++/src/objtools/readers/agp_validate_reader.cpp
+++ b/c++/src/objtools/readers/agp_validate_reader.cpp
@@ -300,7 +300,7 @@ void CAgpValidateReader::OnGapOrComponent()
       int prev_comp_file=spans.rbegin()->file_num;
       int prev_comp_line=spans.rbegin()->line_num;
       if(prev_comp_file < m_last_scaf_start_file || prev_comp_line < m_last_scaf_start_line) {
-        sameComId_otherScaf="; previous occurance at ";
+        sameComId_otherScaf="; previous occurrence at ";
         if(prev_comp_file && prev_comp_file!=m_AgpErr->GetFileNum()) {
           sameComId_otherScaf += m_AgpErr->GetFile(prev_comp_file);
           sameComId_otherScaf += ":";

diff --git a/c++/src/util/compress/api/compress.cpp b/c++/src/util/compress/api/compress.cpp
index 5da4619ec0cb1528fb2aa5cf18ff9528f8ffd0e0..6a1817ae83ef7cf87cf8f80ff0d395f5bdd484c5 100644 (file)
--- a/c++/src/util/compress/api/compress.cpp
+++ b/c++/src/util/compress/api/compress.cpp
@@ -165,7 +165,7 @@ bool CCompression::x_DecompressFile(CCompressionFile& src_file,
     while ( (nread = src_file.Read(buf.get(), file_io_bufsize)) > 0 ) {
         os.write(buf.get(), nread);
         if ( !os.good() ) {
-            SetError(-1, "Error writing to ouput file");
+            SetError(-1, "Error writing to output file");
             return false;
         }
     }