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Modelzilla Project - Change Log
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6-2-2004
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Modelzilla - The long standing anoyance of having to remember to unlink linked properties
is fixed. The various paths to property editing GUI's now un-link properties (so that they
are kept indendantly) for you so there should never be a problem of the model file
opening with properties still linked causing you to loose your colors, etc. This
should help end comments like, "I hate your program!".
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Modelzilla - Objects containing properties that are linked to other properties upon
instantiation but are not linked in the source object are now properly unlinked
during copy operations.
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Modelzilla - A "Geometry Link" shape is now availible. Or maybe "geometry
pass-through" would be a better term. It keeps a list of shapes or groups and
reuses the geometries except with a separate coordinate system and visibility setting.
The copy and transform functions offer the ability to create it. This enables
many copies of the same shape to be placed in a scene while using very little
additional memory and maintains the homogenaity of the shapes.
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Modelzilla - It is now possible to disable all data flow execution by using the
"Enable Validation" and "Disable Validation" functions in the objects menu.
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GridZilla - Can now read unsigned 16 bit data values in the AVS format. This is
not an AVS standard ability. It was added for a German archeologist with funny data
files. Use "short" for data type.
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GridZilla - Point cloud visualization is now intended for finding the hot spots of
huge data sets. A 10,000 point random sampling is the standard mode.
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3-10-2004
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Modelzilla - 3D graphics on Mac are correctly positioned now, due to
fix in JOGL.
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Modelzilla - Dialog frame size on Mac is now correct.
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2-19-2004
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Modelzilla - The user's manual is replaced.
2-06-2004
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Modelzilla - The framework is now OPEN SOURCE, at http://www.sourceforge.net/projects/modelzilla. This is to
encourage application developers to use it. Note this does not include the
applications. (VvM, CADZilla, GridZilla, ZillaTracer). But the Basic Controls
module (the yellow area) is also Open Source. Hopefully I haven't screwed up any
chance of comercializing the applications. The way I see it, they are more valueble
running over a popular open source framework.
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Modelzilla - The MVG saver didn't get changed to use the new image aquisition system
from the last revision. Fixed.
1-26-2004
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VVM - Can write PDB files now.
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Jython Console - A new Jython Console application module is availble. It enables
one to write macros in the Python programing language, and use Jython interactivly.
This is usefull for automating database node creation and making animations.
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Modelzilla - All Jython references have been removed from the framework and ap-mods
other than the new Jython Console, so that Modelzilla has no inherent Jython dependancy.
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Modelzilla - A new MZ_HighLevels macro method set is availible.
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CAD-Zilla - A new CAD_HighLevels macro method set is availible.
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VincentVanMol - A new VVM_HighLevels macro method set is availible.
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Modelzilla - The newest JOGL library in the distribution
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Modelzilla - Complex polygons now render reliably. (This broke when JOGL replaced gl4java.)
The newest JOGL library restores the triangulation ability that was lost. It is better
than the triangulation routine in the Modelzilla math library.
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Modelzilla - Tested to run ok on Mac OSX, with a few problems. (10.3 is required.)
The viewport 3D graphics area is sized wrong, the image aquisition ability
gets the background color wrong, anti aliasing does not work, the 2D graphics
are a bit ugly, the mouse message and repaint queing are messed up.
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Modelzilla - Screen Shot function is working correctly again. The JOGL OpenGL binding
requires frame buffer grabs be done in within its own repaint call - so the new
system uses a flag and grab system rather than the old render and grab system.
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Modelzilla - Thumnail images are now saved correctly with the MVG files, because of the fix
listed above.
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Modelzilla - MZ_HighLevels can dump images in the course of an animation, because of the fix
listed above.
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Modelzilla - The bug of a dark model upon opening an MVG file is fixed. The depth cue points
were not being computed properly. Now they are.
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Modelzilla - Scene anti-aliasing is working again, for tests and image saving.
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Modelzilla - Color data out of bounds errors have been changed to warnings. VvM
ribbons were sometimes not being rendered to graphics because of overly stringent
errors. Now they should render regardless.
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12-05-2003
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CAD-Zilla - Fixed grid snap. The gui switch was disconnected.
