1.0.1 SVN log

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r2497 | ospjuth | 2007-02-01 11:10:19 +0100 (Thu, 01 Feb 2007) | 1 line

Select 3D childresource on parse if exists. Solves 1649551.


r2495 | ospjuth | 2007-02-01 11:05:17 +0100 (Thu, 01 Feb 2007) | 1 line

Fixed javadoc and removed unused code


r2494 | ospjuth | 2007-02-01 10:02:20 +0100 (Thu, 01 Feb 2007) | 1 line

Set up listeners with TODOs for strand and monomer highlighting, pending CDK bugs 1649507 and 1649511.


r2493 | ospjuth | 2007-01-31 18:04:03 +0100 (Wed, 31 Jan 2007) | 1 line

Fixed saveAs in TextEditor. Works for Mol->CML but not the other way around...


r2492 | ospjuth | 2007-01-31 17:35:36 +0100 (Wed, 31 Jan 2007) | 1 line

Fixed creation of Resources with a dedicated type and parsedObject without parsing. This solves some errors in the SaveAs bug.


r2490 | egonw | 2007-01-31 15:23:51 +0100 (Wed, 31 Jan 2007) | 2 lines

Fix: don't try to write XYZ when no 3D coords are given. That fails. This should use the DataFeature approach, but that is outside the scope of 1.0.1.


r2489 | egonw | 2007-01-31 15:22:17 +0100 (Wed, 31 Jan 2007) | 2 lines

Try to write a ChemFile first, before resorting to getAllInOneAtomContainer. It should be a bit more fine grained really, though. But that's outside the scope of 1.0.1.


r2488 | egonw | 2007-01-31 15:20:36 +0100 (Wed, 31 Jan 2007) | 2 lines

One more try: added missing get method for the field originalResource.


r2487 | egonw | 2007-01-31 15:17:03 +0100 (Wed, 31 Jan 2007) | 2 lines

Revert patch r2486: that was supposed to commit just one file :(


r2486 | egonw | 2007-01-31 15:15:17 +0100 (Wed, 31 Jan 2007) | 2 lines

Added missing get method for original resource.


r2485 | ospjuth | 2007-01-31 13:54:12 +0100 (Wed, 31 Jan 2007) | 1 line

Fixed correct formats supported in SaveAs


r2484 | ospjuth | 2007-01-31 13:47:17 +0100 (Wed, 31 Jan 2007) | 1 line

Added for SaveAs commit


r2483 | ospjuth | 2007-01-31 13:45:33 +0100 (Wed, 31 Jan 2007) | 3 lines

Updated the SaveAsDialog with implementations for CDK, JCP, and TextEditor. Saving in other molecular formats is not working, seems like a serialization problem. This patch must be applied to trunk after fixing CDKResource.saveInFormat(IBioResourceFormat) is fixed.


r2481 | ospjuth | 2007-01-31 11:43:57 +0100 (Wed, 31 Jan 2007) | 1 line

Fixed PDBExtractor to work with DNA SEQRES


r2456 | ospjuth | 2007-01-28 15:56:21 +0100 (Sun, 28 Jan 2007) | 1 line

Added .bin to .svnignore


r2437 | egonw | 2007-01-27 00:34:18 +0100 (Sat, 27 Jan 2007) | 1 line

Better output on the CML validation action. Closes #1639424.


r2436 | egonw | 2007-01-27 00:18:53 +0100 (Sat, 27 Jan 2007) | 1 line

Fixed typo.


r2434 | egonw | 2007-01-26 23:39:15 +0100 (Fri, 26 Jan 2007) | 1 line

Fix a problem with servers that don't use Content-Length:


r2433 | egonw | 2007-01-26 22:28:06 +0100 (Fri, 26 Jan 2007) | 1 line

Applied patch in trunk/ to fix Atom 1.0 reading from blogger.com


r2428 | egonw | 2007-01-26 21:29:27 +0100 (Fri, 26 Jan 2007) | 1 line

Ported use of the ChildResourceCreator (path 1804)


r2423 | ospjuth | 2007-01-26 16:01:21 +0100 (Fri, 26 Jan 2007) | 1 line

Updated for Eclipse 3.2.1


r2422 | ospjuth | 2007-01-26 15:30:18 +0100 (Fri, 26 Jan 2007) | 1 line

Adapted for Eclipse Europa (3.2.1)


r2421 | egonw | 2007-01-26 15:29:00 +0100 (Fri, 26 Jan 2007) | 1 line

Added Chemical blogspace.


r2420 | ospjuth | 2007-01-26 15:28:59 +0100 (Fri, 26 Jan 2007) | 1 line

Adapted for Eclipse Europa (3.2.1)


r2419 | ospjuth | 2007-01-26 15:27:54 +0100 (Fri, 26 Jan 2007) | 1 line

Adapted for Eclipse Europa (3.2.1)


r2418 | ospjuth | 2007-01-26 15:24:07 +0100 (Fri, 26 Jan 2007) | 1 line

Updated for Eclipse 3.2.1


r2417 | ospjuth | 2007-01-26 15:17:38 +0100 (Fri, 26 Jan 2007) | 1 line

Removed organic folder from bc_data as it is now in bc_blueobelisk_data


r2414 | ospjuth | 2007-01-26 13:41:14 +0100 (Fri, 26 Jan 2007) | 1 line

Setup for Save As... redesign


r2409 | ospjuth | 2007-01-26 11:30:14 +0100 (Fri, 26 Jan 2007) | 1 line

Fixed starting NULL's when PDB converted into sequence. Solves 1640833.


r2402 | egonw | 2007-01-25 16:25:31 +0100 (Thu, 25 Jan 2007) | 2 lines

Deleted obsolete files, which completely confusing me.


r2401 | ospjuth | 2007-01-25 15:59:39 +0100 (Thu, 25 Jan 2007) | 2 lines

Fixed disallowing of double-click for childResources SequenceExtractor and PDBCDKChildCreator. Solves 1640850.


r2398 | ospjuth | 2007-01-25 15:37:01 +0100 (Thu, 25 Jan 2007) | 1 line

Added isParsable() and isEditable() to IBioResource with default=true.


r2397 | ospjuth | 2007-01-25 15:23:45 +0100 (Thu, 25 Jan 2007) | 1 line

Fixed AA highlighting in Jmol for correct resource only. Solves 1640839.


r2395 | egonw | 2007-01-25 15:20:52 +0100 (Thu, 25 Jan 2007) | 2 lines

Fixes problem with creating new spectrum resources with peaks of zero (=unknown?) intensity (closes #1548402).


r2390 | ospjuth | 2007-01-25 12:53:30 +0100 (Thu, 25 Jan 2007) | 1 line

Make SequenceViewer send IBioresource with scripts


r2388 | ospjuth | 2007-01-25 12:52:13 +0100 (Thu, 25 Jan 2007) | 1 line

Set up JmolScruptEngine and JmolView to use new scripting functionality with an additional IBioResource


r2387 | ospjuth | 2007-01-25 12:49:33 +0100 (Thu, 25 Jan 2007) | 1 line

Adapted delegator for new scripting functionality


r2385 | ospjuth | 2007-01-25 12:48:13 +0100 (Thu, 25 Jan 2007) | 1 line

Allows to run scripts on a specific resource


r2383 | ospjuth | 2007-01-25 11:22:38 +0100 (Thu, 25 Jan 2007) | 1 line

Added convenience method to retrieve child by name


r2379 | egonw | 2007-01-23 12:48:56 +0100 (Tue, 23 Jan 2007) | 2 lines

OK, it now properly handles multiple TOC EPs per plugin.


r2378 | egonw | 2007-01-23 12:24:40 +0100 (Tue, 23 Jan 2007) | 1 line

OK, Mac OS/X does not have the cp -t option, so just copy the whole lot. Ola, does it have rsync?


r2375 | egonw | 2007-01-23 09:58:23 +0100 (Tue, 23 Jan 2007) | 1 line

Created script to create help website for Bioclipse


r2374 | edrin_t | 2007-01-23 00:37:35 +0100 (Tue, 23 Jan 2007) | 1 line

this script should work


r2373 | edrin_t | 2007-01-23 00:36:25 +0100 (Tue, 23 Jan 2007) | 1 line

not compatible with webservice version


r2372 | edrin_t | 2007-01-23 00:35:32 +0100 (Tue, 23 Jan 2007) | 1 line

not compatible with webservice version


r2371 | edrin_t | 2007-01-23 00:34:45 +0100 (Tue, 23 Jan 2007) | 1 line

wrong folder


r2370 | edrin_t | 2007-01-23 00:34:09 +0100 (Tue, 23 Jan 2007) | 1 line

sample scripts


r2369 | edrin_t | 2007-01-23 00:33:13 +0100 (Tue, 23 Jan 2007) | 1 line

not compatible script


r2368 | edrin_t | 2007-01-23 00:31:55 +0100 (Tue, 23 Jan 2007) | 1 line

sample scripts


r2367 | edrin_t | 2007-01-23 00:28:17 +0100 (Tue, 23 Jan 2007) | 1 line

javascript sample scripts


r2366 | ospjuth | 2007-01-22 16:36:00 +0100 (Mon, 22 Jan 2007) | 1 line

Fixed CMLValidationAction to allow for visibility for a SpectrumResource


r2364 | ospjuth | 2007-01-22 16:32:28 +0100 (Mon, 22 Jan 2007) | 1 line

Adapted SpectrumResource for CMLValidationAction


r2362 | ospjuth | 2007-01-22 16:13:19 +0100 (Mon, 22 Jan 2007) | 1 line

Fixed CMLValidationAction to allow for visibility for a CDKResource


r2360 | ospjuth | 2007-01-22 16:07:02 +0100 (Mon, 22 Jan 2007) | 1 line

Adapted CDKResource for IS_CML_FORMAT to allow for CMLValidationAction of a CDKResource


r2358 | tohel | 2007-01-22 11:56:24 +0100 (Mon, 22 Jan 2007) | 1 line

added some comments and did some cleanup


r2357 | tohel | 2007-01-22 10:47:03 +0100 (Mon, 22 Jan 2007) | 1 line

on opening res in editor, res gets loaded now


r2355 | ospjuth | 2007-01-22 09:52:48 +0100 (Mon, 22 Jan 2007) | 1 line

NewFileWizard now sets InMemoryResource instead of ParsedResourse before save(). Solves 1640829.


r2354 | egonw | 2007-01-21 11:27:17 +0100 (Sun, 21 Jan 2007) | 3 lines

Ported sequence support for PDB files, with residue highlighting in the Jmol view. Applied patches: 1929, 1954, 2046-2048.


r2353 | egonw | 2007-01-21 11:18:31 +0100 (Sun, 21 Jan 2007) | 3 lines

Ported ChildResourceCreatorExtension, and move PDB stuff to Bioclipse to make use of this new extension. Applied patches: 1804, 1810-1816, 1818-1820, 1837.


r2352 | egonw | 2007-01-21 10:54:39 +0100 (Sun, 21 Jan 2007) | 2 lines

Cleaned up imports.


r2351 | ospjuth | 2007-01-21 01:38:19 +0100 (Sun, 21 Jan 2007) | 1 line

Tried adding key bindings (not working)


r2349 | ospjuth | 2007-01-20 19:59:09 +0100 (Sat, 20 Jan 2007) | 1 line

Refresh BioResource Navigator after NewSpectrumWizard


r2345 | egonw | 2007-01-19 17:02:59 +0100 (Fri, 19 Jan 2007) | 3 lines

Switched layout: first file name, then tree. This solves a problem here that only the tree is shown, because the tree has no max vertical size.


r2341 | egonw | 2007-01-19 14:51:22 +0100 (Fri, 19 Jan 2007) | 3 lines

OK, another attempt to delete those two bin/ dirs. Apparently, eclipse copies src/.svn files into bin/.svn, so the local SVN client thinks it is deleting the bin/, while the SVN server actually receives commands to delete src/ :(


r2340 | egonw | 2007-01-19 14:39:21 +0100 (Fri, 19 Jan 2007) | 2 lines

Removed autogenerated bin dirs.


r2338 | egonw | 2007-01-19 14:09:06 +0100 (Fri, 19 Jan 2007) | 2 lines

Backported patch to highlight residues in Jmol when clicked in the sequence viewer of biojava (r2047).


r2337 | egonw | 2007-01-19 14:03:20 +0100 (Fri, 19 Jan 2007) | 2 lines

Backported the scripting engine extension point (r2044) and the Jmol engine (r2045).


r2334 | ospjuth | 2007-01-19 11:05:22 +0100 (Fri, 19 Jan 2007) | 1 line

If no default type, return unknown.


r2332 | ospjuth | 2007-01-19 10:37:35 +0100 (Fri, 19 Jan 2007) | 1 line

Deleting of base folders is now disallowed.


r2329 | ospjuth | 2007-01-18 18:56:22 +0100 (Thu, 18 Jan 2007) | 1 line

Fixed Jmol to display selection on first startup.


