This describes the revision history of the CmpSpots program of
released or soon to be released versions. Generally, only the most
recent versions are kept on the Web site (see Version). Documentation for
unresolved bugs and requested functionality is found in the status Web page.
V.0.2.9 12-21-2005: Used more robust LMset/DbLM code
and read TIFF before GIF or JPEG.
V.0.2.6 08-05-2005: Fixed several bugs in zoom; 6x zoom
filtered spots were incorrect; scroller alignment did not work. When
Image Veiwer was closed it would not continue correctly when
V.0.2.4 05-29-2005: Fixed bugs in Image Viewer when change
magnification and also histogram spot filtering.
V.0.2.3 05-29-2005: Fixed bugs in XML SPF writer in the
V.0.2.2 05-27-2005: Fixed bugs in Image Viewer GUI.
V.0.2.1 05-09-2005: Fixed bugs in AP and US pairing that
occured a small percentage of the time. Also modified the SPF XML schema
in the O2Plib.db.DbPairSamples and DbPspot library. Fixed display of
spot pairs for Sample in the popup viewer (it previously only displayed
those in the Rsample). Modified the font size for labeling in the
image in the popup viewer as the zoom factor increased.
V.0.1.16 04-20-2005: Fixed bugs in library and
synchronized with O2Plibrary. Added Zoom feature and changed layout of
Image Viewer popup slightly.
V.0.1.12 03-21-2005: Fixed bug in -usage and -version
switches. Changed SSF input files so it looks for
<sample-name>-SSL.xml rather than <sample-name>.xml.
V.0.1.7 01-18-2005: Cleanup and sync with O2Plib.
V.0.1.6 12-20-2004: Improved secondary pairing.
V.0.1.5 12-17-2004: Fixed pairing errors introduced when
refactored the code during cleanup.
V.0.1.3 12-08-2004: Cleanup and refactored code using
new O2Plib modules. Fixed bugs which improves pairing. This may result
is new pairing results.
V.0.1.1 11-22-2004: Cleanup and refactored code so uses new
O2Plib methods. Added new switch -dtd (default is -nodtd) to add
(omit) Open2Dprot-SPF.dtd when generate the SSF files.
V.0.0.9.1 10-29-2004: Cleanup the manual and library
V.0.0.9 10-12-2004: Now using the Open2Dprot library O2Plib
instead of all code being in CmpSpots. Also changed the XML schema
V.0.0.8 08-25-2004: enabled the command line processing
using the CmpSpots.exe file for running it in batch. Run the command
with "-nodemo" and other switches you need as well as the gel image or
gel sample name (if using the -accession file option). A new switch
-default was added to give you the -demo options but with -nogui and
with no -rsample and no -sample options prespecified.
V.0.0.7 08-11-2004: The new SAX XML readers work for
SSF, accession and landmark XML input files. The new default is set to
inputFormat:X,X,X to read all three files as XML.
V.0.0.6 08-10-2004: Changed accession database input
file format so that the sample name is now "Sample" instead of
"PubPixFileName". Changed landmark database input file format so that
the Sample and Rsample names are now "Sample" and "Rsample".
V.0.0.4 08-05-2004: Generalized the program to other
types of 2D data where the objects used in an experiment are a set of
samples rather than just a set of gels. Refactored code by renaming
all references to (Gel Segmentation File, GSF, gsf) to (Sample
Spot-list File, SSF, ssf), and (Gel Comparison File, GCF, gcf) to
(Sample Paired-spot list File, SPF, spf) including both the Java code,
DTD and documentation. NOTE: This must be synced with changes in the
Seg2Dgel subproject. Fixed misc. bugs with command line options GUI
editor, refresh with Image Viewer, re-initialization problems when
rerunning it multiple times or after changing the command line
V.0.0.3 07-30-2004: Generalized the program to other
types of 2D data. Refactored code by renaming all references to (Rgel
and gel) to (Rsample and Sample).
V.0.0.2 07-29-2004: Cleanup and fixed some of the XML
readers with Epilogue errors. Added
V.0.0.1 07-28-2004: This is a pre-alpha version. The
data is hardwired for now. The histogram is not fully working. It
requires tab-delimited accession and landmark database files for now.
It will accept either -gsfFormat:X or -gsfFormat:F GSF files. It will
generate either -gcfFormat:X or -gcfFormat:F GCF.y