CmpSpots Image Viewer icon

CmpSpots Reference Manual

The following description will tell you what the options are for the CmpSpots and how to run the program - both interactively and from the command line. If you interact with it through the windowing system, then Figure 1 shows a screen view of the CmpSpots reporting window. 




CmpSpots labeled Report Window





Figure 1. Screen view of the CmpSpots program Report Window interface 

 This screen shot shows the status of CmpSpots in the
Report Window graphical user interface after a spot pairing of the
demo samples which are 2D PAGE gels. The reference sample or Rsample
is gel-HM-019. The other sample denoted Sample is gel-HM-071) has
completed. The pairing threshold parameters are shown at the top with
the list of Switches.  The summary statistics on the spot list
pairing is summarized in the window including the run time [Run on a
1Ghz Pentium-4 Windows 2000 system]. The Report window has five pull-down menus at the top of the window used to
invoke menus: File, Edit, View, Pair, and Help
operations.  Although, the button commandss at the bottom of the
window are also available in the menus, they are replicated as buttons
for convenience. The Clear button will clear the window.
SaveAs will let you save the Report Window text in a text file.
The Edit options button pops up a window to let you edit the
options including the sample name, computing window, sizing thresholds
etc.  The Pair spots button starts the spot pairing on the
current options. You can stop the spot pairing by pressing the Stop
spot pairing button. After you have paired the spot lists, you can
review the paired spot data by pressing the Image Viewer to
popup the image viewing window.  A status area appears in the lower
left corner and reports the current state of the spot pairing during
an analysis. It shows "Done" since the spot pairing had completed.










1. Introduction


CmpSpots is an open source Java 2D spot list matching program for
finding and pairing spots between the two quantified spot lists.  It
is part of the Open2Dprot project (
http://open2dprot.sourceforge.net/). CmpSpots is derived the the
GELLAB-II 2D gel spot pairing program cmpgl2 described in
[3]. CmpSpots has been generalized to other types of samples besides
2D gels. While the original program was written in C, CmpSpots is
written in Java, uses XML input and output files and has an optional
graphical user interface. This initial open-source CmpSpots program
code could be used as the basis for more advance spot pairing
methods.


The program may be run either interactively (-gui) or under an OS
shell command line interface to implement batch (-nogui). If the
default -gui mode is used, after the spot pairing is finished, the
user has the option of interactively examining the paired spot data
overlayed on the original sample images.  The user may also modify the
input switch options and save the new options in a
"CmpSpots.properties" file in the current project directory when they
exit so that the last used options may be used as the default switch
options in subsequent running of CmpSpots.


In the analysis of 2D image samples (whether real or virtual), the
matching of spots between these samples by pairing spots between their
spot lists is difficult to perform manually when there are more than a
few spots. Automation is necessary when the samples contain a large
number of spots, spots which are at best only locally congruent from
sample to sample, when the spots can not be counted on to maintain
their "shape" or density and contain little infrastructure on which to
build a characterization [3]. There is at best a local congruence
between two samples related by some a priori undetermined affine
transformation. Some of this description is derived from [3].




Partitioned search - dividing the 2D space into local regions


Aside  from  the number  of  spots to  be  examined,  a major  problem
complicating spot  localization may be  the global distortions  in the
samples.  However, if  we are  locally well-behaved  data, neighboring
spots in  one sample will likely  be neighbors in another  gel but the
intervening  distances  between  them  will  change to  to  a  greater
degree. The spot pairing problem can be handled various ways.


One method would be to warp (using a non-linear affine transform) one
sample image to the geometry of the reference sample image. Then when
these images are analyzed by quantifying segmentmented spots, the
spots will be congruent. This method won't work if there are no images
(e.g., the 2D spot lists are derived from non-image data (e.g., 2D
LC-MS data).



Another method would do a similar warping, but using only the spot
lists themselves.




CmpSpots method: A landmark driven spot pairing algorithm


An alternative method is to partition the spot lists into local
regions and pair spots within these regions. Within a region, spots
surrounding a spot that is known to be paired can most frequently be
reliably paired between samples. We will call these spots in the
center of the regions "landmarks". The method uses an abstract (x,y)
space rather than actual images. Spot (x,y) coordinates are mapped
from the sample to the reference sample. This is done, for each
landmark, by assigning the landmark spots in the two samples, the
cartesian coordinate (0,0). Then using simple linear vector
arithmetic, the set of sample spots coordinates are mapped to the
reference sample. A set of landmark spots increases the efficiency of
inter-sample spot matching by providing an empirical basis for the
partitioning of a virtual sample images into tractable corresponding
subregions.


	
A landmark spot may be defined in various ways. In one current
empirical procedure for choosing landmarks, it is a morphologically
distinctive spot such that neighboring spots and the landmark spot
form a consistent morphological structure.  Moreover, this structure
should be easily recognized across the set of samples used in an
experiment consisting of a number of gels (> 2). The landmark spots
are selected to cover the regions of interest of the sample fairly
evenly if there is uniform distortion between samples. If there are
some regions with a lot of distortion, more landmarks should be used
in these regions. Depending of the similarity and distortions between
the samples, a few to a larger number may be required. This set of
landmarks is called the landmark set.




Landmark region


The landmark region is a 2D space surrounding a landmark spot. It is
defined as a fuzzy region having more certainty closer in toward the
landmark spot. The effective-radius of certainty Ri for landmark i is
a distance defined to be half the distance from landmark i to the
nearest neighbor landmark. Figure 2 illustrates the effective-radius
concept. Images of a spot within the effective-radius of a landmark
set would have a higher probability of being aligned (since the
landmarks have "perfect" alignment) than if the spot were outside of
this radius. Thus, using this heuristic concept of partitioning the
spots by landmark region, it is possible to pair the spots
automatically once the landmarks are established. The landmark spots
are then compared with the two spot lists from the two Sample
Spot-list Files (SSF) and the best segmented spot is used rather than
the coordinates manually produced. If no spot can be found for a
landmark within specified error bounds (currently the maximum latch
distance defined using the -latchLandmarkSpots:maxLatchDist
distance), the landmark coordinate is used in the pairing process. It
is possible to check how reliable the particular spot pairing actually
was by backchecking paired spots using the Image Viewer.


	
The probability of finding the same spot in two samples relative to
the aligned images of a closeby landmark is greater than if the entire
sample spot space were to be searched. This partitioned search has the
added advantage that landmark regions contain an order of magnitude
fewer spots than the total sample space. Thus the combinatorics of
performing the spot matching is greatly decreased as well.



Landmarks could be supplied either using a manual "landmark
definition" interactive program (not described here) or might be
generated using methods for discovering a subset of robust
paired-spots that might be putative landmarks. 









Effective Radii of landmarks





Figure 2. Definition of the effective-radii of a set of landmarks. 


The effective-radii of certainty of a landmark Ri is 1/2 the minimum
distance from landmark i to its nearest adjacent landmark j. In this
example, radius Ra > Rb and Rb=Rc. The nearest neighbor of landmark A
is B and its next nearest neighbor landmark is C. Estimates of spot
pairs within landmark radii are more reliable.
 





Implementation of landmark-oriented spot pairing between two samples


The spot pairing algorithm is described  below.

The actual pairing is performed in two passes through the landmark
sets data called the primary and gelssecondary
pairing procedures. Each procedure operates on one landmark set at a
time.



