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Commits on Nov 12, 2015

• Fixing broken path

  josemduarte

  committed
  4045e7a

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• Merge commit '248cc08c7fbbdc02249bcac0f10481127b7d3ac7'

  josemduarte

  committed
  3abb93f

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Commits on Nov 10, 2015

• Fixing #344

  

  Jose Duarte

  committed
  4dadf22

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Commits on Nov 1, 2015

• Increased type checking.

  paolopavan

  committed
  248cc08

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Commits on Oct 31, 2015

• Changed logger to slf4j

  paolopavan

  committed
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Commits on Oct 30, 2015

• IOEs in IOUtils now thrown and not repacked into a RE, #111.

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  josemduarte

  committed
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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

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Commits on Oct 6, 2015

• Converting all line endings to Unix.

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  sbliven

  committed
  124269e

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• Added setter method for parsing fine tuning configuration.

  paolopavan

  committed
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Commits on Oct 5, 2015

• Change in the way equals() is evaluated for Results, Hits, Hsps.Modified tests accordingly.

  paolopavan

  committed
  26eaebf

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• bugfix

  paolopavan

  committed
  b78d387

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Commits on Sep 28, 2015

• Tests enhancement.

  paolopavan

  committed
  d9c17d7

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Commits on Sep 24, 2015

• Better exception handling.

  paolopavan

  committed
  911ba72

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Commits on Sep 22, 2015

• Modified method with more appropriate access level.

  paolopavan

  committed
  42f3337

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Commits on Sep 17, 2015

• Merge branch 'API_variation' into SearchIO_branch

  paolopavan

  committed
  dd5b463

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• Slight API change.

  paolopavan

  committed
  2f0909a

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Commits on Sep 16, 2015

• Massive refactoring: moved alignment data structures from biojava-alignment to biojava-core.

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  paolopavan

  committed
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Commits on Sep 9, 2015

• Deleted test files that can be delegated to superclass

  paolopavan

  committed
  51262c5

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• Comments and credits.

  

  paolopavan

  authored and

  unknown

  committed
  8026d8f

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Commits on Sep 8, 2015

• Import fixes

  paolopavan

  committed
  5bea7f3

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Commits on Aug 21, 2015

• Deleted unuseful file.

  paolopavan

  committed
  3898b2e

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• Further tests refinements.

  paolopavan

  committed
  70e106c

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Commits on Jul 31, 2015

• Completed procedure for SearchIO constructor with Factory guess. This will allow auto selection of the appropriate parser based on file extension. Tests added.

  paolopavan

  committed
  9080b37

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Commits on Jul 29, 2015

• Add of BlastTabularParser

  paolopavan

  committed
  24fab31

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• Modified test after improvement of object hashing

  paolopavan

  committed
  ef99f09

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• Improvement of object hashing

  paolopavan

  committed
  bc4dafd

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• method getAlignment(): included pattern singleton

  paolopavan

  committed
  3546510

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Commits on Jul 28, 2015

• Fixing type to interface for Results. Forgot.

  paolopavan

  committed
  1176206

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• Fixing type to interface for Results.

  paolopavan

  committed
  598a263

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• Fixing type to interface for Hits.

  paolopavan

  committed
  621560e

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Commits on Jul 27, 2015

• Updated builder with properties Double percentageIdentity, Integer mismatchCount.

  paolopavan

  committed
  79651d7

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• Updated builder with properties Double percentageIdentity, Integer mismatchCount.

  paolopavan

  committed
  15db2f1

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• Added properties Double percentageIdentity, Integer mismatchCount. They are loaded or calculated if possible.

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  paolopavan

  committed
  c47afcd

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Commits on Jul 24, 2015

• Changed method name from getFactory() to more explicative guessFactory()

  paolopavan

  committed
  c2ae786

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Commits on Jul 23, 2015

• test improvement.

  paolopavan

  committed
  c2099e2

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