r2328 | ospjuth | 2007-01-18 18:30:38 +0100 (Thu, 18 Jan 2007) | 1 line

Removed unnecessary logging/error reporting on new folder creation


r2326 | ospjuth | 2007-01-18 17:32:13 +0100 (Thu, 18 Jan 2007) | 1 line

Added logging on parsing failed.


r2325 | ospjuth | 2007-01-18 17:30:45 +0100 (Thu, 18 Jan 2007) | 1 line

Removed BundleRequiredEnvironment 1.5 since this does not work on Mac. Postponed to a future version.


r2323 | ospjuth | 2007-01-18 17:16:00 +0100 (Thu, 18 Jan 2007) | 1 line

Fixed reacting on preference updates in FileRootPath. Solves 1549856.


r2321 | ospjuth | 2007-01-18 16:51:01 +0100 (Thu, 18 Jan 2007) | 1 line

Make NewFileWizard invoke editor based on preferences


r2319 | ospjuth | 2007-01-18 16:45:43 +0100 (Thu, 18 Jan 2007) | 1 line

A new preference option for autoloading


r2317 | ospjuth | 2007-01-18 16:44:01 +0100 (Thu, 18 Jan 2007) | 1 line

Fixed overriding preferences for autoloading


r2314 | ospjuth | 2007-01-18 11:16:16 +0100 (Thu, 18 Jan 2007) | 1 line

Removed unused temp database testing code that was commented out


r2312 | ospjuth | 2007-01-18 10:47:06 +0100 (Thu, 18 Jan 2007) | 1 line

Fixed NewFileWizard to increment trailing digit if exists, and automatic selection in BioResView


r2310 | ospjuth | 2007-01-18 09:34:21 +0100 (Thu, 18 Jan 2007) | 1 line

merge with trunk


r2308 | ospjuth | 2007-01-18 09:26:31 +0100 (Thu, 18 Jan 2007) | 1 line

Fixed unloading of subresources and output for failed parsing now redirected to console instead of dialog.


r2306 | ospjuth | 2007-01-17 14:53:02 +0100 (Wed, 17 Jan 2007) | 1 line

Solves bug 1590856.


r2304 | egonw | 2007-01-15 15:27:04 +0100 (Mon, 15 Jan 2007) | 2 lines

Depend on all plugins to be in the 1.0.x releases.


r2303 | egonw | 2007-01-15 15:24:52 +0100 (Mon, 15 Jan 2007) | 2 lines

Removed redundant/eclipse only bin dir.


r2302 | egonw | 2007-01-15 15:24:06 +0100 (Mon, 15 Jan 2007) | 2 lines

Copied bc_rhino from trunk/ to be part of 1.0.1.


r2301 | egonw | 2007-01-15 15:05:59 +0100 (Mon, 15 Jan 2007) | 2 lines

Added missing docs + license statement.


r2238 | edrin_t | 2006-12-12 16:05:12 +0100 (Tue, 12 Dec 2006) | 1 line

adapted wsdbfetch to the server-side changes at abi server


r1798 | egonw | 2006-08-18 15:11:47 +0200 (Fri, 18 Aug 2006) | 1 line

Applied patch 1794:1795


r1718 | tohel | 2006-08-11 16:26:20 +0200 (Fri, 11 Aug 2006) | 1 line

added possibility to us non modifiable documentProvider


r1713 | ospjuth | 2006-08-11 15:35:10 +0200 (Fri, 11 Aug 2006) | 1 line

Added css to build props


r1712 | ospjuth | 2006-08-11 14:50:29 +0200 (Fri, 11 Aug 2006) | 1 line

Added docu for help, preferences, console and progress windows


r1707 | ospjuth | 2006-08-11 12:31:25 +0200 (Fri, 11 Aug 2006) | 1 line

Removed SequenceTableView. Solves 1538288.


r1706 | ospjuth | 2006-08-11 12:25:29 +0200 (Fri, 11 Aug 2006) | 4 lines

Fixed parsing and display of BioJava resources. - Virtual resources work using a tempfile - SequenceView is updated and cleared depending on parsed status Solves 1538062.


r1705 | ospjuth | 2006-08-11 11:35:27 +0200 (Fri, 11 Aug 2006) | 1 line

Added docu for more extension points


r1704 | ospjuth | 2006-08-11 11:34:56 +0200 (Fri, 11 Aug 2006) | 1 line

Added docu for more extension points


r1703 | ospjuth | 2006-08-11 11:33:08 +0200 (Fri, 11 Aug 2006) | 1 line

Updated about text


r1702 | ospjuth | 2006-08-11 11:32:04 +0200 (Fri, 11 Aug 2006) | 1 line

Updated installation guide


r1701 | ospjuth | 2006-08-11 11:15:21 +0200 (Fri, 11 Aug 2006) | 1 line

Updated the getting started guide


r1699 | ospjuth | 2006-08-11 10:47:24 +0200 (Fri, 11 Aug 2006) | 1 line

Removed -consoleLog from product definition


r1698 | ospjuth | 2006-08-11 10:45:48 +0200 (Fri, 11 Aug 2006) | 1 line

Update version to 1.0.0 and set minimum execution environment to J2SE 1.5


r1697 | ospjuth | 2006-08-11 10:44:08 +0200 (Fri, 11 Aug 2006) | 1 line

Set version to 1.0.0


r1696 | egonw | 2006-08-10 21:12:11 +0200 (Thu, 10 Aug 2006) | 1 line

Documented (closes #1538149).


r1692 | ospjuth | 2006-08-10 17:56:44 +0200 (Thu, 10 Aug 2006) | 1 line

Added schema.css and extension point description for BioResource EP


r1690 | egonw | 2006-08-10 17:14:19 +0200 (Thu, 10 Aug 2006) | 1 line

Added a CML spect from the NMRShiftDB (which can be read)


r1689 | tohel | 2006-08-10 16:44:47 +0200 (Thu, 10 Aug 2006) | 1 line

jcp works again


r1686 | ospjuth | 2006-08-10 16:34:32 +0200 (Thu, 10 Aug 2006) | 1 line

Updated BiojavaResources to also support file extension 'refseq'


r1682 | tohel | 2006-08-10 16:33:06 +0200 (Thu, 10 Aug 2006) | 1 line

updated cdk-control.jar


r1681 | ospjuth | 2006-08-10 16:29:19 +0200 (Thu, 10 Aug 2006) | 1 line

Updated preference page for BioRes Navigator


r1680 | ospjuth | 2006-08-10 16:24:29 +0200 (Thu, 10 Aug 2006) | 1 line

added an anchor "contribs" in tocDev.xml


r1679 | ospjuth | 2006-08-10 16:23:22 +0200 (Thu, 10 Aug 2006) | 1 line

Updated preference page for Bioclipse


r1678 | ospjuth | 2006-08-10 16:16:51 +0200 (Thu, 10 Aug 2006) | 1 line

Refactoring of plugin appearance in Preferences dialog


r1677 | ospjuth | 2006-08-10 16:16:13 +0200 (Thu, 10 Aug 2006) | 1 line

Added documentation for Bioclipse plugin


r1670 | tohel | 2006-08-10 12:32:42 +0200 (Thu, 10 Aug 2006) | 1 line

hopefully solves bug 1533802


r1664 | ospjuth | 2006-08-09 16:00:24 +0200 (Wed, 09 Aug 2006) | 1 line

Updated manifest and product with missing help plugins that were lost


r1648 | egonw | 2006-08-08 14:07:07 +0200 (Tue, 08 Aug 2006) | 1 line

Applied stylesheet, so that our help is readable when using an external browser too (closes #1535925)


r1646 | tohel | 2006-08-08 13:29:54 +0200 (Tue, 08 Aug 2006) | 1 line

some adaptation to new cdk jars


r1645 | tohel | 2006-08-08 13:28:15 +0200 (Tue, 08 Aug 2006) | 1 line

some cleanup


r1644 | tohel | 2006-08-08 13:19:03 +0200 (Tue, 08 Aug 2006) | 1 line

updated to newest cdk jars - because of changes in SimpleController2D


r1631 | egonw | 2006-08-05 14:56:44 +0200 (Sat, 05 Aug 2006) | 1 line

Fixed COMPLETE-ing for file://'s.


r1630 | egonw | 2006-08-05 14:41:06 +0200 (Sat, 05 Aug 2006) | 1 line

There is now a 30 second time out on downloading feeds.


r1629 | egonw | 2006-08-05 12:22:08 +0200 (Sat, 05 Aug 2006) | 1 line

Uploaded a recent CDK version that fixes file IO that was broken in the upload in r1625


r1627 | shk3 | 2006-08-04 13:55:43 +0200 (Fri, 04 Aug 2006) | 1 line

change due to new cdk


r1626 | shk3 | 2006-08-04 13:55:14 +0200 (Fri, 04 Aug 2006) | 1 line

change due to new cdk


r1625 | shk3 | 2006-08-04 13:53:20 +0200 (Fri, 04 Aug 2006) | 1 line

changes in cdk made an update necessary


r1622 | egonw | 2006-08-03 21:00:17 +0200 (Thu, 03 Aug 2006) | 1 line

Java 1.6 (aka 6.0) should be fine too.


r1621 | ospjuth | 2006-08-03 18:24:49 +0200 (Thu, 03 Aug 2006) | 1 line

Removed testData (haven't I done this already?)


r1620 | ospjuth | 2006-08-03 18:08:49 +0200 (Thu, 03 Aug 2006) | 1 line

Updated product for 0.9.10


r1619 | ospjuth | 2006-08-03 17:57:36 +0200 (Thu, 03 Aug 2006) | 1 line

Updated name of install action


r1618 | ospjuth | 2006-08-03 17:56:31 +0200 (Thu, 03 Aug 2006) | 1 line

Added CSS and tried including it in some docs for bioclipse and bc_cdk. Not working so far.


r1616 | ospjuth | 2006-08-03 17:03:19 +0200 (Thu, 03 Aug 2006) | 1 line

Fixes refresh on rename.


r1615 | ospjuth | 2006-08-03 17:00:19 +0200 (Thu, 03 Aug 2006) | 1 line

New icons for installingData


r1614 | edrin_t | 2006-08-03 16:58:23 +0200 (Thu, 03 Aug 2006) | 1 line

new labeling of error msg


r1613 | shk3 | 2006-08-03 16:47:41 +0200 (Thu, 03 Aug 2006) | 1 line

removed old logo


r1611 | shk3 | 2006-08-03 16:43:16 +0200 (Thu, 03 Aug 2006) | 1 line

changed a logo


r1610 | ospjuth | 2006-08-03 16:22:25 +0200 (Thu, 03 Aug 2006) | 1 line

Fixed SpectrumParsing and CMLResource editor input. Solves 1533879.


r1608 | shk3 | 2006-08-03 16:14:48 +0200 (Thu, 03 Aug 2006) | 1 line

removed sample.gif, don't think we need this


r1606 | ospjuth | 2006-08-03 16:04:46 +0200 (Thu, 03 Aug 2006) | 1 line

Fixed copy/past updating from RSSfeeds. Solves 1532500.


r1605 | ospjuth | 2006-08-03 15:47:44 +0200 (Thu, 03 Aug 2006) | 1 line

Fixed DnD in Bioclipse. Now also for virtual resources.


r1601 | edrin_t | 2006-08-03 13:42:59 +0200 (Thu, 03 Aug 2006) | 1 line

some cleanup!


r1598 | edrin_t | 2006-08-03 13:19:57 +0200 (Thu, 03 Aug 2006) | 1 line

just some sample code for axis1 async mechanism...


r1597 | edrin_t | 2006-08-03 13:15:48 +0200 (Thu, 03 Aug 2006) | 1 line

now axis async mechanism is used. it is now possible to abort a webservice call.


r1596 | edrin_t | 2006-08-03 13:14:50 +0200 (Thu, 03 Aug 2006) | 1 line

this class will use the WSDbfetch Web Service directly and not use the by WSDL2Java generated code. This was done to get the undocumented axis async to work. Now it is possible to abort a search.


r1595 | edrin_t | 2006-08-03 13:14:39 +0200 (Thu, 03 Aug 2006) | 1 line

this class will use the WSDbfetch Web Service directly and not use the by WSDL2Java generated code. This was done to get the undocumented axis async to work. Now it is possible to abort a search.


r1594 | edrin_t | 2006-08-03 09:40:39 +0200 (Thu, 03 Aug 2006) | 1 line

another axis stubgenerator script


r1593 | ospjuth | 2006-08-02 20:49:47 +0200 (Wed, 02 Aug 2006) | 1 line

Removed debug outs


r1592 | ospjuth | 2006-08-02 20:32:49 +0200 (Wed, 02 Aug 2006) | 1 line

Fixed parsing of resources from bc_webservices with new API. Solves 1532465.