In the primary pairing algorithm (figure
3), the spots are first mapped to the Cartesian coordinate system
defined by making the landmark spot (0,0) relative to the origin in
the two samples: Rsample (G1) and Sample (G2).  Each spot in G1 is
provisionaly paired to the spot that is its nearest neighbor in the
projected image of G2. Because of possible asymmetry of the two sets
the reverse comparison is also performed so that each spot in G2 is
provisionally paired with its nearest neighbor spot in Rsample. The
nearest neighbor distance is called dP (pair distance). The distance
dL is the distance from the landmark spot to the mean locus of the two
spots in the provisional pair. Two parameter distances are empirically
defined: dTsp and dTpp. Spots closer than dTsp are relatively well
paired. Spots greater than dT2 are very poorly paired and possibly
should not be paired. The default values of dTsp and dTpp (5 and 10
pixels respectively) were determined empirically, by examination of
the nearest neighbor values of several sets of paired samples under a
wide variety of conditions. Figure 4 shows various cases which can
occur. Four types of pairing labels can be assigned. There are sure
pair "SP", possible pair "PP", ambiguous pair "AP" and unresolved spot
"US". The primary spot pair labeling assignments are defined in figure
3.









A) Definition of DP - distance between spots









B) Definition of DL - distance between spot pair and landmark









C) Spot pairing rules







Figure 3. Spot pairing rules. 


Spot pairing is peformed using several features of landmarks and spots
in these landmark sets.  A) Shows the definition of dP or the
distance between spots of a spot pair mapped to the same space.
B) Shows the definition of dL or the distance from a landmark
to the spot pair mapped to the same space.  C) Spot pair
primary labeling assignment definitions. Each potential nearest
neighbor spot pair in a landmark set has one of four labels: SP - sure
pair, PP - possible pair, AP - ambiguous pair, US - unresolved
spot. Rk is the effective radius for a landmark set k.  The dTsp is
the threshold distance for SP spots -thrSP: value.  The dTpp is
the threshold distance for PP spots -thrPP: value.  primary pairing is described below.
The labeling cases are defined by the following cases:





       Case
	[1]  US  is unresolved spot (no dP) for either sample,
	[2]  SP  is dL2  <= Rk and dP2 <= dTsp,
	[3]  PP  is dL3  >= Rk and dP3 <= dTpp,
	[4]  PP  is dL4  <= Rk and dP4 >= dTsp and dP4 <= dTpp,
	[5]  PP  is dL5  >= Rk and dP5 <= dTsp,
	[6]  PP  is dL6  >= Rk and dP6 <= dTpp. For the other spot
	     AP' is dL6' >= Rk and dP6' <= dTpp and dP6' >= dP6.







Secondary spot pairing optimization


A second pass through the data is peformed to optimize the spot
pairing. Secondary spot pairing can be used to further resolve AP and
US labels in adjacent landmark sets into SP or PP labels which are
then placed in either of the two sets. There are four cases: (a) two
unresolved spots (US and US), (b) two ambiguous pairs (AP and AP),
(c-d) one ambiguous spot (AP) and one unresolved spot (US). The new
spot pair is upgraded to a SP or PP pairing label and is put into
whichever landmark set has the smallest dL for the putative pair. Each
landmark set is tested. Each spot has a list of adjacent landmarks, so
these are tested to see if pairing can be optimized for that spot. The
secondary pairing algorithm
is described below.









Secondary spot pairing rules 





Figure 4. Secondary spot-pairing rules. 


A second pass through the data is peformed to optimize the
pairing. Secondary spot pairing can be used to further resolve AP and
US labels in adjacent landmark sets into SP or PP labels which are
then placed in either of the two sets. There are four cases: (a) two
unresolved spots (US and US), (b) two ambiguous pairs (AP and AP),
(c-d) one ambiguous spot (AP) and one unresolved spot (US). The new
spot pair is upgraded to a SP or PP pairing label and is put into
whichever landmark set has the smallest dL for the putative pair. Each
landmark set is tested. Each spot has a list of adjacent landmarks, so
these are tested to see if pairing can be optimized for that spot.
 







Project directory structure for Open2Dprot and CmpSpots


All Open2Dprot programs assume a project directory structure. This
must exist for the program to proceed. You can either create the
structure prior to running any of the programs or you can create it on
the fly using the -projDir:user-project-directory. It will
lookup and/or create the following sub-directories inside of
theuser-project-directory.



    batch/ directory holding temporary batch files - [NOT USED by CmpSpots]
    cache/ directory holding temporary CSD cache files - [NOT USED by CmpSpots]
    ppx/ directory holding your original gel input files
    rdbms/ directory holding CSD database RDBMS files - [NOT USED by CmpSpots]
    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 CmpSpots




The use of these directories is discussed in the rest of this
document.






Input spot list files


The spot lists to be paired are specified by their sample names (e.g.,
plasma27).

The sample and reference samples to be paired is specified by its
image file name using the -sample and -rsample switches with or
without the file extension (e.g., -sample:plasma27.tif or
-sample:plasma27). The file extension is determined by looking up the
image in the ppx/ project subdirectory at run time.


 The application looks up the sample in the accession database (in
xml/accession.xml or as specified using the -accessionFile switch) and
gets additional information about the sample. The Open2Dprot

http://open2dprot.sourceforge.net/Accession pipeline module is 
used for entering samples into the accession database.


[Status: The Open2Dprot Accession module program is not released yet.
The accession database could be edited manually as either XML
(accession.xml), or tab-delimited text (accession.txt) with Excel.]


The samples correspond to Sample Spot-list Files (SSF) and should be
found in the user-project-directory/xml/ sub-directory.  The
SSF format is described in the Open2Dprot Seg2Dgel
program. SSF files may be used by CmpSpots as either XML or full
tab-delimited data formats.



There may be images associated with the samples that can be used with
the Image Viewer. This is the case if the spots were derived from real
images (e.g., 2D gels) or virtual images (e.g., from synthesized 2D
LC-MS data), etc. These images may be in TIFF (.tif, .tiff), JPEG
(.jpg), GIF (.gif), or PPX (.ppx GELLAB-II) format. TIFF images may be
8-bits/pixel through 16-bits/pixel, whereas JPEG, GIF, and PPX are
8-bit images. Gray values in the image files have black as 0. This is
mapped to 0 for white and the maximum pixel value for black.


The input sample image files, if any, are kept in the
user-project-directory/ppx/ sub-directory.  This database
directory structure is consistent with and is used by the other
Open2Dprot analysis pipeline programs.






Landmark database


A small (5 to 25 depending on the rubber-sheet distortion between
samples) set of corresponding landmark spots is required for the
Sample and Rsample. These are defined in a landmark database
(xml/landmark.xml) that is uses the same sample names as used in the
accession database.  The Open2Dprot

http://open2dprot.sourceforge.net/Landmark pipeline module is used
for defining landmark pairs for (Rsample, Sample) into the landmark
database.






Output paired-spot list file - the Sample Pairs File (SPF)


The CmpSpots output is a quantified paired-spot list in various ASCII
formats including XML and tab-delimited as well as the historical
GELLAB-II SPF formats.


The data output file is called the Sample Pairs File (SPF) and is
saved in the user-project-directory/xml/ directory.  The
generated name the same as the base name of the image file but with a
different extension depending on the output format. The possible
extensions are: .spf (for ASCII format compatible with GELLAB-II),
.xml (XML format), and .txt (tab-delimited format). One of these
formats are specified specified by the -spfFormat:{F | G
| T | X} command line switch.


[STATUS: -spfFormat:X is the default. Note that the XML
generated will change with changes in MIAPE.]





