Instant JChem Changes

See also Marvin changes and JChem changes.
These changes will also be included in IJC as IJC uses Marvin and JChem.

2.X Releases

June 26 2009: 2.5.1.1

Hot fix update for IJC 2.5.1

Fixed problem with module versions which prevented table regeneration working correctly.
Added support for additional MySQL column types

May 29 2009: 2.5.1

Minor bug fix release.

Marvin/JChem 5.2.2 are used. JChem tables will not be regenerated from IJC 2.5

Bugs fixed

Some actions were not enabled in the project explorer context menu.
Fixed problem with list renderer when values were null.
Fixed problem when clicking outside widget in form did not cause widget to leave edit mode.

May 14 2009: 2.5

Major version release. This is a rollup of all the previous fixes and improvements since IJC 2.4 and includes a new installer to fix installer related problems on Windows Vista. This version is only available as a new installer or as the Java Web Start version. It is not available using autoupdate.

Marvin/JChem 5.2.1.1 are used. Some JChem tables will be regenerated.

New features and improvements

Added ability to copy a view (form or grid view) from one data tree to another. See here for details (Forum topic).
Query builder and Query as text windows are not shown by default. If you want to use these you can show them using the appropriate items in the Window menu.
Improved tooltips for form and grid view in query mode.

Bugs fixed

Fixed problems with installer under Windows Vista which resulted in updates not being applied correctly.
Fixed problem with querying dates on some databases (Forum topic).
Fixed problem with database connection being randomly closed (Forum topic).
Fixed problems relating to accessing files on Windows using UNCs (Forum topic).
Fixed problem when column renderer in table could become null when value for multiple columns was set.
Fixed problem with chemical terms columns not being deleted from the database.
Fixed memory leak that could cause IJC to die when schema editor was used extensively.
MaxPermGen memory size increased to 120m to avoid potential out of memory errors. If running on 64 bit Java then this setting may need to be be increased further. Edit the etc/instantjchem.conf file to do this.

March 19 2009: 2.4.3.1

Minor bug fix release

Marvin/JChem 5.2 are used. JChem tables will not be regenerated from IJC 2.4.3.

Bugs fixed

Fixed problem deleting last column in grid view on Linux when using Java 1.6 (Forum topic).
Fixed bug preventing promption of foreign key to relationship in some cases.
Location of promote foreign key button changed to be consistent with other promote buttons
Fixed problem the setting dates with new row dialog with certain locales (Forum topic).
Fixed problem with chemical terms expressions that use structure search not being enabled (Forum topic).

March 12 2009: 2.4.3

This is primarily a bug fix release

Marvin/JChem 5.2 are used. JChem tables will be regenerated.

Bugs fixed

Fixed error preventing printing (Forum topic).
Fixed problems with hit alignment sometimes failing with Markush table types.
Improvements to showing license errors during query execution.
Fix for problem when chem terms values were recacluated even if chem terms expression was not altered.

New features and improvements

Added display option for showing/hiding R/S labels on atoms for structures (Forum topic).
Structure search names changed to be consistent with the new names used in JChem (see JChem documentation).
Added security configuration template for Microsoft Active Directory.
New chemical terms editor from JChem 5.2 is used

February 18 2009: 2.4.2

This is primarily a bug fix release

Marvin/JChem 5.1.5 are used. JChem tables will not be regenerated from IJC 2.4.

Bugs fixed

Fixed problems with converting field type not copying values correctly.
Improvements in handling NUMBER columns in Oracle:
- Fixed problem creating number column with a non-zero scale component.
- Number columns can be promoted to decimal number fields.
Fixed problems with validation of query values (e.g. for Between operator).
Fixed problem with hit alignment of Markush structures caused by 2.4.1 upgrade (Forum topic).
Fixed problem with temporary lists and queries not being created unless query builder was showing.
Fixed problem with structures not being correctly coloured when a chemical terms only search had been run.
Provide warning when proxy server settings may need attention.
Structure editor opens wider when editing reactions.
Fixed random exception that sometimes prevented a project being opened.
Improvements in display of some dialogs on Mac.
Fixed some problems with using date editor in query mode.
Improved promote foreign key function to allow creation of many-to-one relationship.
Fixed problems running using latest Java versions (e.g. 1.6.0_12).
Added "rdf" to available file extensions during export.

December 22 2008: 2.4.1

This is primarily a bug fix release

Marvin/JChem 5.1.4 are used. JChem tables will not be regenerated from IJC 2.4.