r1588 | ospjuth | 2006-08-02 19:29:31 +0200 (Wed, 02 Aug 2006) | 1 line

Fixed UNKOWN resource to open in editor if of type byte[] and not String


r1587 | ospjuth | 2006-08-02 19:25:21 +0200 (Wed, 02 Aug 2006) | 1 line

Updates for texteditor and input for save() to be more general


r1586 | ospjuth | 2006-08-02 19:24:14 +0200 (Wed, 02 Aug 2006) | 1 line

Override parsing of PDB's on save()


r1585 | egonw | 2006-08-02 19:06:14 +0200 (Wed, 02 Aug 2006) | 1 line

Overwrite getParsedResourceAsString() to return a String of the byte[], instead of trying defaulting to returning null (closes #1532494).


r1584 | ospjuth | 2006-08-02 18:33:02 +0200 (Wed, 02 Aug 2006) | 1 line

Fixed a bug returning empty editor for UKNOWN resources.


r1583 | ospjuth | 2006-08-02 17:44:59 +0200 (Wed, 02 Aug 2006) | 1 line

Fixed bug with unknown resources not getting opened at all


r1576 | ospjuth | 2006-08-01 18:28:43 +0200 (Tue, 01 Aug 2006) | 1 line

Fixed build properties


r1575 | ospjuth | 2006-08-01 18:28:12 +0200 (Tue, 01 Aug 2006) | 1 line

Fixed correct textEditor if parse failed


r1572 | tohel | 2006-08-01 16:47:06 +0200 (Tue, 01 Aug 2006) | 1 line

added source tab


r1570 | tohel | 2006-08-01 15:57:36 +0200 (Tue, 01 Aug 2006) | 3 lines

- specMol assignment editor shows now the spectrum chart as well - SpecMol- and cml based SpectrumResource will show up in xmlEditor indented - some debugging


r1569 | ospjuth | 2006-08-01 15:45:23 +0200 (Tue, 01 Aug 2006) | 1 line

Fixed a bug that could not handle ChemFileCDO (when trying to visualize CML from chemical-structures) so casted to ChemFile.


r1568 | ospjuth | 2006-08-01 15:14:14 +0200 (Tue, 01 Aug 2006) | 1 line

Fixed delete action to correctly delete folders with hidden content


r1567 | ospjuth | 2006-08-01 14:54:03 +0200 (Tue, 01 Aug 2006) | 2 lines

Fixed startup to not configure logger if already configured. Also moved 'bioclipse started on...' from Activator to Application.


r1566 | tohel | 2006-08-01 14:50:20 +0200 (Tue, 01 Aug 2006) | 1 line

structures are now centered as well :)


r1565 | ospjuth | 2006-08-01 14:44:52 +0200 (Tue, 01 Aug 2006) | 1 line

added bc_blueobelisk_data to product


r1564 | ospjuth | 2006-08-01 14:43:11 +0200 (Tue, 01 Aug 2006) | 1 line

Refactoring of abstract data installer action and helpers


r1563 | ospjuth | 2006-08-01 14:40:37 +0200 (Tue, 01 Aug 2006) | 1 line

Removed chemical-stuctures data and action


r1562 | ospjuth | 2006-08-01 14:36:36 +0200 (Tue, 01 Aug 2006) | 1 line

Added chemical structures data and action to install it


r1561 | ospjuth | 2006-08-01 14:35:41 +0200 (Tue, 01 Aug 2006) | 1 line

Initial import.


r1560 | ospjuth | 2006-08-01 14:03:44 +0200 (Tue, 01 Aug 2006) | 1 line

Set version to 0.9.10


r1558 | egonw | 2006-08-01 13:41:04 +0200 (Tue, 01 Aug 2006) | 1 line

Uses 16x16 now


r1556 | egonw | 2006-08-01 13:38:52 +0200 (Tue, 01 Aug 2006) | 1 line

Added 16x16 version


r1555 | tohel | 2006-08-01 12:55:10 +0200 (Tue, 01 Aug 2006) | 1 line

some code cleanup and removed logging jar


r1554 | ospjuth | 2006-08-01 12:46:15 +0200 (Tue, 01 Aug 2006) | 1 line

Removed jars now available in com.tools.logging plugin


r1552 | ospjuth | 2006-08-01 12:42:52 +0200 (Tue, 01 Aug 2006) | 1 line

Added commons-logging and moved log4j jar to jars/


r1551 | ospjuth | 2006-08-01 12:40:59 +0200 (Tue, 01 Aug 2006) | 1 line

Cleanup of plugin dependencies


r1550 | egonw | 2006-08-01 12:38:09 +0200 (Tue, 01 Aug 2006) | 1 line

Cleaned up dependencies


r1549 | egonw | 2006-08-01 12:37:47 +0200 (Tue, 01 Aug 2006) | 1 line

Removed tests, now in trunk/bc_cmlrss_tests


r1546 | ospjuth | 2006-08-01 12:03:28 +0200 (Tue, 01 Aug 2006) | 1 line

Cleaned unused dependencies, removed a lot of ant-jars relating to bug 1531684


r1545 | edrin_t | 2006-08-01 11:46:06 +0200 (Tue, 01 Aug 2006) | 1 line

i just cleaned this file from unneeded comments, however the bug in BioResourceView.executeDoubleClick(newResource); remains


r1542 | ospjuth | 2006-08-01 11:35:11 +0200 (Tue, 01 Aug 2006) | 1 line

Removed testData, to be uploaded in trunk/bc_testdata


r1540 | egonw | 2006-08-01 10:47:24 +0200 (Tue, 01 Aug 2006) | 1 line

Removed another duplicate jar


r1539 | tohel | 2006-08-01 10:40:15 +0200 (Tue, 01 Aug 2006) | 1 line

removed some jars


r1538 | ospjuth | 2006-08-01 10:36:17 +0200 (Tue, 01 Aug 2006) | 1 line

Removed unused jars


r1537 | ospjuth | 2006-08-01 10:31:11 +0200 (Tue, 01 Aug 2006) | 1 line

Removed sampleData dir in bioclipse as it is duplicate of bc_data


r1536 | egonw | 2006-08-01 10:11:49 +0200 (Tue, 01 Aug 2006) | 1 line

Removed unneeded jars


r1532 | ospjuth | 2006-07-31 14:01:44 +0200 (Mon, 31 Jul 2006) | 1 line

New ID. Solves 1531682


r1529 | tohel | 2006-07-31 11:40:40 +0200 (Mon, 31 Jul 2006) | 1 line

hopefully finally solving bug 1529047


r1522 | ospjuth | 2006-07-27 22:12:05 +0200 (Thu, 27 Jul 2006) | 1 line

Fixed typy in toc.xml


r1521 | ospjuth | 2006-07-27 22:03:47 +0200 (Thu, 27 Jul 2006) | 1 line

Fixed export issues and perspective startup


r1520 | ospjuth | 2006-07-27 21:44:08 +0200 (Thu, 27 Jul 2006) | 1 line

Updated product and plugin for 3.2 delta pack export


r1515 | ospjuth | 2006-07-27 16:41:18 +0200 (Thu, 27 Jul 2006) | 1 line

Added icons for Windows and Mac OS X


r1514 | tohel | 2006-07-27 16:19:26 +0200 (Thu, 27 Jul 2006) | 1 line

now sync seems really to work...


r1513 | tohel | 2006-07-27 15:59:52 +0200 (Thu, 27 Jul 2006) | 1 line

save on textEditor and sync works again


r1512 | ospjuth | 2006-07-27 15:29:04 +0200 (Thu, 27 Jul 2006) | 1 line

Set version to 0.9.9


r1511 | ospjuth | 2006-07-27 15:24:32 +0200 (Thu, 27 Jul 2006) | 1 line

Fixed a bug on instance creation


r1510 | ospjuth | 2006-07-27 15:10:49 +0200 (Thu, 27 Jul 2006) | 1 line

Commented out HueckelAromaticityDetector.detectAromaticity(..)


r1508 | shk3 | 2006-07-27 14:44:43 +0200 (Thu, 27 Jul 2006) | 1 line

uses new cdk


r1507 | shk3 | 2006-07-27 14:41:56 +0200 (Thu, 27 Jul 2006) | 1 line

new cdk


r1506 | ospjuth | 2006-07-27 13:12:42 +0200 (Thu, 27 Jul 2006) | 2 lines

Updated saving to ask for confirmation in BioResourceDocumentProvider if resource could not be parsed after edit


r1504 | shk3 | 2006-07-26 22:07:19 +0200 (Wed, 26 Jul 2006) | 1 line

solves problem that aromaticity dipslay changes when changing tabs; has the implicit h handling as in jcp


r1503 | shk3 | 2006-07-26 21:58:52 +0200 (Wed, 26 Jul 2006) | 1 line

solves problem that aromaticity dipslay changes when changing tabs; has the implicit h handling as in jcp


r1501 | ospjuth | 2006-07-26 17:29:06 +0200 (Wed, 26 Jul 2006) | 1 line

Fixes casting of objects in createChildren


r1500 | tohel | 2006-07-26 17:14:58 +0200 (Wed, 26 Jul 2006) | 1 line

fixed NewMoleculeWizard and NewMoleculeFromSmilesWizard


r1499 | tohel | 2006-07-26 16:48:21 +0200 (Wed, 26 Jul 2006) | 1 line

switching between editors results in selection of the reagrding resources in bioResView and vice versa


r1498 | ospjuth | 2006-07-26 16:03:59 +0200 (Wed, 26 Jul 2006) | 1 line

Added constant for CDK_RESOURCE


r1497 | tohel | 2006-07-26 15:30:14 +0200 (Wed, 26 Jul 2006) | 2 lines

- added calculation of integrals - some debugging


r1496 | ospjuth | 2006-07-26 15:30:16 +0200 (Wed, 26 Jul 2006) | 1 line

Fixed NewJmolScriptWizard


r1495 | ospjuth | 2006-07-26 15:24:09 +0200 (Wed, 26 Jul 2006) | 1 line

Fixed NewFolderWizard


r1494 | ospjuth | 2006-07-26 15:16:39 +0200 (Wed, 26 Jul 2006) | 1 line

Fixed parsing of JmolScriptResources


r1493 | ospjuth | 2006-07-26 14:55:43 +0200 (Wed, 26 Jul 2006) | 1 line

Fixes resource creation when content is provided on object basis. See NewSpectrumWizard.performFinish() for new syntax.


r1491 | tohel | 2006-07-26 11:10:42 +0200 (Wed, 26 Jul 2006) | 1 line

showing xvalue as peak label makes more sense ;-)


r1490 | tohel | 2006-07-25 17:11:24 +0200 (Tue, 25 Jul 2006) | 3 lines

- upgraded jfreechart jars - added possibility to show peak labels - label threshold setable via preference page


r1476 | tohel | 2006-07-24 13:07:24 +0200 (Mon, 24 Jul 2006) | 1 line

patched cdk newWizards to work with new resource objects


r1467 | ospjuth | 2006-07-23 22:15:47 +0200 (Sun, 23 Jul 2006) | 1 line

Code cleanup


r1466 | ospjuth | 2006-07-23 22:07:38 +0200 (Sun, 23 Jul 2006) | 1 line

Added a general error dialog that doesn't seem to work at the moment...


r1465 | ospjuth | 2006-07-23 21:51:44 +0200 (Sun, 23 Jul 2006) | 1 line

Fixed logger


r1464 | ospjuth | 2006-07-23 21:46:47 +0200 (Sun, 23 Jul 2006) | 1 line

Fixed parsing and perspective to work with new parsing design. Solves 1525931.


r1463 | ospjuth | 2006-07-23 21:38:27 +0200 (Sun, 23 Jul 2006) | 1 line

Fixed date format on startup


r1462 | ospjuth | 2006-07-23 21:32:32 +0200 (Sun, 23 Jul 2006) | 1 line

Caught a NPE. Solves 1524666.


r1461 | ospjuth | 2006-07-23 21:25:24 +0200 (Sun, 23 Jul 2006) | 1 line

Fixed a bug that made >64K copy loose a byte per slice


r1460 | ospjuth | 2006-07-23 21:12:31 +0200 (Sun, 23 Jul 2006) | 1 line

Removed isParsedListener that gave multiple selections


r1459 | ospjuth | 2006-07-23 21:11:53 +0200 (Sun, 23 Jul 2006) | 1 line

Added a createChildResource(name,content) to simplify creation of new resources


r1458 | ospjuth | 2006-07-23 21:10:50 +0200 (Sun, 23 Jul 2006) | 1 line

Fixed to check for equals() on selectionChanged


r1457 | ospjuth | 2006-07-23 21:10:19 +0200 (Sun, 23 Jul 2006) | 1 line

Updated to not listen for same object clicked twice


r1456 | ospjuth | 2006-07-23 21:09:44 +0200 (Sun, 23 Jul 2006) | 1 line

Fixed creation of Resources


r1455 | ospjuth | 2006-07-23 20:08:41 +0200 (Sun, 23 Jul 2006) | 1 line

Updated selection with setFocus() to retain focus in BioResView


r1454 | ospjuth | 2006-07-23 20:07:25 +0200 (Sun, 23 Jul 2006) | 1 line

Fixed Cut and Paste, now also for >64K molecules.