1.1 Investigating spot pairing using the paired-spot Image Viewer


Spot pairing may be investigated using the Image Viewer button
which pops up the Image Viewer window. This lets you select spots to
review the pairing data including the quantified spot data. You may
add overlays for (subsets of) pairing labels, pairing vectors,
landmarks names, landmarks radii. The current selected spot's landmark
may be used to filter the spots belonging to that landmark set. There
is also a pairing feature histogram that may be used for spot
filtering as well. There are four Image Viewer pull-down menus:

UL>

  •  File menu

  •  View menu

  •  Filter menu

  •  Histogram menu


    



    

    1.1.1 Image viewer - File menu
    

These commands are used to change the sample image being displayed.

 
    



    

    1.1.2 Image viewer - View menu
    

These commands are used to change the sample image overlays being
displayed.

 
    



    

    1.1.3 Image viewer - Filter menu
    

These commands are used to change the histogram filter.

 
    




    

    1.1.4 Image viewer - Histogram menu
    

These commands are used to change the histogram filtering criteria.

 
    
 


    

    2. CmpSpots spot pairing algorithm
    

The spot pairing algorithm is described in two parts. The first part
describes the global processing operations. The second part describes
individual spot pairing operations.
    


    Global processing algorithm
    


      

    1.  The program first loads a sample accession file that contains the
names of all samples in the database.
      


    2.  The program then loads the two sample SSF spot-list files after
verifying them with the accession database. One for the Reference
sample and one for the sample being paired. We refer to these as
"Rsample" and "Sample". 
      


    3. It then loads the set of landmarks for the (Rsample,Sample) pair
of samples.

      


    4. The landmark effective radii are computed by finding the distance
from each landmark to its closest landmark (for both the Rsample and
the Sample). Then a landmark's radius is estimated as 1/2 the minimum
of these minimum distances for that landmark (for Rsample and
Sample). [Spot pairs inside of this radius can become SP pairs,
otherwise they can only become at best PP pairs. This is not counting
AP pairs which can occure both inside and outside the radius.]
      


    5. The spots for each sample are assigned to their closest landmark
and the spots associated with each landmark are called its landmark
set. Each spot also tracks a list of next-nearest landmarks used in
secondary pairing.

      


    6.  For each landmark, spots in its associated landmark set are
optimally paired with spots in its corresponding landmark set in the
other sample.  Mutually-paired spots are assigned Sure-Pair (SP) and
Possible-Pair (PP) labels if distances (described below) are within
threshold ranges; The case of N:1 or 1:N paired spots between samples
are assigned Ambiguous-Pair (AP) labels (i.e., N spots in one sample
are optimally paired with 1 spot in the other sample);
Unresolved-Spots (US) are what remains.
      


    7. Secondary pairing is attempted for adjacent landmark sets. For
each landmark, we attempt to re-pair or pair spots as SP or PP or (AP
and US) with their next-best landmark set. If the pairing is better
than the current pairing, we move the spot and upgrade the pairing to
a SP or PP. The pairing quality labels are ordered as: SP > PP > (AP
or US).
      


    8.  Finally it writes out the paired-spot list in the format
specified by the -spfFormat switch option. If images are to be saved
in disk files, these are also written out at this time. 
      


    
         


    

    2.1 Spot pairing within a landmark set - algorithm
    

This describes the primary spot pairing within a given landmark
set j. This algorithm is applied for each landmark set in turn.  See
    Figure 3C which illustrates pairing
geometry for two spots in the same landmark set between the two
samples.  The decision rules use the pairing cases listed in that figures legend.
Note the symmetry of the algorithm is such that that each sample views
the other sample the same way.


      


    1.  For each spot i in the Rsample landmark set j set j find the spot
k in the Sample landmark set j with the smallest dP. Then note the dP
and Sample spot k in Rsample spot i.


    2.  For each spot i in the Sample landmark set j set j find the spot
k in the Rsample landmark set j with the smallest dP. Then note the dP
and Sample spot k in Sample spot i.


    3.  For each spot i in the Rsample landmark set j and its optimal
spot k in Sample landmark set j, apply the case rules and assign the
pairing label. Note: for a spot to be a SP or PP, both spots
must point to each other. If spot k does not point to spot i, then
assign a AP label. If dP is > the dTpp threshold, assign the US
label to spot i.


    4.  For each spot i in the Sample landmark set j and its optimal
spot k in Rample landmark set k, apply the case rules and assign the
pairing label. Note: since SP or PP spots were paired in the previous
step, we don't do it again - instead only look for spots that
do not point to each other. If spot k does not point to spot i, then
assign a AP label. If dP is > the dTpp threshold, assign the US
label to spot i.


     

Note: the Image viewer used with the -gui option lets the user
interactively investigate this data.
        
     

    

    2.2 Secondary Spot pairing - algorithm
    

This describes the secondary spot pairing. Secondary spot pairing is
used to further resolve AP and US labels in adjacent landmark sets
into PP labels that are then placed in either of the two sets. There
are four cases: (a) two unresolved spots (US and US), (b) two
ambiguous pairs (AP and AP), (c-d) one ambiguous spot (AP) and one
unresolved spot (US). The new spot pair is upgraded to a PP pairing
label and is put into whichever landmark set has the smallest dL for
the putative pair. The four cases are described in     Figure 4. This procedure is
applied to each landmark set in the Rsample and then each landmark set
in the Sample. Again, the algorithm is symmetric and is applied to
each sample for each landmark set.
    


      


    1.  For each spot i in the Rsample landmark set j that has a US or AP
pairing label, for all landmark sets m (such that j is not equals to
m) do a trail test or each spot k in the Sample that has a US or AP
label.  If the trial test has a minimum dP <= dTpp, then the two
spots are a candidate for secondary pairing.


    2.  Then pair the two spots i and k with a PP label and assign the
pair to either landmark set j or landmark set m - whichever has a
lower dL value. Remove the spot from the landmark set from which it
was removed.


    3.  For each spot i in the Sample landmark set j that has a US or AP
pairing label, for all landmark sets m (such that j is not equals to
m) do a trail test or each spot k in the Rample that has a US or AP
label.  If the trial test has a minimum dP <= dTpp, then the two
spots are a candidate for secondary pairing.


    4.  Then pair the two spots i and k with a PP label and assign the
pair to either landmark set j or landmark set m - whichever has a
lower dL value. Remove the spot from the landmark set from which it
was removed.


                  


    

    3. Running CmpSpots and specifying parameter options via the 
command line
    

The program may be run either interactively (-gui) with a graphical
user interface (GUI) or under an OS shell command to implement batch
(-nogui) depending on how it was started. In the former case, after
the spot pairing is finished, the user has the option of interactively
viewing the paired spot data using the Image Viewer.  The user may
also modify the input switch options and save the new options in a
"CmpSpots.properties" file in the current project directory so that it
may be used as the default switch options in subsequent running of the
program.

[Status: the CmpSpots.properties file is not enabled.]

All options including the input reference sample and other sample to
be paired are specified via GNU/Unix style switches on the command
line (-switch{optional ':parameters'} and its negation as
-noswitch). However, if GUI mode is used, you can interactively
specify the switches and their options. It is assigned previously by
software that generated the SSF spot lists.




    

    The computing window region of interest
    

The computing window is a rectangular region or interest in the SSF
spot list (real or virtual) image where data is considered to be
valid. Spots in this region should be paired.  Any spots outside of
this region are ignored.
    

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.]
    


    

    Local Folders and files created and used by CmpSpots
     

When CmpSpots is first started, it will check for the following folders
and files in the installation directory and create them if they can
not be found.



