Assemble 1.0.4 (02-09-2011)
===========================

Bugs fixed
----------

- if the user canceled the opening or saving of a file, the 3D scene was frozen
- the result of a search for RNA motifs contained redundant hits for some queries (if the two lengths for an internal loop are equal for example)
- the residues deleted from the 3D model were still present in memory. Consequently, these "ghost" residues were sent to algorithms like RNART.
- the refinement of 3D models containing several RNA molecules produced freaky results (due to different order of the molecules in the GLOBAL.PDB and NUCLIN.DAT files)
- the ability to merge several secondary structures is fixed (2D Model -> Import...)

Improvements
------------

- the MyPDB library and all its related code are now managed by the Paradise component. Assemble migrates the data during the first start of this version of Assemble
- for the index of MyPDB, the "Location" property of the helix/single-strand nodes contains now the name of the molecule (paradise_id#molecule_name). MyPDB is reindexed during the first start of this version of Assemble.
- if the refinement algorithm cannot handle an atom (no match found), the refinement is aborted and the user is warned
- the concept "UnknownInteraction" has been added for the PARADISE engine
- the update system has been improved to use beta versions of releases

Assemble 1.0.3 (06-09-2010)
===========================

Bugs fixed
----------

- the update system has been fixed for Windows. Windows is locking files when Assemble is running. It is not possible to update files like assemble.jar or paradise.jar

Assemble 1.0.2 (06-07-2010)
===========================

Bugs fixed
----------

* the button to restore the undo state has been recovered
* the phosphodiester bonds in a chain were not managed by the undo engine
* to create an RNA motif, it is now possible to use non-english characters in the comment (french accents for example)

Improvements
------------

* the automatic update system has been improved. If a new version is available, the user has to confirm the update. Moreover, the update system can now add/delete files in the hidden directories .assemble and .paradise. This will allow us to provide automatically new RNA motifs to the MyPDB library (for example)
* Shift key + left mouse button pressed and dragged: this combination activates a lasso selection for the 2D panel. Depending on the selection mode activated, the lasso will select a set of "Residues", "Interactions" or "Structural Domains"
* for the mouse and keyboard shortcuts, the user can now decide to use the "Ctrl" key each time the "Alt" key was necessary. This option has been added to the lateral preferences panel
* if RNAVIEW has modified the sequence of the tertiary structure to annotate, an rnaview.log file is created in the directory of Assemble. This file contains details that should help the user to localize and fix the problem
* The MyPDB library is now indexed with the neo4j library (http://neo4j.org/). Based on this index, Assemble is able to search for three-way and four-way junctions separately. Moreover, the construction of the query has also been improved for all the categories of single-strands. Instead to search for single-strands with a precise length, we allow now the use of the characters Ô=Õ, Ô<Õ and Ô>Õ.

Assemble 1.0.1 (05-21-2010)
===========================

Bugs fixed
----------

* Problem to load a 3D model where parts of the 2D are not present in the 3D. A "position" attribute has been added to the "base" elements used to save the 3D data in the ParadiseProject directory. 
* the ability to export single residues in the 3D scene has been restored. The user has to activate the "Residues" selection mode, select the residues to export and click on the "Generate 3D from 2D" button.

Improvements
------------

* the communication with S2S has been improved. The residues selected are exchanged as an array of string (absolute_position+" "+long value of the ParadiseID of the molecule)
* if several tools are connected (one S2S and one Assemble for example), the tool that initiated the working session has to be stopped after all the other ones. A test has been added to warn the user.
* the binary file format to save 3D models has been removed
* a button has been added to reload the RNA Motifs library. This is useful to display the motifs created/deleted from a second Assemble application launched in parallel. 
* when a new tertiary structure is imported into the MyPDB library, its secondary structure is calculated during the import (with the 1.0 version, this was done when the 3D was loaded for the first time). Consequently, once imported, this new 2D/3D can be targeted by the Search panel. 
* the current version of Assemble is displayed in the title before the first file loaded
* the update system has been improved. If no file elements are found for a given version in the updates.xml file, the user is warned that this version has to be downloaded 

