add more unit tests
Changed behavior of gt_feature_node_set_source
Merge pull request #28 from Garonenur/xdrop

add more unit tests
Merge branch 'master' of https://github.com/genometools/genometools
Merge pull request #29 from standage/master

Change behavior or gt_feature_node_set_source to enable resetting source value
refactor and rename

removed indirection for reading and writing were possible
Merge pull request #30 from Garonenur/dw

refactor and rename
change Sascha Kastens' mail address
Merge pull request #31 from satta/master

change Sascha Kastens' mail address
add gt_tir_stream_get_encseq()
add gt_ltrdigest_pdom_visitor_set_{root_type,source_tag}()
fix bug in GtLTRdigestPdomVisitor

some pHMMs contain consensus annotation -- in this case
there is an additional line in the output which must be taken
into account
extend `gt tirvish' tool with pHMM search

This commit adds profile HMM search to the TIRvish tool,
much similar to the implementation in the LTRdigest tool.
It allows for the detection of internal transposase (e.g.
DDE) domains inside de novo detected candidates.
Merge pull request #32 from satta/tir_pdom

add pHMM protein domain search to TIRvish
genometools.h wrapped in #ifdef __cplusplus

allows to include genometools.h into C++ projects