r1453 | ospjuth | 2006-07-23 19:00:15 +0200 (Sun, 23 Jul 2006) | 1 line

Added dispose() method


r1452 | ospjuth | 2006-07-23 18:59:28 +0200 (Sun, 23 Jul 2006) | 1 line

Removed NotifyBioResViewer as it seemed unneccesary


r1451 | ospjuth | 2006-07-21 18:57:45 +0200 (Fri, 21 Jul 2006) | 1 line

Updated text when switching perspectives.


r1450 | ospjuth | 2006-07-21 18:49:21 +0200 (Fri, 21 Jul 2006) | 1 line

Removed support for .gz for 1.0.


r1449 | ospjuth | 2006-07-21 18:25:24 +0200 (Fri, 21 Jul 2006) | 1 line

Fixed NewFileWizards. Solves 1525467.


r1448 | ospjuth | 2006-07-21 18:00:34 +0200 (Fri, 21 Jul 2006) | 1 line

Creation of NewSpectrumWizard is now parsed correctly and appears in BioResView. Solves #1518187.


r1447 | ospjuth | 2006-07-21 17:14:19 +0200 (Fri, 21 Jul 2006) | 1 line

Caught a ParsingException


r1446 | ospjuth | 2006-07-21 16:00:07 +0200 (Fri, 21 Jul 2006) | 1 line

Fixes a NPE


r1445 | tohel | 2006-07-21 14:53:40 +0200 (Fri, 21 Jul 2006) | 1 line

flipping of selected atoms/bonds works again


r1444 | tohel | 2006-07-21 12:02:14 +0200 (Fri, 21 Jul 2006) | 1 line

some changes on open Perspective for resource preference system


r1443 | tohel | 2006-07-20 16:31:21 +0200 (Thu, 20 Jul 2006) | 1 line

fixed textField height


r1439 | egonw | 2006-07-19 22:20:58 +0200 (Wed, 19 Jul 2006) | 1 line

Turned on aromaticity rendering (closes #1525324).


r1438 | egonw | 2006-07-19 20:09:13 +0200 (Wed, 19 Jul 2006) | 1 line

Give user feedback when the OPML file cannot be read.


r1437 | shk3 | 2006-07-19 18:15:37 +0200 (Wed, 19 Jul 2006) | 1 line

added indenting


r1435 | ospjuth | 2006-07-19 17:14:10 +0200 (Wed, 19 Jul 2006) | 1 line

Fixed debug outs


r1434 | ospjuth | 2006-07-19 17:10:40 +0200 (Wed, 19 Jul 2006) | 1 line

Prevent ChemTree from re-reading resources


r1433 | ospjuth | 2006-07-19 16:57:36 +0200 (Wed, 19 Jul 2006) | 1 line

Fixes NPE in FolderResource.getChildren()


r1432 | ospjuth | 2006-07-19 16:39:42 +0200 (Wed, 19 Jul 2006) | 1 line

Fixed init of children in folders


r1431 | shk3 | 2006-07-19 15:19:44 +0200 (Wed, 19 Jul 2006) | 1 line

all dict entries


r1430 | tohel | 2006-07-19 15:11:05 +0200 (Wed, 19 Jul 2006) | 1 line

more dict entries


r1429 | egonw | 2006-07-19 14:38:21 +0200 (Wed, 19 Jul 2006) | 1 line

Turned on schema validation.


r1428 | egonw | 2006-07-19 14:35:56 +0200 (Wed, 19 Jul 2006) | 1 line

Turned on schema validation. Many of them have problems. Are these in sync with upstream??


r1427 | egonw | 2006-07-19 14:32:19 +0200 (Wed, 19 Jul 2006) | 1 line

Shaped up dict a bit.


r1426 | tohel | 2006-07-19 14:26:43 +0200 (Wed, 19 Jul 2006) | 1 line

replaced "." by "dot" in ids


r1425 | egonw | 2006-07-19 14:20:33 +0200 (Wed, 19 Jul 2006) | 1 line

Added suggested documentation on mapping JCAMP-DX id's to XML id's.


r1424 | egonw | 2006-07-19 14:20:04 +0200 (Wed, 19 Jul 2006) | 1 line

Fixed a number of sematic errors.


r1423 | egonw | 2006-07-19 14:04:40 +0200 (Wed, 19 Jul 2006) | 1 line

Turned on schema validation: three types of problems.


r1422 | tohel | 2006-07-19 14:03:33 +0200 (Wed, 19 Jul 2006) | 1 line

some changes in dict


r1421 | tohel | 2006-07-19 13:57:49 +0200 (Wed, 19 Jul 2006) | 1 line

more dict entries


r1420 | egonw | 2006-07-19 13:44:26 +0200 (Wed, 19 Jul 2006) | 1 line

Removed sources, which we do not need here; they're in the CML repos already


r1419 | tohel | 2006-07-19 13:22:57 +0200 (Wed, 19 Jul 2006) | 1 line

added schema24


r1418 | tohel | 2006-07-19 12:48:04 +0200 (Wed, 19 Jul 2006) | 1 line

added jcamp version to dict entries


r1417 | egonw | 2006-07-19 12:41:21 +0200 (Wed, 19 Jul 2006) | 1 line

Fixed unallowed spaces in IDs.


r1416 | tohel | 2006-07-18 19:39:50 +0200 (Tue, 18 Jul 2006) | 1 line

some debugging


r1415 | ospjuth | 2006-07-18 19:33:19 +0200 (Tue, 18 Jul 2006) | 1 line

Started adapting cut and paste for virtual object support and files larger than 64Kb.


r1414 | ospjuth | 2006-07-18 19:29:45 +0200 (Tue, 18 Jul 2006) | 1 line

Major updates to IBioResources parsing mechanism and new object creation to allow for Virtual objects.


r1413 | ospjuth | 2006-07-18 18:35:18 +0200 (Tue, 18 Jul 2006) | 1 line

Added FIXME for catching error in adapter


r1411 | ospjuth | 2006-07-18 14:03:09 +0200 (Tue, 18 Jul 2006) | 1 line

Fixed a NPE


r1410 | ospjuth | 2006-07-18 13:34:03 +0200 (Tue, 18 Jul 2006) | 1 line

Added TODO to mark commit for testing; NewFile with content should be verified that save() actually saves content.


r1409 | ospjuth | 2006-07-18 13:22:30 +0200 (Tue, 18 Jul 2006) | 1 line

Fixes cut and paste toString() problem related to bug 1524084.


r1408 | tohel | 2006-07-18 13:09:07 +0200 (Tue, 18 Jul 2006) | 1 line

new saveAs dialog for molecules based on the BioclipseSaveAsDialog


r1407 | egonw | 2006-07-17 22:38:42 +0200 (Mon, 17 Jul 2006) | 1 line

Forgot to add this file.


r1406 | egonw | 2006-07-17 22:37:57 +0200 (Mon, 17 Jul 2006) | 1 line

Some final bits


r1405 | egonw | 2006-07-17 22:36:29 +0200 (Mon, 17 Jul 2006) | 1 line

Now also shows content for the feed itself. Also the view now has a title again; it was set the empty, because it is taken from the HTML <head><title>.


r1404 | egonw | 2006-07-17 22:33:06 +0200 (Mon, 17 Jul 2006) | 1 line

Added IFeed.getDescription().


r1403 | egonw | 2006-07-17 21:27:27 +0200 (Mon, 17 Jul 2006) | 1 line

Consider text as text, and not as XML.


r1402 | egonw | 2006-07-17 21:26:53 +0200 (Mon, 17 Jul 2006) | 1 line

Deal with HTML embedded in CDATA as used in the CMLRSS demo Usefulchem Molecules feed.


r1401 | egonw | 2006-07-17 21:26:03 +0200 (Mon, 17 Jul 2006) | 1 line

Give positive feedback on recognized feed formats.


r1400 | egonw | 2006-07-17 21:25:11 +0200 (Mon, 17 Jul 2006) | 1 line

Added an RSS perspective, automatically opened when opening an OPML file.


r1399 | egonw | 2006-07-17 21:24:36 +0200 (Mon, 17 Jul 2006) | 1 line

Added an RSS perspective, automatically opened when opening an OPML file.


r1397 | egonw | 2006-07-17 20:06:42 +0200 (Mon, 17 Jul 2006) | 1 line

Updated after API changes in NewFileWizard, fixes opening auto opening of these files.


r1396 | egonw | 2006-07-17 20:04:49 +0200 (Mon, 17 Jul 2006) | 1 line

You need to save the content before opening it, otherwise the content is lost (closes #152400).


r1395 | tohel | 2006-07-17 18:53:10 +0200 (Mon, 17 Jul 2006) | 1 line

some bugfixing


r1394 | egonw | 2006-07-17 18:48:50 +0200 (Mon, 17 Jul 2006) | 1 line

Removed two format which are not well supported.


r1393 | tohel | 2006-07-17 18:42:12 +0200 (Mon, 17 Jul 2006) | 2 lines

- added new wizard for specMol resource - added dialog for askinng if already existing files should be overwritten to FolderResource


r1390 | ospjuth | 2006-07-17 15:51:50 +0200 (Mon, 17 Jul 2006) | 2 lines

Updated so SaveAsDialog works on IBioResources, IBioResources gets saved with new content, and revealed in BioResView. Note: Updates in interfaces API of IBioResource. Fixed a lookup in refresh operating on a custom equals() for IBioResources.


r1389 | ospjuth | 2006-07-17 14:10:39 +0200 (Mon, 17 Jul 2006) | 1 line

Fixed refresh action to pick up new additions in folders


r1388 | egonw | 2006-07-17 11:11:37 +0200 (Mon, 17 Jul 2006) | 1 line

Enlarger edit box so that all reasonable commands can be entered.


r1387 | ospjuth | 2006-07-17 10:55:04 +0200 (Mon, 17 Jul 2006) | 1 line

Removed deprecated classes


r1385 | tohel | 2006-07-17 10:26:11 +0200 (Mon, 17 Jul 2006) | 1 line

added description to wizards


r1382 | edrin_t | 2006-07-16 15:04:34 +0200 (Sun, 16 Jul 2006) | 1 line

removed unneeded inmport


r1377 | egonw | 2006-07-15 10:17:45 +0200 (Sat, 15 Jul 2006) | 1 line

Added recognition of CONECT and SSBOND.


r1373 | tohel | 2006-07-14 15:48:59 +0200 (Fri, 14 Jul 2006) | 1 line

small correction of the former commit :)


r1372 | tohel | 2006-07-14 15:42:04 +0200 (Fri, 14 Jul 2006) | 2 lines

fixed bug 1522390 & on unloading of resources all related editors are closed as well


r1363 | tohel | 2006-07-14 10:23:09 +0200 (Fri, 14 Jul 2006) | 1 line

on deleting a res, related open editors are closed as well


r1361 | tohel | 2006-07-14 10:13:20 +0200 (Fri, 14 Jul 2006) | 1 line

fixed bug 1518602 and 1518605


r1360 | ospjuth | 2006-07-14 09:51:16 +0200 (Fri, 14 Jul 2006) | 1 line

cleanup


r1359 | ospjuth | 2006-07-14 09:45:48 +0200 (Fri, 14 Jul 2006) | 1 line

Updated PDBEditor highlighting and keywords


r1358 | ospjuth | 2006-07-14 09:45:40 +0200 (Fri, 14 Jul 2006) | 1 line

Renamed category


r1357 | ospjuth | 2006-07-14 09:45:26 +0200 (Fri, 14 Jul 2006) | 1 line

Replaced COT and BioPolTree with ChemTree


r1356 | ospjuth | 2006-07-14 09:42:58 +0200 (Fri, 14 Jul 2006) | 1 line

Added chemical structures 1.0 and adapted actions


r1355 | ospjuth | 2006-07-14 09:41:52 +0200 (Fri, 14 Jul 2006) | 1 line

Removed e.printStackTrace() when parsing failed, since this is a common expected scenario


r1354 | ospjuth | 2006-07-14 09:41:19 +0200 (Fri, 14 Jul 2006) | 1 line

Updated for 3.2 export


r1353 | ospjuth | 2006-07-14 09:41:02 +0200 (Fri, 14 Jul 2006) | 1 line

Removed unused bioclipseLogger


r1352 | ospjuth | 2006-07-14 09:40:49 +0200 (Fri, 14 Jul 2006) | 1 line

added progrss label and bar on startup (3.2)


r1351 | ospjuth | 2006-07-14 09:39:48 +0200 (Fri, 14 Jul 2006) | 1 line

Replaced sysout with logger.debug, and some other updates


r1350 | ospjuth | 2006-07-14 09:38:10 +0200 (Fri, 14 Jul 2006) | 1 line

Fixed startingFilter for content providers


r1349 | ospjuth | 2006-07-14 09:37:29 +0200 (Fri, 14 Jul 2006) | 1 line

Removed unused FileBufferListener


r1348 | ospjuth | 2006-07-14 09:35:45 +0200 (Fri, 14 Jul 2006) | 1 line

Removed unused bioclipseLogger


r1347 | ospjuth | 2006-07-14 09:35:22 +0200 (Fri, 14 Jul 2006) | 1 line

Updated manifest


r1346 | ospjuth | 2006-07-14 09:34:25 +0200 (Fri, 14 Jul 2006) | 2 lines

Opens COT, 2DView and Jmol on start, as these plugins are shipped with Bioclipse (for now). Solves #1520667


r1343 | ospjuth | 2006-07-13 16:39:54 +0200 (Thu, 13 Jul 2006) | 1 line

Solves a NPE in dispose() if BioResView is not open


r1342 | tohel | 2006-07-13 16:07:59 +0200 (Thu, 13 Jul 2006) | 1 line

closed bug 1521210


r1341 | ospjuth | 2006-07-13 16:02:12 +0200 (Thu, 13 Jul 2006) | 1 line

Added startup message and progress bar using 3.2 product definitions


r1340 | egonw | 2006-07-13 15:02:13 +0200 (Thu, 13 Jul 2006) | 1 line

More failsafe error handling


r1339 | egonw | 2006-07-13 14:51:47 +0200 (Thu, 13 Jul 2006) | 1 line

Fixed initialization of the BioJava logger


r1337 | egonw | 2006-07-13 14:25:29 +0200 (Thu, 13 Jul 2006) | 1 line

Added context help for the Jmol Script editor.


