Landmark Reference Manual

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

Local Folders and files created and used by Landmark

• Landmark.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 Landmark.properties file.

Normally the project directory is setup prior to running Landmark and it expects the data to be in the following directories. 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 Landmark]
• cache/ directory holding temporary CSD cache files - [NOT USED by Landmark]
• ppx/ directory holding your original gel input files
• rdbms/ directory holding CSD database RDBMS files - [NOT USED by Landmark]
• tmp/ directory holding generated sample image files
• xml/ directory that holds Landmark DB, landmark DB, SSF spot-list files, and generated SPF paired spot list file generated by Landmark

Landmark command-line arguments switch usage

     Landmark -rsample:Reference-sample -sample:sample [< 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 Landmark.exe file or clicking on the Landmark.jar file, you can't change the default startup memory.

If you are using the Landmark.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 Landmark.jar {additional command line args}

Menu notation

• 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.
  ------------------------------------
• Open landmark file - open a landmark database. Ask to save current landmark database if you have made any changes.
• New landmark file - create a new landmark database. Ask to save current landmark database if you have made any changes.
• Rename landmark file - rename the current landmark database. Ask to save current landmark database if you have made any changes.
  ------------------------------------
• Open Rsample - specify the reference sample from samples in the current accession database.
• Open Sample - specify the current sample from samples in the current accession database.
  ------------------------------------
• Remove Sample-pair from Landmark DB - remove the current (Rsample,Sample) pair from the landmark database.
  ------------------------------------
• Save Landmark DB - explicitly save the Landmark DB if changes were made. Otherwise, it is saved when you press "Done".
  ------------------------------------
• 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
  ------------------------------------
• Update - update Landmark programs and data from open2dprot.sourceforge.net/Landmark server
•      Landmark all files - to get the latest files
•      Landmark program - to get the latest program release (Landmark.jar) and other version dependent files from Landmark server
•      Landmark demo files - get latest demo project data files
•      Landmark documentation - to get the latest documentation (for stand-alone operation)
  ------------------------------------
• Exit - exit the program when in GUI mode.

• Select Rsample from (Rsample,Sample) list in the LMS DB - select the Rsample from a list of available landmark sets in the current landmark database. This set of Rsample landmarks can be used when doing "template" editing (see below).
• Don't edit Rsample landmarks - prevent the user from changing the set of coordinates for the Rsample landmarks. Normally, you would not edit the Rsample landmarks after their initial definition. This lets you use exactly the same landmarks when landmarking other samples in subsequent sessions.
• Use Rsample landmarks as fixed template - when landmarking a new sample, the landmarks from the template Rsampe (see above) will be available for you to match in the Sample (right image). This ensures that all samples will be paired with the same landmarks in the Rsample.
  ------------------------------------
• Landmark - popup the Landmark editor window for the current (Rsample,Sample) pair of samples.
  ------------------------------------
• Options - change the command line options
•      Open options file - read a new options file (this overides the previous options file which could be Landmark.properties).
•      Save options file - write the current options to the current options file (default Landmark.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 thier 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. These are samples that are available for you to define as paired samples.
• List Landmark Samples - list the names of all paired samples in the Landmark database (in the running program). These are listed as pairs of (Rsample,Sample) pairs.
  ------------------------------------
• Show Rsample accession DB data - list accession data for the currently selected Rsample in report window.
• Show Sample accession DB data - list accession data for the currently selected Sample in report window.
• Show landmark DB data - show Landmark pairs for the current (Rsample,Sample)database in in report window.
• Show radii of landmarks - list of Landmark radii for the current (Rsample,Sample) in report window.
  ------------------------------------
• Show Accession DB in popup browser - show Accession database in a popup XML browser.
• Show Landmark DB in popup browser - show Landmark database in a popup XML browser.

• Save Landmark DB - explicitly save the Landmark DB if changes were made. Otherwise, it is saved when you press "Done".
• Log text output to Report window - copy text output to Report window.
  ------------------------------------
• Cancel - exit the Landmark Editor window without saving any changes you may have made
• Exit - exit the Landmark Editor window, but ask to save the landmarks if you made changes.

• Flicker Rsample vs Sample (C-F) - flicker the Rsample and Sample zoom windows (top row) into the upper right zoom window. The flicker rate is determined by the delay scrollers at the bottom.
• Add landmarks radii overlay - add half-radii overlays for the defined landmarks
• Show radii table data for landmark spot - show additional numeric data for a landmark spot in the text area when you click on a landmark.
• Use +# instead of + for landmarks - show landmarks as "+#" rather than "+letter".
  ------------------------------------
• Use mouse draw to select spots - instead of having to click on a spot
• Add focus box to aid landmarking - draw a "focus" box around the area you are editing in the Rsample.
  ------------------------------------
• Separate Flicker Window - use a separate flicker window instead of the upper left image windows. You may resize this separate window to see more detail. It is more useful on higher resolution monitors.
  ------------------------------------
• Guard region color - select the guard region color. This addes a colored region (1/4 of the height or width) to the the image on all four edges so that you can scroll and center the image to data on any of the four edges.
  1. White
  2. Black
  3. Gray
  4. LightGray
  5. DarkGray
  6. Cyan
  7. Mean image

• Add Landmark at current cursor (C-A) - to add a landmark after you have indicated the coordinates in both the Rsample and Sample.
• Delete Landmark at current cursor (C-D) - to delete a landmark after you have indicated the coordinates in both the Rsample and Sample. If you are not allowed to edit the Rsample then only the Sample landmark will be deleted. See Report Window menu (Edit | Don't edit Rsample landmarks).