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Modelzilla - Fixed window title change on saving file.
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CAD-Zilla - Fixed end snap for trimed polygons.
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CAD-Zilla - Fixed trimming of poly-lines.
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Modelzilla - Fixed the color assignment for some objects like the grid
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CAD-Zilla - Polygon join now uses a tolorance to check the possibility of closing polygon ends.
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Modelzilla - Fixed grid update.
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Modelzilla - Fixed explode function.
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CAD-Zilla - Fixed polygon offset. Now reliable for smooth and sharp polygons. An embarassingly
bad bug. Also, end snap now works for polygon offset.
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Modelzilla - STL generator now reverses triangles for objects in a mirrored coordinate system.
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Modelzilla - Fixed the "show in tree" function. Removed a couple functions from shape context menus.
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CAD-Zilla - Point handles are working again.
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Modelzilla - Single property dialog resizes better. Single and multiple dialogs now
have an OK/Cancel panel. Hitting OK now "hits enter" for you in the active control widget.
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CAD-Zilla - New primative objects now are in coordinates of UCS. This was the original system.
The change was accidental. It was hugly problematic for polygons and constructions
based on them. Very embarassing, again. Some creature from the black lagoon must
have removed a couple lines from the code. This fixes many things.
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GridZilla - Now volume operations can be done on grids - any solid can be "intersected" with
a grid and a linear function can be applied to the grid where is is inside or outside
the solid. A "solid" includes a molecular surface, or any solid from CAD-Zilla.
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Modelzilla - Node validater now queries nodes for their expected validation time and
gives messages to the user if time is over a threshold.
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CAD-Zilla - Transientness of primative solids makes it out to the graphics during creation, once
again.
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11-05-2003
Fixed control panel sizing during initialization.
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10-21-2003
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Modelzilla - Made geometric property calculations (suface area, volume) availible for all objects
9-29-2003
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Modelzilla - A nice developer guide is now on the web site and in the distribution.
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Modelzilla - Module auto-loading works again.
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Modelzilla - Viewport settings showing in GUI now follow modification through access functions.
So when VvM turns on depth-cue for you, the user interface that controls this should reflect
the change.
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VvM - Property chart scroll range is fixed so missing rows on bottom can be scene.
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VvM - Ribbons now go to the very last residue in residue rendering set. (Doug's bug.)
There was an error in the control point partitioning array. Also fixed another bug
causing ribbons in chains other than the first to not start on the first residue. (Doug's too.)
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VvM - Improved the ribbon geometry at the tube/strand/helix junction. The junctions
are now always size of the tube diameter. The arrowMinorSize field is now gone. The
arrowMajorSize now controls the arrow size proportionally to the strand thickness in
the region, enabling some strands to be huge with huge arrows, and others to be
thin and delicate with proportionally thin arrows. Arrow boolean field is gone too.
Set the arrowMajorSize to 1.0 to achive no arrows.
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VvM - Tubes elbow option (the default option) is now working beutifully. They used
to fail for large radii. They have sharper bends now. They should now
work up to a tube radius of about 1.5 angstroms, where they might fail by turning inside
out. Also, the secondary structure coloring scheme for tubes is working again.
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VvM - Residue selection by number range is working again.
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VvM - Atom selection now has a filter called "side chain" and "backbone".
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VvM - Color schemes now use the RasMol color scheme (the Shapely color scheme),
and have and added "colorScale" control to control the overall brighness of the
scheme. Added DNA/RNA bases to the mapping table.
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VvM - Tubes now know the difference between Proteins and DNA/RNA - trace element
control is gone. Trace goes through carbon-alpha or phosphorous automatically.
Tubes now check for undeclared chain breaks between nucleic acids.
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VvM - Ribbons now know the difference between Proteins and DNA/RNA - DNA/RNA is
made to be a "helix" trace no matter what the secondary structure assigment. Helix
trace choses different atoms for controling extrusion locaion and twist depending
on whether residues are amino acids or nucleic acids. Ribbons now check for undeclared
chain breaks between nucleic acids.
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VvM - Auto-bonder now bonds P-O3' bond between bases.