r1336 | egonw | 2006-07-13 14:18:38 +0200 (Thu, 13 Jul 2006) | 1 line

Added context help for the JCP editor.


r1335 | egonw | 2006-07-13 14:17:49 +0200 (Thu, 13 Jul 2006) | 1 line

Added context help for the JCP editor.


r1333 | egonw | 2006-07-13 14:03:40 +0200 (Thu, 13 Jul 2006) | 1 line

Added help on mouse gestures.


r1330 | egonw | 2006-07-13 12:55:01 +0200 (Thu, 13 Jul 2006) | 1 line

Enabled context help for the Jmol View


r1323 | egonw | 2006-07-12 23:15:20 +0200 (Wed, 12 Jul 2006) | 1 line

New CDK version (r6652)


r1322 | egonw | 2006-07-12 23:13:46 +0200 (Wed, 12 Jul 2006) | 5 lines

Largely rewritten: - now assumes multi model PDB files to be read as a IChemSequence of

 IChemModel's ('model 3' works!)

- iterates over CDK objects instead of using getAllAtomContainer,

 which enormously speeds up performance

r1321 | egonw | 2006-07-12 23:10:54 +0200 (Wed, 12 Jul 2006) | 1 line

Just reformated.


r1320 | egonw | 2006-07-12 23:08:09 +0200 (Wed, 12 Jul 2006) | 1 line

Some extra debug, useful for timing


r1319 | tohel | 2006-07-12 19:27:42 +0200 (Wed, 12 Jul 2006) | 1 line

some changes for allwoing multiple selections


r1316 | egonw | 2006-07-12 17:03:14 +0200 (Wed, 12 Jul 2006) | 1 line

Treat a sequence of BioPolymer's as one model.


r1314 | egonw | 2006-07-12 16:44:50 +0200 (Wed, 12 Jul 2006) | 1 line

More meaningfull names if getID() returns null.


r1312 | ospjuth | 2006-07-12 16:28:50 +0200 (Wed, 12 Jul 2006) | 1 line

Started merging COT and BioPolymerTree


r1307 | egonw | 2006-07-12 13:25:27 +0200 (Wed, 12 Jul 2006) | 1 line

Removed some commented-out code.


r1306 | egonw | 2006-07-12 13:22:46 +0200 (Wed, 12 Jul 2006) | 1 line

Fixed init of Logger (closes #1521038)


r1305 | egonw | 2006-07-12 13:08:39 +0200 (Wed, 12 Jul 2006) | 1 line

Added reasonable 'Format'.


r1303 | egonw | 2006-07-12 12:54:35 +0200 (Wed, 12 Jul 2006) | 1 line

Better 'Format' feedback (closes #1518609)


r1296 | tohel | 2006-07-12 11:33:53 +0200 (Wed, 12 Jul 2006) | 1 line

added format for cml


r1295 | tohel | 2006-07-12 11:22:27 +0200 (Wed, 12 Jul 2006) | 1 line

added format property thing to bc_spectrum


r1294 | tohel | 2006-07-12 10:26:00 +0200 (Wed, 12 Jul 2006) | 1 line

closing bug 1520668


r1293 | ospjuth | 2006-07-12 10:00:52 +0200 (Wed, 12 Jul 2006) | 1 line

Fixed a NPE


r1289 | ospjuth | 2006-07-11 18:28:19 +0200 (Tue, 11 Jul 2006) | 1 line

Updated for 0.9.3


r1288 | ospjuth | 2006-07-11 18:22:00 +0200 (Tue, 11 Jul 2006) | 1 line

Updated for 0.9.3 export


r1287 | ospjuth | 2006-07-11 18:21:40 +0200 (Tue, 11 Jul 2006) | 1 line

Updated for 0.9.3 export


r1286 | ospjuth | 2006-07-11 18:21:30 +0200 (Tue, 11 Jul 2006) | 1 line

Updated for 0.9.3 export


r1285 | ospjuth | 2006-07-11 18:21:16 +0200 (Tue, 11 Jul 2006) | 1 line

Updated for 0.9.3 export


r1284 | ospjuth | 2006-07-11 18:20:59 +0200 (Tue, 11 Jul 2006) | 1 line

Updated for 0.9.3 export


r1283 | ospjuth | 2006-07-11 18:20:45 +0200 (Tue, 11 Jul 2006) | 1 line

Updated for 0.9.3 export


r1282 | ospjuth | 2006-07-11 18:20:23 +0200 (Tue, 11 Jul 2006) | 1 line

Removed unused file that made export fail


r1281 | ospjuth | 2006-07-11 18:19:47 +0200 (Tue, 11 Jul 2006) | 1 line

Updated for 0.9.3 export


r1280 | ospjuth | 2006-07-11 18:19:17 +0200 (Tue, 11 Jul 2006) | 1 line

Catched a ClassCastException if BioResView not instantiated


r1279 | ospjuth | 2006-07-11 18:18:41 +0200 (Tue, 11 Jul 2006) | 1 line

Updated for 0.9.3 export


r1278 | ospjuth | 2006-07-11 18:18:25 +0200 (Tue, 11 Jul 2006) | 1 line

Updated for 0.9.3 export


r1277 | ospjuth | 2006-07-11 18:18:15 +0200 (Tue, 11 Jul 2006) | 1 line

Updated for 0.9.3 export


r1276 | ospjuth | 2006-07-11 18:02:53 +0200 (Tue, 11 Jul 2006) | 1 line

Updated for 0.9.3 and binary builds


r1269 | tohel | 2006-07-11 16:20:30 +0200 (Tue, 11 Jul 2006) | 1 line

fixed bug 1512964


r1265 | tohel | 2006-07-11 16:00:38 +0200 (Tue, 11 Jul 2006) | 1 line

solved bug 1507140 - "Paste in BioResourceView gives NPE"


r1240 | tohel | 2006-07-10 15:32:32 +0200 (Mon, 10 Jul 2006) | 1 line

further jcamp dict entries


r1239 | tohel | 2006-07-10 14:31:10 +0200 (Mon, 10 Jul 2006) | 1 line

new jcamp dict


r1237 | sba | 2006-07-10 13:11:11 +0200 (Mon, 10 Jul 2006) | 1 line

Added "Reset Perspective" Action.


r1224 | edrin_t | 2006-07-07 16:15:39 +0200 (Fri, 07 Jul 2006) | 1 line

added support for spawning the wizard with database&format preselection


r1223 | edrin_t | 2006-07-07 16:14:38 +0200 (Fri, 07 Jul 2006) | 1 line

updated with axis license information


r1217 | egonw | 2006-07-07 13:55:07 +0200 (Fri, 07 Jul 2006) | 1 line

Gives CML parts better names, like 'molecule1.cml' and 'spectrum2.cml'.


r1215 | tohel | 2006-07-07 13:45:35 +0200 (Fri, 07 Jul 2006) | 1 line

added some more jdx spectra


r1214 | shk3 | 2006-07-07 12:56:51 +0200 (Fri, 07 Jul 2006) | 1 line

changed nmrshiftdb server to production machine


r1213 | shk3 | 2006-07-07 12:47:48 +0200 (Fri, 07 Jul 2006) | 1 line

Also works if a spectrum has no yvalues


r1211 | tohel | 2006-07-07 11:51:08 +0200 (Fri, 07 Jul 2006) | 2 lines

theoretically, new files created via newFileWizard will now be parsed, selected and opened in resp. editor --> doesnt work for some reason


r1210 | egonw | 2006-07-07 11:30:44 +0200 (Fri, 07 Jul 2006) | 1 line

Made namespace public.


r1209 | egonw | 2006-07-07 11:26:48 +0200 (Fri, 07 Jul 2006) | 1 line

Cleaned up debug output.


r1208 | egonw | 2006-07-07 11:20:37 +0200 (Fri, 07 Jul 2006) | 1 line

Allow auto opening if resources created with this wizard.


r1203 | tohel | 2006-07-07 10:49:11 +0200 (Fri, 07 Jul 2006) | 1 line

cleaned up new Wizard categories


r1202 | tohel | 2006-07-07 10:08:25 +0200 (Fri, 07 Jul 2006) | 1 line

removed demo actions and buttons


r1201 | ospjuth | 2006-07-07 09:54:11 +0200 (Fri, 07 Jul 2006) | 1 line

Added and refactored documentation


r1200 | ospjuth | 2006-07-07 09:50:19 +0200 (Fri, 07 Jul 2006) | 1 line

Updated name of actions


r1175 | egonw | 2006-07-06 17:32:19 +0200 (Thu, 06 Jul 2006) | 1 line

More sysout work.


r1174 | egonw | 2006-07-06 17:30:59 +0200 (Thu, 06 Jul 2006) | 1 line

More sysout replacements.


r1173 | egonw | 2006-07-06 17:24:25 +0200 (Thu, 06 Jul 2006) | 1 line

More sysout work.


r1172 | egonw | 2006-07-06 15:38:14 +0200 (Thu, 06 Jul 2006) | 1 line

More sysout work.


r1171 | egonw | 2006-07-06 15:30:07 +0200 (Thu, 06 Jul 2006) | 1 line

More sysout work.


r1170 | egonw | 2006-07-06 15:24:43 +0200 (Thu, 06 Jul 2006) | 1 line

More sysout replacements.


r1169 | tohel | 2006-07-06 15:04:22 +0200 (Thu, 06 Jul 2006) | 1 line

some more debugging


r1168 | egonw | 2006-07-06 14:59:25 +0200 (Thu, 06 Jul 2006) | 1 line

Commented out sysouts.


r1167 | egonw | 2006-07-06 14:58:28 +0200 (Thu, 06 Jul 2006) | 1 line

Converted a lot of SysOut's to logger use.


r1166 | egonw | 2006-07-06 14:56:09 +0200 (Thu, 06 Jul 2006) | 1 line

Added the Useful Chemistry CMLRSS feed in the OPML template.


r1165 | egonw | 2006-07-06 14:52:59 +0200 (Thu, 06 Jul 2006) | 1 line

Converted a lot of SysOut's to logger use.


r1164 | egonw | 2006-07-06 14:36:07 +0200 (Thu, 06 Jul 2006) | 1 line

Removed example code not used in Bioclipse at all.


r1163 | tohel | 2006-07-06 14:34:57 +0200 (Thu, 06 Jul 2006) | 1 line

some debugging


r1162 | egonw | 2006-07-06 14:31:41 +0200 (Thu, 06 Jul 2006) | 1 line

Added output of CDK source code.


r1161 | egonw | 2006-07-06 14:28:49 +0200 (Thu, 06 Jul 2006) | 1 line

Removed sysouts (even in some test classes).


r1160 | egonw | 2006-07-06 14:01:29 +0200 (Thu, 06 Jul 2006) | 1 line

Added a screenshot


r1159 | tohel | 2006-07-06 13:49:15 +0200 (Thu, 06 Jul 2006) | 1 line

solved problem with "phantom res" on overwriting...


r1158 | tohel | 2006-07-06 13:43:29 +0200 (Thu, 06 Jul 2006) | 1 line

opening of newly created res works now correctly :)


r1157 | tohel | 2006-07-06 13:42:59 +0200 (Thu, 06 Jul 2006) | 1 line

debug


r1156 | tohel | 2006-07-06 11:37:40 +0200 (Thu, 06 Jul 2006) | 1 line

solving bug 1517599 - load/unload problem


r1155 | tohel | 2006-07-06 11:34:40 +0200 (Thu, 06 Jul 2006) | 1 line

some docu changes


r1152 | egonw | 2006-07-05 19:24:58 +0200 (Wed, 05 Jul 2006) | 1 line

Check for NP (closes #1505725).


r1151 | egonw | 2006-07-05 19:03:43 +0200 (Wed, 05 Jul 2006) | 1 line

Added views to Show View menu (closes #1507149)


r1150 | egonw | 2006-07-05 18:48:19 +0200 (Wed, 05 Jul 2006) | 1 line

Commented out for now: does not work properly.


