Timeline


and

19-10-10:

19:00 Changeset [644] by tim.te.beek@…
Add TODO for indexes
16:11 Ticket #1 (JSpecView applet keeps using CPU after first spectrum selection) created by tim.te.beek@…
Due to repeated invocation of jspecview.common.JSVPanel.drawPlot(), …
15:50 WikiStart edited by tim.te.beek@…
(diff)

15-10-10:

14:38 WikiStart edited by tim.te.beek@…
(diff)
10:54 Changeset [643] by tim.te.beek@…
Do not ignore return value of file.delete() for temp file
10:53 Changeset [642] by tim.te.beek@…
Set clone() for bincounts int[], to eliminate external mutability

14-10-10:

16:50 Changeset [641] by tim.te.beek@…
2nd try to enable findbugs
15:40 Changeset [640] by tim.te.beek@…
15:40 Changeset [639] by tim.te.beek@…
14:45 Changeset [638] by tim.te.beek@…
Provide a name for speed-test module
14:44 Changeset [637] by tim.te.beek@…
Disable FindBugs? & log reason
14:39 Changeset [636] by tim.te.beek@…
Fix JavaDoc?
14:38 Changeset [635] by tim.te.beek@…
Load & link spectrum automatically
14:34 Changeset [634] by tim.te.beek@…
Fix JavaDoc?
14:06 Changeset [633] by tim.te.beek@…
Add FIXME notice to externally licensed file
14:01 Changeset [632] by tim.te.beek@…
Enable FindBugs? to see if it works
13:20 Changeset [631] by tim.te.beek@…
Added two commented out broken implementations of loading labels & …
13:18 Changeset [630] by tim.te.beek@…
Removed Builder class: No longer needed
13:18 Changeset [629] by tim.te.beek@…
Convert record to map once, instead of repeated split & count incrementing …
10:44 Changeset [628] by tim.te.beek@…
Detect & handle duplicates for mol files & spectra adding

13-10-10:

13:18 Changeset [627] by tim.te.beek@…
Clearly state script value will be replaced
13:11 Changeset [626] by tim.te.beek@…
Store first spectrum reference instead of recreating it
13:09 Changeset [625] by tim.te.beek@…
Log reasons for disabled tests
13:06 Changeset [624] by tim.te.beek@…
Disable complex wildcard testing
12:50 Changeset [623] by tim.te.beek@…
Add test (and executable!) to test compoundpage display for compound …
12:48 Changeset [622] by tim.te.beek@…
Only float jmol to the right if there are spectra
12:38 Changeset [621] by tim.te.beek@…
Remove individual visibility setting for members of JSpecViewPanel, as …
12:24 Changeset [620] by tim.te.beek@…
Rename DAOs to emphasize distinction with interfaces
12:21 Changeset [619] by tim.te.beek@…
Use DAO interfaces instead of implementing classes
12:20 Changeset [618] by tim.te.beek@…
Use DAO interfaces instead of implementing classes
12:16 Changeset [617] by tim.te.beek@…
Create panels for JSpecView & Jmol applets Move JSpecView & Jmol specific …

12-10-10:

16:56 Changeset [616] by tim.te.beek@…
Added two TODOs
16:23 Changeset [615] by tim.te.beek@…
Do not display ChemClass? when null Do not display jspecview applet or tab …
16:20 Changeset [614] by tim.te.beek@…
- Only delete compound if found - Assert ElementCounts? is not empty - …
16:19 Changeset [613] by tim.te.beek@…
Throw legible FNFE when mol file is missing
15:47 Changeset [612] by tim.te.beek@…
Added test for CompoundPage? display for compound without spectra
15:46 Changeset [611] by tim.te.beek@…
Make molfile field @NotEmpty?
14:34 Changeset [610] by tim.te.beek@…
14:34 Changeset [609] by tim.te.beek@…

08-10-10:

12:59 Changeset [608] by tim.te.beek@…
Load jdx spectrum using packaged resource & attribute modifier instead of …
12:01 Changeset [607] by tim.te.beek@…
Disable test while bitwise is disabled
09:47 Changeset [606] by tim.te.beek@…
Use default Hibernate PostgreSQL dialect
09:47 Changeset [605] by tim.te.beek@…
@Ignore tests that use native bitwise search
09:42 Changeset [604] by tim.te.beek@…
No longer store BitSets? as bits(200) in PostgreSQL Deprecate …

07-10-10:

18:28 Changeset [603] by tim.te.beek@…
Removed unused fields COUNTS_SUBSPEC_SCORE etc
18:27 Changeset [602] by tim.te.beek@…
Also generate Compound
18:19 Changeset [601] by tim.te.beek@…
Added additional debug log statement
18:19 Changeset [600] by tim.te.beek@…
Added additional debug log statements
16:59 Changeset [599] by tim.te.beek@…
Added searchBitwiseNatively
16:59 Changeset [598] by tim.te.beek@…
Suppress unused warnings
16:57 Changeset [597] by tim.te.beek@…
Add asserts for the number of hits that should be returned from normal …
16:53 Changeset [596] by tim.te.beek@…
Use mask.set(startBin, endBin, true); to set bits in a range instead of a …
16:46 Changeset [595] by tim.te.beek@…
Limit @SuppressWarnings? scope
16:12 Changeset [594] by tim.te.beek@…
Only print first 5
16:07 Changeset [593] by tim.te.beek@…
Count using i += 50
15:53 Changeset [592] by tim.te.beek@…
Complete documentation
15:48 Changeset [591] by tim.te.beek@…
Renamed method & add binsize as argument
15:29 Changeset [590] by tim.te.beek@…
Add initial Native bit operation search
15:06 Changeset [589] by tim.te.beek@…
Extract public static methods toString & toBitSet to translate between …
14:09 Changeset [588] by tim.te.beek@…
Split up BitSet? definitions for clarity
11:52 Changeset [587] by tim.te.beek@…
Remove @runwith stuff, as it isn't a @Test Directly store Spectra instead …
11:24 Changeset [586] by tim.te.beek@…
Do not clone return value of getBinBits, as it itself is already a clone …
11:24 Changeset [585] by tim.te.beek@…
Return a clone of binBits upon getBinBits
11:17 Changeset [584] by tim.te.beek@…
Remove fields solvent, nmrType, experimentType & compound from …
10:44 Changeset [583] by tim.te.beek@…
Run installer before parser test

06-10-10:

16:35 Changeset [582] by tim.te.beek@…
Use association querying on …
16:32 Changeset [581] by tim.te.beek@…
Log warning on missing JDX file
16:30 Changeset [580] by tim.te.beek@…
Log IOException on failure to read SDF file
16:06 Changeset [579] by tim.te.beek@…
Delete shaded xml files
16:04 Changeset [578] by tim.te.beek@…
16:03 Changeset [577] by tim.te.beek@…
Move usertype package to mapping Update hibernate.cfgs accordingly
15:53 Changeset [576] by tim.te.beek@…
Suppress deprecation warnings as there's no alternative hint yet till …
15:52 Changeset [575] by tim.te.beek@…
Use protected static fields from BitSetUserType? in MyEPSQLDialect
15:51 Changeset [574] by tim.te.beek@…
Add asserts that first hits should have no differences
15:47 Changeset [573] by tim.te.beek@…
Store number of differences in SpectrumHit? as int instead of double
14:37 Changeset [572] by tim.te.beek@…
Add popup jar (33 KB) to remove related errors
14:30 Changeset [571] by tim.te.beek@…
Load first Spectrum on page load
13:36 Changeset [570] by tim.te.beek@…
Extract Compound.Image & Compound.Link to separate classes
13:26 Changeset [569] by tim.te.beek@…
Extract composeLoadSpectrumScript in preparation of Load spectrum on page …
13:12 Changeset [568] by tim.te.beek@…
Reduce visibility of static method
12:58 Changeset [567] by tim.te.beek@…
Remove Suffix from setJmolId method invocation append("jmolApplet") to …

05-10-10:

16:58 Changeset [566] by tim.te.beek@…
Reintroduce setOutputMarkupId in replaced & replacement panels
15:45 Changeset [565] by tim.te.beek@…
Add TODO for loading Spectrum
15:36 Changeset [564] by tim.te.beek@…
Flip Spectrum.Solvent order to alter sort order on webpage
15:34 Changeset [563] by tim.te.beek@…
Make Spectrum Comparable to Spectrum Store Spectra in a SortedSet? to lock …
11:02 Changeset [562] by tim.te.beek@…
Add TODO for zero-padding
10:59 Changeset [561] by tim.te.beek@…
Renamed TBSS to TBSSS
10:58 Changeset [560] by tim.te.beek@…
Add test speed for counts Add easy-toggle to run installer & generator …
09:37 Changeset [559] by tim.te.beek@…
Fix import Types ambiguity

04-10-10:

