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root/owl/trunk/src/owl/core/sequence
r1304
File Last Change (rev)
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alignment/ 1166 (11 years ago) by jmduarteg: Fixed bug: not allowing anymore the presence of gaps when choosing the representative CDS to uniprot match. Now the nucleotide alignments should be always correct (before they were shifted if there were gaps in CDS-to-uniprot)
UniprotHomologList.java 1304 (11 years ago) by jmduarteg: Fixed important bug: we didn't model the blast data properly. A hit is composed of several hsps. Now our classes following that data model properly (before we treated a hit as an hsp).
UniprotHomolog.java 1304 (11 years ago) by jmduarteg: Fixed important bug: we didn't model the blast data properly. A hit is composed of several hsps. Now our classes following that data model properly (before we treated a hit as an hsp).
UniprotEntry.java 1285 (11 years ago) by jmduarteg: Now throwing MatchNotFound exception instead of catching it.
TranslatedFrame.java 1284 (11 years ago) by cvehlow: Overrides removed
ProteinToCDSMatch.java 1273 (11 years ago) by jmduarteg: Fixed buf: EMBL DB fetch returns sequences now in upper case, we were not converting properly to lower case in one place, now should be fixed.
UniprotVerMisMatchException.java 1259 (11 years ago) by jmduarteg: New exception for mismatching uniprot versions
Codon.java 1154 (11 years ago) by jmduarteg: And all other amiguous codons
GeneticCodeType.java 1132 (11 years ago) by jmduarteg: New SelectonRunner class. More taxonomy information retrieved from uniprot.
Sequence.java 1119 (11 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 (11 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.
Translator.java 1119 (11 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.
geneticCode.dat 1114 (11 years ago) by jmduarteg: New feature: code for dna to protein translation
ReadingFrame.java 1114 (11 years ago) by jmduarteg: New feature: code for dna to protein translation
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