Bugs fixed

Fixed problem restoring lists of more than 1000 IDs on Oracle.
Fixed problem writing errors file during import when location was specified using a UNC (Forum topic).
Fixed error that occurred when column size was edited when creating a field.
Fixed problems exporting data from entities in the schema editor (Forum topic).
Fixed problem with converting structures to 2D in import not working (Forum topic).
Introduced a maximum number of deleted rows before undo operation is disabled (too high a value caused excessive memory consumption due to the need to support undo). Limit is 1000.
Added missing project related actions to File menu and projects window context menu.
Fixed problem with search by selected value opening structure editor.
Fixed problem with Command key on Mac switching table cell to edit mode
Added missing support for CHAR columns on Oracle
JWS clears out old IJC installation files before updating to new ones.
Fixed problem with Markush tables when Markush license has been removed or become invalid.

November 21 2008: 2.4

Feature release. This release is almost entirely focused on usability issues based on user feedback.

Marvin/JChem 5.1.3 are used. JChem tables will be regenerated.

New features and improvements

Support for JChem cartridge on Oracle.
- Create JChemBase table with cartridge index on cd_structure column.
- Create standard table with cartridge index on column with structures.
- Promote existing cartridge tables in the database into IJC.
- Support for different table types, standardizer and chemical terms columns.
File import.
- Support for import of chemical names using Name2Structure calculator plugin
- Better determination of whether text files contain structures
- Better determination of JChem table type based on the types of structures found (Forum topic).
- Better determination of data field type where empty values were encountered.
- Changed name normalisation so that fields are always recognised if the file (or similar file) is re-imported into the same entity.
- File import action made less sensitive to context to avoid the risk of importing data into an exisiting entity by mistake. If wanting to import into an existing entity this must be explicitly specified using the r-click action on the node in the project explorer. Otherwise file is always imported into a new entity.
- Parsing for field detection can be cancelled.
- Import into exisiting entity now possible without ROLE_EDIT_SCHEMA rights (new fields cannot be created).
File export.
- Added support for export in smarts format.
- Added support for exporting relational data to flat file formats (SDF, Excel...).
Printing.
- Improved print quality using Jasper Reports print engine.
- Print preview
- Allow footers and headers to be specified.
- Print to PDF.
Grid view
- Discontinuous selection intervals now possible.
- Added ability to auto-estimate the best column widths to use.
- Added popup menu to row header to allow adding and deleting rows.
- Design mode display is now more consistent with browse mode settings.
- Multi-line text display improved.
Form view
- Added warnings when innapropriate widgets were used and would result in not all data being displayed.
- Widget right-click menu options improved.
- Added horizontal alignment to widget display options.
- Added ability to horizontally align multiple widgets.
- Widgets can be selected using Tab key.
Query
- Better support for 'between' queries for dates.
- Date picker tool added to query builder.
- Added progress dialog during data retrieval so that you don't have to wait for all IDs to load for very large tables.
- Query as text window shows structures as (cx)smiles or (cx)smarts as is most appropriate for the search type (Forum topic).
List and Query management
- Added abiity to add/remove a list to/from the current result set (Forum topic).
- Added data tree selector to Lists & queries window to make it easier to see lists and queries from other data trees.
- Added ability to create new list and define the contents for this list.
Project explorer.
- Created 'single project mode' where a simplified representation of the projects tree is displayed when only a single project is open.
- Added default option to close current project when opening a new one so that you stay in single project mode.
- Added option to 'autoconnect' to a schema when IJC is opened.
- Added ability to clean up all unused related artifacts when a data tree is deleted.
Simple Federated Search (SFS).
- Moved SFS window to main window and improved layout.
- SFS window can be specified as start page.
- Added ability to collate all SFS results into a new data set.
UI/Usability.
- Added option to define a default start page. Specified page can be Welcome screen, Simple Federated search or any view (form or grid view). Option to open this start page maximised.
- Added 'Remember this decision' option in many places.
- Added keyboard shortcuts for switching mode in form and grid view (Ctrl-1, Ctrl-2, Ctrl-3).
- Warnings added on startup when licenses have expired or are about to expire.
- Convert type can now be used to create a copy a field of the same type.
- Improved performance when using Copy & Paste for large numbers of cells (Forum topic).
- Added more data flavors when copying single structures from grid and form view so that they paste better.
Other.
- Default maximum memory (heap size) increased to 300MB

Bugs fixed

Many bugs have been fixed, including:

Removed problems related to project contents using absolute file paths.
Fixed problems with temporary list and queries not being created if data from the data tree had not yet been opened.
Improved hit alignment performance for Markush structures.
Fixed problems during file import with empty values causing the automatic detection of the best field type to fail.
Fixed problem with slow scrolling in grid view when 2D structures needed to be generated.
Fixed some problems inserting and deleting rows in detail tables for relational data.
Fixed problem with adding detail table when master table contained data.
Fixed problem using a file url for shared projects (Forum topic).
Fixed problem deploying license file when chemaxon dir did not exist (Forum topic).