    

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.



    



    

    CmpSpots command-line arguments switch usage
    

The command line arguements usage is:

    
     CmpSpots -rsample:Reference-sample -sample:sample [< optional switches >]

    

The complete     list of switches is given
later in this manual and as well as some examples of typical sets of switches. The
user defined default switches may be specified as a resource string
'CmpSpots.properties' file saved in the project directory. For
example:


    
    CmpSpots -rsample:gel-HM-19 -sample:gel-HM-071 -thrSP:5 -thrPP:10 -project:demo/ -gui


    



    

    Options wizard window for setting the command line switches
    

If you invoke the Edit options button in the Report window (or
from the Edit menu), it will popup an options wizard shown in Figure 5
to let you set or change the switch options and then to save these as
the new default switch options. The default is saved in the
CmpSpots.properties file when you exit program.



    

    

    
Popup options wizard window

    

    

Figure 5. Screen view of the popup options wizard window for
setting the command line switches, parameter and specifying input
samples to be paired.

  All of the switches are available in the
scrollable window. Switches are checked if they are enabled and if the
switch requires a value, the current value is shown in the data entry
window to its right. On the right are several threshold sliders for
the the upper sizing values for several parameters including
-thrSP:dTsp, -thrPP:dTpp,
-latchLandmarkSpots:maxLatchDist, and
-altLandmarks:nbrAltLMs. In the middle, are several
Browse buttons to use for specifying a different samples
(-rsample: and -sample:), and directories.  Clicking on
any switch will show a short help message associated with that switch
at the top of the window. Pressing the Set new default button
will pass the new options values back to CmpSpots. Note: for this to
take effect, you must exit and then restart CmpSpots. Then to use
them, press the Pair spots button in the main Report Window.




    



    

    Updating CmpSpots from the Open2Dprot Web server using -update switch
    

As new versions of CmpSpots are developed and put on the Web server,
a more efficient way of updating your version is to use the -update
commands. There are four options:


    
        -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

    

After updating the program, it should be exited and restarted for the
new program to take effect. 
    



    

    Increasing the allowable memory used by CmpSpots
    

If you are working with very large images that require a lot of memory,
you might want to increase the memory available at startup.
    

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

    

However, if you are using the CmpSpots.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 CmpSpots.jar {additional command line args}

    

    

   

    

    4. Command and Report Window - the command center
    

CmpSpots is designed to be used efficiently in a batch mode with
minimal command line output. It is also designed to optionally provide
a graphical user interface (GUI) which creates a  Report Window that captures a report
of the spot pairing output as well as additional output directed to it
by the user. There are a set of pull-down
menus as well as a set of buttons for often used functions.
    

All logged output is sent to the report window in a scrollable text
window that may be saved or used for cut and paste operations.  A set
of command buttons at the bottom of the window are replicates of
commands in the menus, but are easier to access. They include the
following functions:
    


    



    

    5. Pull-down menus in the Graphical User Interface (GUI)
    


The menu bar a the top of the Report Window contains five menus.


      


    1. File menu - to open the samples to be
    paired and other file operations.


    2. Edit menu - to change various options
including command line switches, computing window, and memory size


    3. View menu - to invoke the image viewer
used to inspect the images after spot pairing


    4. Pair menu - to run the spot pairing on
your sample spot lists.


    5. Help menu - popup Web browser
     documentation on CmpSpots

    



    

    Menu notation
    

In the following menus, selections that are sub-menus are
indicated by a 'Indicates that the
menu has a submenu'.  Selections prefaced with a 'Checkbox on' and indicate 'Checkbox off' indicate that the command is a checkbox
that is enabled and disabled respectively.  Selections prefaced with a
'Radio button on' and indicate 'Radio button off' indicate that the command is a
multiple choice "radio button" that is enabled and disabled
respectively, and that only one member of the group is allowed to be
on at a time. The default values set for an initial database are shown
in the menus.  Selections that are not currently available will be
grayed out in the menus of the running program. The command short-cut
notation C-key means to hold the Control key and then
press the specified key.

    



    

    5.1 File menu
    

These commands are used to open the samples to be paired and other
file operations. The current menus and the menu commands (non-working
commands have a '*' prefix) are listed below. You can use either the
"Edit options" button to popup the Options Window editor to change the
input samples or the (File menu | Open Rsample) and (File
menu | Open Sample) commands.
    


 
    



    

    5.2 Edit menu
     

These commands are used to change various defaults. These are saved
when you save the state and when you exit the program.


    




    

    5.3 View menu
     

This menu contains commands to invoke the image viewer used to inspect
the images after spot pairing.

 



    

    5.4 Pair menu
     

This menu is used to run the spot pairing to perform the
analysis. These commands also appear as command buttons at the bottom
of the Report Window.



    



    

    5.5 Help menu
     

These commands are used to invoke popup Web browser documentation on
CmpSpots. Some of the commands will load local documentation in the
the GUI report window.
    

The documentation is kept on the Internet at 
http://open2dprot.sourceforge.net/CmpSpots. Normally, these help
commands should pop up a Web browser that directly points to the
CmpSpots Web page.  If your browser is not configured correctly, it
may not be able to be launched directly from the CmpSpots
program. Instead, just go to the Web site with your Web browser and
look up the information there.


    


    
  


    

    6. Downloading, installing and running CmpSpots
    

The installation packages are available for 

download from the SourceForge Files mirror. Look for the most 
recent release named "CmpSpots-dist-V.XX.XX.zip". These releases include 
the program (both as Windows .exe file and a .jar file), required jar 
libraries, demo data, Windows batch and Unix 
shell scripts. Download the zip file and put the contents where you want 
to install the program. Note that there is a CmpSpots.exe
(for Windows program). You might make a short-cut to this to use in more easily
starting the program. Alternatively, you can use the sample .bat and .sh scripts
to run the program explicitly via the java interpreter. Note that this method
assumes that you have Java installed on your computer and that it is at 
least JDK (Java Development Kit) or JRE (Java Runtime Environment) 
version 1.5.0. If you don't have this, you can download the latest version free 
from the java.sun.com Website.

    



    

    6.3 Running CmpSpots
    

There are several ways to run the program. On Windows, you can start 
CmpSpots by clicking on the startup icon shown in Figure 6 below. 
For Unix systems including MacOS-X, you can start CmpSpots from
the command line by running the CmpSpots.jar file. If your computer is setup
to execute jar files, just type the jar file. In both systems, you can specify
additional command line arguments in Windows .bat and unix .sh scripts (see 
demo examples below.
    


    

    

    
CmpSpots startup icon

    

    

Figure 6. Startup icon for CmpSpots.exe in Windows.  
Clicking on the icon starts CmpSpots. To start CmpSpots, click on the startup 
icon shown in Figure 6 below - or  you can run the demo-CmpSpots.bat 
script. For Unix systems including MacOS-X, you can start CmpSpots from the 
command line by clicking on the CmpSpots.jar file or using the 
demo-CmpSpots.sh script. These two scripts run the program in batch.
There are also GUI versions of the two scripts demo-CmpSpots-GUI.bat
and demo-CmpSpots-GUI.bat that will pop up a user interface.
You could make short-cuts (Windows) or symbolic-links in Unix to make it 
easier to start.


