Accession Reference Manual

    batch/ directory holding temporary batch files - [NOT USED by Accession]
    cache/ directory holding temporary CSD cache files - [NOT USED by Accession]
    ppx/ directory holding your original gel input files
    rdbms/ directory holding CSD database RDBMS files - [NOT USED by Accession]
    tmp/ directory holding generated sample image files    
    xml/ directory that holds  accession DB, landmark DB,
             SSF spot-list files, and generated SPF paired spot list file
             generated by Accession

2.1 Accession information editing popup window

2.1.1.1 Accession Info File menu

• Use values from template sample - use the values from the specified template sample for this sample being edited. It does NOT copy the
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• Log text output to Report window - copy all text out to this popup window to the main Accession Report Window as well.
• Save accession DB - explicitly save the accession DB if changes were made. Otherwise, it is saved when you press "Done".
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• Clear report - clear the report text area so that you can start a new report that will be easier to cut and paste or do save to a file
• Save Accession DB - save the changes in the accession database file.
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• Cancel - exit the accession information popup, do not save any changes.
• Exit - exit the accession information popup, save any changes when exit.

• Assign current Rsample to this sample - assign the current Rsample name to the current sample being edited.
• Clear image computing window ROI entry - clear the image computing window ROI entry. This will force you to define the window using the ROI editor popup.
• Clear calibration wedge ROI entry - clear the image wedge calibration ROI entry. This will force you to define the window using the ROI editor popup.

• Describe accession fields - list the accession database fields and the short descriptions of these fields in the top reporting region of the Accession information popup window.

2.2.1.1 ROI editing File menu

• Log text output to Report window - copy all text out to this popup window to the main Accession Report Window as well.
• Save accession DB - explicitly save the accession DB if changes were made. Otherwise, it is saved when you press "Done".
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• Clear report - clear the report text area so that you can start a new report that will be easier to cut and paste or do save to a file
• Save Accession DB - save the changes in the accession database file.
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• Cancel - exit the ROI popup, do not save any changes.
• Exit - exit the ROI popup, save any changes when exit.

• Draw trial ROI overlay - draw the trial ROI overlay (cyan color).
• Draw CW ROI overlay - draw the computing window (CW) ROI overlay (red color). The CW ROI is used to define the image region to segment or find spots.
• Draw calibration wedge ROI overlay - draw the calibration wedge ROI overlay (blue color). This can be used over a grayscale calibration wedge region in the image.
• Draw measured spot overlays - draw measured spot overlays (magenta color). This is used if calibration if being performed using a list of spot measurements.
• Draw measured spot labels - draw measured spot overlay labels (magenta color). This is used if calibration if being performed using a list of spot measurements. The spot labels are "#1", #2", ... "#n".
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• WinDump pixel window size - if not "none", i.e. "3x3", "5x5", ... "21x21", show the region around the current pixel.

• Set ROI ULHC at current cursor (C-U) - define upper left hand corner of working trial ROI. Draw a upper corner to indicate this. If both ULHC and LRHC are defined, draw the trail ROI region.
• Set ROI LRHC at current cursor (C-L) - define lower right hand corner of working trial ROI. Draw a lower corner to indicate this. If both ULHC and LRHC are defined, draw the trail ROI region.
• Clear working ROI (C-D) - clear the working trial ROI.
• Assign ROI to Computing Window (C-C) - assign the working trial ROI to the computing window. This is saved in the accession DB for this sample.
• Assign ROI to Calibration Wedge ROI (C-W) - assign the working trial ROI to the calibration wedge ROI. This is saved in the accession DB for this sample.
• List current ROI definitions - list the trial, CW and wedge ROIs if defined.