June 16 2008: 2.3.1

This is primarily a bug fix release

Marvin/JChem 5.0.3 are used. This is unchanged from 2.3

New features and improvements

Overlap anaysis: The outputted field can be specified.
Overlap anaysis: Option added to turn off writing hits to console during (Forum topic).
Added action to main toolbar to reset windows (this was present in Windows menu too).
Chemical Terms: Hint about code assist feature added to chemical terms editor
IJC URLs: Generate URL dialog now only allows creation of URLs for shared databases in shared projects.

Bugs fixed

Fixed problem exporting to Excel where sheet name contained illegal characters or was too long
Fixed problem with empty strings not being accepted as values for float fields (they are converted to null).
Fixed problem with copying multi-line text in grid view (Forum topic).
When switching to query mode first used field gets focus.
Corrected wrong license file location property in JNLP file. It should be chemaxon.license.url not ijc.license.url.
License manager window now has Close button, not OK/Cancel.
Fixed problem with hit highlighting when structure was in detail entity and displayed using structure widget.
Query actions sometimes became disabled.
Apply list and query actions sometimes became disabled.
Chemical terms expression is validated during fererated search.
Fixed problems with data in grid view sometimes not displaying when scrolling.
Fixed rare exception when hiding columns in grid view.
Fixed problem with boolean columns in grid view sometimes becoming not editable.
Changed misleading warning message when no standardizer license is present.
Fixed problem with progress going immediately to 100% during import of text files.
Fixed problem cancelling chemical terms queries.
Fixed problems renaming lists and queries.
Fixed exception that occurred when with searches with Ignore operator (Forum topic).
Fixed rare exception when editing values and typing too fast!
Fixed problem when editing values where change was made in DB but old value was sometimes still displayed.
Direct editing of values in fields that are used in relationships is disabled.
Correct JChem table type selected after parsing completes during import.
Fixed problem with branding index page for Java Web Start version.
Deleting project now deletes the files properly.
Excluded null as an option when editing boolean fields which require a value
Fixed potential problem with query when wrong results could be returned
Fixed exception that occurred when in query builder when deleting elements
Fixed exception that occurred when typing in URL when opening shared project

April 25 2008: 2.3

Feature release

Marvin/JChem 5.0.3 are used. JChem tables will be regenerated.

New features and improvements

Marvin/JChem 5 releated features
- Marvin User interfaces are updated.
- New license system is used. Request updated license file if you do not already have one.
- Code assist for chemical terms expressions.
- Query and Markush JChem table types are supported
- Markush enumeration added.
- Structure file import now uses Marvin record parsing interface.
- Hit highlighting now uses JChem chemaxon.util.HitDisplayTool class.
- Hit alignment enabled for superstructure searches.
- JChem search options now uses chemaxon.sss.search.JChemSearchOptions class.
- Mol Formula field is sorted using the new cd_sortable_formula column.
New features
- Shared project deployment.
- License file can be centrally deployed.
- IJC URLs allow you to send a link that opens IJC and shows the view + list/query.
- Schema Editor: Promote foreign key to relationship.
- Form builder: WBLabel widget allowing static text to be put an a form.
Other improvements
- Additional standardizer templates provided.
- Query as text window indicates whether current query has been executed.
- Overlap analysis writes matching IDs to the report.
- Changed the order for chemical terms favourites. The new order is: FLOAT, TEXT, INT, BOOLEAN
- Oracle driver updated to 11g driver (version 11.1.0.6.0)
- Derby database version updated to 10.3.2.1
- Removed dependency on java.awt.Robot class when resizing rows in grid view (Forum topic).
- Option to not show Welcome screen on startup
- Column names also checked for name matches during file import (Forum topic).
- User asked whether to save view when shared view is first modified.
- Table names restricted to proper tables (synonyms, views etc. not listed).
- Show/hide R-group definitions property for Marvin renderer.
- JChem tables are created as InnoDB types on MySQL. InnoDB no longer has to be the default table type.
- Improved consistency between query builder and form based query

Bugs fixed

Remember username/password checkboxes stay sticky when schema is manually disconnected.
Better handling of undo queue for MSketchPane
Workaround for Oracle returning illegal JDBC column types (Forum topic).
Fix for problem for Oracle JDBC metadata where TIMESTAMP columns were being reported as TIMESTAMP(6) (the brackets and size should not be present).
Uninitialized views are closed when connection is closed.
Fixed problems with setting default fingerprint settings for each JChem table type.
Fixed problem with some queries when there were more than 2 levels of hierarchy.
Fixed problems with some Marvin popup windows.
Fixed problem with progress stopping at 99%

Know issues

Feb 14 2008: 2.2.1

Bug fix release

JChem 3.2.12 and Marvin 4.1.14 are used. This is unchanged from 2.2.0.