• . . .

7. List of the command line switches

    Landmark -rsample:reference-sample -sample:sample [< optional switches >]

Command line switches

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

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


-commutativeLMS lets you search the landmark database for sample pairs
      where the Rsample and Sample are swapped. (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/,
         -LandmarkDB:Landmark.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 (Open2Dprot-SPF.dtd) in the output XML
      if -spfFormat:X is set. (Default is -nodtd).
     
-gui to start the spot pairing with a popup Graphical User Interface
      rather than in batch mode.  Landmark does not run in batch
      mode. This captures messages from Landmark.  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 -gui).

-inputFormat: defines the input formats for 
      the Landmark database file accMode). Where mode is: 'F'
      for full tab-delimited data that includes 2 files: the list of
      spots, parameters and statistics. The 'T' for tab-delimited
      (.txt) data, and 'X' for XML (.xml) data. (Default is 
      -noinputFormat:X,X).

-landmarkFile:lmsFile to overide the default landmark
      database file.  (Default is -nolandmarkFile:landmark.xml).

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

-rsample: is name of the reference sample.

-sample: is the name of 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
       Landmark 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:

     Landmark [< opt.-switches >]

The following examples using switches might be useful:     

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

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

8.1 Examples - samples of screen shots

REM File: demo-Landmark.bat - interactively define landmark spots for each of 3 samples 
REM when paired with the reference sample.
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
REM demo image files:
REM      demo/ppx/gel-HM-019 (Reference sample)
REM      demo/ppx/gel-HM-071
REM      demo/ppx/gel-HM-087
REM      demo/ppx/gel-HM-096
REM Accession database file is in:
REM      demo/xml/accession.xml
REM Landmark database file is in:
REM      demo/xml/landmark.xml
REM Sample Spot-list files (SSF) are in:
REM      demo/xml/gel-HM-019-SSF.xml
REM      demo/xml/gel-HM-071-SSF.xml
REM      demo/xml/gel-HM-087-SSF.xml
REM      demo/xml/gel-HM-096-SSF.xml
REM Generated images are saved in:
REM      demo/tmp/
REM
REM P. Lemkin $Date$ 
 
echo "demo-Landmark.bat"

pwd
date /T 
 
java -Xmx256M -jar Landmark.jar -demo -project:demo\ -sample:gel-HM-071 -rsample:gel-HM-019
java -Xmx256M -jar Landmark.jar -demo -project:demo\ -sample:gel-HM-087 -rsample:gel-HM-019
java -Xmx256M -jar Landmark.jar -demo -project:demo\ -sample:gel-HM-096 -rsample:gel-HM-019

echo "-- Finished landmarking the samples ---"
date /T 

#!/bin/sh
# File: demo-Landmark.sh - interactively define landmark spots for each of 3 
# samples when paired with the reference sample.
# This example assumes that all .jar files listed below and demo/ directory are
# in the current directory. Modify for other situations.
#
# JAR files required and mentioned in manifest:
#     xml-apis.jar xercesImpl.jar jai_codec.jar jai_core.jar O2Plib.jar
#
# 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 image files:
#      demo/ppx/gel-HM-019 (Reference sample)
#      demo/ppx/gel-HM-071
#      demo/ppx/gel-HM-087
#      demo/ppx/gel-HM-096
# Accession database file is in:
#      demo/xml/accession.xml
# Landmark database file is in:
#      demo/xml/landmark.xml
# Sample Spot-list files (SSF) are in:
#      demo/xml/gel-HM-019-SSF.xml
#      demo/xml/gel-HM-071-SSF.xml
#      demo/xml/gel-HM-087-SSF.xml
#      demo/xml/gel-HM-096-SSF.xml
# Generated images are saved in:
#      demo/tmp/
#
# P. Lemkin $Date$ 

echo "demo-Landmark.sh"

pwd
date 

java -Xmx256M -jar Landmark.jar -demo -project:demo/ -sample:gel-HM-071 -rsample:gel-HM-019
java -Xmx256M -jar Landmark.jar -demo -project:demo/ -sample:gel-HM-087 -rsample:gel-HM-019
java -Xmx256M -jar Landmark.jar -demo -project:demo/ -sample:gel-HM-096 -rsample:gel-HM-019

echo "-- Finished landmarking the samples ---"

date