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GridZilla - AVS Field reader now alows "rectilinear" to read, evan though it
really can only hold uniform fields in memory. (Because Vickie's file is really
uniform, despite its rectilinear marking.) GridZilla will in the future be improved
to at least be able to hold rectilinear fields.
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9-07-2003
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Modelzilla - Package names and class names have been changed for Modelzilla and
all applications. The idea is to get the interface for developers (API) in
a stable state that enables scientific programmers (such as myself) to
feel good about using the system. I see the real value in the system for
programmers as the access to hard to program things such as the molecular
graphics, grid graphics and geometrical modeling math. I am trying to
give all of the application modules easy and artfull API's to this end.
The programmer should be able to control everthing that is controlable from
the gui from the their code. Getting the package and class name stable
is the first step.
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Modelzilla - MVG file opener now reads a class name remapping table under
Modelzilla/settings/type_remap.
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Modelzilla - package jv changed to harmonic.mz, jar file changed from jv.jar to mz.jar,
some class renamings. Most importantly, class ShapeDef is finally class ShapeNode.
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Vincent Van Mol - package molex changed to scripps.molex, jar file changed from molex.jar to vvm.jar,
some class renamings. All classes ending in Def now end in Shape.
Regular Expression: (\W)(\w+)Def(\W), Shape
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CAD-Zilla - package md changed to harmonic.md, jar file changed from md.jar to cad.jar,
some class renamings. All classes ending in Def now end in Shape.
Regular Expression: (\W)(\w+)Def(\W), Shape
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GridZilla - package contour changed to scripps.grid.
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ViewerCore - package viewport changed to harmonic.viewer3D
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MeshGeom - package meshGeom changed to harmonic.meshGeom
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WidgetLib - widget library is now shared by happy hands and modelzilla. package
widgetLib changed to harmonic.widgetLib. Widget classes now all start with
HW.
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8-26-2003
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Modelzilla - Replaced the Java-OpenGL bindings. Formerly, GL4Java was used.
Now JOGL is used. JOGL is more activly supported. It promises to run
on more systems. The system requirements have accordingly changed.
Java version 1.4.1 is now required. Modelzilla should now run on:
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Any version of Windows from the last 5 years
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Any modern Linux. Tested on SuSE linux.
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Solaris version 5.7 and above. It will never work on 5.6, limited
by the Java 1.4.1 requirements.
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It should work on Mac 0S 10.3 when this comes out. I havn't been
able to test it here because we dont have any Macs running 10.3.
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Modelzilla - Fixed light enabledness boolean for the light objects.
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Modelzilla - All objects now have a material setting field. This data
type used to be used mostly by CAD-Zilla. The material field
has sub fields controling the diffuse, ambient, specular colors,
and the shininess. It is applied differently for different
object types. If an object has per vertex colors, the
diffuse and ambient will have no effect, but the specular
and shininess settings are still applied. An object such
as the VvM ball'n'stick applies only the specular and
shininess because it has different colors for each ball
and cylinder.
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Modelzilla - Added a global specular scale setting that effects how much
light colors are applied to specular highlights. This setting
is required because the Solaris OpenGL interprets these parameters
quite differently than on Windows and Liunx.
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Modelzilla - Changed default light directions to come more from the front
and higher.
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Modelzilla - Some OpenGL rendering settings had been disconnected from
user control. They are now reconnected. The OpenGL renderer now
pulls settings from the more general rendering settings under
the general settings list.
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Modelzilla - For some reason special lighting for fully selected objects had been
disabled. Fixed.
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Modelzilla - Depth Cue is improved. You should now get full depth cue regardless
of overall object depth. The "depthCueBug" setting (which forces the back depth
cue point to zero to fix an old bug on a Sun) was being applied always, a bug.
It seams that this bad hardware no longer exists, and this "bug fix" was
actually causing a bug, so the "depthCueBug" setting has been removed.
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Modelzilla - There are now settings for the main dialog background colors,
under the Settings/"Colors and Fonts".
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ZillaTracer - Now installs properly.
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VvM - Helicies in the ribbon trace were recently broken in some cases. Fixed.
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VvM - Wire rendition now defaults to coloring by residue type.