r1149 | egonw | 2006-07-05 18:12:53 +0200 (Wed, 05 Jul 2006) | 1 line

Updated CDK to r6596


r1148 | tohel | 2006-07-05 17:59:04 +0200 (Wed, 05 Jul 2006) | 1 line

piped e.printStackTrace to logger


r1147 | tohel | 2006-07-05 17:55:31 +0200 (Wed, 05 Jul 2006) | 1 line

removed more sys.out


r1146 | tohel | 2006-07-05 17:51:16 +0200 (Wed, 05 Jul 2006) | 1 line

removed some sys.out


r1145 | tohel | 2006-07-05 17:43:26 +0200 (Wed, 05 Jul 2006) | 1 line

restricting CDKFormatdetector to CDKResources


r1144 | egonw | 2006-07-05 17:29:56 +0200 (Wed, 05 Jul 2006) | 1 line

Updated CDK to r6595


r1143 | egonw | 2006-07-05 17:26:59 +0200 (Wed, 05 Jul 2006) | 1 line

Removed sysout calls.


r1139 | egonw | 2006-07-05 16:23:30 +0200 (Wed, 05 Jul 2006) | 3 lines

Tobias and I made the SaveAs now use getSupported-() and getRequiredDataFeatures(): the wizard will not show formats it cannot save to (missing required features), and it will warn the user when not all features of the model will be saved (data loss because format does not support a certain feature).


r1138 | egonw | 2006-07-05 14:09:26 +0200 (Wed, 05 Jul 2006) | 1 line

Updated CDK to r6590


r1134 | ospjuth | 2006-07-05 12:02:19 +0200 (Wed, 05 Jul 2006) | 1 line

Updated about text (developers)


r1133 | ospjuth | 2006-07-05 12:01:23 +0200 (Wed, 05 Jul 2006) | 1 line

Updated old docu


r1132 | ospjuth | 2006-07-05 12:00:51 +0200 (Wed, 05 Jul 2006) | 1 line

Added documentation


r1124 | tohel | 2006-07-04 15:55:48 +0200 (Tue, 04 Jul 2006) | 1 line

some debugging


r1122 | ospjuth | 2006-07-04 14:37:05 +0200 (Tue, 04 Jul 2006) | 1 line

Updated documentation


r1120 | egonw | 2006-07-04 12:28:33 +0200 (Tue, 04 Jul 2006) | 1 line

Details on supported data features


r1119 | egonw | 2006-07-04 12:23:25 +0200 (Tue, 04 Jul 2006) | 1 line

Updated list


r1113 | tohel | 2006-07-03 14:22:17 +0200 (Mon, 03 Jul 2006) | 1 line

added dataFeature checking to SaveAs wizard


r1112 | egonw | 2006-07-03 13:21:17 +0200 (Mon, 03 Jul 2006) | 1 line

Updated for static method in DataFeaturesTool


r1111 | egonw | 2006-07-03 13:06:11 +0200 (Mon, 03 Jul 2006) | 1 line

New CDK version


r1102 | egonw | 2006-06-29 20:13:15 +0200 (Thu, 29 Jun 2006) | 1 line

Added missing license and copyright notices.


r1101 | egonw | 2006-06-29 20:06:39 +0200 (Thu, 29 Jun 2006) | 1 line

Some missing license files


r1100 | egonw | 2006-06-29 20:05:49 +0200 (Thu, 29 Jun 2006) | 1 line

Added missing license and copyright notices.


r1099 | egonw | 2006-06-29 20:05:22 +0200 (Thu, 29 Jun 2006) | 1 line

Added missing license and copyright notices.


r1098 | egonw | 2006-06-29 19:58:44 +0200 (Thu, 29 Jun 2006) | 1 line

Added missing license and copyright notices.


r1097 | egonw | 2006-06-29 19:51:47 +0200 (Thu, 29 Jun 2006) | 1 line

Added missing license and copyright notices.


r1096 | egonw | 2006-06-29 19:39:08 +0200 (Thu, 29 Jun 2006) | 1 line

Added missing license and copyright notices.


r1081 | tohel | 2006-06-28 13:37:36 +0200 (Wed, 28 Jun 2006) | 1 line

added file formats page to bc_spectrum


r1077 | ospjuth | 2006-06-27 12:39:58 +0200 (Tue, 27 Jun 2006) | 1 line

Removes debugs out


r1076 | ospjuth | 2006-06-27 12:39:28 +0200 (Tue, 27 Jun 2006) | 1 line

Fixes wizard finish to parse resources into correct type before open in editor


r1075 | tohel | 2006-06-27 11:44:06 +0200 (Tue, 27 Jun 2006) | 3 lines

changed smilesWizard -> smiles string is not anymore checked on every change, but on trying to finish the wizard -> activated "Test Smiles" button


r1074 | shk3 | 2006-06-27 10:40:59 +0200 (Tue, 27 Jun 2006) | 1 line

revert


r1073 | shk3 | 2006-06-27 10:35:33 +0200 (Tue, 27 Jun 2006) | 1 line

fixes bug #1483297


r1072 | shk3 | 2006-06-26 19:36:02 +0200 (Mon, 26 Jun 2006) | 1 line

new classes for plugins


r1071 | shk3 | 2006-06-26 17:43:05 +0200 (Mon, 26 Jun 2006) | 1 line

even better help


r1070 | shk3 | 2006-06-26 17:39:52 +0200 (Mon, 26 Jun 2006) | 1 line

more help improvments


r1069 | shk3 | 2006-06-26 17:37:07 +0200 (Mon, 26 Jun 2006) | 2 lines

removed obsolete help text


r1068 | shk3 | 2006-06-26 17:21:13 +0200 (Mon, 26 Jun 2006) | 1 line

jcp plugins work in bioclipse. The aminoacidtemplates plugin does not work; internal problem with loading templates, I suppose classpath or so.


r1067 | shk3 | 2006-06-26 17:19:58 +0200 (Mon, 26 Jun 2006) | 1 line

new cdk


r1066 | tohel | 2006-06-26 15:11:35 +0200 (Mon, 26 Jun 2006) | 1 line

new jfreechart jar


r1065 | tohel | 2006-06-26 14:41:17 +0200 (Mon, 26 Jun 2006) | 1 line

added FIXME for unloading of object from jmol on load of new non-jmol resource


r1064 | tohel | 2006-06-26 14:29:36 +0200 (Mon, 26 Jun 2006) | 1 line

added missing action


r1063 | tohel | 2006-06-26 13:46:44 +0200 (Mon, 26 Jun 2006) | 1 line

debugged new mol wizards


r1062 | tohel | 2006-06-26 13:24:50 +0200 (Mon, 26 Jun 2006) | 2 lines

debuged logging opening of empty mols works again


r1061 | edrin_t | 2006-06-26 12:38:29 +0200 (Mon, 26 Jun 2006) | 2 lines

some GUI changes... nothing important


r1060 | tohel | 2006-06-26 12:10:23 +0200 (Mon, 26 Jun 2006) | 1 line

with wizard created files are now opened in editor past creation


r1059 | egonw | 2006-06-26 12:02:26 +0200 (Mon, 26 Jun 2006) | 1 line

Removed unneeded and troublesome 'Required-Bundle'.


r1058 | edrin_t | 2006-06-26 11:54:34 +0200 (Mon, 26 Jun 2006) | 1 line

added wsplugin.html for docu


r1057 | edrin_t | 2006-06-26 11:38:59 +0200 (Mon, 26 Jun 2006) | 1 line

docu with tutorial


r1056 | edrin_t | 2006-06-26 11:37:40 +0200 (Mon, 26 Jun 2006) | 1 line

documentation with tutorial


r1055 | tohel | 2006-06-26 11:16:56 +0200 (Mon, 26 Jun 2006) | 3 lines

added missing logger.properties file some refactoring


r1054 | tohel | 2006-06-26 10:53:41 +0200 (Mon, 26 Jun 2006) | 1 line

replaced all sys.out by log messages


r1053 | tohel | 2006-06-26 10:42:54 +0200 (Mon, 26 Jun 2006) | 1 line

replaced all sys.out by log messages


r1052 | edrin_t | 2006-06-26 09:57:14 +0200 (Mon, 26 Jun 2006) | 1 line

added a progressmonitor for the open-resource wizardpage


r1051 | edrin_t | 2006-06-25 20:23:26 +0200 (Sun, 25 Jun 2006) | 1 line

Added functionality to finish the job with a wizard where you can decide how to handle the web service result (make it a Resource, set filename and open it)


r1050 | edrin_t | 2006-06-25 20:20:20 +0200 (Sun, 25 Jun 2006) | 1 line

renamed to IDoPerformFinish


r1047 | tohel | 2006-06-23 13:34:12 +0200 (Fri, 23 Jun 2006) | 1 line

removed non 1.0 functionality


r1046 | tohel | 2006-06-23 11:00:32 +0200 (Fri, 23 Jun 2006) | 1 line

fixed bug 1510546


r1037 | miguelrojasch | 2006-06-22 17:27:34 +0200 (Thu, 22 Jun 2006) | 1 line

update of cdk jars. And example data for reaction


r1036 | shk3 | 2006-06-22 17:03:12 +0200 (Thu, 22 Jun 2006) | 1 line

solves bug #1510542


r1035 | shk3 | 2006-06-22 16:51:00 +0200 (Thu, 22 Jun 2006) | 1 line

switch between jcp and text also works when having detachted elements


r1032 | tohel | 2006-06-22 14:46:21 +0200 (Thu, 22 Jun 2006) | 1 line

non jcamp notes are included into metadata


r1030 | egonw | 2006-06-21 17:49:26 +0200 (Wed, 21 Jun 2006) | 1 line

Full name, for branding purposes.


r1029 | egonw | 2006-06-21 17:45:32 +0200 (Wed, 21 Jun 2006) | 1 line

Added docs on the views.


r1028 | tohel | 2006-06-21 16:00:38 +0200 (Wed, 21 Jun 2006) | 1 line

peak picking on ir spectra debugged


r1025 | egonw | 2006-06-21 15:44:10 +0200 (Wed, 21 Jun 2006) | 1 line

Fixed hierarchy: the scripting reference is not a tutorial


r1024 | tohel | 2006-06-21 15:40:56 +0200 (Wed, 21 Jun 2006) | 1 line

more debugging, cleanup and logging


r1023 | egonw | 2006-06-21 15:39:45 +0200 (Wed, 21 Jun 2006) | 1 line

Fixed escaping of < in the OPML example code.


r1022 | egonw | 2006-06-21 15:39:08 +0200 (Wed, 21 Jun 2006) | 1 line

Added docs for the 'New OPML Resource' wizard.


r1021 | ospjuth | 2006-06-21 14:07:44 +0200 (Wed, 21 Jun 2006) | 1 line

Implemented virtual storage and parsing of results + open in editors


r1020 | ospjuth | 2006-06-21 14:07:00 +0200 (Wed, 21 Jun 2006) | 1 line

Added virtual folder functionality


r1019 | tohel | 2006-06-21 13:01:40 +0200 (Wed, 21 Jun 2006) | 1 line

added logging, debugged, new jcamp jar...


r1018 | edrin_t | 2006-06-20 16:01:09 +0200 (Tue, 20 Jun 2006) | 1 line

icon for progress view


r1017 | edrin_t | 2006-06-20 12:54:16 +0200 (Tue, 20 Jun 2006) | 1 line

added ws_ebi.png icon used in bc_webservices


r1016 | edrin_t | 2006-06-20 12:53:17 +0200 (Tue, 20 Jun 2006) | 1 line

finally adapted classpathes to get it compile, removed debug output to console, removed "common" exceptions that were written to bioclipse console


r1015 | edrin_t | 2006-06-20 10:34:54 +0200 (Tue, 20 Jun 2006) | 1 line

updated classpath and removed wsdl stuff that is not required


r1014 | egonw | 2006-06-19 20:35:03 +0200 (Mon, 19 Jun 2006) | 1 line

Updated CDK version


r1013 | tohel | 2006-06-19 17:09:39 +0200 (Mon, 19 Jun 2006) | 1 line

new spectrum perspective


r1012 | egonw | 2006-06-19 16:11:32 +0200 (Mon, 19 Jun 2006) | 1 line

Added missing bits: note that src-axis1 is not the axis1 source, but the classes generated for the EMBL webservices, which uses Axis1.4


r1011 | tohel | 2006-06-19 15:11:34 +0200 (Mon, 19 Jun 2006) | 1 line

peak table entries are now rounded


r1010 | egonw | 2006-06-19 14:30:41 +0200 (Mon, 19 Jun 2006) | 1 line

OK, first copy; have to check things yet


r1009 | tohel | 2006-06-19 13:46:04 +0200 (Mon, 19 Jun 2006) | 1 line

unload on resources shown in textEditor works again


r1008 | egonw | 2006-06-18 13:26:06 +0200 (Sun, 18 Jun 2006) | 2 lines

Ported edrin's 1005:1006 patch to the b1 branch, so that bc_webservices works nicely with this branch too. Having the progress viewer working in b1/ is a nice touch anyway, would be nice if other time consuming tasks would use it too, e.g. opening PDB files :)


r999 | tohel | 2006-06-14 14:03:24 +0200 (Wed, 14 Jun 2006) | 1 line

writing of cont data works, now - and the written data can be read in again!


