--- /dev/null
+From: Michael R. Crusoe <michael.crusoe@gmail.com>
+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<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",
+ "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<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
+ 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("<<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,
+--- 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;
+ }
+ }
projects / ncbi-blast+.git / commitdiff