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8-14-2003
The new ZillaTracer application module has arived on the scene. Its giving POV-Ray a work out.
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7-22-2003
- Modelzilla - Made alot of progress in eliminating memory leaks, using the memory debuging tool JProfile.
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User interface elements are now fully detached from data nodes by clearing listener arrays, and vice versa.
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There are no tables of data nodes anymore.
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Data nodes are now recursivly purged when deleted.
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User interface components are recursivly purged as well.
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The task management system now calls new function Task.cleanTask() to
give tasks chance to unregister themselves in listener arrays.
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Viewports are now compleatly detatached when closed.
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The text message box now properly will not accept editing, and thus doesn't
keep an undo history, which was costing at least 5MB.
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Deleted objects are now purged from the undo system as they are pushed off the undo stack.
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Closing a file now automatically purges undo history.
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The memory instrumentation now tool indicates that deleting files, closing
viewports and closing temporary user interfaces do indeed enable the
associated objects to be garbage collected, but still there is a ways to go.
The goal is to be able to use the program "untill kingdom come" without
loosing usefull memory.
- Modelzilla - Changed the basic controls panel to use the square tabs
instead of the honey comb.
- Modelzilla - Each application module's user interface panel now has a
different color.
- Modelzilla - User interface is cleaned up to be more readable.
- Modelzilla - Added a new prototyping system. The new system offers
a "Make Default" button in various spots that will make a prototype copy
of the the object of focus (in whatever specialized interface). The
prototype is then used as the template for subsequent creation of new
objects. Prototypes are saved to the users settings directory, under
Modelzilla/Modelzilla/prototypes/. This
means that if use make the perfect color map with GridZilla, or have the
perfect ribbon colors for VincentVanMol, you can save your color map or
your ribbons as a template that will automatically be applied when you
make the next ones. (And the general section "pushDistance".)
7-7-2003
- VVM - data structure that keeps molecular graphics properties like
atom color, radii, strand thickness, etc has been replaced. These properties
are now kept in a relational database system that is a new member of the
framework's built in datatypes. For those who have the development API, it
is called the TableNode. It is a generalized row/column system. It is much
more memory effient that the old system, requireing a heap allocation for
each column, intead of each row as before. Also, the "show element" property
has been removed. An element is now understood to be shown if a corrisponding
row for it exisits in the table. This way, a ball and stick showing only
a small part of a molecule will keep only a few rows, rather than 1000's of
rows with the "show element" column turned mostly off. This further reduces
memory requirements and file size.
- VVM - the user interface now separates the idea of what portion of a molecule
is shown in a rendition object from the properties controling how it is
shown. The "per element" panel has been split into three parts:
- (a) a show/hide panel for adding and removing elements
- (b) an element property set selection panel
- (c) an element property value panel, controing the values to apply to the panel (b)
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It is now virtually impossible to mess up and unintentionally add or remove
a bunch of elements.
- VVM - the user interface tabs are now more readable and look better.
- VVM - the general set selection system has been improved. It now has
a sub-setting ability that alows one to narrow down the selection in steps.
A separate expression box is used for each type.
- VVM - the default "max-balls" setting for the CPK and B'n'S renditions has
a new default of 10,000 instead of 100.
- VVM - the "fancy blend" setting in ribbons now defaults to 0.0 intead of 0.5,
making residues colored purly by local properties.
- VVM - the residue color scheme is now "color by secondary structure" by default
- VVM - fixed offset of a quarter residue in color application to ribbons with sharp colors.
Note this works if the path quality is between 5-8 samples per residue. Beyond this
is is still a bit wrong. Also, a quarter residue push is now done in color sampling
for smooth case.
- VVM - ribbon rendition no longer erroniously drops sections as it is
updated incrementally, which was disconcerting and a nuisance. This bug has been around
for a couple years now! Its fixed! It updates perfectly now!
- VVM - ball'n'stick rendition now has a quality setting
- VVM - ball'n'stick will now automatically render bonds between any two atoms
in it's atom table, if the "autoBond" setting is true, which is the default. Adding
a bond setting to the table further specifies how it drawn - its thickness and
color and halfness. A new "defaultBondThickness", "defaultBondColor",
and "defaultBondHalfness" whole object properties are used when rendering
bonds automatically.