r996 | tohel | 2006-06-14 10:53:41 +0200 (Wed, 14 Jun 2006) | 1 line

some docu & bc_spectrum debugging


r995 | tohel | 2006-06-14 10:50:29 +0200 (Wed, 14 Jun 2006) | 1 line

started making editors aware of changes realized in views


r966 | shk3 | 2006-06-08 16:02:42 +0200 (Thu, 08 Jun 2006) | 1 line

new ckd, which should do the better ring layout again


r964 | egonw | 2006-06-07 17:37:56 +0200 (Wed, 07 Jun 2006) | 1 line

Script help


r963 | egonw | 2006-06-07 17:33:43 +0200 (Wed, 07 Jun 2006) | 1 line

Script help


r962 | ospjuth | 2006-06-07 17:20:33 +0200 (Wed, 07 Jun 2006) | 1 line

Updated for 0.9.2 release


r961 | ospjuth | 2006-06-07 17:19:47 +0200 (Wed, 07 Jun 2006) | 1 line

Removed debug outs


r960 | ospjuth | 2006-06-07 17:13:27 +0200 (Wed, 07 Jun 2006) | 1 line

Removed debug outs


r959 | ospjuth | 2006-06-07 17:11:46 +0200 (Wed, 07 Jun 2006) | 1 line

Updated binary build


r958 | ospjuth | 2006-06-07 16:49:54 +0200 (Wed, 07 Jun 2006) | 1 line

Updated versioning for 0.9.2 release


r957 | ospjuth | 2006-06-07 16:37:45 +0200 (Wed, 07 Jun 2006) | 1 line

Constributed a PDBEditor for PDB-files with line highlighting and code completion


r956 | ospjuth | 2006-06-07 16:37:06 +0200 (Wed, 07 Jun 2006) | 1 line

Contributed an abstract KeywordEditor


r955 | tohel | 2006-06-06 19:05:48 +0200 (Tue, 06 Jun 2006) | 1 line

some docu


r954 | tohel | 2006-06-06 16:19:39 +0200 (Tue, 06 Jun 2006) | 1 line

debugging


r953 | shk3 | 2006-06-06 14:19:38 +0200 (Tue, 06 Jun 2006) | 1 line

printing of jcp now possible


r952 | tohel | 2006-06-06 13:28:45 +0200 (Tue, 06 Jun 2006) | 1 line

jcp is now capable of opnening files containing an empty molecule/model e.g. newly created chemical files


r951 | shk3 | 2006-06-06 12:48:36 +0200 (Tue, 06 Jun 2006) | 1 line

Refactored help


r950 | tohel | 2006-06-06 12:34:28 +0200 (Tue, 06 Jun 2006) | 2 lines

removed requirements.html


r949 | tohel | 2006-06-06 12:33:19 +0200 (Tue, 06 Jun 2006) | 1 line

removed jcp wizard - not needed


r948 | tohel | 2006-06-06 11:38:35 +0200 (Tue, 06 Jun 2006) | 1 line

some more changes in help


r947 | shk3 | 2006-06-06 11:37:47 +0200 (Tue, 06 Jun 2006) | 1 line

Changes in help


r946 | shk3 | 2006-06-06 10:49:06 +0200 (Tue, 06 Jun 2006) | 1 line

I removed the Molecular List view. If anybody likes this one, he may re-add it with some usefull content


r945 | shk3 | 2006-06-06 10:35:29 +0200 (Tue, 06 Jun 2006) | 1 line

help


r944 | shk3 | 2006-06-06 10:35:02 +0200 (Tue, 06 Jun 2006) | 2 lines

added help for cml


r943 | tohel | 2006-06-06 10:03:14 +0200 (Tue, 06 Jun 2006) | 1 line

corrected icon for cml files


r942 | egonw | 2006-06-05 21:35:24 +0200 (Mon, 05 Jun 2006) | 1 line

Has a template, otherwise it can't be openend because of an XML parsing error.


r941 | egonw | 2006-06-05 21:34:46 +0200 (Mon, 05 Jun 2006) | 1 line

Files can now have a template content.


r940 | egonw | 2006-06-05 21:07:08 +0200 (Mon, 05 Jun 2006) | 1 line

Attempt to get it auto rebonding


r939 | egonw | 2006-06-05 21:05:53 +0200 (Mon, 05 Jun 2006) | 1 line

Latest CDK: working PDB reader with Rebond as default turned on, because I can't get Jmol to cooperate


r938 | egonw | 2006-06-05 21:04:41 +0200 (Mon, 05 Jun 2006) | 1 line

Fixed an ArrayIndexOutOfBounds source, and set limit to number of atoms for calculating SMILES.


r937 | egonw | 2006-06-05 19:07:34 +0200 (Mon, 05 Jun 2006) | 1 line

Default no rebonding


r936 | egonw | 2006-06-05 19:07:16 +0200 (Mon, 05 Jun 2006) | 1 line

Allow customize reading: PDB does not auto rebond, and uses a nonotify data class


r935 | egonw | 2006-06-05 18:42:19 +0200 (Mon, 05 Jun 2006) | 1 line

Be more fault tolerant towards CDK input.


r932 | ospjuth | 2006-06-02 16:43:11 +0200 (Fri, 02 Jun 2006) | 1 line

Prepared for a PDBEditor very similar to JmolEditor but with other KeyWords


r931 | ospjuth | 2006-06-02 16:42:29 +0200 (Fri, 02 Jun 2006) | 1 line

Fixed a classcastException bug when parsing CML into molecule


r930 | ospjuth | 2006-06-02 16:41:51 +0200 (Fri, 02 Jun 2006) | 1 line

Refactored constants to plugins


r929 | ospjuth | 2006-06-02 16:41:26 +0200 (Fri, 02 Jun 2006) | 1 line

Refactored constants to plugins


r928 | ospjuth | 2006-06-02 16:40:57 +0200 (Fri, 02 Jun 2006) | 1 line

Fixed NullpointerException if BioResView is closed before dispose() in other views is called


r927 | ospjuth | 2006-06-02 16:36:08 +0200 (Fri, 02 Jun 2006) | 1 line

Fixed a classcastException bug when parsing CML into molecule


r926 | ospjuth | 2006-06-02 15:30:10 +0200 (Fri, 02 Jun 2006) | 1 line

Added new icon for BaseFolder


r925 | ospjuth | 2006-06-02 15:17:23 +0200 (Fri, 02 Jun 2006) | 1 line

Updated to use a new CML-icon


r924 | ospjuth | 2006-06-02 14:51:55 +0200 (Fri, 02 Jun 2006) | 1 line

Fixed tab-style and perspective placement


r921 | tohel | 2006-06-01 15:36:20 +0200 (Thu, 01 Jun 2006) | 1 line

all spectrum related views are now cleaned up on unloading a spectrumResource


r920 | tohel | 2006-06-01 15:00:45 +0200 (Thu, 01 Jun 2006) | 1 line

unloading of spectra is now working


r919 | tohel | 2006-06-01 14:45:16 +0200 (Thu, 01 Jun 2006) | 1 line

added gifs for cml files


r918 | shk3 | 2006-06-01 14:33:45 +0200 (Thu, 01 Jun 2006) | 1 line

updated help-


r917 | ospjuth | 2006-06-01 14:24:53 +0200 (Thu, 01 Jun 2006) | 1 line

Removed CDK-like properties


r916 | shk3 | 2006-05-31 23:10:57 +0200 (Wed, 31 May 2006) | 1 line

started editing help


r914 | ospjuth | 2006-05-31 16:16:16 +0200 (Wed, 31 May 2006) | 1 line

Fixed copyright, javadoc, and JmolEditor so that JmolKeywords are used directly


r913 | ospjuth | 2006-05-31 16:15:23 +0200 (Wed, 31 May 2006) | 1 line

Fixed comments and javadoc


r912 | shk3 | 2006-05-31 14:54:44 +0200 (Wed, 31 May 2006) | 1 line

correct handling of highligthing action with non-highlighted acitons like periodic table


r910 | shk3 | 2006-05-31 14:49:27 +0200 (Wed, 31 May 2006) | 1 line

new cdk


r909 | shk3 | 2006-05-31 14:48:42 +0200 (Wed, 31 May 2006) | 1 line

removed unecessary images


r906 | shk3 | 2006-05-31 14:00:01 +0200 (Wed, 31 May 2006) | 1 line

avoids a npe


r905 | tohel | 2006-05-31 13:20:19 +0200 (Wed, 31 May 2006) | 1 line

cml metadata can be edited, too


r904 | tohel | 2006-05-31 12:49:55 +0200 (Wed, 31 May 2006) | 1 line

editing and displaying of metadata for jcamp spectry should work correctly now


r903 | ospjuth | 2006-05-31 10:32:05 +0200 (Wed, 31 May 2006) | 1 line

Added image for doc


r902 | ospjuth | 2006-05-31 10:31:22 +0200 (Wed, 31 May 2006) | 1 line

Added 1ale to pdb


r901 | ospjuth | 2006-05-31 10:30:39 +0200 (Wed, 31 May 2006) | 1 line

Added NewOPMLWizard


r900 | ospjuth | 2006-05-31 10:30:10 +0200 (Wed, 31 May 2006) | 1 line

Removed error stacktrace on parse of CMLRSS


r899 | ospjuth | 2006-05-30 22:14:57 +0200 (Tue, 30 May 2006) | 1 line

Refactored NewFileWizard to be easily overridden by plugins


r898 | ospjuth | 2006-05-30 22:10:15 +0200 (Tue, 30 May 2006) | 1 line

Fixed recursive copying of files and directories


r897 | ospjuth | 2006-05-30 22:09:35 +0200 (Tue, 30 May 2006) | 1 line

Added NewJmolScriptAction


r896 | ospjuth | 2006-05-30 22:09:06 +0200 (Tue, 30 May 2006) | 1 line

Added dots on/off action


r895 | ospjuth | 2006-05-30 21:16:28 +0200 (Tue, 30 May 2006) | 1 line

Recursive copy of directories now operational. All InstallActions now works.


r894 | tohel | 2006-05-30 15:05:31 +0200 (Tue, 30 May 2006) | 1 line

some more metadata debugging


r893 | tohel | 2006-05-30 14:40:40 +0200 (Tue, 30 May 2006) | 1 line

fixed a metadata bug


r892 | ospjuth | 2006-05-29 23:32:20 +0200 (Mon, 29 May 2006) | 1 line

Working on docs for bioclipse


r890 | ospjuth | 2006-05-29 22:14:00 +0200 (Mon, 29 May 2006) | 1 line

Working on docs for bioclipse


r889 | ospjuth | 2006-05-29 22:13:27 +0200 (Mon, 29 May 2006) | 1 line

Removed text field above tree (why has this not been done before?)


r888 | shk3 | 2006-05-29 21:44:31 +0200 (Mon, 29 May 2006) | 1 line

removed comment


r887 | shk3 | 2006-05-29 19:01:17 +0200 (Mon, 29 May 2006) | 1 line

Shows active JCP button


r886 | tohel | 2006-05-29 16:28:56 +0200 (Mon, 29 May 2006) | 1 line

started with jcp docu


r885 | shk3 | 2006-05-29 16:19:16 +0200 (Mon, 29 May 2006) | 1 line

better c&p


r884 | shk3 | 2006-05-29 14:53:19 +0200 (Mon, 29 May 2006) | 1 line

copy&paste works


r883 | tohel | 2006-05-29 14:20:39 +0200 (Mon, 29 May 2006) | 1 line

rest of docu


r882 | tohel | 2006-05-29 14:17:27 +0200 (Mon, 29 May 2006) | 1 line

on dispose unregister the view at bioResView


r881 | ospjuth | 2006-05-29 13:55:11 +0200 (Mon, 29 May 2006) | 1 line

Added removeSelectionChanged methods for cleanup on dispose in other views


r880 | tohel | 2006-05-29 13:50:34 +0200 (Mon, 29 May 2006) | 1 line

added docu fpr bc_spectrum


r879 | ospjuth | 2006-05-28 23:56:33 +0200 (Sun, 28 May 2006) | 1 line

Changed output on start to CML


r878 | ospjuth | 2006-05-28 23:53:17 +0200 (Sun, 28 May 2006) | 1 line

Fixed disposal of JmolView to unregister listeners


r875 | tohel | 2006-05-24 14:21:25 +0200 (Wed, 24 May 2006) | 1 line

if molecule could not be opened in jcp, open file in text menu and show errorMessage to the user


r874 | shk3 | 2006-05-24 14:07:52 +0200 (Wed, 24 May 2006) | 1 line

centering now also works when loading with scrollbars


r873 | shk3 | 2006-05-24 13:40:53 +0200 (Wed, 24 May 2006) | 1 line

vertical scroll works again


r872 | tohel | 2006-05-24 11:55:13 +0200 (Wed, 24 May 2006) | 1 line

if the user tries to save not valid (to the regardign file format) txtEditor content form the jcp instance, msgbox stating an error is poping up and nothing will be saved...


