{"push_id":623992124,"size":46,"distinct_size":46,"ref":"refs/heads/master","head":"b1f10f10f6b00c21ce78d36137759ae4457cd5e9","before":"d513726edbc36a6334f6fb50ac2104d34b41c987","commits":[{"sha":"273dc2d83247ff09db873bc9bbc20dd160d4546d","author":{"email":"741eca2f5b7d96cecce15a60ae98ba1a7e50de37@ucsd.edu","name":"Spencer Bliven"},"message":"Excluding ECOD tests from compilation\n\nDownloading two 70MB files is slow and prone to connection errors.","distinct":true,"url":"https://api.github.com/repos/heuermh/biojava/commits/273dc2d83247ff09db873bc9bbc20dd160d4546d"},{"sha":"ec0da5bb8cece767caa2ca768d6d3e8dfd9f9aa6","author":{"email":"38dd49c8e608e145033926106a20601c57740a61@gmail.com","name":"lafita"},"message":"Changed the DisplayAFP, line 76, to color correctly the alignment\n(because if the alignment is not FatCat the unaligned residues were\ncolored as well).","distinct":true,"url":"https://api.github.com/repos/heuermh/biojava/commits/ec0da5bb8cece767caa2ca768d6d3e8dfd9f9aa6"},{"sha":"91c727c0645eb1e2af1e1e6bddee0ac0f827dab8","author":{"email":"38dd49c8e608e145033926106a20601c57740a61@gmail.com","name":"lafita"},"message":"Modified the updateSuperposition method to calculate also the RMSD and\nTMscores for each alignment block (subunit).","distinct":true,"url":"https://api.github.com/repos/heuermh/biojava/commits/91c727c0645eb1e2af1e1e6bddee0ac0f827dab8"},{"sha":"97924c5a1045c3c8dd05f70e4da63ce9f8123a67","author":{"email":"741eca2f5b7d96cecce15a60ae98ba1a7e50de37@ucsd.edu","name":"Spencer Bliven"},"message":"First round of fixes to ECOD format\n\nFormat was updated slightly in response to our testing, but some\nproblems and inconsistencies remain.","distinct":true,"url":"https://api.github.com/repos/heuermh/biojava/commits/97924c5a1045c3c8dd05f70e4da63ce9f8123a67"},{"sha":"ae8ca434f54e63d03d5fb19f87b06885f2a9ba1a","author":{"email":"741eca2f5b7d96cecce15a60ae98ba1a7e50de37@ucsd.edu","name":"Spencer Bliven"},"message":"More ECOD format changes\n\nAll files now have the proper 14-field format","distinct":true,"url":"https://api.github.com/repos/heuermh/biojava/commits/ae8ca434f54e63d03d5fb19f87b06885f2a9ba1a"},{"sha":"7ee97557d6b31d3c031917612178031a97fe8483","author":{"email":"38dd49c8e608e145033926106a20601c57740a61@gmail.com","name":"lafita"},"message":"Moved the notifymatrix listener and added some comments to the trace\nmanipulation in the CECalculator, in order to find were the blackout\nregions were being ignored and because of that the optimization used\nthem.","distinct":true,"url":"https://api.github.com/repos/heuermh/biojava/commits/7ee97557d6b31d3c031917612178031a97fe8483"},{"sha":"5e1631fa7dad22b9a61b28049aa30ace50737173","author":{"email":"741eca2f5b7d96cecce15a60ae98ba1a7e50de37@ucsd.edu","name":"Spencer Bliven"},"message":"Improving memory efficiency of EcodFactory\n\nSwitch to a soft cache to avoid OutOfMemoryErrors.","distinct":true,"url":"https://api.github.com/repos/heuermh/biojava/commits/5e1631fa7dad22b9a61b28049aa30ace50737173"},{"sha":"f9eef59572f922c02c945ef7f5e7b5469057b308","author":{"email":"741eca2f5b7d96cecce15a60ae98ba1a7e50de37@ucsd.edu","name":"Spencer Bliven"},"message":"Merge branch 'noEcodTest' into minor","distinct":true,"url":"https://api.github.com/repos/heuermh/biojava/commits/f9eef59572f922c02c945ef7f5e7b5469057b308"},{"sha":"1f8d0e9893be8157f40dca95993765052eff4812","author":{"email":"3bc6f2208b90542717470de5278f48ae0e983c97@bliven.us","name":"Spencer Bliven"},"message":"Merge pull request #261 from sbliven/minor\n\nECOD updates + merge patch","distinct":true,"url":"https://api.github.com/repos/heuermh/biojava/commits/1f8d0e9893be8157f40dca95993765052eff4812"},{"sha":"ca1f9c7450e186a41419fbcc96ca196b0d5f0a1e","author":{"email":"91f813dc766ff6406c0f23361489fabb3e8e75b9@gmail.com","name":"dmyersturnbull"},"message":"Added a more complex test for NeedlemanWunsch using an alignment done by