    



    

    6.4 Requirements: minimum hardware and software requirements
    

A Windows PC, MacIntosh with MacOS-X, a Linux computer or a Sun
Solaris computer having a display resolution of at least
1024x768.  We find that a 1024x768 is adequate, but a 1280x1024 screen
size much better since you can see the Popup Report window, Options
window, and Image Viewer window at the same time. At least 30 Mb of
memory available for the application is required and more is desirable
for comparing large images or performing transforms. If there is not
enough memory, it will be unable to load the images, the transforms
may crash the program or other problems may occur.
    

An Internet connection is required to download the program from the
Open2Dprot CmpSpots Web site. New versions of the program and
associated demo data will become available on this Web site and can be
uploaded to your computer using the various
(File | Update | ...) menu commands. We currently distribute CmpSpots 
so that it uses up to 256Mb. See discussion on 
increasing memory.
    


    

    6.5 Files included in the download
    

The following files are packaged in the distribution you install. 
you can periodically a (File | Update from Web server | ...
program) menu command to update the files from the open2dprot.sourceforge.net
Web server. 
    


    



    

    7. List of the command line switches
    

The command line usage is:

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

    

where the order of arguments is not relevant. In the following list,
items in bold are specific values which must be used (e.g., for
-spfFormat:{X | F | T | G}, whereas
variable values in italics indicate that a numeric value for
that variable should be used (e.g., for -thrSP:t1threshold it
might be -thrSP:5). Some switches have several alternate fixed choices
in which case this indicated as a list of bolded items inside of a set
of '{...}' with '|' separating the items.  You must pick one of the
items and do not include the '{}' brackets. Also, do NOT include any
extra spaces in the arguments of the switch - it will be counted as if
it were another switch.


    Command line switches
    


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

-altLandmarks:NbrOfLandmarkSets specifies the number of alternate
      landmarks to check. (Default is -altLandmarks:3).


-commutativeLMS lets you search the landmark database for sample pairs
      where the Rsample and Sample are swapped. (Default is
      -commutativeLMS).

-csamplePrimeData indicates that the SSF data are canonical Csample'
      data created from replicate samples in the Composite Sample
      Database (CSD).  (Default is -nocsamplePrimeData).

-debugBits:bits,optLandmarkNbr dumps various conditional
      debugging parameters onto the report window as well as the
      output SPF file. The debugging is active for all landmarks
      unless optLandmarkNbr is specified.  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
          -thrSP:5 -thrPP:10 -inputFormat:X,X,X
      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. This captures messages from CmpSpots.
      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).

-histGUI will bring the the dynamic histogram graphical user interface 
      when the Image Viewer is requested. (Default is -histGUI).

-inputFormat:ssfMode,accMode,lmsMode defines the input formats
      for the Sample Spot-list File (ssfMode), accession database file
      (accMode), and landmark database file (lmsMode). Where mode is:
      F for full tab-delimited data that includes the 3 files:
      list of spots, parameters, and statistics.  The T for
      tab-delimited (.txt) data, and X for XML (.xml)
      data. (Default is -noinputFormat:X,T,T).

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

-latchLandmarkSpots:maxLatchDist is the maximum distance to use
       when trying to latch a landmark to its closest spot. (Default
       is -nolatchLandmarkSpots:6).

-percentDensity to output percent density instead of OD values.
       (Default is -nopercentDensity).

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

-rsample: is the reference sample.

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

-spfFormat:{F | G | T | X} defines the output format for the
       Sample Pairs File (SPF) where mode is: F for full
       tab-delimited data that includes the list of spots but also the
       same information as the G format), G for
       GELLAB-II (.spf), T for tab-delimited (.txt) spots-only,
       and X for XML (.xml).  (Default is -spfFormat:X). The
       Open2Dprot-SPF.dtd file is included only if -dtd switch is set.

-secondaryPairing to perform secondary pairing. (Default is
      -secondaryPairing).

-ssfCW:x1,x2,y1,y2 to ignore spots outside of this window for
       both SSF input files. This is a debugging tool. (Default is
       -nossfCW).

-thrSP:dTsp specifies the minimum distance thresholdbetween
       paired spots for them to be considered a Sure-Pair.  (Default
       is -thrSP:5).

-thrPP:dTpp specifies the minimum distance threshold between
       paired spots for them to be considered a Possible-Pair.
       (Default is -thrPP:10).

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

-unCorrectedDensity use uncorrected density in the pairing output.
       (Default is -nounCorrectedDensity).

-update:{all | program | demo | doc} specifies that all of the
       CmpSpots 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).


    

    



    

    7.1 Examples of some typical sets of switches
    


    
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:

     CmpSpots input-sample-image-file [< opt.-switches >]

The following examples using switches might be useful:
     

     CmpSpots -rsample:gel-HM-019 -sample:gel-HM-071 -nogui -project:demo/
  # Pair two samples into a SPF file using "-spfFormat:X" XML format.
  # This is what is normally used in batch mode

     CmpSpots -rsample:gel-HM-019 -sample:gel-HM-071 -gui -project:demo/
  # Pair two samples into a SPF file, popup up Report window and then
  # use may pop up Image viewer to display sample images with paired spot
  # overlays including spot labels, vectors and landmark sets

     CmpSpots -rsample:gel-HM-019 -sample:gel-HM-071 -spfFormat:G 
              -project:demo/
  # Pair two samples into a SPF file using the GELLAB format.

     CmpSpots -rsample:gel-HM-019 -sample:gel-HM-071 -thrSP:10 -thrPP:20 \
               -altNbrLMs:2 -project:demo/
  # Pair two samples as above, but use new thresholds thrSP, thrPP and
               the alternate number of landmarks.


    

    



    

    7.2 Debug option bits for the -debug switch
    

The following are the orthogonal octal -debug option code bits.  This
means you can add them together (in octal) and use that computed octal
number (it will also accept decimal). The
-debug:bits,landmarkNbr option is meant only for serious
programmers reading or modifying the source code.


    

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 =  assignCodes()
bit:            02 =  assignSSFtoLMS()
bit:            04 =  computeRadii()
bit:           020 =  dumpSPF()
bit:           040 =  findLMSinSSFs()
bit:          0100 =  switchAnalysis()
bit:          0200 =  initialSpotPairing() and convolveG1G2spots()
bit:          0400 =  -free-
bit:         01000 =  printAt()
bit:         02000 =  cvtLMsetSpotsToStr()
bit:         04000 =  cvprintSpot()
bit:        010000 =  -free-
bit:        020000 =  readSSFdata()
bit:        040000 =  readLandmarks()
bit:       0100000=   secondarySpotPairing()
bit:       0200000 =  main()
bit:       0400000 =  dumpLMsetSpots()
bit:      01000000 =  dumpSPFpreface() and dumpStatisticsToSPFfile 
=======================================================================


    


    

    8. Demonstrations
    

 
    *** BEING REWRITTEN ***
    


    

    8.1 Examples - samples of screen shots
    

To give the flavor of running the spot pairing program, we provide a
few screen shots of the graphical user interfaces and some images
generated by the program. 
    

You can these images in the list below or  view all of the screen shots in a
single Web page.
    


    

    


    

    8.2 Example - output of the Report Window for a spot pairing
    

The following Report Window output was generate for the images in the
above example.


