[Biojava-l] Typos - the saga continues

[Tony Watkins]

More for the trunk .....

Package org.biojava.bio.search

Interface SeqSimilaritySearcher

method search

(original)
db - the sequence database against which the similarity search will be performed. May not be null otherwise an IllegalArgumentException is thrown. Must also be an element of the set of searchable dbs returnes by getSearchableDBs().

(suggested correction)
... Must also be an element of the set of searchable dbs *returned* by getSearchableDBs().

Interface SeqSimilaritySearchHit

Method getSubHits

(original)
a List of SeqSimilaritySearchSubHit objects containing all sub-hits for this hit. Never returns null and the List is guaranteed to contain at least 1 entry

(suggested change)
... Never returns null and the List is guaranteed to contain at least *one* entry

Interface SeqSimilaritySearchSubHit

method getScore

(original)
the score of this sub-hit. This is a mandatory piece of information and may hence not be NaN

(suggested change)
.... This is a mandatory piece of information and *hence may* not be NaN

Class SequenceDBSearchHit

Constructor detail SequenceDBSearchHit

(original)
sStrand - the strand of the sub-hits on the subject sequence, which may be null for protein similarities. If they are no all positive or all negative, then this should be the unknown strand

(suggested correction for non Scottish readers)
... If they are *not* all positive or all negative, then this should be the unknown strand

method getScore

(original)
the overall score of this hit. This is a mandatory piece of information and may hence not be NaN

(suggested change)
.... This is a mandatory piece of information and  *hence may* not be NaN

Class SequenceDBSearchSubHit

method getScore

(original)
the score of this sub-hit. This is a mandatory piece of information and may hence not be NaN.

(suggested change)
the score of this sub-hit. This is a mandatory piece of information and *hence may* not be NaN.

Class SimpleSeqSimilaritySearchHit

Constructor detail

(original)
qStrand - the strand of the sub-hits on the query sequence, which may be null for protein similarities. If they are no all positive or all negative, then this should be the unknown strand.

(suggested correction)
... If they are *not* all positive or all negative, then this should be the unknown strand.

(ditto for sStrand)

(also for score the suggested change in word ordering for *hence may*)

method getSubHits

(original)
a List of SeqSimilaritySearchSubHit objects containing all sub-hits for this hit. Never returns null and the List is guaranteed to contain at least 1 entry

(suggested change)
... Never returns null and the List is guaranteed to contain at least *one* entry

Class SimpleSeqSimilaritySearchResult

(Constructor detail)

(original)
sequenceDB - the sequence database against the search that produced this results was done, which may not be null

(suggested change)

sequenceDB - the sequence database against *which* the search that produced this *result* was done, which may not be null

method getQuerySequence

(original)
Return the sequence with which the search that produced this search result was performed

(suggested changes which may prove too simplistic)
Return the *original query sequence used to produce this search result*

method getSequenceDB

(original)
Return the sequence database against which the search that produced this search result was performed

(suggested change - ditto on above comment, and I'm not 100% happy with the suggestion)
Return the sequence database *queried for this search result*

Class SimpleSeqSimilaritySearchSubHit

method getScore

(original)
the score of this sub-hit. This is a mandatory piece of information and may hence not be NaN

(suggested re-ordering)
the score of this sub-hit. This is a mandatory piece of information and hence may not be NaN

That's all folks....