hand.","distinct":true,"url":"https://api.github.com/repos/heuermh/biojava/commits/ca1f9c7450e186a41419fbcc96ca196b0d5f0a1e"},{"sha":"d520274d95c959b6adb347abdb3f086214424f70","author":{"email":"741eca2f5b7d96cecce15a60ae98ba1a7e50de37@ucsd.edu","name":"Spencer Bliven"},"message":"Merge branch 'patch' into minor","distinct":true,"url":"https://api.github.com/repos/heuermh/biojava/commits/d520274d95c959b6adb347abdb3f086214424f70"},{"sha":"6a429ff3a4391ce33f602a10ca501a9047b8a228","author":{"email":"741eca2f5b7d96cecce15a60ae98ba1a7e50de37@ucsd.edu","name":"Spencer Bliven"},"message":"Merge branch 'minor' into master","distinct":true,"url":"https://api.github.com/repos/heuermh/biojava/commits/6a429ff3a4391ce33f602a10ca501a9047b8a228"},{"sha":"d28a601a8334f475cdcf8e96bf2bf4b3333a90fd","author":{"email":"398770e7cdca9ffd35e14fa1d0ab99f50437e27f@gmail.com","name":"josemduarte"},"message":"Added another test for CrystalBuilder","distinct":true,"url":"https://api.github.com/repos/heuermh/biojava/commits/d28a601a8334f475cdcf8e96bf2bf4b3333a90fd"},{"sha":"70fe0fdf0b0ce26a15cd87e4120398c68daf7c79","author":{"email":"398770e7cdca9ffd35e14fa1d0ab99f50437e27f@gmail.com","name":"josemduarte"},"message":"Merge branch 'patch' into minor","distinct":true,"url":"https://api.github.com/repos/heuermh/biojava/commits/70fe0fdf0b0ce26a15cd87e4120398c68daf7c79"},{"sha":"1c86ee5b156c1d8e1b0ddb99499b96230ae9000a","author":{"email":"398770e7cdca9ffd35e14fa1d0ab99f50437e27f@gmail.com","name":"josemduarte"},"message":"Merge branch 'minor'","distinct":true,"url":"https://api.github.com/repos/heuermh/biojava/commits/1c86ee5b156c1d8e1b0ddb99499b96230ae9000a"},{"sha":"bc96c5122fb7d307a92396157fcf4779d293c53f","author":{"email":"38dd49c8e608e145033926106a20601c57740a61@gmail.com","name":"lafita"},"message":"Added a new parameter to the AFPChain class to control the color of the\nsubunits (blocks) in the jmol and alignment panel for the CE-Symm. This\nparameter is used in StructureAlignmentJmol and AligPanel to set the\ncolor of the blocks (if the parameter is null the default color is set).\nA bug in the coloring of the blocks in AligPanel has ben fixed, because\na variables was incremented before a statement. Furthermore, when\ncoloring the gaps the spaces in the symb variable of AFPChain are not\nconsidered if the alignment is not FatCat, which has also been changed.","distinct":true,"url":"https://api.github.com/repos/heuermh/biojava/commits/bc96c5122fb7d307a92396157fcf4779d293c53f"},{"sha":"30cc0b46db42ec0051ffe6b9205043e262cfca96","author":{"email":"38dd49c8e608e145033926106a20601c57740a61@gmail.com","name":"lafita"},"message":"Added new methods to the AlignmentTools class: a method to calculate the\ngaps in each block of an optimal alignment and a method to replace the\noptimal alignment of an AFPChain.","distinct":true,"url":"https://api.github.com/repos/heuermh/biojava/commits/30cc0b46db42ec0051ffe6b9205043e262cfca96"},{"sha":"576fbd3e0ec20d1a698bd89a58512fdee6ef4b3d","author":{"email":"741eca2f5b7d96cecce15a60ae98ba1a7e50de37@ucsd.edu","name":"Spencer Bliven"},"message":"Add CrystalCell method to convert operators to function on the unit cell","distinct":true,"url":"https://api.github.com/repos/heuermh/biojava/commits/576fbd3e0ec20d1a698bd89a58512fdee6ef4b3d"},{"sha":"2fa8dd3c6edf82702ae2c6f16f801d84bed81b1b","author":{"email":"3bc6f2208b90542717470de5278f48ae0e983c97@bliven.us","name":"Spencer Bliven"},"message":"Merge pull request #262 from sbliven/minor\n\nAdd CrystalCell method to convert operators to function on the unit cell","distinct":true,"url":"https://api.github.com/repos/heuermh/biojava/commits/2fa8dd3c6edf82702ae2c6f16f801d84bed81b1b"},{"sha":"487246e741226dd463743960d71a003a9cf6b201","author":{"email":"741eca2f5b7d96cecce15a60ae98ba1a7e50de37@ucsd.edu","name":"Spencer Bliven"},"message":"Merge branch 'minor' into master","distinct":true,"url":"https://api.github.com/repos/heuermh/biojava/commits/487246e741226dd463743960d71a003a9cf6b201"}]}