 ../
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alignment/
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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)
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UniprotHomologList.java
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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).
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UniprotHomolog.java
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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).
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UniprotEntry.java
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1285
(11 years ago)
by jmduarteg:
Now throwing MatchNotFound exception instead of catching it.
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TranslatedFrame.java
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1284
(11 years ago)
by cvehlow:
Overrides removed
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ProteinToCDSMatch.java
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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.
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UniprotVerMisMatchException.java
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1259
(11 years ago)
by jmduarteg:
New exception for mismatching uniprot versions
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Codon.java
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1154
(11 years ago)
by jmduarteg:
And all other amiguous codons
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GeneticCodeType.java
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1132
(11 years ago)
by jmduarteg:
New SelectonRunner class. More taxonomy information retrieved from uniprot.
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Sequence.java
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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.
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TranslationException.java
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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.
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Translator.java
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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.
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geneticCode.dat
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1114
(11 years ago)
by jmduarteg:
New feature: code for dna to protein translation
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ReadingFrame.java
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1114
(11 years ago)
by jmduarteg:
New feature: code for dna to protein translation
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