ViewVC Help
View Directory | Revision Log | Download Tarball | View Changeset | Root Listing
root/owl/trunk/src/owl/core/sequence
r1137
File Last Change (rev)
 ../
alignment/ 1116 (12 years ago) by jmduarteg: Now properly translating all frames and finding the best translation match in checkEmblCDSMatching. New class doing all the matching of protein to CDS.
UniprotEntry.java 1137 (12 years ago) by jmduarteg: Now checking the sequence identity of the representative CDS to be above a minimum value.
Codon.java 1136 (12 years ago) by jmduarteg: New ambiguous nucleotide w.
UniprotHomologList.java 1133 (12 years ago) by jmduarteg: Fixed bug: getNucleotideAlignment was nullpointing when encountering a null return from getRepresentativeCDS() (which happens whenever there is no representative CDS for the particular UniprotEntry). Now checking for nulls before using the homolog in the alignment.
GeneticCodeType.java 1132 (12 years ago) by jmduarteg: New SelectonRunner class. More taxonomy information retrieved from uniprot.
ProteinToCDSMatch.java 1126 (12 years ago) by jmduarteg: New code to obtain the nucleotide alignment by mapping the aminoacid alignment to the nucleotide sequences.
TranslatedFrame.java 1122 (12 years ago) by jmduarteg: Some refactoring
UniprotHomolog.java 1120 (12 years ago) by jmduarteg: New class UniprotEntry. Things make a lot more sense now...
Sequence.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.
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.
geneticCode.dat 1114 (12 years ago) by jmduarteg: New feature: code for dna to protein translation
ReadingFrame.java 1114 (12 years ago) by jmduarteg: New feature: code for dna to protein translation
         12 files shown