 ../
|
alignment/
|
1564
(9 years ago)
by jmduarteg:
Minor fixes in entropy calculation
|
geneticCode.dat
|
1114
(12 years ago)
by jmduarteg:
New feature: code for dna to protein translation
|
|
UnirefEntryClusterMember.java
|
1557
(10 years ago)
by jmduarteg:
Fixed bug: for a uniref100 cluster member, was taking the representative's uniprot id/tax id instead of the member's. Database was not correctly modelled -> need also the tax ids for cluster members (and then to query the tax ids from members and not from representative)
|
|
UnirefEntry.java
|
1557
(10 years ago)
by jmduarteg:
Fixed bug: for a uniref100 cluster member, was taking the representative's uniprot id/tax id instead of the member's. Database was not correctly modelled -> need also the tax ids for cluster members (and then to query the tax ids from members and not from representative)
|
|
UniprotVerMisMatchException.java
|
1259
(11 years ago)
by jmduarteg:
New exception for mismatching uniprot versions
|
|
UniprotEntry.java
|
1534
(10 years ago)
by jmduarteg:
Now the reference entry in HomologList is also a UnirefEntry. Not using anymore UniprotEntry
|
|
Translator.java
|
1119
(12 years ago)
by jmduarteg:
Now checking also for ambiguous nucleotide codes (n, m) when translating. Changed implementation of translation by using the new Codon class.
|
|
TranslationException.java
|
1119
(12 years ago)
by jmduarteg:
Now checking also for ambiguous nucleotide codes (n, m) when translating. Changed implementation of translation by using the new Codon class.
|
|
TranslatedFrame.java
|
1306
(11 years ago)
by jmduarteg:
Added Serializable interface to many classes. To be able to serialize classes containing objects of these types.
|
|
Sequence.java
|
1597
(9 years ago)
by jmduarteg:
Several changes related to blast:
- now supporting blast+ blastp.
- blast xml parser can now ignore the DTD url, avoiding unnecessary network access if desired
- refactoring: legacy blast related stuff is now refactored to contain "legacy", runBlastp refers to blast+
Also updated uniprot jar.
|
|
ReadingFrame.java
|
1114
(12 years ago)
by jmduarteg:
New feature: code for dna to protein translation
|
|
ProteinToCDSMatch.java
|
1306
(11 years ago)
by jmduarteg:
Added Serializable interface to many classes. To be able to serialize classes containing objects of these types.
|
|
HomologList.java
|
1630
(9 years ago)
by jmduarteg:
New feature: now blast xml parser can read either raw xml or gzipped xml files. Also HomologList will use xml.gz files only as cache files
|
|
Homolog.java
|
1599
(9 years ago)
by jmduarteg:
Fixed important issues with searching and alignment of homologs:
- ids and coverage were calculated wrongly, based on all BlastHsps for a hit. Now based on single Hsps
- fixed bug in BlastHsp.getQueryCoverage: was miscalculating the coverage by 1 unit
- the useHspsOnly parameter in alignment didn't make much sense. We need always to use the hsp segments only, extending to the full sequence is dangerous and in any case does not make sense at all if the clustering is done in hsps only
|
|
GeneticCodeType.java
|
1132
(12 years ago)
by jmduarteg:
New SelectonRunner class. More taxonomy information retrieved from uniprot.
|
|
Codon.java
|
1154
(11 years ago)
by jmduarteg:
And all other amiguous codons
|