Boolean field is queryable in form based query
Boolean field null state handled better in browse mode
Queries for boolean field = false no longer return rows where values are null
Date field is queryable in form based query
Date formats handled in more consistent format throughout IJC (Forum topic)
Improvements to editing date fields
Text array fields exported correctly in Excel export
Fixed bug preventing new rows being added in multi-user mode (Forum topic)
Less confusing error message when setting a duplicate structure
Improved formatting of float fields during display and editing
List is applied with entries in correct order
Printed forms are prettier
Improvement to layout of some dialogs on Mac
Fixed various memory leaks
Fixed problems reordering columns under Java 1.6 (Forum topic)
Name in border can be changed for tables in forms (Forum topic)
RDF import is more tolerent of bad entries
Fixed performance regression in overlap analysis (Forum topic)
Fixed potential issue with database connections that were idle for long periods
Fixed problem with tab separated format text file import with empty values
Fixed problem with query by example not being enabled for fields from detail tables
Fixed problem with editing queries following fedorated search
Fixed problems with project groups (Forum topic)
Fixed problem with export where all records were sometimes exported, not current result set
View toolbar rearranged by relocating some global actions to main toolbar
Fixed problem with pasting multiple values causing multiple screen refreshes
Fixed problem with windows opened by Marvin Sketch remaining open after sketch closes. These windows are now closed when the sketch closes
Fixed problem with queries not being cancellable
Fixed potential problem when creating new entity or field fails
Fixed problems with export to excel (Forum topic)

Feb 14 2008: 2.2.0.1

Autoupdate upgrade to allow upgrade to 2.2.1

January 10 2008: 2.2

Feature release

JChem 3.2.12 and Marvin 4.1.14 are used. JChem tables will be regenerated.

New features and improvements

Query
- Form based query
- Added Starts with, Ends with and Contains operators for text fields
- Query panel re-worked to simplify query builder and make it work in conjunction with form based query
- Structure can be directly pasted into empty structure query widget
- Added federated search feature allowing structure searches to be run across multiple data trees
Security
- Support for authentication using LDAP
- Added ability to ROLE_ADMIN to log out a user (Forum topic)
- Users can be added/deleted/modified from multi-user mode
File export
- Option to generate missing coordinates during SDF, MRV... export
- Export to Excel format (structures included as images)
Standard import
- Records with errors are writen to a file
- Duplicate records are writen to a file
RDF import
- Improved auto-determination of field types and sizes
- Mechanism added to prevent naming conflicts
- Records with errors are writen to a file
Java Web Start
Startup performance improved during reading of information from DatabaseMetaData
Form printing
Views (form and grid view), queries and lists are directly sharable, allowing all users to see a standard set of forms
Description attribute added for things like entity, data tree etc.
General improvements to relational data management
Added ability to refresh data (e.g. if a different user has edited values)

Bugs fixed

Fixed problem with Integer values specified using scientific notation being handled as decimal numbers
Unrestricted searched permitted in remote databases
Clean2D done before passing structure to Marvin for display in form or grid view (forum topic)
Fixed some problems in relationship creation
Fixed problems with copy & paste and export of Text Array fields
Fixed problem dropping IJC tables from database
Fixed problem recognising some boolean chemical terms functions
Fixed error preventing clearing data in grid view
Many-to-many relationships now prevent duplicate values in join table
Fixed problem clearing molecules (forum topic)
Fixed problems with reported statistices during import (forum topic)

Know issues

Form printing limited to single record at a time
Printed forms are not very beautiful
Progress finishes at 99% (bug in Netbeans library)
Boolean and Date fields are not queryable in form based query
Error message when setting a duplicate structure is misleading
Some UI elements don't look nice on Mac OSX

October 23 2007: 2.1.1

Bug fix release

JChem 3.2.11 and Marvin 4.1.13 are used. This is unchanged from 2.1

October 2 2007: 2.1

Feature release

JChem 3.2.11 and Marvin 4.1.13 are used. JChem tables will be regenerated.

New features

Query management feature added
List management feature added
Query by example feature added
Queries can be restricted to a particular list (search domain)
Goto row feature added in grid and form views
Option to encrypt database connection details
Import and export of InChI format structures
Added additional Marvin display options for structures
Added option to strip quotes from data during import of text files
IJC can now run using Java 1.6.
Windows and Linux installers use Java 1.6

Bugs fixed

Notification icon when updates are available
Improvements to wrapping of multi-line text display
Removed limit of deleting more than 1000 rows
Perfect search options work correctly
Fixed poblem on Oracle with queries not working when data was sorted
Query widget borders now visible on Mac
Entity deletion in Oracle now more fault tolerant
Fixed problem with Oracle reporting wrong max size for CLOB columns
Cursor changes when re-sizing form widgets in design mode
Missing show user list action restored
Fixed problems with windows opened by Marvin Sketch e.g. calculator plugin windows

August 27 2007: 2.0.2

Bug fix release

JChem 3.2.10 and Marvin 4.1.12 are used. This is unchanged from 2.0.1.

