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asterix-gerrit.ics.uci.edu / hyracks / daaaade0ad7c65e40aa8580eacf0261d5dfecb8a / genomix / genomix-pregelix
  1. daaaade Merge with code review by Anbang Xu · 12 years ago
  2. b41f87f Code review on removeTip -- 2013.9.25 by Anbang Xu · 12 years ago
  3. 01927ed Add log to removetip by Anbang Xu · 12 years ago
  4. 0d1f7ba Apply logReadIds to EdgeWritable by Anbang Xu · 12 years ago
  5. f65b2e5 Add logReadIds option to driver by Anbang Xu · 12 years ago
  6. bf8d060 ADD #iteration to log by Anbang Xu · 12 years ago
  7. 6b5caff Extract common method for P1 and P4 by Anbang Xu · 12 years ago
  8. aafca2f Add logging to P1 by Anbang Xu · 12 years ago
  9. 9614206 Merge branch 'genomix/fullstack_genomix' of https://code.google.com/p/hyracks into genomix/fullstack_genomix by Anbang Xu · 12 years ago
  10. ed271fd ADD some comments by Anbang Xu · 12 years ago
  11. 08d4d04 reformat code and remove some debug checks (msgs only from neighbors anyway) by Jake Biesinger · 12 years ago
  12. 8ba5da2 fix NPE for debugKmers by Jake Biesinger · 12 years ago
  13. 09036bb add cmdline option to specify kmers to log by Jake Biesinger · 12 years ago
  14. a3ec17d Merge branch 'genomix/fullstack_genomix' into wbiesing/refactor_p4 by Jake Biesinger · 12 years ago
  15. 807b452 Add more restriction for chooseMergedir by Anbang Xu · 12 years ago
  16. 59ee6a1 Prepare to run P1 by Anbang Xu · 12 years ago
  17. fd9229e Clean up code and move to cluster to test P0 by Anbang Xu · 12 years ago
  18. 82a9005 P0(refactor version of P1) pass all small testcases by Anbang Xu · 12 years ago
  19. e5ddfc4 Sender msg edgetype need to fix by Anbang Xu · 12 years ago
  20. 671cf67 Simply P1 and add throw Exception to it by Anbang Xu · 12 years ago
  21. 8009477 Refactor P1 by Anbang Xu · 12 years ago
  22. 0a04676 use a list of kmers for verbose mode by Jake Biesinger · 12 years ago
  23. 65a8336 Keep old version of ComplexBubbleMerge by Anbang Xu · 12 years ago
  24. b6a3caff Refactoring BubbleMerge by Anbang Xu · 12 years ago
  25. a128e4b Simplify the main compute function of removetip and removelowcoverage by Anbang Xu · 12 years ago
  26. 1c73130 Refactor removeLowCoverage by Anbang Xu · 12 years ago
  27. 9908512 Refactor tipremove by Anbang Xu · 12 years ago
  28. 14f3c71 Add DIR.edgeType() to covert dir to edgeTypew by Anbang Xu · 12 years ago
  29. f91c5bb Refactor broadcaseMerge to sendMergeMsg by Anbang Xu · 12 years ago
  30. cb7ebcd Finish integration by Anbang Xu · 12 years ago
  31. 0958af1 Pass tests by Anbang Xu · 12 years ago
  32. 88e742e Fix other pattherns by Anbang Xu · 12 years ago
  33. 205471f Apply EDGETYPE to P4 by Anbang Xu · 12 years ago
  34. f7d0baf Add enum EDGETYPE by Anbang Xu · 12 years ago
  35. ada697a add option for verbose and log (one of) the problem kmer(s) by Jake Biesinger · 12 years ago
  36. f709d73 Merge with Jake's refactor branch by Anbang Xu · 12 years ago
  37. af493b5 Prepare to integrate by Anbang Xu · 12 years ago genomix/anbangx/before-pathmerge-refactor genomix/old-code v1.4
  38. ba2b0a7 only check for tandem repeats at start and after merge (not after updates) by Jake Biesinger · 12 years ago
  39. a4a5ae9 more consistent voteToHalt/activate in P4 by Jake Biesinger · 12 years ago
  40. 4494560 code review on P4 refactor by Jake Biesinger · 12 years ago
  41. f54b5e9 Fix syntax errors in P1 (probably still broken though) by Jake Biesinger · 12 years ago
  42. 6a19516 refactor of P4 passes test cases (P1 broken) by Jake Biesinger · 12 years ago
  43. db9186e Merge updateState and sendMsg into on step by Anbang Xu · 12 years ago
  44. ec97be2 Integrate with Jake's enum mergeDir by Anbang Xu · 12 years ago
  45. bc17671 Add some function util by Anbang Xu · 12 years ago
  46. 8fa68de use getDest by Anbang Xu · 12 years ago
  47. 3b5c6bd WIP: refactor P4 (broken) by Jake Biesinger · 12 years ago
  48. 6efdb29 fix logging file for pregelix test cases by Jake Biesinger · 12 years ago
  49. ff90e10 Add an iterable for Edge keys by Jake Biesinger · 12 years ago
  50. 21e8120 getDestVertexId has some issues, which may cause problem on P4 by Anbang Xu · 12 years ago
  51. ecdc0f6 Make setReplaceDir and setDeleteDir by Anbang Xu · 12 years ago
  52. 88640f6 Use mergeDir in check condition and move setMergeDir and sendUpdateMsg out of check condition by Anbang Xu · 12 years ago
