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May 20, 2009 11:21
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| $ git log | |
| commit e67014fc4a1040dd129a1e57d1994bed2831662b | |
| Author: shk3 <shk3@fcb5ba71-d80d-0410-8237-ba3920747fcc> | |
| Date: Wed May 20 09:47:15 2009 +0000 | |
| now using dept and formula information | |
| git-svn-id: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/bioclipse2/trunk@10609 fcb5ba71-d80d-0410-8237-ba3920747fcc | |
| commit c3eb7a1653cd185dd447c0788c1cc1e97b18abcf | |
| Author: jonalv <jonalv@fcb5ba71-d80d-0410-8237-ba3920747fcc> | |
| Date: Wed May 20 09:28:23 2009 +0000 | |
| abort to next method when run out of parameters to check in the method. fixes bug 1079 and most likely a bunch of other problems as well. | |
| git-svn-id: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/bioclipse2/trunk@10608 fcb5ba71-d80d-0410-8237-ba3920747fcc | |
| commit 078cc16e1a785673a1823ced5e209a8ff44264da | |
| Author: shk3 <shk3@fcb5ba71-d80d-0410-8237-ba3920747fcc> | |
| Date: Wed May 20 09:09:34 2009 +0000 | |
| added real-world seneca example | |
| git-svn-id: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/bioclipse2/trunk@10607 fcb5ba71-d80d-0410-8237-ba3920747fcc | |
| commit f79e65d791c02dcfb78a59dfbda5c6d94d02c844 | |
| Author: jonalv <jonalv@fcb5ba71-d80d-0410-8237-ba3920747fcc> | |
| Date: Wed May 20 09:00:00 2009 +0000 | |
| rewrote testLoadATPInWorkspaceJob into rethrowing any exceptions thrown in the WorkSpaceJob | |
| git-svn-id: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/bioclipse2/trunk@10606 fcb5ba71-d80d-0410-8237-ba3920747fcc | |
| commit 3342d1c7fb4c137f2ae1f61fd4869519181d4f9f | |
| Author: goglepox <goglepox@fcb5ba71-d80d-0410-8237-ba3920747fcc> | |
| Date: Wed May 20 08:48:37 2009 +0000 | |
| Changed Add bond toolbar button to use AddBondDragModule | |
| Also added PhantomGenerator to show to be added bonds | |
| Fixes bug #590 | |
| git-svn-id: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/bioclipse2/trunk@10605 fcb5ba71-d80d-0410-8237-ba3920747fcc | |
| commit 4806c6763a794d4cbfc4f04dfba0a8ef7cd395e9 | |
| Author: goglepox <goglepox@fcb5ba71-d80d-0410-8237-ba3920747fcc> | |
| Date: Wed May 20 08:48:06 2009 +0000 | |
| Added module to choose direction when adding bonds and a generator to show none commited changes | |
| [jchempaint-primary] jchempaint-primary@14593 | |
| git-svn-id: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/bioclipse2/trunk@10604 fcb5ba71-d80d-0410-8237-ba3920747fcc | |
| commit b2c284a780fbed705ba7e41d7eb63679fc09df86 | |
| Author: goglepox <goglepox@fcb5ba71-d80d-0410-8237-ba3920747fcc> | |
| Date: Wed May 20 08:47:35 2009 +0000 | |
| Removed source.include | |
| git-svn-id: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/bioclipse2/trunk@10603 fcb5ba71-d80d-0410-8237-ba3920747fcc | |
| commit ad16e3f59a518c5af937181140d6b6f05f8a6cfa | |
| Author: goglepox <goglepox@fcb5ba71-d80d-0410-8237-ba3920747fcc> | |
| Date: Wed May 20 08:46:48 2009 +0000 | |
| Added alternative generate star method | |
| git-svn-id: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/bioclipse2/trunk@10602 fcb5ba71-d80d-0410-8237-ba3920747fcc | |
| commit bf06fb1a6da1c4c327eb1255f7308a72e416d117 | |
| Author: goglepox <goglepox@fcb5ba71-d80d-0410-8237-ba3920747fcc> | |
| Date: Wed May 20 08:46:08 2009 +0000 | |
| Made inner class static and defined default color | |
| git-svn-id: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/bioclipse2/trunk@10601 fcb5ba71-d80d-0410-8237-ba3920747fcc | |
