 ../
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alignment/
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1147
(12 years ago)
by jmduarteg:
Implemented logging with log4j library
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UniprotEntry.java
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1162
(12 years ago)
by jmduarteg:
Allowing plasmids as gene encoding organelles without having to treat them especially as they don't have a different genetic code.
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UniprotHomologList.java
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1159
(12 years ago)
by jmduarteg:
Reverting change made in last revision. It intended to fix a bug for a particular test case (don't know anymore which one!) but it actually broke most other cases.
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Codon.java
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1154
(12 years ago)
by jmduarteg:
And all other amiguous codons
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UniprotHomolog.java
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1143
(12 years ago)
by jmduarteg:
New methods to check for reliability of positions with respect of the CDS matching
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TranslatedFrame.java
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1143
(12 years ago)
by jmduarteg:
New methods to check for reliability of positions with respect of the CDS matching
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GeneticCodeType.java
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1132
(12 years ago)
by jmduarteg:
New SelectonRunner class. More taxonomy information retrieved from uniprot.
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ProteinToCDSMatch.java
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1126
(12 years ago)
by jmduarteg:
New code to obtain the nucleotide alignment by mapping the aminoacid alignment to the nucleotide sequences.
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Sequence.java
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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.
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TranslationException.java
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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.
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Translator.java
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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.
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geneticCode.dat
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1114
(12 years ago)
by jmduarteg:
New feature: code for dna to protein translation
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ReadingFrame.java
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1114
(12 years ago)
by jmduarteg:
New feature: code for dna to protein translation
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