    
CmpSpots V.0.0.4-pre-Alpha - $Date$ - $Revision$ (Open2Dprot)
Today's date is 08/04/04 14:37:34
Switches:  -thrSP:5 -thrPP:10 -projDir:demo/ -rsample:gel-HM-019
           -sample:gel-HM-071 -gui -spfFormat:X,T,T -spfFormat:G

CmpSpots V.0.0.4-pre-Alpha - $Date$ - $Revision$ (Open2Dprot)
Today's date is 08/04/04 14:37:34
Sample Pairs File is: demo\xml\gel-HM-071.spf from gel-HM-019 and gel-HM-071
Distance sizing limits: dT1= 5.00, dT2= 10.00

Switches:  -thrSP:5 -thrPP:10 -projDir:demo/ -rsample:gel-HM-019 -sample:gel-HM-071 -gui -spfFormat:X,T,T -spfFormat:G
Reading accession database file: demo\xml\accession.txt
Reading landmark database file: demo\xml\landmark.txt
Reading Rsample file: demo\xml\gel-HM-019.xml
Reading Sample file: demo\xml\gel-HM-071.xml
Spot lists parameters and statistics
------------------------------------
Rsample Window [14:475,74:505] (pixels) [rows,cols]=[512,512] PixelSizeMicrons=0.00
NbrSpots=2015 NbrSpotsPrime=933 NbrSpotsOmitted= 1082
TotSampleDensity=61294.00 TotSampleDensityPrime=13292.00 TotOmittedDensity=119.40
TotSampleArea=11752 TotSampleAreaPrime=76350 TotSampleAreaOmitted=23119

Sample Window [14:475,74:505] (pixels) [rows,cols]=[512,512] PixelSizeMicrons=0.00
NbrSpots=2143 NbrSpotsPrime=2143 NbrSpotsOmitted= 0
TotSampleDensity=69184.00 TotSampleDensityPrime=37056.90 TotOmittedDensity=0.00
TotSampleArea=24976 TotSampleAreaPrime=138368 TotSampleAreaOmitted=0

Sample pairs threshold sizing parameters
----------------------------------------
Threshold Sure-Pair (SP) sizing limit, thrSP: 5.0 (pixels)
Threshold Possible-Pair (PP) sizing limit, thrPP: 10.0 (pixels)
Number of alternate landmark sets to check: 1

Summary: of paired-spot statistics
----------------------------------
Rsample has 933, Sample 2143 spots in all landmark sets.
After Initial pairing:
  US 853
  SP 242
  PP 1028
  AP 792
  CP 0
  EP 0
0.5(SP+PP)/(|G1| MIN |G2|)=68.06%

After secondary pairing:
  US 834
  SP 242
  PP 1082
  AP 757
  CP 0
  EP 0

After secondary pairing: 0.5(SP+PP)/(|G1| MIN |G2|)=71.0%
mean dP(SP+PP)=4.66, mean dP'((|G1|+|G2|)/(SP+PP))=8.39

List of image files and generated files
---------------------------------------
Input Rsample pix file  [demo\ppx\gel-HM-019.gif]
Input Sample pix file   [demo\ppx\gel-HM-071.gif]
Input Rsample SSF file  [demo\xml\gel-HM-019.xml]
Input Sample SSF file   [demo\xml\gel-HM-071.xml]
Output SPF file         [demo\xml\gel-HM-071.spf]

FINISHED! The Sample Pairs File (SPF), is demo\xml\gel-HM-071.spf
Run time =0:0:3 (H:M:S) or 3.1 seconds

Finished pairing gel-HM-019 with gel-HM-071.
Output SPF: demo\xml\gel-HM-071.spf


    

    




    

    8.3 Examples - part of Sample Pairs File XML format 
    

This is part of a Sample Pairs File to illustrate the type of data
available as output. This used the default -spfFormat:X option
with the XML DTD file Open2Dprot-SPF.dtd.

    


    

Open2Dprot-SPF.dtd (if -dtd switch used), else

<?xml version="1.0" ?>
<SpotList_Pairing>
<Pairing_parameters>
 <date>"05/10/05 11:18:32"</date>
 <Open2Dprot_SPF_Version>"1.5"</Open2Dprot_SPF_Version>
 <Project_directory>"demo\"</Project_directory>
 <Sample_Pairs_File>"gel-HM-071-SPF.xml"</Sample_Pairs_File>
 <thrSP_threshold>5.0</thrSP_threshold>
 <thrPP_threshold>10.0</thrPP_threshold>
 <nbrAltLandmarks>1</nbrAltLandmarks>
 <nbrLandmarks>22</nbrLandmarks>

 <Rsample>
   <Sample_Type>"Rsample"</Sample_Type>
   <Sample_Name>"gel-HM-019"</Sample_Name>
   <Simple_FileName>"gel-HM-019.gif"</Simple_FileName>
   <Sample_Pix_FileName>"demo\ppx\gel-HM-019.gif"</Sample_Pix_FileName>
   <Sample_SSF_FileName>"demo\xml\gel-HM-019-SSF.xml"</Sample_SSF_FileName>
   <cwx1>14</cwx1>
   <cwx2>475</cwx2>
   <cwy1>74</cwy1>
   <cwy2>509</cwy2>
   <Pix_Height>512</Pix_Height>
   <Pix_Width>512</Pix_Width>
   <PixelSizeMicrons>0.00</PixelSizeMicrons>
   <NbrSpots>1588</NbrSpots>
   <NbrSpotsPrime>738</NbrSpotsPrime>
   <NbrSpotsOmitted>850</NbrSpotsOmitted>
   <TotSampleDensity>8838.70</TotSampleDensity>
   <TotSampleDensityPrime>5670.40</TotSampleDensityPrime>
   <TotOmittedDensity>91.90</TotOmittedDensity>
   <TotSampleArea>36158</TotSampleArea>
   <TotSampleAreaPrime>23019</TotSampleAreaPrime>
   <TotSampleAreaOmitted>13139</TotSampleAreaOmitted>
   <PctOmittedToDprimeAcceptedSpots>1.62   </PctOmittedToDprimeAcceptedSpots>
   <Nbr_Spots_Failing_Area_Sizing>
     <nbr_below_t1Area_thr>3316     </nbr_below_t1Area_thr>
     <nbr_above_t2Area_thr>0     </nbr_above_t2Area_thr>
     <nbr_below_t1Density_thr>4214     </nbr_below_t1Density_thr>
     <nbr_above_t2Density_thr>0     </nbr_above_t2Density_thr>
     <nbr_below_t1Range_thr>0     </nbr_below_t1Range_thr>
     <nbr_above_t2Range_thr>0     </nbr_above_t2Range_thr>
  </Nbr_Spots_Failing_Area_Sizing>
</Rsample>

 <Sample>
   <Sample_Type>"Sample"</Sample_Type>
   <Sample_Name>"gel-HM-071"</Sample_Name>
   <Simple_FileName>"gel-HM-071.gif"</Simple_FileName>
   <Sample_Pix_FileName>"demo\ppx\gel-HM-071.gif"</Sample_Pix_FileName>
   <Sample_SSF_FileName>"demo\xml\gel-HM-071-SSF.xml"</Sample_SSF_FileName>
   <cwx1>6</cwx1>
   <cwx2>450</cwx2>
   <cwy1>68</cwy1>
   <cwy2>503</cwy2>
   <Pix_Height>512</Pix_Height>
   <Pix_Width>512</Pix_Width>
   <PixelSizeMicrons>0.00</PixelSizeMicrons>
   <NbrSpots>3059</NbrSpots>
   <NbrSpotsPrime>1590</NbrSpotsPrime>
   <NbrSpotsOmitted>1469</NbrSpotsOmitted>
   <TotSampleDensity>31534.10</TotSampleDensity>
   <TotSampleDensityPrime>23052.90</TotSampleDensityPrime>
   <TotOmittedDensity>131.30</TotOmittedDensity>
   <TotSampleArea>80117</TotSampleArea>
   <TotSampleAreaPrime>51342</TotSampleAreaPrime>
   <TotSampleAreaOmitted>25905</TotSampleAreaOmitted>
   <PctOmittedToDprimeAcceptedSpots>0.5694   </PctOmittedToDprimeAcceptedSpots>
   <Nbr_Spots_Failing_Area_Sizing>
     <nbr_below_t1Area_thr>2567     </nbr_below_t1Area_thr>
     <nbr_above_t2Area_thr>0     </nbr_above_t2Area_thr>
     <nbr_below_t1Density_thr>4107     </nbr_below_t1Density_thr>
     <nbr_above_t2Density_thr>0     </nbr_above_t2Density_thr>
     <nbr_below_t1Range_thr>0     </nbr_below_t1Range_thr>
     <nbr_above_t2Range_thr>0     </nbr_above_t2Range_thr>
  </Nbr_Spots_Failing_Area_Sizing>
</Sample>
</Pairing_parameters>