  53. 3afaa26 Simply sendMergeMsg() by Anbang Xu · 12 years ago
  54. 1848aa3 Process information before sending message by Anbang Xu · 12 years ago
  55. af88e04 Aggregate all the incomingMsgs first, then make a decision based aggregateMsg by Anbang Xu · 12 years ago
  56. 9703a5c Change non-head to path by Anbang Xu · 12 years ago
  57. 1491f7f refactor to use general NEXT and PREVIOUS directions by Anbang Xu · 12 years ago
  58. 2876f0e Merge branch 'anbangx/code_review2' into genomix/fullstack_genomix by Anbang Xu · 12 years ago
  59. f307307 Clean up some code by Anbang Xu · 12 years ago
  60. efbeca5 Simplifying sendSettleMsgs by Anbang Xu · 12 years ago
  61. ee1e1e1 bit clean and move the member of subclass to derived class by Anbang Xu · 12 years ago
  62. 53cc7e3 Merge branch 'wbiesing/debug' into genomix/fullstack_genomix by Jake Biesinger · 12 years ago
  63. 2bdc6fb Combine setNext/PrevToMeDir to setNeighborToMeDir(boolean) and throw exception when the merge dir degree is not 1 by Anbang Xu · 12 years ago
  64. deeb3c8 REMOVE isfilp in sendMergeMsg() by Anbang Xu · 12 years ago
  65. 5dbc4e9 Call node.updateEdges directly by Anbang Xu · 12 years ago
  66. 7b773fd Change Num_TandemRepeat to Num_Cycles by Anbang Xu · 12 years ago
  67. b237604 Seperate function for each block in each iteration by Anbang Xu · 12 years ago
  68. 4273653 add ThreeNodesCycle, and it succeeds to pass test by Anbang Xu · 12 years ago
  69. 87dace3 Whenever detect the cycle, don't remove tandem repeats but DO stop merging by Anbang Xu · 12 years ago
  70. 065aaeb Clean up some feedbacks from code review by Anbang Xu · 12 years ago
  71. 05f3eff Move all the setCounter to the end of this iteration by Anbang Xu · 12 years ago
  72. 0e9ff97 Use incomingMsg as a parameter in processMerge() by Anbang Xu · 12 years ago
  73. 1b8fc71 Move the checking condition outside the loop by Anbang Xu · 12 years ago
  74. 63c251c Pass incomingMsg as parameter in processUpdate() by Anbang Xu · 12 years ago
  75. daabce7 Simplifying all the setSateAsMergeDir by Anbang Xu · 12 years ago
  76. 6d3e6da Simplifing all the sendUpdateMsg by Anbang Xu · 12 years ago
  77. 4e0d144 add structural constraints to update directions by Jake Biesinger · 12 years ago
  78. 50e83b4 Combine ifFlipWithNext/Prev() to ifFlipWithNeighbor(boolean withPredecessor) and combine configureUpdateMsgFroPredecessor/Successor to sendUpdateMsg by Anbang Xu · 12 years ago
  79. aea52c1 fix P4 to use (already available) cmdline random seed by Jake Biesinger · 12 years ago
  80. de16f37 add AlreadyInEdge test case by Jake Biesinger · 12 years ago
  81. 972050a DON'T NEED TO SEARCH for this edge when sendUpdateMsg, so change it to get dir directly by Anbang Xu · 12 years ago
  82. 89e09d0 Code review on P4 -- 2013.9.16 by Anbang Xu · 12 years ago
  83. d8f9809 Merge with debug branch, which has one testcase and add real randomSeed by Anbang Xu · 12 years ago
  84. 21c030c clean up the code by Anbang Xu · 12 years ago
  85. aeb6a54 Seperate set state's MergeDir and sendUpdateMsgToNeighbor by Anbang Xu · 12 years ago
  86. 2250399 Change head/halt flag to check the vertex internal structure by Anbang Xu · 12 years ago
  87. 4575fb7 Extend flag of headMergeDir from 1-bit to 2-bit by Anbang Xu · 12 years ago
  88. c079e59 Change state/message flag from byte to short by Anbang Xu · 12 years ago
  89. bdecb7f Prepare to change state by Anbang Xu · 12 years ago
  90. e53a2fb Try to use check condition in vertex state instead of give a isHalt state flag, but it occurs some errors by Anbang Xu · 12 years ago
  91. 84539c0 Add isUnMergeVertex() by Anbang Xu · 12 years ago
  92. eca45b7 Change should to can, make it more meaningful by Anbang Xu · 12 years ago
  93. 8efea88 Move isHaltNode() outside the function in initState() by Anbang Xu · 12 years ago
  94. 0f1f820 clean up code by Anbang Xu · 12 years ago
  95. 43b3f56 Keep only one isTandemRepeat() by Anbang Xu · 12 years ago
  96. a7e295c Make getCopyWithoutTandemRepeats() function by Anbang Xu · 12 years ago
  97. a20c75e Remove some unnecessary flag by Anbang Xu · 12 years ago
  98. a864eb2 Move extra logic(check if it is a valid head) to inside of the function by Anbang Xu · 12 years ago
  99. a3b5878 change curKmer/preKmer/nextKmer from deep copy to shallow copy by Anbang Xu · 12 years ago
  100. e929dfc don't need to create "randGenerator" every iteration by Anbang Xu · 12 years ago