Promote table bug fixed

August 27 2007: 2.0.1

Bug fix release

JChem 3.2.10 and Marvin 4.1.12 are used. JChem tables will be regenerated.

Fix bugs preventing multi user access with read-only access.
Fixed wrong expression for TPSA chemical terms favourite.
Fix for query panel occassionally throwing exception when query being reinstated.
Fixed problem with parser properties not being displayed during import.
IJC will run on Java 1.6.
Fixed problem with wrong number of records being reported during import.
Fixed problem with exporting string array fields

August 7 2007: 2.0

Public release

Patched version of JChem 3.2.9 and Marvin 4.1.11 are used

Fixed problems with nbm files on update center not being recognised as signed by ChemAxon certificate.
Changes to Welcome screen
Fixed problem with failures with Chemical terms calculations in Derby database
New Chemical terms favourite for Lipinski variant

July 26 2007: 2.0 Beta 8

Private beta release

JChem 3.2.9 and patched version of Marvin 4.1.11 are used. JChem tables will need regenerating.

Improvements to relational data handling:
- Row insert and delete for many-to-many relationships
- Add a simplified process for creating a detail entity
- Improved enabling the add and delete row actions depending on context
- Fixes to relationship creation and display
- Fixes to data retrieval for many-to-many relationships when fields are not the ID fields
Fixed problems with unique index creation
Improved ability to execute some complex advanced queries
- Structure queries can be part of an OR expression
- Multiple structure queries can be specified
Improved descriptions and messages when clearing data in grid view
Fixed problems with focus handling making editing form contents difficult
Fixed problems with large structures in Oracle JChem tables
Minor import and merge improvements
Fixed problem in query when Marvin Sketch was close with More window open
Fixed problem pasting multi-line text
Fixed problem on Windows with options not being able to find the instantjchem.conf file
Updated user guides
Updated developer guides

July 4 2007: 2.0 Beta 7 release

Public beta release

JChem 3.2.7 and patched version of Marvin 4.1.9 are used. JChem tables will need regenerating.
Various form builder usability improvements.
Chemical terms favourites can be edited
More complete version info now present in About box
Netbeans platform updated to 6.0. Major changes include:
- Autoupdate UI changed (now Tools -> Plugins)
- User settings editor improved
Query:
- Query UI and implementation re-written
- Hit alignment bugs fixed
- Return non-hits for structure query
- Standard and Advanced query modes
- Relational query now possible
- AND and OR queries now possible
Schema Editor enhancements:
- Index management
- Improved handling of Relationships
- Promote standard table now works
- Sequence definition for standard Oracle tables
Minor improvements to RDF import
Various UI and usability improvements
Better support for dates
Better support for list fields
Improvements to multi-threaded database connections
Improvements to Undo/Redo support
Extensibility improvements:
- Improvements to APIs and SPIs
- API code examples
- Developer tutorials

Known bugs

Not all advanced queries that can be built will execute:
- Only one structure query can be specified as part of AND element
Marvin Sketch panel does not appear correctly in standardizer editor when used for defining standardizer for a JChem table
Marvin Sketch and Standardizer editors are slow to load
Problems are seen with modal Marvin calcualtor plugin windows on some platforms
Some aspects of many-to-many relationships are not yet working

June 4 2007: 2.0 Milestone 3g release

Hot fix update for IJC 2.0M3

JChem 3.2.5 and Marvin 4.1.7 are used (this is unchanged from M3a).
Fixed problem with data retrieval with Relationships where the field was not the primary key column.

May 24 2007: 2.0 Milestone 3f release

Hot fix update for IJC 2.0M3

JChem 3.2.5 and Marvin 4.1.7 are used (this is unchanged from M3a).
Better errror tolerance and error reporting when initializing IJC schema.
Added ignore directive to RDF import template.
RDF import continues after error.

May 17 2007: 2.0 Milestone 3e release

Hot fix update for IJC 2.0M3

JChem 3.2.5 and Marvin 4.1.7 are used (this is unchanged from M3a).
Problem with scrolling "out of range" in a table causing inconsistency between row header and main table fixed.
Export to file now works in multi-user mode.
Sketcher remembers last drawn structure if it has nothing better to display.
Option to reload results when data is imported into existing table.
Fixed discrepancy in number of rows reported at end of import.