22:29 Changeset [558] by tim.te.beek@…
Add Type mapping to BitSet?
22:28 Changeset [557] by tim.te.beek@…
Add MyExtendedPostgreSQLDialect
16:42 Changeset [556] by tim.te.beek@…
Added TODO for counts test
16:32 Changeset [555] by tim.te.beek@…
Add method to test countByChemClass
16:29 Changeset [554] by tim.te.beek@…
Correctly cast & return Long values from (row)Count Projections
16:06 Changeset [553] by tim.te.beek@…
Remove padding setType to varbit
16:00 Changeset [552] by tim.te.beek@…
Do not cast Long to Integer
15:51 Changeset [551] by tim.te.beek@…
Remove unnecessary @Setter
15:33 Changeset [550] by tim.te.beek@…
Replaced @Data with getter & setter Renamed BitSetMapper? to BitSetUserType?
15:32 Changeset [549] by tim.te.beek@…
Print done
15:31 Changeset [548] by tim.te.beek@…
Update Hibernate versions
15:28 Changeset [547] by tim.te.beek@…
Recreate lucene index dir after install to remove a warning
10:29 Changeset [546] by tim.te.beek@…
Use actual Object equals again now Lazy Fetching is disabled again in …
10:23 Changeset [545] by tim.te.beek@…
Remove lazy fetching: Gives a 4 second boost from 89 to 85 seconds, with …
09:33 Changeset [544] by tim.te.beek@…
Compare spectrumhits based on toString implementation
08:50 Changeset [543] by tim.te.beek@…
Fix JavaDoc? related imports
07:49 Changeset [542] by tim.te.beek@…
Added untested experimental BitSetMapper?
07:47 Changeset [541] by tim.te.beek@…
Added (fetch=FetchType?.LAZY)//TODO Test performance benefits/repercussions …

01-10-10:

22:44 Changeset [540] by tim.te.beek@…
Make container a field
22:39 Changeset [539] by tim.te.beek@…
Organize imports 100% width on CompoundsDataTablePanel? Move <h2>Search …
22:35 Changeset [538] by tim.te.beek@…
log.debug number of returned MassHits?

30-09-10:

16:18 Changeset [537] by tim.te.beek@…
Removed logger, which shouldnt have been committed in the first place
16:17 Changeset [536] by tim.te.beek@…
Move adduct label back to MassSearchPanel? Correctly paginate mass & …
15:50 Changeset [535] by tim.te.beek@…
Added null check for Compound
15:43 Changeset [534] by tim.te.beek@…
Renamed fields to mirror SpectrumSearchPanel?
15:33 Changeset [533] by tim.te.beek@…
Harmonize likewise code between TablePanels?
15:26 Changeset [532] by tim.te.beek@…
Move adduct label to MassHitTablePanel? using constructor argument
14:30 Changeset [531] by frank_van_zimmeren@…
Renamed JMOL_APPLET_ID to JMOL_APPLET_ID_SUFFIX and changed value
14:18 Changeset [530] by tim.te.beek@…
Do not Override detach() with empty implementation
13:38 Changeset [529] by tim.te.beek@…
Initially hide SpectrumHitTablePanel? on SpectrumSearchPanel?
13:09 Changeset [528] by frank_van_zimmeren@…
Fixed error that occurred when clicking on download button without having …
12:41 Changeset [527] by tim.te.beek@…
remove readonly instrumentation on @Transactional as there's no speed …
12:15 Changeset [526] by tim.te.beek@…
Added altered SpectrumSearch? test that searches for the first 10 spectra
12:00 Changeset [525] by tim.te.beek@…
Removed shadowing conflict by renaming second StringBuilder? variable Not …
11:57 Changeset [524] by tim.te.beek@…
Use IndicatingAjaxButton? instead of AjaxSubmitLink?
10:59 Changeset [523] by tim.te.beek@…
Added List<T> get(int first, int count) to GenericHibernateDAO to support …

28-09-10:

17:04 Changeset [522] by tim.te.beek@…
Oops: only generate 100K binnedSpectra instead of 5 million
16:50 Changeset [521] by tim.te.beek@…
Added initial generator using MersenneTwisterFast?
15:41 Changeset [520] by tim.te.beek@…
Use @Override @SuppressWarnings?("unchecked") public T find(Long id) { …
15:13 Changeset [519] by frank_van_zimmeren@…
Removed unused JMol jar
14:51 Changeset [518] by frank_van_zimmeren@…
JSpecView to JMol callback now works, so both callbacks now work
09:58 Changeset [517] by tim.te.beek@…
Disable FindBugs? due to OutOfMemory? Exception
09:20 Changeset [516] by frank_van_zimmeren@…
JMol to JSpecView pick callback now works

27-09-10:

16:57 Changeset [515] by frank_van_zimmeren@…
Load JMol applet using javascript supplied with JMol
16:50 Changeset [514] by tim.te.beek@…
Added Stub class with TODO
16:42 Changeset [513] by tim.te.beek@…
Add speed test base
14:36 Changeset [512] by tim.te.beek@…
load .mol file in JMol Applet after page is loaded
09:28 Changeset [511] by tim.te.beek@…
Wrap DownloadPage? in ModalWindow? to circumvent broken back-button on mass …
08:40 Changeset [510] by tim.te.beek@…
Use clone to retrieve binCounts to avoid externally mutable reference Do …
08:35 Changeset [509] by tim.te.beek@…
Do not ignore result of FileInputStream?.read(byte[])