Assemble 1.0 (04-21-2010)
=========================

Bugs fixed
----------

* with no 3D displayed, it wasn't possible to export a selection in a FASTA file
* each time the model project is saved with the same name ("Save Model" choice), Assemble created new rnaml files in the Molecules subdirectory of the project.
* Assemble was not able to parse PDB files with atom's positions described like "47A", "47B",.... (like the PDB file with ID 3A3A)
* single-H bonds whose residues are stacked in an helix were described as cisWW interactions

Improvements
------------

* Assemble is fully compatible with Java 1.6
* the OpenGL drivers have been updated for Mac OSX 10.6 "Snow Leopard"
* a samples directory is available to quickly play with Assemble
* an Assemble plugin can store its own libraries in a lib subdirectory inside the plugin's directory. These libraries are added to the classpath of the GroovyShell loading the plugin.
* each plugin is associated to its own GroovyShell "session". This should avoid libraries' conflicts.
* a panel to set the preferences of Assemble has been added. At now, it allows to change the thickness of the covalent bonds and of the line representing the backbone.
  It allows also to choose if the view has to be centered automatically on the selection
* when Assemble is properly closed, the files created by the JADE framework in the working directory are deleted (APDescription.txt and MTPs-* files)
* to start Assemble, it is now possible to click on the launch_Assemble_for_XXX files
* it is not anymore necessary to specify the suffix of a file during an export/save step (.ct, .fasta, .pdb,...). Assemble adds them automatically.
* a new file listing modified nucleotides is used by Assemble. This file is copied to the .paradise directory and is adapted from a file provided by P. Auffinger and Y. Hashem and used with their SWS project (http://tatooine.u-strasbg.fr/~sws/)
* single-H Bonds are displayed in the 2D panel. At now, they're not used for the refinement process
* since the 2D drawing algorithms are not able to manage multi-molecular 2D, the inter-helices are not redrawn when a reorganization of helices is asked for.
* Assemble can load a model (saved with the textual or binary format) containing only a secondary structure
* the Undo history panel was not so practical, so it has been removed for now. The new undo mechanism is the following:
  Ctrl+Z: define the current 3D model state as the new undo state
  Alt+Z : come back to the undo state
  Shift+Z : come back to the current state
* the way to hide/display residues has been improved. The residues hidden don't block the mouse picking anymore.
* when a 3D model is exported with the PDB format, a checkbox allows to decide if the original numbering system is kept or if each molecular chain is renumbered from 1.
* Assemble is now able to load PDB files created by PyMOL
* the way to develop plugins has been improved. Now plugins can be a new menu item in the plugins menu or a new menu with sub-items
* the panel to browse the RNA motifs has been improved
* creation of a new panel named MyPDB allowing to browse and organize a local PDB repository
* new options in the Preferences Panel to :
    - display/hide single-h bonds
    - display/hide tertiary interactions
    - change the frequency of residue labeling in the 2D panel
    - change the numbering system (absolute numbering system or the one defined in the original PDB file)
* the speed to display a 3D model when a file is loaded has been improved
* the usage of mouse buttons and keyboard shortcuts to manipulate the 2D and 3D scenes have been updated
* Assemble is now fully compatible with Windows 7, XP, Linux Ubuntu and MacOSX Tiger, Leopard and Snow Leopard
* the way to automatically move a selection of residues has been improved (this ability is available with the new button with the plug icon)
* when an RNA motif is applied, the phosphodiester bonds are cut for the residues that don't belong to this new motif

Assemble 1.0 Release Candidate 3 (08-05-2009)
=============================================

Bugs fixed
----------

* Assemble was not able to export as a PDB a 3D model created by S2S
* the RNAVIEW algorithms was not able to annotate efficiently a tertiary structure with, at least, twice the same molecule