| commit 518626dafcd92e646806b10e9b682b20fc1d2930 | |
| Author: jonalv <jonalv@fcb5ba71-d80d-0410-8237-ba3920747fcc> | |
| Date: Wed May 20 08:45:01 2009 +0000 | |
| commented out and removed Structuredb references for now since structuredb is not compiling for the moment | |
| git-svn-id: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/bioclipse2/trunk@10600 fcb5ba71-d80d-0410-8237-ba3920747fcc | |
| commit 5bcd6ced81b16627f72bf7de551cfacdfe54cf57 | |
| Author: jonalv <jonalv@fcb5ba71-d80d-0410-8237-ba3920747fcc> | |
| Date: Wed May 20 08:44:14 2009 +0000 | |
| indentation | |
| git-svn-id: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/bioclipse2/trunk@10599 fcb5ba71-d80d-0410-8237-ba3920747fcc | |
| commit 7f6fac2443b39e6f35438e538cfc27ce9cb29f2c | |
| Author: ospjuth <ospjuth@fcb5ba71-d80d-0410-8237-ba3920747fcc> | |
| Date: Wed May 20 08:36:47 2009 +0000 | |
| Set feature version to 2.0.0.B20090520 and update bioclipse.product version. | |
| git-svn-id: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/bioclipse2/trunk@10598 fcb5ba71-d80d-0410-8237-ba3920747fcc | |
| commit 4d65bfc9cd2077c5eb42ad6f7ef612b0e1d99921 | |
| Author: egonw <egonw@fcb5ba71-d80d-0410-8237-ba3920747fcc> | |
| Date: Wed May 20 08:30:07 2009 +0000 | |
| Removed temporary test: again properly checks if instance location is set | |
| git-svn-id: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/bioclipse2/trunk@10597 fcb5ba71-d80d-0410-8237-ba3920747fcc | |
| commit 84139e56571480137d4f3f29e65b05f1a11d98e8 | |
| Author: ospjuth <ospjuth@fcb5ba71-d80d-0410-8237-ba3920747fcc> | |
| Date: Wed May 20 08:03:59 2009 +0000 | |
| Set version to 2.0.0.B20090520. | |
| git-svn-id: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/bioclipse2/trunk@10596 fcb5ba71-d80d-0410-8237-ba3920747fcc | |
| commit 9a6d4f2352258bd4d0122a07ff48e111e199cf3d | |
| Author: ospjuth <ospjuth@fcb5ba71-d80d-0410-8237-ba3920747fcc> | |
| Date: Wed May 20 08:03:18 2009 +0000 | |
| Set version to 2.0.0.B20090520. | |
| git-svn-id: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/bioclipse2/trunk@10595 fcb5ba71-d80d-0410-8237-ba3920747fcc | |
| commit f02004218c32a89e072d1bc73c7efca67f6e36da | |
| Author: ospjuth <ospjuth@fcb5ba71-d80d-0410-8237-ba3920747fcc> | |
| Date: Wed May 20 07:34:32 2009 +0000 | |
| Commented out deleteVirtalProject since causing exception on startup. It was put there 'just to be sure' that virtual project would be empt | |
| git-svn-id: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/bioclipse2/trunk@10594 fcb5ba71-d80d-0410-8237-ba3920747fcc | |
| commit 29d7909be5ef329aab9454da4c957e8a98b2c9bb | |
| Author: ospjuth <ospjuth@fcb5ba71-d80d-0410-8237-ba3920747fcc> | |
| Date: Wed May 20 07:17:25 2009 +0000 | |
| Delete temp file upon completed prediction. | |
| git-svn-id: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/bioclipse2/trunk@10593 fcb5ba71-d80d-0410-8237-ba3920747fcc | |
| commit dc623de23eeb0b768a6295f5d7c2845186c11b4f | |
| Author: ospjuth <ospjuth@fcb5ba71-d80d-0410-8237-ba3920747fcc> | |
| Date: Wed May 20 07:12:35 2009 +0000 | |
| Cleaned up instantiation, added comments, and removed static declarations. | |
| git-svn-id: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/bioclipse2/trunk@10592 fcb5ba71-d80d-0410-8237-ba3920747fcc | |
| commit 9f521704a4818c5feeb66cbd53b180923c0e517b | |
| Author: ospjuth <ospjuth@fcb5ba71-d80d-0410-8237-ba3920747fcc> | |
| Date: Wed May 20 07:09:22 2009 +0000 | |
