Commits

Breadcrumbs

History for

onbiojava-3.0.4

User selector

All users

All time

Commit History

Commits on Mar 8, 2012

• added sanity check to Alignments, throws IllegalArgumentException if compound sets mismatch (instead of just failing silently)

  Show description for 6b1ae69
  brandstaetter

  committed
  6b1ae69

  Copy full SHA for 6b1ae69

Commits on Feb 24, 2012

• unified indentation in pom.xml; added some Test cases for DNA Alignments

  Show description for 2dd546d
  brandstaetter

  committed
  2dd546d

  Copy full SHA for 2dd546d

Commits on Oct 6, 2011

• new unit test for DNA alignments

  Show description for aab05d0
  andreasprlic

  committed
  aab05d0

  Copy full SHA for aab05d0

Commits on Oct 5, 2011

• adding a unit test that aligns a DNA sequence

  Show description for 2f68ad6
  andreasprlic

  committed
  2f68ad6

  Copy full SHA for 2f68ad6

• Added missing intra-package import (Thanks to Hannes Brandstätter-Müller)

  Show description for 27d81eb
  sbliven

  committed
  27d81eb

  Copy full SHA for 27d81eb

Commits on Jul 6, 2011

• Contributing new framework for loading amino acid substitution matrices from the AAINDEX database.

  Show description for c185c8b
  andreasprlic

  committed
  c185c8b

  Copy full SHA for c185c8b

Commits on Nov 2, 2010

• Modified in line with latest version of biojava3-core's Sequence interface

  Show description for ee47db7
  andrewyatz

  committed
  ee47db7

  Copy full SHA for ee47db7

Commits on Sep 28, 2010

• extending junit tests with conversion info

  Show description for bcc9ffe
  andreasprlic

  committed
  bcc9ffe

  Copy full SHA for bcc9ffe

Commits on Aug 20, 2010

• finished with linear space (anchored) alignments

  Show description for 16b6ae0
  markchapman

  committed
  16b6ae0

  Copy full SHA for 16b6ae0

Commits on Aug 12, 2010

• added alignment output formatting; outputs to CLUSTALW's ALN, FASTA, and GCG's MSF formats

  Show description for 7a4693e
  markchapman

  committed
  7a4693e

  Copy full SHA for 7a4693e

Commits on Aug 11, 2010

• refactored alignment routines: granted access to all score matrices, reduced memory requirement

  Show description for 7697759
  markchapman

  committed
  7697759

  Copy full SHA for 7697759

Commits on Jul 29, 2010

• refactored aligner, scorer, and refiner enum types

  Show description for 8312ae9
  markchapman

  committed
  8312ae9

  Copy full SHA for 8312ae9

Commits on Jul 28, 2010

• improvements to memory usage during multiple sequence alignment

  Show description for d73eca4
  markchapman

  committed
  d73eca4

  Copy full SHA for d73eca4

• improvements to memory usage during multiple sequence alignment

  Show description for d067eca
  markchapman

  committed
  d067eca

  Copy full SHA for d067eca

Commits on Jul 27, 2010

• cookbook programs

  Show description for 21ad1b7
  markchapman

  committed
  21ad1b7

  Copy full SHA for 21ad1b7

• updated tests to use SubstitutionMatrixHelper

  Show description for 0118cdb
  markchapman

  committed
  0118cdb

  Copy full SHA for 0118cdb

Commits on Jul 22, 2010

• refactored AlignedSequence to have a Sequence generic type in addition to a Compound generic type

  Show description for ae20365
  markchapman

  committed
  ae20365

  Copy full SHA for ae20365

Commits on Jul 10, 2010

• added concurrent progressive multiple sequence alignment

  Show description for 40c3e58
  markchapman

  committed
  40c3e58

  Copy full SHA for 40c3e58

Commits on Jul 9, 2010

• added caching of profile vectors

  Show description for ed9e23e
  markchapman

  committed
  ed9e23e

  Copy full SHA for ed9e23e

• refactored and commented GuideTree and GuideTreeNode, added Iterator from leaves to root

  Show description for 7c64af3
  markchapman

  committed
  7c64af3

  Copy full SHA for 7c64af3

Commits on Jul 7, 2010

• implemented GuideTree as wrapper for forester's Phylogeny

  Show description for ff58f3e
  markchapman

  committed
  ff58f3e

  Copy full SHA for ff58f3e

• implemented profile-profile alignment

  Show description for d64c0f7
  markchapman

  committed
  d64c0f7

  Copy full SHA for d64c0f7

Commits on Jun 30, 2010

• tests for alternate scorers

  Show description for c6c2469
  markchapman

  committed
  c6c2469

  Copy full SHA for c6c2469

• minor: use String.format("%n") for line separator

  Show description for c85d649
  markchapman

  committed
  c85d649

  Copy full SHA for c85d649

Commits on Jun 29, 2010

• tests for profile-profile alignment data structure

  Show description for 7f53cff
  markchapman

  committed
  7f53cff

  Copy full SHA for 7f53cff

• tests for local alignment and improved max and min alignment scores

  Show description for db65080
  markchapman

  committed
  db65080

  Copy full SHA for db65080

• fixed tests in maven

  Show description for 2b8ae33
  markchapman

  committed
  2b8ae33

  Copy full SHA for 2b8ae33

• minor: performance improvements from FindBugs

  Show description for 10a1802
  markchapman

  committed
  10a1802

  Copy full SHA for 10a1802

• tests, 1 bug fix, and minor updates

  Show description for 9253c9b
  markchapman

  committed
  9253c9b

  Copy full SHA for 9253c9b

Commits on Jun 21, 2010

• Location refactoring

  Show description for 2136be1
  markchapman

  committed
  2136be1

  Copy full SHA for 2136be1

Commits on Jun 19, 2010

• test files

  Show description for bffa577
  markchapman

  committed
  bffa577

  Copy full SHA for bffa577

Commits on Jun 17, 2010

• tests

  Show description for 966a6f8
  markchapman

  committed
  966a6f8

  Copy full SHA for 966a6f8

• simplified defaults (loads blosum62)

  Show description for d85bd95
  markchapman

  committed
  d85bd95

  Copy full SHA for d85bd95

• simplified defaults

  Show description for fb61f44
  markchapman

  committed
  fb61f44

  Copy full SHA for fb61f44

Commits on Jun 16, 2010

• tests

  Show description for b62bc0b
  markchapman

  committed
  b62bc0b

  Copy full SHA for b62bc0b

Pagination

Previous

Next