Improvements
------------

* Assemble uses now only RNA algorithms exposed as Web Services (for details see http://serialized-thoughts.blogspot.com/2009/07/forget-installation-of-rna-algorithms.html)
* for the 2D prediction, the Contrafold algorithm has been added (http://contra.stanford.edu/contrafold/)
* for the 2D drawing, the VARNA tool has been added (http://varna.lri.fr/)
* by right-clicking on the Motif Browser panel, it is now possible to reload the repository. Practical to recover a new motif created by a second Assemble application
* the way to apply RNA motifs has been improved. The secondary structure displayed in the 2D panel is automatically modified once the motif applied.
* when a new RNA motif is created, the screenshot displays the residue ids if they are at the 5' or 3' ends of a sub-sequence.
* when an helix is removed in the 2D panel, the secondary interactions can be kept as tertiary ones. For details see http://serialized-thoughts.blogspot.com/2009/07/new-features-to-edit-rna-secondary.html
* a new helix created in the 2D panel can overlap existing ones. For details see http://serialized-thoughts.blogspot.com/2009/07/new-features-to-edit-rna-secondary.html

Assemble 1.0 Release Candidate 2 (07-06-2009)
=============================================

Bugs fixed
----------

* the user was not able to browse directories when he wanted to save or export some data
* 2D edition: if an helix deleted is at the 5'-end of an RNA, the full molecule became a single-strand
* saving of an Assemble model using the textual data: it was done one directory too high
* the parser of the XPLOR format for density maps has been fixed to be able to read the files generated by the map2map tool provided by the Situs package (http://situs.biomachina.org/). For details see http://serialized-thoughts.blogspot.com/2009/06/using-saxs-data-with-assemble.html
* the refinement of the 3D model has been fixed and improved


Improvements
------------

* when an RNA algorithm has no solution, a dedicated message is displayed (and not an error)
* if a sequence contains an unknown modified residue, if the user doesn't know the unmodified version (A, U, G or C), he can choose "?". But to be used carefully
* a plugin system is now available (check http://www.bioinformatics.org/assemble/plugins.html for details)
* it is now possible to use the embedded paradise platform to run user-defined groovy scripts (by typing "java -jar paradise.jar" in the lib directory)
* when a selection is made from the 2D panel, the atoms are displayed automatically if they were invisible
* to load FASTA files, the suffix of the files can be ".fasta", ".fna", ".fas",".fa" or ".txt"
* an "Undo History" panel is available. When the button "Accept current 3D model" is clicked, Assemble asks for a name. This construction step will be listed in the Undo panel.
  When the user double-click on a construction step listed, the corresponding state of the 3D model is restored (for details see http://serialized-thoughts.blogspot.com/2009/05/undo-history-panel-of-assemble.html).
* the way to apply an RNA motif is more flexible. To make the link with a subsequence of an RNA motif, select a set of residues in the 3D scene, even if they're not contiguous and/or in the same molecular chain.
  One constraint: the number of residues selected has to be equal to the length of the subsequence you want to link.
* the algorithms_installation.sh script has been improved to warn the user if it is not launched from its own directory
* when Assemble starts, it checks if the user has started it from its own directory. This is necessary to manage some algoritms like the SVG export of RNAplot (at least, until we find another workaround)
* two new icons to quickly tile horizontally or vertically the two widows of Assemble
* the Map panel has been reorganized and improved
* it is now possible to modify the opacity of a density map rendered as a mesh
* the 3D model can be centered on the density map. The center of the density map is calculated according to the triangles displayed (with the mesh mode). If they change, so will the center of the map
* the 2D model can be exported in an SVG file
* Assemble can load an RNA secondary Structure stored in a FASTA file and described with the bracket notation (for details see http://serialized-thoughts.blogspot.com/2009/06/load-secondary-structure-described-with.html)