May 8 2007: 2.0 Milestone 3d release

Hot fix update for IJC 2.0M3

JChem 3.2.5 and Marvin 4.1.7 are used (this is unchanged from M3a).
Fixed problem with hit highlighting and alignment.
Fixed problem with display not always updating after chemical terms calculation.
Optimum separator is selected when parsing text file.
Improved error reporting during RDF import.
Fixed problem when structures without coordinates are opened in sketcher.

April 27 2007: 2.0 Milestone 3c release

Hot fix update for IJC 2.0M3

JChem 3.2.5 and Marvin 4.1.7 are used (this is unchanged from M3a)
Fixed problem with graph library version when updating from 2.0M2

April 25 2007: 2.0 Milestone 3b release

Hot fix update for IJC 2.0M3

JChem 3.2.5 and Marvin 4.1.7 are used (this is unchanged from M3a)
RDF import improvements:
- Empty structures are allowed.
- Fixed memory leak preventing import of large files.
- Better handling of Cancel and Finish buttons in wizard.
- Improved progress notification.
Fix for possible problem adding fields in Overlap analysis.

April 17 2007: 2.0 Milestone 3a release

Hot fix update for IJC 2.0M3

JChem 3.2.5 and Marvin 4.1.7 are used. JChem table regeneration is required.
New features:
- Copy form from other user.
- Clone form.
- Template based import now supports SDF files as well as RDF.
- IUPAC name added as chemical terms expression favourite.
- Improved documentation.
Bugs fixed:
- Marvin update fixes infinite loop problem when parsing some files.
- "Unsupported file format" problem for non-structure files solved.
- Hit alignment now works in grid view.
- Improved layout of demo project for Windows.
- Fixed potential problem with lower case table names.
- Improved editing of checkbox widget.
Known issues and limitations:
- Many-to-many relationships are not supported.
- Schema Editor lacks managment of indexes.
- Limited support for editing relational data.
- Performance needs optimising in some areas.
- Problems exist with views not updating when data is changed (e.g. during import/merge).
- Some threading issues when updating and reading data need resolving.
- Various bugs exist.

April 3 2007: 2.0 Milestone 3 release

Second public preview (alpha) release of IJC 2.0

JChem 3.2.4 and Marvin 4.1.6 are used. JChem table regeneration is required.
New features:
- Form builder.
- Relational data.
- RDF import prototype.
- Improved schema editor.
- Data Tree editor.
- Improved user documentation.
- Initial developer documentation.
Known issues and limitations:
- Many-to-many relationships are not supported.
- Schema Editor lacks managment of indexes
- Limited support for editing relational data.
- Performance needs optimising in some areas.
- Various bugs exist.

February 6 2007: 2.0 Milestone 2 release

First public preview (alpha) release of IJC 2.0

New features:
- Multi-user access and security.
- Many usability improvements, particularly for adding fields (esp. chem terms fields), file import and connecting to databases .
- General improvements in responsiveness and feedback.
- Better concurrent access (ability to do multiple things at once).

1.0 Releases

February 1 2007: 1.0.7

Redesigned file export to avoid bug on Apple Mac.

January 22 2007: 1.0.6

JChem version updated to 3.2.3. This upgrade requires jchem tables to be regerated which will happen when you first connect to the database. You will be asked to confirm you wnat the regeneration to proceed. Please backup your data first if it contains important information that you cannot easy re-create.
Bugs fixed
- Fixed problem with display of overlap analsis results.
- Improved editing of multi-line text fields.
Know issues
- Marvin Space fails to load in IJC on Linux. If you need to use Marvin Space then please contact us via the forum and we will try to povide a fix. This will be solved in a future version.

December 11 2006: 1.0.5

Improved support for non-english languages (including non-western languages)
Added ability to specify file encoding for file import and export (e.g. for reading files containing Japanese text).
Improved validation of file names
Minor documentation updates
Bugs fixed
- Fix bug with merging data from text files where header line was present.

November 30 2006: 1.0.4

Better performance for chem terms calculations and table regeneration on multi-cpu/core machines.
Right-click popup menu in grid view providing view, edit and copy & paste functions.
Minor documentation updates
Imporovements to copy & paste
Bugs fixed
- Fixed possibility of wrong values being updated when data is changed (e.g new query executed, or re-sorted) whilst in the middle of an edit (or undo/redo) operation.
- Fix to allow deletion of structures where JChem table allows it.
- Fixes to ensure files are closed and released in various places.

November 17 2006: 1.0.3

Bugs fixed
- Chem terms expression for donor and acceptor counts were transposed.
- Fixed ArrayIndexOutOfBoundsException exception with Copy & Paste of complete rows.
- .stndzr extension automatically added when saving a standardizer file if .stndzr or .xml extension not present.

