Holds definition of sequence output.
| Name | Type | Description |
|---|---|---|
| Name | Name (ID) | |
| Acc | Accession number (primary only) | |
| Sv | SeqVersion number | |
| Gi | GI NCBI version number | |
| Desc | One-line description | |
| Tax | Main taxonomy (species) | |
| Taxid | Main taxonomy (species) id in NCBI taxonomy | |
| Organelle | Organelle taxonomy | |
| Type | Type N or P | |
| Outputtype | Output sequence known type | |
| Molecule | Molecule type | |
| Class | Class of entry | |
| Division | Database division | |
| Evidence | Experimental evidence (e.g. from UniProt) | |
| Db | Database name from input name | |
| Setdb | Database name from input command line | |
| Setoutdb | Database name from command line | |
| Full | Full name | |
| Date | Dates | |
| Fulldesc | Dates | |
| Doc | Obsolete - see TextPtr | |
| Rev | true: to be reverse-complemented | |
| Circular | true: circular nucleotide molecule | |
| Usa | USA for re-reading | |
| Ufo | UFO for re-reading | |
| Fttable | Feature table | |
| Ftquery | Feature table output | |
| FtFormat | Feature output format (if not in UFO) | |
| FtFilename | Feature output filename (if not in UFO) | |
| Informatstr | Input format | |
| Formatstr | Output format | |
| EType | unused, obsolete | |
| Format | Output format index | |
| Filename | Output filename (if not in USA) | |
| Directory | Output firectory | |
| Entryname | Entry name | |
| Acclist | Secondary accessions | |
| Keylist | Keyword list | |
| Taxlist | Taxonomy list | |
| Genelist | Gene list | |
| Reflist | References (citations) | |
| Cmtlist | Comment block list | |
| Xreflist | Database cross reference list | |
| Seq | The sequence | |
| File | Output file | |
| Knownfile | Already open output file (we don't close this one) | |
| Single | If true, single sequence in each file (-ossingle) | |
| Features | If true, save features with sequence or in file | |
| Extension | File extension | |
| Accuracy | Accuracy values (one per base) from base calling | |
| Savelist | Previous sequences saved for later output (e.g. MSF format) | |
| Count | Number of sequences | |
| Offset | offset from start |
| Name | Description |
|---|---|
| ajSeqoutNew | Default constructor |
| Name | Description |
|---|---|
| ajSeqoutDel | Default destructor |
| Name | Description |
|---|---|
| ajSeqoutUsa | Resets using a new USA |
| ajSeqoutClear | Resets ready for reuse. |
| ajSeqoutOpen | If the file is not yet open, calls seqoutUsaProcess |
| Name | Description |
|---|---|
| ajSeqoutCheckGcg | Calculates the GCG checksum for a sequence set. |
| Name | Description |
|---|---|
| ajSeqWrite | Master sequence output routine |
| ajSeqsetWrite | Master sequence set output routine |
| ajSeqFileNewOut | Opens an output file for sequence writing. |
| Name | Description |
|---|---|
| AjPSeq | Sequences |
| Name | Type | Description |
|---|---|---|
| Cleanup | Function to write remaining lines on closing |