[med-svn] [giira] branch upstream updated (a315672 -> 54ea890)

[Andreas Tille]

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tille pushed a change to branch upstream
in repository giira.

      from  a315672   Imported Upstream version 0.0.20140210
       new  54ea890   New upstream version 0.0.20140625

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 src/geneFinder/ExtractGeneCandidates.java       |   3 +
 src/geneFinder/FrameSearch.java                 | 236 ++++++++++++++++++++++++
 src/geneFinder/GeneFinder.java                  |  10 +-
 src/geneFinder/Giira.java                       |   5 +-
 src/geneFinder/ProkaryoteExtraction.java        |   3 +
 src/geneFinder/Prokaryote_Specials.java         | 211 +++++++++++++++++++++
 src/geneFinder/ReadInParameters_GeneFinder.java |  88 ++++++++-
 src/geneFinder/SamParser.java                   |  76 ++++++--
 src/types/Rna.java                              |   2 +-
 9 files changed, 612 insertions(+), 22 deletions(-)

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