• Add measured spot at current cursor (C-M) - add spot of current measurement size at the current cursor position to the measurement spot list.
• Remove measured spot at current cursor (C-R) - remove selected spot from the measurement spot list.
• Define common mean background spot at current cursor (C-B) - define a spot to measure mean background to subtract from all spots (optional).
• List measured spots - List all of the spots and their values in the spot measurement list.
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• Clear list of measured spots - clear list of measured spots.
• Clear background spot - clear background spot (used for background correction).
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• Measurement square size - to one of "1x1", "3x3", "5x5", ... "29x29" values. The spot density measurement is the sum of gray values under this square.
• Recompute spot-list measurements with common size - recompute spot-list with the same common size. This lets you change the spot measurement size for all spots and the corresponding total densities after the spot list was defined.
• Recompute spot-list measurements with background correction - recompute spot-list with background correction. This lets you add or remove the background correction after the spot list was defined.
• Sort spot-list measurements - sort the spot-list by density. This lets you keep a sorted spot list - even if they were defined out of order.

• N.A. - (none available yet).

2.3.1.1 File menu

• Log text output to Report window - copy all text out to this popup window to the main Accession Report Window as well.
• Save calibration - explicitly save the calibration into the accession DB if changes were made. Otherwise, it is saved when you press "Done".
  ------------------------------------
• Cancel - exit the grayscale calibration popup editor, do not save any changes.
• Exit - exit the grayscale calibration popup editor, save any changes when exit.

• N.A. - Not available yet.

• Analyze histogram - computes the grayscale histogram of the wedge in the sample image and updates the table on the right with the histogram peaks that were found.
• Add peak (C-A) - adds a peak value to the table on the right if you have selected a peak with the mouse in the histogram prior to pressing this button. It will insert a peak if the value you select is between two existing peaks. It redraws the histogram and calibration curve.
• Delete peak (C-D) - deletes a peak value to the table on the right if you have selected a peak with the mouse in the histogram prior to pressing this button. It will remove a peak if the value you select is between two existing peaks. It redraws the histogram and calibration curve.
• Refresh peak table - refreshes the histogram. This is useful if you manually edit the table.
• Generate linear calibration - [***EDIT***]

• N.A. - Not available yet.

The computing window region of interest

The computing window is defined as [x1:x2, y1:y2]. You can set the computing window using the -cw:x1,x2,y1,y2 command line switch. If you have not defined it or it is not defined in the accession database (if the -accessionFile option is used), it is defined as [0:pixWidth-1 x 0:pixHeight-1] where the virtual image is of size pixWidth x pixHeight.

[STATUS: The computing window for each sample entry is defined in the accession database. The Accession program will allow users to define the computing window.]

• Accession.properties - is the default command line switch options to be used (if present). You can edit the default switch options and then save them into the Accession.properties file.

If you specify an image to be semented, it will check whether it is in a ppx/ subdirectory. If not, it will ask you if you want to create a project directory and will then set up the following four directories and copy your image into the ppx/ directory. You can also use the -projDir:user-project-directory switch to specify a (possibly new) project directory.

• batch/ directory holding temporary batch files - [NOT USED by Accession]
• cache/ directory holding temporary CSD cache files - [NOT USED by Accession]
• ppx/ directory holding your original gel input files
• rdbms/ directory holding CSD database RDBMS files - [NOT USED by Accession]
• tmp/ directory holding generated sample image files
• xml/ directory that holds accession DB (created or edited by Accession), landmark DB, SSF spot-list files, and SPF paired-spot list files.

Accession command-line arguments switch usage

     Accession  [< optional switches >]

Options wizard window for setting the command line switches

        -update:program      to update the program jar file
        -update:demo         to update the demonstration files
        -update:doc          to update the documentation files
        -update:all          to update all of the above

If you are using the Windows Accession.exe file or clicking on the Accession.jar file, you can't change the default startup memory.