  <Paired_Spot>
    <LandmarkSet>A</LandmarkSet>
    <R_spotNbr>188</R_spotNbr>
    <R_dxLM>-2</R_dxLM>
    <R_dyLM>-25</R_dyLM>
    <R_xC>207.0</R_xC>
    <R_yC>166.0</R_yC>
    <R_merX1>205</R_merX1>
    <R_merX2>210</R_merX2>
    <R_merY1>163</R_merY1>
    <R_merY2>168</R_merY2>
    <S_spotNbr>759</S_spotNbr>
    <S_dxLM>-2</S_dxLM>
    <S_dyLM>-25</S_dyLM>
    <S_xC>226.0</S_xC>
    <S_yC>166.0</S_yC>
    <S_merX1>224</S_merX1>
    <S_merX2>229</S_merX2>
    <S_merY1>152</S_merY1>
    <S_merY2>158</S_merY2>
    <PairingCode>P</PairingCode>
    <DP>3.0</DP>
    <DL>25.1</DL>
    <R_area>18</R_area>
    <S_area>25</S_area>
    <R_dens>1.560</R_dens>
    <S_dens>8.352</S_dens>
    <R_dPrime>0.826</R_dPrime>
    <S_dPrime>3.515</S_dPrime>
    <R_volume>1.347</R_volume>
    <S_volume>6.484</S_volume>
    <R_MaxDens>0.132</R_MaxDens>
    <S_MaxDens>0.480</S_MaxDens>
    <R_MinDens>0.043</R_MinDens>
    <S_MinDens>0.225</S_MinDens>
    <R_MeanBkgDens>0.041</R_MeanBkgDens>
    <S_MeanBkgDens>0.193</S_MeanBkgDens>
    <R_stdDev_X>1.229</R_stdDev_X>
    <R_stdDev_Y>1.173</R_stdDev_Y>
    <S_stdDev_X>1.292</S_stdDev_X>
    <S_stdDev_Y>1.473</S_stdDev_Y>
  </Paired_Spot>
  <Paired_Spot>
    <LandmarkSet>A</LandmarkSet>
    <R_spotNbr>190</R_spotNbr>
    <R_dxLM>-7</R_dxLM>
    <R_dyLM>-24</R_dyLM>
    <R_xC>202.0</R_xC>
    <R_yC>167.0</R_yC>
    <R_merX1>201</R_merX1>
    <R_merX2>203</R_merX2>
    <R_merY1>164</R_merY1>
    <R_merY2>169</R_merY2>
    <S_spotNbr>759</S_spotNbr>
    <S_dxLM>-2</S_dxLM>
    <S_dyLM>-24</S_dyLM>
    <S_xC>226.0</S_xC>
    <S_yC>167.0</S_yC>
    <S_merX1>224</S_merX1>
    <S_merX2>229</S_merX2>
    <S_merY1>152</S_merY1>
    <S_merY2>158</S_merY2>
    <PairingCode>A</PairingCode>
    <DP>5.4</DP>
    <DL>25.0</DL>
    <R_area>11</R_area>
    <S_area>25</S_area>
    <R_dens>1.470</R_dens>
    <S_dens>8.352</S_dens>
    <R_dPrime>0.961</R_dPrime>
    <S_dPrime>3.515</S_dPrime>
    <R_volume>1.125</R_volume>
    <S_volume>6.484</S_volume>
    <R_MaxDens>0.186</R_MaxDens>
    <S_MaxDens>0.480</S_MaxDens>
    <R_MinDens>0.043</R_MinDens>
    <S_MinDens>0.225</S_MinDens>
    <R_MeanBkgDens>0.046</R_MeanBkgDens>
    <S_MeanBkgDens>0.193</S_MeanBkgDens>
    <R_stdDev_X>0.704</R_stdDev_X>
    <R_stdDev_Y>1.209</R_stdDev_Y>
    <S_stdDev_X>1.292</S_stdDev_X>
    <S_stdDev_Y>1.473</S_stdDev_Y>
  </Paired_Spot>
     
     . . .

  <Paired_Spot>
    <LandmarkSet>V</LandmarkSet>
    <R_spotNbr>0</R_spotNbr>
    <R_dxLM>0</R_dxLM>
    <R_dyLM>0</R_dyLM>
    <R_xC>0.0</R_xC>
    <R_yC>0.0</R_yC>
    <R_merX1>0</R_merX1>
    <R_merX2>0</R_merX2>
    <R_merY1>0</R_merY1>
    <R_merY2>0</R_merY2>
    <S_spotNbr>1422</S_spotNbr>
    <S_dxLM>159</S_dxLM>
    <S_dyLM>0</S_dyLM>
    <S_xC>446.0</S_xC>
    <S_yC>0.0</S_yC>
    <S_merX1>441</S_merX1>
    <S_merX2>448</S_merX2>
    <S_merY1>493</S_merY1>
    <S_merY2>499</S_merY2>
    <PairingCode>U</PairingCode>
    <DP>166.5</DP>
    <DL>166.5</DL>
    <R_area>0</R_area>
    <S_area>33</S_area>
    <R_dens>0.000</R_dens>
    <S_dens>0.630</S_dens>
    <R_dPrime>0.000</R_dPrime>
    <S_dPrime>0.395</S_dPrime>
    <R_volume>0.000</R_volume>
    <S_volume>0.601</S_volume>
    <R_MaxDens>0.000</R_MaxDens>
    <S_MaxDens>0.041</S_MaxDens>
    <R_MinDens>0.000</R_MinDens>
    <S_MinDens>0.000</S_MinDens>
    <R_MeanBkgDens>0.000</R_MeanBkgDens>
    <S_MeanBkgDens>0.007</S_MeanBkgDens>
    <R_stdDev_X>0.000</R_stdDev_X>
    <R_stdDev_Y>0.000</R_stdDev_Y>
    <S_stdDev_X>1.512</S_stdDev_X>
    <S_stdDev_Y>1.365</S_stdDev_Y>
  </Paired_Spot>

<Global_Spot_pairing_statistics>
 <NbrRsampleSpotsInLMS>738</NbrRsampleSpotsInLMS>
 <NbrSampleSpotsInLMS>1427</NbrSampleSpotsInLMS>

 <Landmark_set_sizes>
   <Landmark>
     <Landmark_name>A</Landmark_name>
     <Landmark_nbr>1</Landmark_nbr>
     <Nbr_Rsample_spots>12</Nbr_Rsample_spots>
     <Nbr_Sample_spots>18</Nbr_Sample_spots>
   </Landmark>
   <Landmark>
     <Landmark_name>B</Landmark_name>
     <Landmark_nbr>2</Landmark_nbr>
     <Nbr_Rsample_spots>34</Nbr_Rsample_spots>
     <Nbr_Sample_spots>77</Nbr_Sample_spots>
   </Landmark>

    . . .