November 16 2006: 1.0.2

Bugs fixed
- Fixed occasional problem with viewing data in grid view (NullPointerException).
- Fixed alignment problem in Welcome screen when viewed at narrow size.
- Possible safe fix for un-reproducable bug report in grid view where data was being requested for row that didn't exist.
- Fixed problem importing of some types of reaction files.
- Fixed problem with structure file viewer not displaying the correct number of strucutures
- Fixed problems with files not being released during import and export

November 7 2006: 1.0.1

Changed user dir to ijc_1_0 to prevent possible conflict with pevious updates from Update Center
Removed r-click popup from structure editor panel in grid view
Bugs fixed
- Fixed occasional problem with queries not being executed and Show All button not functioning.
- Fixed problem restoring Chem Terms filter in query panel when no strucutre is specified
- Fixed problem with grid view not updating
- Fixed problem with row count being one too many after import
- Fixed problem with not being able to close standardizer editor when changes were present

November 3 2006: 1.0

Hit alignment now supports link groups
Delete row in grid view now prompts for whether to delete row from db.
Text values truncated during import when too long for column size.
Message presented to user when opening HSQL database.
IJC license will be found if located in Marvin licenses.dat file.
Improved import performance.
Documentation updates.
Query structures displayed without implicit hydrogens.
All modules use the same EULA, which refers to 3rd party libraries and licenses.
IN LIST queries added for integer and text fields.
Bugs fixed
- UpdateHandler closed immediatly following import
- Cell selection for 2D structures in grid view now works properly
- Adding row in grid view now scrolls to correct row
- Disabled sorting of structure fields
- StandardizeForDisplay now uses default standardization when none is specified.
- Changing StandardizeForDisplay setting now updates structure display immediately.
- Workaround for problem with My Documents directory apprearing read-only on Windows XP
- Fixed bug resulting in creation of local database files when using remote database.
- Fixed bug with missing values in standard import.
- Fixed bug with default values for non-text fields in standard import.
- Fixed bug with merging with delineated text files.
- Fixed bug with updating date fields in some database types.
- Fixed bug with date editor in grid view
- Fixed rare startup deadlock when table editor was open and HSQL database had been shutdown incorrectly.
- Fixed problem setting default values and required status of fields with Derby databases

October 17 2006: 0.8.0

Derby in now local database for new projects resulting in improved performance for large data sets

Adding fields is much faster
Shutdown is much faster
Restart after improper shutdown is much faster

Added JChem tables types which are present in JChem 3.2
Improvements to display of 3D structures in grid view
Hit highlighting and alignment for 3D structures
Improved usability of editing structures in grid view
Explicit hydrogens not displayed in query panel
Improved documentation for grid view display settings
Improved documentation for query
Improved documentation for memory mamagement
Added documentation about Derby and HSQL based projects
Faster loading of entity editor by lazy loading of standardizer editor
Quick import is cancellable
CLogP renamed to LogP in Chemical Terms favourites
Chemical Terms editor now available in query panel
Java memory settings can now be specified using Tools -> Options
Bugs fixed
- Fixed problem importing files greater than 2GB in size.
- Fixed problem with grid linces not being displayed in grid view on Mac
- Chem Terms fields excluded from fields displayed in Add Row dialog in grid view

The JChem version used is 3.2

September 20 2006: 0.7.4

Chemical terms filters can now be run without a structure query
Queries are cancellable
Improved management of favourites in Chemical Terms editor
Field type/editability indicators removed from grid view column headers
3D strucutres can be displayed as 2D without converting permanantly to 2D
Editing structures in grid view now more consistent with editing other data types
Improved documentation on license keys
Various bugs fixed

The JChem version used is the jchemTEST_2006_08_17 build

September 12 2006: 0.7.3

Added chemical terms filter to query
Various bugs fixed

The JChem version used is the jchemTEST_2006_08_17 build

August 1 2006: 0.7.0

Welcome screen
Quick import wizard
Merge data during import
Standardizer editor
Overalp analysis to compare 2 databases for identical or similar structures
Improved structure search options
Copy & Paste and Undo in grid view
Find function in grid view
Improved performance for large data sets

The JChem version used is the jchemTEST_2006_08_17 build

Version 0.6.1

Added row height zooming in grid view.
Added possibiltiy for horizontal scrolling in grid view.
Added ability to delete field directly form grid view.
Added chemical terms fields based on JChem chemical terms columns.
Added abilitiy to standardize structure files using standardizer files.
Native molecule format used in import where possible.
Grid view can be printed.
Added Exact Fragment structure search mode.
Creating entity from exisiting table now adds fields for all column types that IJC understands.
Grid view only asks for data when view is shown.
Improved notification on progress during field adding/editing.
Better validation during file import.
Better error recovery when database cannot be connected etc.
Bugs fixed
- Better validation of field names in file import
- Improved handling of required status and default values for fields.