- VVM - made separate settings controling whether entire molecule is added to
rendition automatically when it is created from user interface button, instead of
the single "autoShowAll". According to the default settings, all renditions
span the molecule entirly, except the CPK and Ball'n'Stick.
- VVM - element selection list boxes now altrenate in item background color
to group atoms by residue, bonds by residue, and residue by chain.
- VVM - scheme color parameters are now "ColorField" types instead of "MaterialField"
types, since VVM only used one color from the MaterialField anyway.
- VVM - tube trace can now be set to go through atoms named "P", for DNA
- VVM - made new pictures for new renditions menu, and used the famous hex-rect buttons widget instead
of the honey comb widget.
- Modelzilla - all list boxes now show tooltips if list item is too wide to be
read
- GridZilla - renamed all fields previously called "spaceField" to "grid". Please
do a find and replace in your ".mvg" files if you need to.
6-13-2003
- Modelzilla - added a windows executable starter with exe4j. This
starter scans the intallation directory for .jar files, so new application modules
can now be installed without changing the start script classpath.
(Put .jar file of app in installation directory)
- GridZilla - fixed a discontinuity on color map that caused a erronious
color value at highest map position
- GridZilla - color ducks are now sorted as color spectrum is computed
so user cannot mix up the ducks.
- GridZilla - user is dis-allowed from moving the color ducks too low
or too high
- GridZilla - interactive drawing of color map curve is now compleatly
reliable - mouse position mapping is fixed
- GridZilla - general section function now explicitly asks for the
sectioning object
- GridZilla - a color legend is now avalaible as as a regular object
created from the color map control panel. It can be moved around like
any other object and has a number of settings like text font, color and spacing.
- GridZilla - now longer gets confused with multiple grids loaded. Color
map min/max points are now in same units as grid values, rather than being
parameterized between zero and one. (Of couse mulpltile color maps can be
created to enable a different min/max for each grid.)
4-28-2003
- Modelzilla - added the new database spreadsheet/network interface.
- Modelzilla - added some tooltips
4-7-2003
- Modelzilla - added drag and drop ability to transfer shapes from one
viewport to another. (One model sub tree to another.)
- Modelzilla - added a new geometry exporter and importer, using a new
geometry format created for the purpose. The new geometry format
is (or will soon be) described in the developers guide (that isn't
avalible yet). It only describes boundry type geometry but has the
special feature of alowing any number of per vertex values to be
expressed, alowing arbitrary data such as "happyness" to be associated
with every vertex.
- Modelzilla - added a raw geometry shape type database node, that
being a database node persists in the model files. The raw geometry
shape has no idea how it was computed and cannot be intelligently
modified from its own parameters, but can still be modified by external
operators. (Other intelligent data nodes.) It is usefull for geometry imports.
- Modelzilla - added a copy function that copies any type of data node.
Has the option to make a regular copy, a link copy, or a raw geometry copy.
- Modelzilla - fixed filename field to operate relative to filename of
owning model
- VVM - fixed a specialized VVM database type to copy properly so
VVM objects can be easily copied too
- Modelzilla - fixed coordinate system list gui to update when current file changes
- Modelzilla - fixed behaviour of window close X on new main viewport.
- Modelzilla - viewpoint movements pan and zoom can be done by hoding down shift and control (as it was a couple years ago!) - fixed mouse mapping in general
- Modelzilla - selection lights now come from the top as well as the bottom
- Modelzilla - fixed some things involving viewport closing file save confirm, exit confirm
3-22-2003
- Modelzilla - fixed and expanded multiple viewport ability. Can now open
model files in new viewport, open mulptile viewports to see the same model
file, and see multiple model files in one viewport
- Modelzilla - got rid of "main viewport" idea, that had one viewport attached
to main controls. Now all viewports are equal.
- Modelzilla - fixed light model in ViewerCore. Objects may now each have
an entirly independant set of lights. This change alowed the easy fixing of
a long stading bug in Modelzilla selection system.
- Modelzilla - fixed positioning reliability of lights and drag rect and other viewport
stationary objects, by fixing ViewCoordSystem to quickly update every redraw.