| SmartsHit should always be colored in same color. | |
| git-svn-id: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/bioclipse2/trunk@10590 fcb5ba71-d80d-0410-8237-ba3920747fcc | |
| commit 3b1245941a3995f59b022206603b9d5a1a5ad979 | |
| Author: ospjuth <ospjuth@fcb5ba71-d80d-0410-8237-ba3920747fcc> | |
| Date: Wed May 20 07:09:00 2009 +0000 | |
| Added method 'public Color getHighlightingColor(IAtom atom);' so that ISubStructure can supply a color for the highlighting. | |
| git-svn-id: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/bioclipse2/trunk@10589 fcb5ba71-d80d-0410-8237-ba3920747fcc | |
| commit b874305b3295c1bf454fc00d69afcbedab177e84 | |
| Author: egonw <egonw@fcb5ba71-d80d-0410-8237-ba3920747fcc> | |
| Date: Wed May 20 06:47:54 2009 +0000 | |
| Remove debug output to STDOUT | |
| git-svn-id: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/bioclipse2/trunk@10587 fcb5ba71-d80d-0410-8237-ba3920747fcc | |
| commit c29fab5881c610b4b59fa6c1122c20dba7269ae7 | |
| Author: miguelrojasch <miguelrojasch@fcb5ba71-d80d-0410-8237-ba3920747fcc> | |
| Date: Wed May 20 06:08:55 2009 +0000 | |
| Updated to new manager | |
| git-svn-id: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/bioclipse2/trunk@10586 fcb5ba71-d80d-0410-8237-ba3920747fcc | |
| commit 97f49514b21d9280dd2f5b4c1a14b3b522457ab7 | |
| Author: miguelrojasch <miguelrojasch@fcb5ba71-d80d-0410-8237-ba3920747fcc> | |
| Date: Wed May 20 00:33:59 2009 +0000 | |
| removed bundle manager | |
| git-svn-id: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/bioclipse2/trunk@10585 fcb5ba71-d80d-0410-8237-ba3920747fcc | |
| commit 76d950c1b3dea755b38f729d5ceb4533c03db688 | |
| Author: lc69 <lc69@fcb5ba71-d80d-0410-8237-ba3920747fcc> | |
| Date: Tue May 19 23:05:59 2009 +0000 | |
| This is a working version except that the color is the same regardless of the prediction. The code still needs restructuring, comments etc. | |
| git-svn-id: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/bioclipse2/trunk@10584 fcb5ba71-d80d-0410-8237-ba3920747fcc | |
| commit 4187b556a51a2d9574c4abc9970609a32bc8222c | |
| Author: miguelrojasch <miguelrojasch@fcb5ba71-d80d-0410-8237-ba3920747fcc> | |
| Date: Tue May 19 22:52:34 2009 +0000 | |
| added needed bundle | |
| git-svn-id: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/bioclipse2/trunk@10583 fcb5ba71-d80d-0410-8237-ba3920747fcc | |
| commit 5be42429b12fe8ae913b7db196c8f38f43f0235e | |
| Author: miguelrojasch <miguelrojasch@fcb5ba71-d80d-0410-8237-ba3920747fcc> | |
| Date: Tue May 19 22:14:39 2009 +0000 | |
| Removed scaled coordinates for reactions. The File should have already the corrected coordinates. | |
| git-svn-id: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/bioclipse2/trunk@10582 fcb5ba71-d80d-0410-8237-ba3920747fcc | |
| commit 661966fe2894237be1de02a1857d3801c945bad4 | |
| Author: lc69 <lc69@fcb5ba71-d80d-0410-8237-ba3920747fcc> | |
| Date: Tue May 19 21:57:50 2009 +0000 | |
| Cleared a couple of lists and hashmaps that grow too much. | |
| git-svn-id: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/bioclipse2/trunk@10581 fcb5ba71-d80d-0410-8237-ba3920747fcc | |
| commit 4336ba594dd4705bac1873141f7f20bfb499d972 | |
| Author: miguelrojasch <miguelrojasch@fcb5ba71-d80d-0410-8237-ba3920747fcc> | |
| Date: Tue May 19 21:45:58 2009 +0000 | |
| Difference in dimension between boxes for width and height | |
| git-svn-id: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/bioclipse2/trunk@10580 fcb5ba71-d80d-0410-8237-ba3920747fcc | |