Version 0.6.0

Structure support module providing basic support for viewing structure files
Various UI changes to improve usability
Standardizer license detection now works
IJC license required for connecting to remote databases
Major documentation update
Added new project template with sample data
Passwords for remote datbases not stored
Bugs fixed

Notification about emtpy structure files during import

This is a beta release ready for the ChemAxon UGM

May 22 2006: 0.5.5

Create entity from exisitng JChem table
Project template with local db
Bugs fixed

JChem properties table configuration missing when creating connection to a datbase that already has a properties table.

Version 0.5.4

Initial support for MySQL databases
Bugs fixed

Field name specification in import now works

May 22 2006: 0.5.3

Grid view and results now synchronised with changes in the table editor
JChem tables updated when new version of JChem is found
jchem.jar updated to latest development build
Table editor enhancements

Icons for adding fields
Standardizer tab now displays warnign about needing a standardizer license

Grid view enhancements

Column header now displays sort info on second line
Selected rows now highlight

Oracle separated as a separate module to enable licensing
Restricted to local database only unless IJC license key is entered (any text will do currrently)
HSQL local database searches run unrestricted
Sort directives now retained when a new query is exectuted
ChemAxon update center URL set to http://www.chemaxon.com/jchem/ijc/updatecenter/updates.xml (update center does not yet exist)
Added link to IJC forum in Help menu
Improved validation when editing and creating various artifacts
Added ability to display structures in standarrdized form
Bugs fixed

Fixed some problems in file import wizard
Fixed bug when editing structures with duplicate detection turned on
Non-standard JChemProperties table names now work OK

May 10 2006: 0.5.2

File import enhancements

Added create new table from file capability
Added RDF format
Progress bar shows actual progresss
Field type can be chosen during import
Grid view can be opened after import to display data

File export enhancments

Added RDF format
Fixed problem with exporting MRV format

Import and export are global actions in main toolbar and file menu.
Reworked project explorer nodes and editors according to discussions in Budapest

DataTree now displays the table it represents
Grid view opens as default action (double click) on a table node

Transparant support for embedded HSQL database
Ability to define license keys as options. These are useed as defaults when creating new JChemProperties table.
Hit hightlighting colours configurable as options.
Similarity threshold disabled unless similarity search selected.
More context sensitive help in wizards
Tooltips in table toolbar
JChem table editor uses tabbed view - expert features not displayed unless needed
Added settings for ChemAxon update center. Removed Netbeans update centers
Initial support for editing and updating standardizer

April 10 2006: 0.5

Table settings are persistent.
Enhancements to schema editor

Most field and column properties are editable, where appropriate
Convert field function (e.g text -> integer)

Export to file
Boolean and date field types
Hit alignment and substructure highlighting
Improved documentation
Improved error handling

March 17 2006: 0.4

Major enhancements to the table viewer.

Configurable renderer types for all fields

Marvin display options
Multi-line text fields
Alignment, colours, fonts etc.

Configurable row height and column widths.
Show/hide columns
Cell editing, row addition/deletion

Cached result set, allowing all data in large table to be viewed

Querying and sorting reworked to use cached result set

Sort manager dialog allows multi column sorting

Performance excellent for thousands of rows
Performance reasonable for 10's of thousands of rows (depending on database speed/location)

Application almost completely localized. English only current langauge.
Minor enhancements/bugfixes to schema editor
Reworked Getting Started Guide (available from the Help menu)

March 2 2006: 0.3

Enhanced schema editor.

Element properties are displayed when selected from the explorer.
Inital editing of some element proeprties. More work is needed to make all the properties editable.

New project wizard now operational
Standard entities are now supported, in addition to JChemBase entities
JChemProperties table can now be created when a new schema is created. license keys can be specified.
Enhancements to file import

CSV and TAB separated files now supported
Additional import options available
Abiltiy to specify default values
Improved user interface
Improvements to import performance

Improvements to datasource configuration and management
Some unncessary menu and toolbar items have been removed.
There are sensible items in the Help menu and the basics of a help system are in place.

February 15 2006: 0.2

Clarification/definition of key concepts/terms, and major refactoring to accommodate this.

Schema
Entity
Property Categeory
Field

Support for the key IJC use case

Creating a new IJC Entity
Importing an SD file into it
Adding/creating Fields
Viewing the data in a table
Executing queries on the data.

SD file import capabilties
Major refactoring of the DataLoader and DataObjects used in the Project Explorer
Major refactoring and clean up of the DIF tier
Options/settings/L&F made to match those of jcman as far as it possible.

The version of JChem used is 3.1.