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Commits on Jul 25, 2014

• simplify Makefile for publication

  crclark

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Commits on Jul 15, 2014

• dynparams no longer makes rates larger than input rates, and add experimental objectives Rob Patro suggested

  crclark

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Commits on Jul 11, 2014

• removed unused functions in Alignment class and refactored slightly.

  crclark

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  9e9d831

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• remove superfluous v1Unaligned data structure from Alignment class

  crclark

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Commits on Jul 10, 2014

• optimized conservedCount and inducedCount

  crclark

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• replaced strings with enumerated types for tracking fitness objectives

  crclark

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• store GOC and bitscore data in multi_array for performance increase

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Commits on Jul 9, 2014

• separate reporting of objectives from optimization of objectives in .info file. Can now report objectives that are not optimized. Added new args to specify goc and blastsum objectives separately fr…

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Commits on Jun 30, 2014

• more work on seed-and-extend

  crclark

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Commits on Jun 27, 2014

• starting seed-and-extend algo

  crclark

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Commits on Jun 25, 2014

• added S3's denominator as a separate objective to be minimized, allowing us to ensure EC always goes up

  crclark

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Commits on Jun 21, 2014

• forgot a semicolon

  crclark

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• Added S3 score from MAGNA

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Commits on Jun 20, 2014

• remove check for node of degree 0 -- impossible with network input format

  crclark

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  59bf4b8

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• Now using currInducedCount to compute ICS

  crclark

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  5143cea

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• currInducedCount works after partial mutation and crossover

  crclark

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• currInducedCount now consistent after crossover. Not yet tested on partial alignments, however.

  crclark

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  4b4b064

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• currInducedCount now consistent after doSwap and mutate. Not yet implemented for crossover.

  crclark

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  e7b5b45

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• induced count function. Not added to mutation, doSwap, or crossover functions, yet.

  crclark

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  49bea07

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• currInducedCount added, and correct after aln initialization. Not yet working after modifications to aln.

  crclark

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  95d81fc

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• fixed bug in alnInv updating in doSwap

  crclark

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  4ce2c4e

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• beginning memoization of ics denominator. Bug in alnInv still, though

  crclark

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  fd80f09

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Commits on Jun 19, 2014

• deleted some old comments

  crclark

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Commits on Jun 18, 2014

• hillclimbing that actually works

  crclark

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  971a9b3

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• replace explicit choice of prng type with typedef in Network.h

  crclark

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Commits on Jun 17, 2014

• modified greedy matching function to use either bitscores or GOC

  crclark

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Commits on Jun 16, 2014

• drastically simplified conserved edge counting. Also fixes self-loop bugs.

  crclark

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• remove debug cout statement

  crclark

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• GOC confirmed working when local search turned off. Next, need it to work with local search on.

  crclark

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  0c60305

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Commits on Jun 15, 2014

• adding GOC objective. Currently broken.

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Commits on Jun 13, 2014

• fixed stupid performance bug

  crclark

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  e5b568d

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Commits on Jun 11, 2014

• rewrote greedy bitscore match algorithm

  crclark

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Commits on Jun 10, 2014

• proportional time local search and one half fast matching

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Commits on Jun 9, 2014

• tracking which nodes of v1 are unaligned so as to speed up local search optimization of alignment size.

  crclark

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Commits on Jun 6, 2014

• added local seearch to loop, optionally

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