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SearchIO module - #329

Merged

josemduarte merged 13 commits into

biojava:masterfrom

paolopavan:SearchIO_branch

Nov 12, 2015

Merged

SearchIO module#329
josemduarte merged 13 commits into
biojava:masterfrom
paolopavan:SearchIO_branch

Commits on Sep 9, 2015
- Deleted test files that can be delegated to superclass
  paolopavan
  committed
  51262c5
Commits on Sep 16, 2015
- Massive refactoring: moved alignment data structures from biojava-alignment to biojava-core.
  paolopavan
  committed
  5ad3cc9
Commits on Sep 17, 2015
- Merge branch 'API_variation' into SearchIO_branch
  paolopavan
  committed
  dd5b463
Commits on Sep 18, 2015
- Fixed reference to resource file.
  paolopavan
  committed
  967168d
Commits on Sep 22, 2015
- Modified method with more appropriate access level.
  paolopavan
  committed
  42f3337
Commits on Sep 24, 2015
- Better exception handling.
  paolopavan
  committed
  911ba72
Commits on Sep 28, 2015
- Tests enhancement.
  paolopavan
  committed
  d9c17d7
Commits on Oct 5, 2015
- bugfix
  paolopavan
  committed
  b78d387
- Change in the way equals() is evaluated for Results, Hits, Hsps.Modified tests accordingly.
  paolopavan
  committed
  26eaebf
Commits on Oct 6, 2015
- Added setter method for parsing fine tuning configuration.
  paolopavan
  committed
  31f3729
Commits on Oct 9, 2015
- Refactoring proposed by Jose Manuel Duarte to separate this module from the old implementation in org.biojava.nbio.genome.query.BlastXMLQuery.
  paolopavan
  committed
  f059f0e
Commits on Oct 31, 2015
- Changed logger to slf4j
  paolopavan
  committed
  9cbd9ee
Commits on Nov 1, 2015
- Increased type checking.
  paolopavan
  committed
  248cc08