24-09-10:

17:32 Changeset [508] by tim.te.beek@…
Remove test with dash commented out: Not the source of the problem
15:19 Changeset [507] by tim.te.beek@…
Add test that searches for inchikey
15:19 Changeset [506] by tim.te.beek@…
Do not tokenize identifiers
13:41 Changeset [505] by tim.te.beek@…
Move Lucene indices one folder up
13:13 Changeset [504] by tim.te.beek@…
Use varargs as arg to main
13:07 Changeset [503] by tim.te.beek@…
Dependency manage metidb-parser
12:39 Changeset [502] by tim.te.beek@…
Make id protected instead of private
12:10 Changeset [501] by tim.te.beek@…
wicket.version++
11:19 Changeset [500] by tim.te.beek@…
Add JBoss repo to parent Update hibernate search version
11:03 Changeset [499] by tim.te.beek@…
Switch test case to known problematic instance

23-09-10:

16:38 Changeset [498] by tim.te.beek@…
Print hits just before returning from find(...)
16:21 Changeset [497] by tim.te.beek@…
Replace ’ with ' in names
16:19 Changeset [496] by tim.te.beek@…
Typo
15:15 Changeset [495] by tim.te.beek@…
Add help link for Query parser syntax
15:03 Changeset [494] by tim.te.beek@…
Add additional test case to replicate Velitchka's wildcard problems
15:03 Changeset [493] by tim.te.beek@…
Upgrade lucene to 2.9.3
14:08 Changeset [492] by tim.te.beek@…
Move refine button to MassSearchPanel? (where adducts label & resultspanel …
12:47 Changeset [491] by tim.te.beek@…
Alter check condition before download
12:29 Changeset [490] by tim.te.beek@…
Comment out resource polling & remove associated TODO
12:27 Changeset [489] by tim.te.beek@…
remove <? extends ...> Limit scope of @SuppressWarnings?
12:24 Changeset [488] by tim.te.beek@…
Move @SuppressWarnings? to limit scope
11:37 Changeset [487] by tim.te.beek@…
Merged RefiningSearchPanel? & SpectrumSearchPanel? back into one
11:36 Changeset [486] by tim.te.beek@…
Added FIXME about thrown IAE
11:36 Changeset [485] by tim.te.beek@…
Actually refine using counts instead of copy-past-error …

22-09-10:

18:40 Changeset [484] by tim.te.beek@…
Similar <h2>Search results</h2>'s
18:37 Changeset [483] by tim.te.beek@…
Place a header above Spectrum Search results
18:36 Changeset [482] by tim.te.beek@…
Make refinement link a button and move to top Hide buttons upon activating …
18:04 Changeset [481] by tim.te.beek@…
Suppress PMD warning on documented if-if
18:01 Changeset [480] by tim.te.beek@…
Supply proper null models to prevent NPE
16:11 Changeset [479] by tim.te.beek@…
Spec package moved
16:08 Changeset [478] by tim.te.beek@…
Extract ShiftsModel? as separate class
16:02 Changeset [477] by tim.te.beek@…
Include call to WicketTester?
15:14 Changeset [476] by tim.te.beek@…
Mirror extraction of defaultSolvent field
14:43 Changeset [475] by tim.te.beek@…
Extract refining search to separate package
14:38 Changeset [474] by tim.te.beek@…
Added Proof of Concept combined Mass & Spec search UI
14:37 Changeset [473] by tim.te.beek@…
Experiment selection is optional: Handle null Improved logging

21-09-10:

18:49 Changeset [472] by tim.te.beek@…
Added TODO to kickstart development tomorrow
17:45 Changeset [471] by tim.te.beek@…
Made getData protected in SpectrumHitProvider? to allow for overriding Made …
16:00 Changeset [470] by tim.te.beek@…
Added method to extract relevant spectra
15:54 Changeset [469] by tim.te.beek@…
Added similarly implemented counts refinement Added test for counts …
15:39 Changeset [468] by tim.te.beek@…
Do not print Spectra with Compound.toString

20-09-10:

17:24 Changeset [467] by tim.te.beek@…
Added a rocking combined Mass / Spectrum search mode!
13:50 Changeset [466] by tim.te.beek@…
Added test to find the 60 Compounds with mass 330.xyz
13:41 Changeset [465] by tim.te.beek@…
Added preliminary test for combined mass & spec search to find Mass with …
12:24 Changeset [464] by tim.te.beek@…
Update test file for parsing
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