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Commit 3c3d354b authored by Marco Del Tufo's avatar Marco Del Tufo
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1 merge request!40SSDM-13578 : 2PT : Database and V3 Implementation - include the new AFS "free"...
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docs/software-developer-documentation/legacy-server-side-extensions/search-domain-services.md
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......@@ -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. |
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