[Biojava-l] Typos - the saga continues

Fri, 15 Feb 2002 00:04:29 +0000

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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....

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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&nbsp; *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.... 
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