However, if you are using the Accession.jar in a script using the java interpreter as in the following example which uses the -Xmx256M (specifying using 256Mbytes at startup). Change 256 to a larger size if you want to increase startup memory.

   java -Xmx256M -jar Accession.jar {additional command line args}

Menu notation

• Create project (directory) - create a new project directory and create the new directory and (batch/, cache/, ppx/, rdbms/, tmp/ and xml/) subdirectories. See the -projDir:new_project-directory switch that you can use to do this on startup.
• Set project directory - set the new default project directory and create the new directory and (batch/, cache/, ppx/, rdbms/, tmp/ and xml/) subdirectories if needed. See the -projDir:new_project-directory switch that you can use to do this on startup.
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• Open accession file - Open an accession file in the current project directory. Close the old accession file first if it was open.
• New accession file - Create a new accession database file in the current project directory. Close the old accession file first if it was open.
• Rename of current accession file - rename the current accession database. This lets you support multiple accession databases in the same project directory.
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• Add sample to the accession DB - add a new sample name to the accession DB. This does not specify the accession info, ROI, or calibrations. You must make this the active sample and then assign these values using the Edit functions.
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• Set Rsample - specify the reference sample from samples in the current accession database.
• Set Sample - specify the current sample from samples in the current accession database.
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• Save accession DB - explicitly save the accession DB if changes were made. Otherwise, it is saved when you press "Done".
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• Clear report - clear the report text area so that you can start a new report that will be easier to cut and paste or do save to a file
• Save report to a file - save the report to a text file
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• Update - update Accession programs and data from open2dprot.sourceforge.net/Accession server
•      Accession all files - to get the latest files
•      Accession program - to get the latest program release (Accession.jar) and other version dependent files from Accession server
•      Accession demo files - get latest demo project data files
•      Accession documentation - to get the latest documentation (for stand-alone operation)
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• Exit - exit the program when in GUI mode.

• Accession info - popup the Accession info editor for the current Sample.
• Regions of interest - popup the Regions Of Interest (ROI) info editor for the current Sample.
  ------------------------------------
• Calibrate by step wedge - popup the Calibrate by Step Wedge editor to calibrate grayscale by computing the peaks in a calibration wedge scanned with the image for the current Sample.
• Calibrate by spot list - popup the Calibrate by spot list editor to calibrate grayscale by a list of measured spots for the current Sample.
• Calibrate by file data - popup the Calibrate by file data editor to calibrate grayscale from a file for the current Sample.
• Calibrate by manual entry - popup the Calibrate by manual entry of the calibration for the current Sample.
• Read calibration values from file - calibrate data from a file.
  ------------------------------------
• Options - change the command line options
•      Open options file - read a new options file (this overides the previous options file which could be Accession.properties).
•      Save options file - write the current options to the current options file (default Accession.properties)
•      SaveAs options file - write the current options to a new file you specify
•      Edit options - popup the an Options wizard window to to edit the switch options and their parameters, threshold parameter sliders, and input image file
•      *Reset default options - reset options to the initial default

• List accession samples - list the names of all samples in the accession database (in the running program). If you have added samples, this may contain samples not yet in the accession database file.
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• Show Rsample accession DB data - show accession data for the currently selected Rsample.
• Show Sample accession DB data - show accession data for the currently selected Sample.
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• Show accession DB in popup browser - show accession database in a popup XML browser.
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• Show list of measured spots - show list of measured spots used for calibration.

7. List of the command line switches

    Accession  [< optional switches >]

Command line switches

-accessionFile:accFile to overide the default accession
      database file.  (Default is -noaccessionFile:accession.xml).

-backupDatabases makes backups of the accession and landmark databases "+
      "if they are edited. (Default is -commutativeLMS).

-debugBits:bits,optLandmarkNbr dumps various conditional
      debugging parameters onto the report window.  The 'bits' are the
      debug bits specified as either octal or decimal and enable
      particular debugging output if the program was compiled with
      debugging enabled.  (Default is -nodebug).

-default sets the default switches to a specific configuration:+
         -nodemo
         -inputFormat:X -projDir:demo/,
         -accessionDB:accession.xml.
      This disables -demo if it was set. (Default -nodefault).

-demo sets the default switches and sample input sample to a specific 
      configuration. This may be overriden by turning off the -demo
      switch in the Options Wizard.

-dtd adds the XML DTD file in the output XML file. (Default is -nodtd).
     
-gui to start the spot pairing with a popup Graphical User Interface
      rather than in batch mode. This captures messages from Accession.
      You can then cut and paste the results or save it to a text
      file.  The GUI is also used to change the switch options, re-run
      the spot pairing and view images after each analysis.  (Default
      is -nogui).

