diff --git a/docs/software-developer-documentation/legacy-server-side-extensions/search-domain-services.md b/docs/software-developer-documentation/legacy-server-side-extensions/search-domain-services.md index 5df71d38e4e50d573448f36dbef5189065b0ee3a..80bc9f8f467eacee73aa0b467e52ff22b60a90c9 100644 --- a/docs/software-developer-documentation/legacy-server-side-extensions/search-domain-services.md +++ b/docs/software-developer-documentation/legacy-server-side-extensions/search-domain-services.md @@ -109,12 +109,12 @@ retrieved for each match: |BLAST output column|Access in Java |Description | |-------------------|----------------------------------------------------------------------------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| -|score |SearchDomainSearchResult.getScore().getScore() |=HYPERLINK("http://homepages.ulb.ac.be/~dgonze/TEACHING/stat_scores.pdf","Score. See http://homepages.ulb.ac.be/~dgonze/TEACHING/stat_scores.pdf for an explanation of score, bit-score and evalue.")| -|bitscore |SearchDomainSearchResult.getScore().getBitScore() | | -|evalue |SearchDomainSearchResult.getScore().getEvalue() | | -|sstart |SearchDomainSearchResult.getResultLocation().getAlignmentMatch().getSequenceStart() |Start of alignment in found sequence | -|send |SearchDomainSearchResult.getResultLocation().getAlignmentMatch().getSequenceEnd() |End of alignment in found sequence | -|qstart |SearchDomainSearchResult.getResultLocation().getAlignmentMatch().getQueryStart() |Start of alignment in search string. | -|qend |SearchDomainSearchResult.getResultLocation().getAlignmentMatch().getQueryEnd() |End of alignment in search string. | -|mismatch |SearchDomainSearchResult.getResultLocation().getAlignmentMatch().getNumberOfMismatches()|Number of mismatches. | -|gaps |SearchDomainSearchResult.getResultLocation().getAlignmentMatch().getTotalNumberOfGaps() |Total number of gap. | +|`score` |`SearchDomainSearchResult.getScore().getScore()` |=HYPERLINK("http://homepages.ulb.ac.be/~dgonze/TEACHING/stat_scores.pdf","Score. See http://homepages.ulb.ac.be/~dgonze/TEACHING/stat_scores.pdf for an explanation of score, bit-score and evalue.")| +|`bitscore` |`SearchDomainSearchResult.getScore().getBitScore()` | | +|`evalue` |`SearchDomainSearchResult.getScore().getEvalue()` | | +|`sstart` |`SearchDomainSearchResult.getResultLocation().getAlignmentMatch().getSequenceStart()` |Start of alignment in found sequence | +|`send` |`SearchDomainSearchResult.getResultLocation().getAlignmentMatch().getSequenceEnd()` |End of alignment in found sequence | +|`qstart` |`SearchDomainSearchResult.getResultLocation().getAlignmentMatch().getQueryStart()` |Start of alignment in search string. | +|`qend` |`SearchDomainSearchResult.getResultLocation().getAlignmentMatch().getQueryEnd()` |End of alignment in search string. | +|`mismatch` |`SearchDomainSearchResult.getResultLocation().getAlignmentMatch().getNumberOfMismatches()`|Number of mismatches. | +|`gaps` |`SearchDomainSearchResult.getResultLocation().getAlignmentMatch().getTotalNumberOfGaps()` |Total number of gap. |