(This bug must have happend during the rearchitecuring 6 months ago.)
- Modelzilla - fixed drag rect behaviour.
- Modelzilla - VRML dumper adds gamma correction now. (For 3D printer.)
3-12-2003
- VVM - optimized property table assignment code - 6 times faster - by
sharing operations between get row, compare row, and set row steps.
- VVM - reduced memory requirement for holding a molecule by 2 times, by
extending SimpleNode (only ~12 bytes in size) type instead of ModelMode (~80 bytes).
- VVM and Modelzilla - reduced update for interactive ribbon, cpk, ball'n'stick by
up to 10 times. Fixed geometry update/transfer down to viewer core
layer. It used to be clearing all geometries of any shape and rebuilding
all display lists if any changed. It now properly only re-transfers the
ones that actually changed.
- Modelzilla - restored sceene anti-aliasing ability. There is a new
viewport setting called "jitterCount" to control it.
- VVM - improved ribbon diagram geometry. Fixed strange bulbous tubes that
resulted from a splining array mismatch.
3-6-2003
- GridZilla now reads the AVS .fld file format, for uniform binary or ascii fields, one file of referenced files.
2-25-2003
- Modelzilla now installs and runs on the Mac OS 10 platform.
12-14-2002
- VVM: Added an atom/residue color by hydrophobicity scheme
- Added MagnetMaker small demo
- Standard Controls: Added a selection monitor gui
- Fixed a bad bug in Modelzilla selection system that thrwarted some users.
12-10-2002
- Wrote Grid Zilla user's manual.
11-25-2002
- Fixed holes in polygons on Solaris by using slower java based poyygon triangulater
- Fixed all capital ALL_LIBS.JAR file
- Fixed problem with finding new module stubs
11-21-2002
- Fixed a bad lighting bug
- VVM - Fixed an error in DSSP connection when loading an MVG file
- VVM - Fixed an error installing DSSP under windows
- GridZilla is re-released
- Changed GridZilla so it uses the regular VisAD library, rather than our funcky hacked version
- GridZilla color map now saves/opens from MVG file properly
- GridZilla produced objects can now be used with CAD-Zilla
- GridZilla in general with the regular VisAD can become more powerfull
11-14-2002
- Improved transparency by reviving triangle sorter
- Fixed a bug on saving MVG file
- Changed default rendition properties for VVM ribbons and tubes to not outline
11-10-2002
- Fixed: write no files to installation directory at all (for nfs install)
- VVM split panes fixed
- VVM new runs DSSP if PDB file has no secondary structure
- No longer hangs on Linux when viewport is resized
11-5-2002
Added -nfs (network file system) option to the install program
that installs binaries for all platforms (the non java binaries)
to enable entire lab or office to use the same installation of Modelzilla.
10-31-2002
Fixed some intallation problems.
- Installs properly on Linux now.
- Removed ICE Browser library.
- Removed Visual Numerics library.
- Install program now requires Java 1.4
- Install program now uses Swing and our regular widget library.
- Updated the gl4java binaries
10-22-2002
Second big update. Fixed many things, including:
- VVM Incremental update of ribbons fixed
- VVM Residue picking of viewport fixed
- VVM Secondary Structure element picking added
- CAD Zilla solid ops no longer effect input geometry
- Fixed coordinate system bug in all CAD Zilla composite ops that appeared due to new architeture
- CAD Zilla polygon relators fixed
- Lights are now proper on open
9-27-2002
First update. Fixed bugs:
- Fixed CAD Zilla Boolean math to handle larger intersection region
- Fixed VRML Exporter
- Changed Grid
- Change selection graphics to use lighting change
- UCS set to view new only changes rotation
- Added snap to surface point snap option
- Fixed Ribbon Backbone incremental update in VVM
- Fixed transparency to work for any object
- Made navigation of basic control module easier
- Fixed a terrible memory leak
- Fixed handy transform by eye function
9-20-2002
Modelzilla replaces StarModel.
September 2001 - September 2002
The first effort, StarModel, is re-architectured, re-designed, and re-documented.
September 1998 - September 2001
The task of writing a general Java viewer is enthusiasticly pursued.
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