r871 | tohel | 2006-05-24 11:21:08 +0200 (Wed, 24 May 2006) | 1 line

removed copy & paste error


r870 | tohel | 2006-05-24 10:40:56 +0200 (Wed, 24 May 2006) | 1 line

dialog asking if res related perspective should be opened is just popping up, if the regarding perspective is not already open


r869 | tohel | 2006-05-24 10:05:01 +0200 (Wed, 24 May 2006) | 1 line

deleted jcp translations - we do not support anythiong else than english at the moment


r868 | ospjuth | 2006-05-24 01:02:12 +0200 (Wed, 24 May 2006) | 1 line

Some cleanups


r867 | ospjuth | 2006-05-24 01:01:35 +0200 (Wed, 24 May 2006) | 1 line

Added doc to exported folders


r866 | ospjuth | 2006-05-24 01:00:57 +0200 (Wed, 24 May 2006) | 1 line

Fixed activator and binary build


r865 | ospjuth | 2006-05-24 01:00:23 +0200 (Wed, 24 May 2006) | 1 line

Fixed activator for bc_cml


r864 | tohel | 2006-05-23 17:16:34 +0200 (Tue, 23 May 2006) | 2 lines

-removed annoying output from chemObjectTree -fixed focus prob with jmol - if jmolpanel is clicked, the view gets focussed now


r863 | shk3 | 2006-05-23 14:56:59 +0200 (Tue, 23 May 2006) | 1 line

mew cdk, fixes problems with drawing bonds


r862 | ospjuth | 2006-05-23 14:43:39 +0200 (Tue, 23 May 2006) | 1 line

Adde filenamefilter for .meta files


r861 | tohel | 2006-05-23 12:50:51 +0200 (Tue, 23 May 2006) | 2 lines

- added simple dialogs asking if regarding perspective should be opened on loading a resource - selection is not stored to preferences at the moment


r860 | ospjuth | 2006-05-23 12:37:07 +0200 (Tue, 23 May 2006) | 1 line

Fixed documentation structure and new additions for Bioclipse plugin


r859 | ospjuth | 2006-05-23 12:36:12 +0200 (Tue, 23 May 2006) | 1 line

Added tutorial for running external applications in Bioclipse


r858 | ospjuth | 2006-05-23 12:34:56 +0200 (Tue, 23 May 2006) | 1 line

Fixed preliminary icons for bioclipe window and manager


r857 | ospjuth | 2006-05-23 12:33:56 +0200 (Tue, 23 May 2006) | 1 line

Added documentation structure for Jmol and started documentation


r856 | ospjuth | 2006-05-23 12:32:53 +0200 (Tue, 23 May 2006) | 1 line

Commented out unused extension


r855 | tohel | 2006-05-23 11:15:18 +0200 (Tue, 23 May 2006) | 1 line

focussing of jcpEditor now works from all other views (views have to override setFocus() method, please ensure, that this method sets the focus to the main component of that view!)


r854 | shk3 | 2006-05-22 17:45:14 +0200 (Mon, 22 May 2006) | 1 line

contains a new cdk; this avoids problems with scaling when switching between jcp and test editor


r848 | tohel | 2006-05-22 15:00:59 +0200 (Mon, 22 May 2006) | 1 line

added FIXME


r837 | ospjuth | 2006-05-19 18:15:54 +0200 (Fri, 19 May 2006) | 1 line

Updated for binary build


r836 | ospjuth | 2006-05-19 18:15:20 +0200 (Fri, 19 May 2006) | 1 line

Updated product with bc_data


r835 | ospjuth | 2006-05-19 18:06:16 +0200 (Fri, 19 May 2006) | 1 line

Factored out InstallDataAction to new plugin bc_data


r834 | ospjuth | 2006-05-19 17:59:06 +0200 (Fri, 19 May 2006) | 1 line

Import of data files and setup of actions to install sample data and organic data


r833 | ospjuth | 2006-05-19 17:56:02 +0200 (Fri, 19 May 2006) | 1 line

Initial import.


r832 | ospjuth | 2006-05-19 15:22:07 +0200 (Fri, 19 May 2006) | 1 line

Removed Toolbar icon for sample data installation; a menu alternative is sufficient


r831 | ospjuth | 2006-05-19 15:20:16 +0200 (Fri, 19 May 2006) | 1 line

Removed BioSearch for now; postponed to a later version


r820 | tohel | 2006-05-18 16:03:12 +0200 (Thu, 18 May 2006) | 1 line

some bug fixing on bioPolymerTree


r819 | ospjuth | 2006-05-18 15:58:36 +0200 (Thu, 18 May 2006) | 1 line

Fixed icons and versioning, about text etc for 0.9.1 release


r814 | ospjuth | 2006-05-18 15:22:17 +0200 (Thu, 18 May 2006) | 1 line

Updated icon for JmolView and removed standard icon for actions


r813 | ospjuth | 2006-05-18 15:21:31 +0200 (Thu, 18 May 2006) | 1 line

Removed annotations view


r811 | tohel | 2006-05-16 18:08:28 +0200 (Tue, 16 May 2006) | 2 lines

adapted new SpectrumWizard bugfixes in bc_spectrum


r805 | tohel | 2006-05-15 17:01:37 +0200 (Mon, 15 May 2006) | 2 lines

added a new ContentProvider for the folder tree in new wizards to bioclipse package


r804 | tohel | 2006-05-15 17:00:42 +0200 (Mon, 15 May 2006) | 4 lines

changed newMoleculeWizard -> is just working on resources now dir selection is now done on tree just showing all folders below actual root


r791 | ospjuth | 2006-05-15 13:45:15 +0200 (Mon, 15 May 2006) | 1 line

External applications preferences updated and works now


r790 | ospjuth | 2006-05-15 13:44:23 +0200 (Mon, 15 May 2006) | 1 line

Removed unused actions (Generate 3D coordinates, Create descriptors) as they are not implemented


r783 | tohel | 2006-05-15 11:11:18 +0200 (Mon, 15 May 2006) | 1 line

some bugfixes


r781 | tohel | 2006-05-14 18:43:11 +0200 (Sun, 14 May 2006) | 3 lines

saveAs of jchempaint is now unsing a wizard, too added MoleculeSaveAsWizard to bc_cdk - should be used by all plugins for saveAs... cdk molecules removed former saveAsDialog from build path


r780 | tohel | 2006-05-14 17:46:53 +0200 (Sun, 14 May 2006) | 1 line

removed unneeded code


r779 | tohel | 2006-05-14 17:43:45 +0200 (Sun, 14 May 2006) | 2 lines

added new molecule wizard added confirm dialog in new spectrum wizard if file already exists


r778 | tohel | 2006-05-14 17:42:06 +0200 (Sun, 14 May 2006) | 2 lines

added new molecule wizard added confirm dialog in new spectrum wizard if file already exists


r777 | tohel | 2006-05-14 16:44:58 +0200 (Sun, 14 May 2006) | 1 line

current root dir is now pre selected in new Spectrum Wizard


r772 | tohel | 2006-05-12 18:02:09 +0200 (Fri, 12 May 2006) | 2 lines

new jcampParser jar expanded new spectrum wizard by two more spectrum types (UV & IR)


r771 | tohel | 2006-05-12 17:48:40 +0200 (Fri, 12 May 2006) | 2 lines

some bugfixing


r770 | tohel | 2006-05-12 17:47:50 +0200 (Fri, 12 May 2006) | 2 lines

updated cdk jars


r769 | tohel | 2006-05-12 17:43:07 +0200 (Fri, 12 May 2006) | 2 lines

ome bugfixes


r768 | tohel | 2006-05-12 16:01:06 +0200 (Fri, 12 May 2006) | 2 lines

new spectrum wizard is now fully functional creation of jdx and cml spectra works


r767 | egonw | 2006-05-12 11:27:54 +0200 (Fri, 12 May 2006) | 1 line

Updated jars from CDK SVN r6243.


r766 | egonw | 2006-05-12 07:42:08 +0200 (Fri, 12 May 2006) | 1 line

Ignore .svn dirs too. Linux has lower cases.


r765 | egonw | 2006-05-12 07:39:22 +0200 (Fri, 12 May 2006) | 1 line

Cool patch to give the file size in the Props.


r762 | tohel | 2006-05-11 17:42:34 +0200 (Thu, 11 May 2006) | 1 line

started a new spectrum wizard


r761 | egonw | 2006-05-10 14:31:22 +0200 (Wed, 10 May 2006) | 1 line

Updated for new CDK.


r760 | egonw | 2006-05-10 14:27:00 +0200 (Wed, 10 May 2006) | 1 line

Updated for new CDK.


r759 | egonw | 2006-05-10 14:25:34 +0200 (Wed, 10 May 2006) | 1 line

Updated for new CDK.


r758 | egonw | 2006-05-10 14:17:22 +0200 (Wed, 10 May 2006) | 1 line

Updated CDK


r757 | ospjuth | 2006-05-09 16:44:24 +0200 (Tue, 09 May 2006) | 1 line

Makes selection of TextEditor based on format in BioResource possible


r756 | ospjuth | 2006-05-09 16:44:03 +0200 (Tue, 09 May 2006) | 1 line

Makes selection of TextEditor based on format in BioResource possible


r755 | ospjuth | 2006-05-09 16:37:21 +0200 (Tue, 09 May 2006) | 1 line

Select editor for source tab by getting it from CDKResource.getTextEditor().


r754 | ospjuth | 2006-05-09 15:59:37 +0200 (Tue, 09 May 2006) | 1 line

Updated for IChemFormat.isXMLBased(), see FIXME


r753 | ospjuth | 2006-05-09 15:45:24 +0200 (Tue, 09 May 2006) | 1 line

Open with... now closes any open editors of wrong type, or else activates the workbench part


r752 | ospjuth | 2006-05-09 15:30:52 +0200 (Tue, 09 May 2006) | 1 line

Added getTextEditorID to accommodate for different editors in e.g. JCP source tab


r751 | ospjuth | 2006-05-09 15:27:07 +0200 (Tue, 09 May 2006) | 1 line

Echo output from command line to BioclipseConsole


r750 | ospjuth | 2006-05-09 14:32:23 +0200 (Tue, 09 May 2006) | 1 line

Updated binary build


r749 | egonw | 2006-05-09 14:24:19 +0200 (Tue, 09 May 2006) | 1 line

Merged patches 728,729-733: Atom 1.0 support + a NPE fixes and use of Logger


r747 | egonw | 2006-05-09 14:17:42 +0200 (Tue, 09 May 2006) | 1 line

Removed method getMolecule() and getAtomContainer() which were not well defined.


r746 | ospjuth | 2006-05-09 14:06:59 +0200 (Tue, 09 May 2006) | 1 line

2DStrucureView is now emptied when only 3D-coordinates are available


r745 | ospjuth | 2006-05-09 13:39:56 +0200 (Tue, 09 May 2006) | 1 line

On Unload, open editors are closed and user is asked to save() if isDirty


r744 | ospjuth | 2006-05-09 13:38:58 +0200 (Tue, 09 May 2006) | 1 line

Changed Filtering to use ViewFilters for TreeViewer and rewrote UnwantedNamesFilters


r743 | ospjuth | 2006-05-09 13:37:29 +0200 (Tue, 09 May 2006) | 1 line

Fixed bug in display and deletion of Folders with hidden content


r742 | ospjuth | 2006-05-09 13:36:05 +0200 (Tue, 09 May 2006) | 1 line

Fixed a bug if no squences in a BioJavaResource


r741 | ospjuth | 2006-05-08 15:23:51 +0200 (Mon, 08 May 2006) | 1 line

Fix the ExternalApplication and preferences bug.


r740 | ospjuth | 2006-05-08 15:22:37 +0200 (Mon, 08 May 2006) | 1 line

Added functionality to react on application arguments on command line start


r739 | ospjuth | 2006-05-08 09:50:28 +0200 (Mon, 08 May 2006) | 1 line

Update javadoc of JmolScriptActions


r738 | ospjuth | 2006-05-08 09:46:55 +0200 (Mon, 08 May 2006) | 1 line

This fixes the RunJmolScriptAction


r736 | egonw | 2006-05-07 21:40:21 +0200 (Sun, 07 May 2006) | 1 line

Split up cartoons|ribbons on/off into two menu items (closes #1483299)


r727 | ospjuth | 2006-05-05 13:00:58 +0200 (Fri, 05 May 2006) | 1 line

Added OPML icon to export build


r726 | egonw | 2006-05-04 18:24:17 +0200 (Thu, 04 May 2006) | 1 line

Setup up content for the Bioclipse 1.x (b1) branch


r725 | egonw | 2006-05-04 18:21:09 +0200 (Thu, 04 May 2006) | 1 line

Setup dir for stable Bioclipse 1.x branch


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