find the release info.  Fixed.

http://www.ebi.ac.uk/GOA/uniprot_release.html

used together with pipline code ( prevent that dbcon to pipeline db will be cleared as well)

new routines for getting the sql querys and their times. Note you need to uncomment the relevant sections to use this. By default this is all commented out as intended fro debuging and profiling

"Bio::EnsEMBL::Util::Eprof".  Change in comments.

No functional change.

Fixed comment.

genomic_end() on translations.

Current API and test DB passes the tests.

    $translation->cdna_start();    # or...
    $translation->cdna_start($transcript);
        # Returns the start position of the translation in cDNA
        # coordinates.  Providing the transcript explicitly speeds
        # things up a bit.  The transcript is used in a call to
        # $exon->cdna_coding_start($transcript);

    $translation->cdna_end();    # or...
    $translation->cdna_end($transcript);
        # Returns the end position of the translation in cDNA
        # coordinates.  Providing the transcript explicitly speeds
        # things up a bit.  The transcript is used in a call to
        # $exon->cdna_coding_end($transcript);


    $translation->genomic_start();
        # Returns the start position of the translation in genomic
        # coordinates on the forward strand.

    $translation->genomic_end();
        # Returns the end position of the translation in genomic
        # coordinates on the forward strand.

cdna_coding_end(), coding_region_start(), and coding_region_end() on
exons.

Current API and test DB passes the tests.

    $exon->cdna_start($transcript);
        # Returns the start position of the exon in cDNA coordinates.

    $exon->cdna_end($transcript);
        # Returns the end position of the exon in cDNA coordinates.


    $exon->cdna_coding_start($transcript);
        # Returns the start position of the coding region of the exon
        # in cDNA coordinates.  Returns undef if the whole exon is
        # non-coding.

    $exon->cdna_coding_end($transcript);
        # Returns the end position of the coding region of the exon
        # in cDNA coordinates.  Returns undef if the whole exon is
        # non-coding.


    $exon->coding_region_start($transcript);
        # Returns the start position of the coding region of the exon in
        # genomic coordinates on the forward strand.  Returns undef if
        # the whole exon is non-coding.

    $exon->coding_region_end($transcript);
        # Returns the end position of the coding region of the exon in
        # genomic coordinates on the forward strand.  Returns undef if
        # the whole exon is non-coding.


Since an exon may be part of one or more transcripts, the relevant
transcript must be given as argument ot these methods.