| Name | Type | Description |
|---|---|---|
| seq1start | ajuint | match start point in original sequence |
| seq2start | ajuint | match start point in comparison sequence |
| sequence | const AjPSeq | need in case we build multiple matches here so we know which one the match belongs to |
| length | ajint | length of match |
| Padding | char[4] | Padding to alignment boundary |
| Name | Type | Description |
|---|---|---|
| fword | const char* | Original word |
| seqlocs | AjPTable | Table of word start positions in multiple sequences |
| count | ajint | Total number of locations in all sequences |
| Padding | char[4] | Padding to alignment boundary |
| Name | Type | Description |
|---|---|---|
| seq | const AjPSeq | Sequence for word start positions |
| locs | AjPList | List of word start positions in the sequence |
Possible improvements could be achieved by scanning all other words during preprocessing to find out a minimum length that can be skipped safely when a word is matched.
The first 5 fields (seqindxs-nseqs) are set during initialisation, and the last 3 fields (nMatches, lenMatches, nSeqMatches) are calculated during search.
| Name | Type | Description |
|---|---|---|
| word | const EmbPWord | Original word object |
| seqindxs | ajuint* | Positions in the seqset for each sequence the word has been seen |
| nnseqlocs | ajuint* | Number of word start positions for each sequence |
| locs | ajuint** | List of word start positions for each sequence |
| hash | ajulong | Hash value for the word |
| nseqs | ajuint | Number of pattern-sequences word has been seen |
| nMatches | ajuint | Number of matches in query sequences |
| lenMatches | ajulong | Total length of extended matches |
| nSeqMatches | ajuint* | Number of matches recorded on per pattern-sequence base |