-inputFormat: defines the input formats for
      the accession database file accMode). Where mode is: 'T'
      for tab-delimited (.txt) data, and 'X' for XML (.xml) data.
      (Default is -noinputFormat:X)

-projDir:alternate project directory path to specify the
       project directory to use instead of the default 'demo/' file in
       the installation directory. (Default is -noprojDir).

-propertiesFile:alternate 'Accession.properties' file to specify
       the alternate startup properties file to use instead of the
       default 'Accession.properties' file. (Default is
       -nopropertiesFile).

-rsample: is the reference sample.

-sample: is the Sample to be paired with the Rsample.

-timer enables a timer to capture processing times for each step.
       (Default is -notimer).

-update:{all | program | demo | doc} specifies that all of the
       Accession files, the program jar files, the documentation files
       or the demonstration files should be updated from the
       Open2Dprot Web server.  The program should be exited and
       restarted after updating the program for this to take
       effect. (Default is -noupdate).

-usage prints all of the switches. (Default is -nousage).

The following shows a few examples of useful combinations of command
line switches.

Any case-independent switch may be negated by preceeding it with
a 'no' eg. '-notimer'.

The command line syntax used to invoke it is:

     Accession [< opt.-switches >]

The following examples using switches might be useful:
     

     Accession -gui -project:demo/
  # Start Accession and load the accession database from the demo project.

     Accession -rsample:gel-HM-019 -sample:gel-HM-071 -gui -project:demo/
  # Start Accession with two samples already in the accession database

Debugging option bits used with the "-dbug:" command line command
-----------------------------------------------------------------------------

The following are the orthogonal -debug option code bits in octal.
This means you can add them together (in octal) and use that number.

         Octal code   Methods traced
         ==========   ================
bit:            01 =  -free-
bit:            02 =  -free-
bit:            04 =  -free-
bit:           010 =  -free-
bit:           020 =  -free-
=======================================================================

8. Demonstrations

8.1 Examples - samples of screen shots

REM File: demo-Accession.bat - accession a sample gel 
REM
REM This example assumes that all .jar files listed below and demo/ directory are
REM in the current directory. Modify for other situations. 
REM 
REM The JDK should be installed and version 1.4 or later is required.
REM You can download the latest JDK from http://java.sun.com/
REM
REM The files needed are listed below:
REM JAR files required and mentioned in manifest:
REM     xml-apis.jar xercesImpl.jar jai_codec.jar jai_core.jar O2Plib.jar
REM demo Files:
REM      demo/ppx/gel-HM-019
REM Accession database file is in:
REM      demo/xml/accession.xml
REM Generated Sample Spot-list Files (SSF) are saved in:
REM      demo/xml/
REM Generated images are saved in:
REM      demo/tmp/
REM
REM P. Lemkin $Date$ 

echo "demo-Accession.bat"

pwd
date /T 

java -Xmx256M -jar Accession.jar -demo -gui -project:demo\ 

echo "-- Finished accessioning the samples ---"

date /T

#!/bin/sh
# File: demo-Accession.sh - accession a sample gel 
#
# This example assumes that all .jar files listed below and demo/ directory are
# in the current directory. Modify for other situations.
# 
# The JDK should be installed and version 1.4 or later is required.
# You can download the latest JDK from http://java.sun.com/
#
# The files needed are listed below:
# JAR files required and mentioned in manifest:
#     xml-apis.jar xercesImpl.jar jai_codec.jar jai_core.jar O2Plib.jar
#
# demo Files:
#      demo/ppx/gel-HM-019
# Accession database file is in:
#      demo/xml/accession.xml
# Generated Sample Spot-list Files (SSF) are saved in:
#      demo/xml/
# Generated images are saved in:
#      demo/tmp/
#
# P. Lemkin $Date$ 

echo "demo-Accession.sh"

pwd
date

java -Xmx256M -jar Accession.jar -demo -gui -project:demo/ 

echo "-- Finished accessioning the samples ---"

date