From: Michael R. Crusoe Date: Wed, 4 Dec 2019 13:36:24 +0000 (+0100) Subject: fix some spelling typos X-Git-Tag: archive/raspbian/2.16.0+ds-7+rpi1~1^2~129 X-Git-Url: https://dgit.raspbian.org/?a=commitdiff_plain;h=91a3709182cd43b2175ccee75ceac2d7ddb8ef6a;p=ncbi-blast%2B.git fix some spelling typos --- diff --git a/debian/patches/series b/debian/patches/series index db6b7513..6038260b 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -12,3 +12,4 @@ optionally_keep_sequence fix_unit_tests system_mbedtls_only reprobuild +spelling diff --git a/debian/patches/spelling b/debian/patches/spelling new file mode 100644 index 00000000..5fc13266 --- /dev/null +++ b/debian/patches/spelling @@ -0,0 +1,239 @@ +From: Michael R. Crusoe +Subject: Spelling fixes +--- ncbi-blastplus.orig/c++/include/objtools/alnmgr/seqids_extractor.hpp ++++ ncbi-blastplus/c++/include/objtools/alnmgr/seqids_extractor.hpp +@@ -232,7 +232,7 @@ + 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); + } +--- ncbi-blastplus.orig/c++/src/algo/blast/api/blast_setup_cxx.cpp ++++ ncbi-blastplus/c++/src/algo/blast/api/blast_setup_cxx.cpp +@@ -784,7 +784,7 @@ + if(warning != kEmptyStr){ + warning += ": "; + } +- warning += "Subject sequence contians no data"; ++ warning += "Subject sequence contains no data"; + ERR_POST(Warning << warning); + continue; + } +--- ncbi-blastplus.orig/c++/src/algo/winmask/seq_masker_ostat_factory.cpp ++++ ncbi-blastplus/c++/src/algo/winmask/seq_masker_ostat_factory.cpp +@@ -75,7 +75,7 @@ + } + 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 @@ + } + else NCBI_THROW( CSeqMaskerOstatFactoryException, + eBadName, +- "unkown unit counts format" ); ++ "unknown unit counts format" ); + } + catch( CException & e ) { + NCBI_RETHROW( e, CSeqMaskerOstatFactoryException, eCreateFail, +--- ncbi-blastplus.orig/c++/src/app/blastdb/blastdbcheck.cpp ++++ ncbi-blastplus/c++/src/app/blastdb/blastdbcheck.cpp +@@ -232,7 +232,7 @@ + "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()); +--- ncbi-blastplus.orig/c++/src/app/blastdb/makeprofiledb.cpp ++++ ncbi-blastplus/c++/src/app/blastdb/makeprofiledb.cpp +@@ -546,13 +546,13 @@ + + if(!pssm.IsSetQuery() || (0 == pssm.GetQueryLength())) + { +- string err = filename + " contians no bioseq data"; ++ string err = filename + " contains no bioseq data"; + NCBI_THROW(CInputException, eInvalidInput, err); + } + + if(!pssm.IsSetNumRows() || !pssm.IsSetNumColumns()) + { +- string err = filename + " contians no info on num of columns or num of rows"; ++ string err = filename + " contains no info on num of columns or num of rows"; + NCBI_THROW(CInputException, eInvalidInput, err); + } + +@@ -605,13 +605,13 @@ + + if(sm_invalid == sm) + { +- string err = filename + " contians no pssm or residue frequencies"; ++ string err = filename + " contains no pssm or residue frequencies"; + NCBI_THROW(CInputException, eInvalidInput, err); + } + } + else + { +- string err = filename + " contians no scoremat"; ++ string err = filename + " contains no scoremat"; + NCBI_THROW(CInputException, eInvalidInput, err); + } + +@@ -1563,7 +1563,7 @@ + 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; + } + +--- ncbi-blastplus.orig/c++/src/connect/ncbi_lbos.c ++++ ncbi-blastplus/c++/src/connect/ncbi_lbos.c +@@ -951,7 +951,7 @@ + sizeof(char) * (strlen(buf) + 1))) ) + { + CORE_LOG(eLOG_Warning, "s_LBOS_UrlReadAll: Buffer shrink error, using " +- "original stirng"); ++ "original string"); + } else { + buf = realloc_result; + } +--- ncbi-blastplus.orig/c++/src/objects/seqalign/Dense_seg.cpp ++++ ncbi-blastplus/c++/src/objects/seqalign/Dense_seg.cpp +@@ -988,7 +988,7 @@ + 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"); + } + } +--- ncbi-blastplus.orig/c++/src/objects/seqalign/Seq_align.cpp ++++ ncbi-blastplus/c++/src/objects/seqalign/Seq_align.cpp +@@ -872,7 +872,7 @@ + if (dim != ss.GetDim() || row != dim) { + NCBI_THROW(CSeqalignException, eInvalidInputAlignment, + "CreateDensegFromStdseg(): " +- "Inconsistent dimentions!"); ++ "Inconsistent dimensions!"); + } + + if (widths_determined[seg]) { +--- ncbi-blastplus.orig/c++/src/objects/seqfeat/institution_codes.inc ++++ ncbi-blastplus/c++/src/objects/seqfeat/institution_codes.inc +@@ -661,7 +661,7 @@ + "BPS\ts\tCalifornia Department of Food and Agriculture\t\t\t", + "BPU\ts\tEoetvoes Lorand University, Department of Plant Taxonomy and Ecology\t\t\t", + "BR\ts\tBotanic Garden Meise\t\t\t", +-"BR\tc\tJohanna Dobereiner Biological Resouce Center (CRB-JD)\t\t\t", ++"BR\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", + "BRC\ts\tBotanical Record Club\t\t\t", +--- ncbi-blastplus.orig/c++/src/objects/seqfeat/institution_codes.txt ++++ ncbi-blastplus/c++/src/objects/seqfeat/institution_codes.txt +@@ -628,7 +628,7 @@ + BPS s California Department of Food and Agriculture + BPU s Eoetvoes Lorand University, Department of Plant Taxonomy and Ecology + BR s Botanic Garden Meise +-BR c Johanna Dobereiner Biological Resouce Center (CRB-JD) ++BR c Johanna Dobereiner Biological Resource Center (CRB-JD) + BRA s Slovak National Museum, Botany Department + BRAD s University of Bradford, Biology Department + BRC s Botanical Record Club +--- ncbi-blastplus.orig/c++/src/objmgr/util/sequence.cpp ++++ ncbi-blastplus/c++/src/objmgr/util/sequence.cpp +@@ -274,7 +274,7 @@ + if ( best_feats.empty() ) { + NCBI_THROW_FMT(CObjMgrException, eFindFailed, + "GetProteinName("< 1 ) { + NCBI_THROW_FMT(CObjMgrException, eFindConflict, +--- ncbi-blastplus.orig/c++/src/objtools/align_format/taxFormat.cpp ++++ ncbi-blastplus/c++/src/objtools/align_format/taxFormat.cpp +@@ -587,7 +587,7 @@ + } + } + 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; + +--- ncbi-blastplus.orig/c++/src/objtools/format/flat_file_config.cpp ++++ ncbi-blastplus/c++/src/objtools/format/flat_file_config.cpp +@@ -614,7 +614,7 @@ + + // from + arg_desc->AddOptionalKey("from", "From", +- "Begining of shown range", CArgDescriptions::eInteger); ++ "Beginning of shown range", CArgDescriptions::eInteger); + + // to + arg_desc->AddOptionalKey("to", "To", +--- ncbi-blastplus.orig/c++/src/objtools/readers/agp_converter.cpp ++++ ncbi-blastplus/c++/src/objtools/readers/agp_converter.cpp +@@ -728,7 +728,7 @@ + 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; +--- ncbi-blastplus.orig/c++/src/objtools/readers/agp_util.cpp ++++ ncbi-blastplus/c++/src/objtools/readers/agp_util.cpp +@@ -67,7 +67,7 @@ + + "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", + +@@ -88,7 +88,7 @@ + // 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", +--- ncbi-blastplus.orig/c++/src/objtools/readers/agp_validate_reader.cpp ++++ ncbi-blastplus/c++/src/objtools/readers/agp_validate_reader.cpp +@@ -295,7 +295,7 @@ + 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 += ":"; +--- ncbi-blastplus.orig/c++/src/util/compress/api/compress.cpp ++++ ncbi-blastplus/c++/src/util/compress/api/compress.cpp +@@ -160,7 +160,7 @@ + while ( (nread = src_file.Read(buf.get(), buf_size)) > 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; + } + }