| commit b04a886399ee7077828bf3577443aaa92de1c3d0 | |
| Author: miguelrojasch <miguelrojasch@fcb5ba71-d80d-0410-8237-ba3920747fcc> | |
| Date: Tue May 19 21:36:23 2009 +0000 | |
| Implement synchronization between boxes and JCP | |
| git-svn-id: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/bioclipse2/trunk@10579 fcb5ba71-d80d-0410-8237-ba3920747fcc | |
| commit a31707bbce9326a2afffd44aeebc24c725a89805 | |
| Author: lc69 <lc69@fcb5ba71-d80d-0410-8237-ba3920747fcc> | |
| Date: Tue May 19 20:55:33 2009 +0000 | |
| Checking in a preliminary prototype. It needs restructuring and removal of a lot of print statements. | |
| git-svn-id: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/bioclipse2/trunk@10578 fcb5ba71-d80d-0410-8237-ba3920747fcc | |
| commit 864bd068640c4c5bf6c93d65214a919dbe5122b7 | |
| Author: egonw <egonw@fcb5ba71-d80d-0410-8237-ba3920747fcc> | |
| Date: Tue May 19 20:37:30 2009 +0000 | |
| Disabled recording right now, as it is giving NullPointerExceptions for me (see #1086) | |
| From: Egon Willighagen <egon.willighagen@gmail.com> | |
| git-svn-id: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/bioclipse2/trunk@10577 fcb5ba71-d80d-0410-8237-ba3920747fcc | |
| commit fbdc4baf0c9de1d6169e21225291fe048d7c5d63 | |
| Author: egonw <egonw@fcb5ba71-d80d-0410-8237-ba3920747fcc> | |
| Date: Tue May 19 20:37:07 2009 +0000 | |
| Moved spring config file in the correct location (Jonathan's great idea! jonalv++) | |
| From: Egon Willighagen <egon.willighagen@gmail.com> | |
| git-svn-id: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/bioclipse2/trunk@10576 fcb5ba71-d80d-0410-8237-ba3920747fcc | |
| commit dd89dab60bd33dd963d268fcfe6abf5bd9a3ffdc | |
| Author: egonw <egonw@fcb5ba71-d80d-0410-8237-ba3920747fcc> | |
| Date: Tue May 19 20:36:42 2009 +0000 | |
| moved pick workspacedialog to ui plugin because that's where it's needed for setting up the workspace before depending code is run. | |
| Also moved Spring extender starting code from ui to core to no success... :( | |
| From: jonalv <jonalv@fcb5ba71-d80d-0410-8237-ba3920747fcc> | |
| git-svn-id: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/bioclipse2/trunk@10575 fcb5ba71-d80d-0410-8237-ba3920747fcc | |
| commit 1e6b3cb88f44d66afbc11073e808f25557a14cbb | |
| Author: egonw <egonw@fcb5ba71-d80d-0410-8237-ba3920747fcc> | |
| Date: Tue May 19 20:35:58 2009 +0000 | |
| removed remains of net.bioclipse.managers and net.bioclipse.recording plugins. | |
| From: jonalv <jonalv@fcb5ba71-d80d-0410-8237-ba3920747fcc> | |
| git-svn-id: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/bioclipse2/trunk@10574 fcb5ba71-d80d-0410-8237-ba3920747fcc | |
| commit 5409031becdf18f1e9817f4c7ed4c7b04531a36f | |
| Author: egonw <egonw@fcb5ba71-d80d-0410-8237-ba3920747fcc> | |
| Date: Tue May 19 20:35:25 2009 +0000 | |
| merged net.bioclipse.recording into net.bioclipse.core | |
| From: jonalv <jonalv@fcb5ba71-d80d-0410-8237-ba3920747fcc> | |
| git-svn-id: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/bioclipse2/trunk@10573 fcb5ba71-d80d-0410-8237-ba3920747fcc | |
| commit 9de521b49a8cca5b23b48030dddd8ddac58e8d51 | |
| Author: egonw <egonw@fcb5ba71-d80d-0410-8237-ba3920747fcc> | |
| Date: Tue May 19 20:33:29 2009 +0000 | |
| merged net.bioclipse.managers into net.bioclipse.core | |
| From: jonalv <jonalv@fcb5ba71-d80d-0410-8237-ba3920747fcc> | |
| git-svn-id: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/bioclipse2/trunk@10572 fcb5ba71-d80d-0410-8237-ba3920747fcc | |
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