   <Landmark>
     <Landmark_name>V</Landmark_name>
     <Landmark_nbr>22</Landmark_nbr>
     <Nbr_Rsample_spots>39</Nbr_Rsample_spots>
     <Nbr_Sample_spots>93</Nbr_Sample_spots>
   </Landmark>
 </Landmark_set_sizes>

 <InitialpairingStats>
   <Nbr_US_spotsPri>608</Nbr_US_spotsPri>
   <Nbr_SP_spotsPri>230</Nbr_SP_spotsPri>
   <Nbr_PP_spotsPri>764</Nbr_PP_spotsPri>
   <Nbr_AP_spotsPri>563</Nbr_AP_spotsPri>
   <Nbr_CP_spotsPri>0</Nbr_CP_spotsPri>
   <Nbr_EP_spotsPri>0</Nbr_EP_spotsPri>
 </InitialpairingStats>

 <SecondarypairingStats>
   <Nbr_US_spotsSec>594</Nbr_US_spotsSec>
   <Nbr_SP_spotsSec>230</Nbr_SP_spotsSec>
   <Nbr_PP_spotsSec>810</Nbr_PP_spotsSec>
   <Nbr_AP_spotsSec>531</Nbr_AP_spotsSec>
   <Nbr_CP_spotsSec>0</Nbr_CP_spotsSec>
   <Nbr_EP_spotsSec>0</Nbr_EP_spotsSec>
 </SecondarypairingStats>
 <Primary_SP_PP_pairRate>67.3</Primary_SP_PP_pairRate>
 <Secondary_SP_PP_pairRate>70.5</Secondary_SP_PP_pairRate>
 <meanDP_SP_PP>10.9</meanDP_SP_PP>
 <meanDPprime_SP_PP>17.6</meanDPprime_SP_PP>
</Global_Spot_pairing_statistics>
</SpotList_Pairing>


    

    


    

    8.4 Examples - part of Sample Pairs File GELLAB-II format 
    

This is part of a Sample Pairs File to illustrate the type of data
available as output. This used the default -spfFormat:X option.


    
CmpSpots V.0.1.0-pre-Alpha - $Date$ - $Revision$ (Open2Dprot)
Input Rsample file: gel-HM-019.gif
Input Sample file: gel-HM-071.gif
Output Sample Pairs File: demo\xml\gel-HM-071.spf

Spot lists parameters and statistics
------------------------------------
Rsample Window [14:475,74:509] (pixels) [rows,cols]=[512,512] PixelSizeMicrons=0.00
NbrSpots=3072 NbrSpotsPrime=1717 NbrSpotsOmitted= 1355
TotSampleDensity=80411.00 TotSampleDensityPrime=26247.40 TotOmittedDensity=121.00
TotSampleArea=29974 TotSampleAreaPrime=55093 TotSampleAreaOmitted=22282

Sample Window [6:450,68:503] (pixels) [rows,cols]=[512,512] PixelSizeMicrons=0.00
NbrSpots=1484 NbrSpotsPrime=864 NbrSpotsOmitted= 620
TotSampleDensity=44242.00 TotSampleDensityPrime=16980.60 TotOmittedDensity=50.80
TotSampleArea=21961 TotSampleAreaPrime=33078 TotSampleAreaOmitted=11164

Sample pairs threshold sizing parameters
----------------------------------------
Threshold Sure-Pair (SP) sizing limit, thrSP: 5.0 (pixels)
Threshold Possible-Pair (PP) sizing limit, thrPP: 10.0 (pixels)
Number of alternate landmark sets to check: 1

Switches:  -noaccessionFile:accession.xml -noaltLandmarks:1 -nocommutativeLMS
           -nocsamplePrimeData -nodebugBits:0,0 -nodefault -demo
           -nodtd -histGUI -inputFormat:X,X,X -nolandmarkFile:landmark.xml
           -latchLandmarkSpots:6.0 -nopercentDensity -noprojDir:demo\
           -nopropertiesFile:CmpSpots.properties -rsample:gel-HM-019
           -sample:gel-HM-071 -spfFormat:G -secondaryPairing -nossfCW:0,0,0,0
           -thrSP:5.00 -thrPP:10.00 -notimer -nounCorrectedDensity
           -noupdate:program

#A R:209 d(xy)LM1[-2,-26] (xy)C1[205.0,164.0]  MER1[202:208,162:167] S:178 d(xy)LM2[-2,-28] (xy)C2[225.0,148.0]  MER2[222:228,147:151]P dP=2.0,dL=28.131area1 22area2 9.190D1gray 5.495D1gray 7.870D'1 1.238D'2 7.756V'1 4.037V'2 0.540Maxd1 0.325Maxd2 0.070MinD1 0.122MinD2 1.348sX1 1.517sX2 1.503sY1 1.155sY2 0.00sdMX,0.00sdMY,0.00sdMD0.00sdMA,0#G,0.043MnBk1 0.193MnBk2
#A R:197 d(xy)LM1[6,-20] (xy)C1[233.0,156.0]  MER1[209:213,164:168] S:219 d(xy)LM2[4,-24] (xy)C2[211.0,166.0]  MER2[230:236,153:160]A dP=4.5,dL=24.343area1 15area2 14.598D1gray 5.336D1gray 7.120D'1 4.780D'2 11.566V'1 3.308V'2 0.540Maxd1 0.376Maxd2 0.174MinD1 0.275MinD2 1.685sX1 1.244sX2 1.792sY1 0.997sY2 0.00sdMX,0.00sdMY,0.00sdMD0.00sdMA,0#G,0.174MnBk1 0.037MnBk2
#A R:233 d(xy)LM1[-1,-19] (xy)C1[206.0,171.0]  MER1[203:208,168:175] S:196 d(xy)LM2[-1,-21] (xy)C2[226.0,155.0]  MER2[224:229,152:158]P dP=2.0,dL=21.034area1 25area2 10.213D1gray 8.352D1gray 8.702D'1 3.515D'2 8.683V'1 6.484V'2 0.480Maxd1 0.480Maxd2 0.122MinD1 0.225MinD2 1.433sX1 1.292sX2 1.779sY1 1.473sY2 0.00sdMX,0.00sdMY,0.00sdMD0.00sdMA,0#G,0.044MnBk1 0.193MnBk2
#A R:234 d(xy)LM1[6,-18] (xy)C1[213.0,172.0]  MER1[209:219,168:176] S:197 d(xy)LM2[6,-20] (xy)C2[233.0,156.0]  MER2[230:236,153:160]P dP=2.0,dL=20.946area1 43area2 18.568D1gray 14.598D1gray 16.779D'1 7.120D'2 17.748V'1 11.566V'2 0.540Maxd1 0.540Maxd2 0.325MinD1 0.174MinD2 2.545sX1 1.685sX2 1.822sY1 1.792sY2 0.00sdMX,0.00sdMY,0.00sdMD0.00sdMA,0#G,0.039MnBk1 0.174MnBk2
#A R:252 d(xy)LM1[9,-13] (xy)C1[216.0,177.0]  MER1[213:219,175:178] S:217 d(xy)LM2[7,-12] (xy)C2[234.0,164.0]  MER2[231:237,161:167]P dP=2.2,dL=15.821area1 37area2 15.298D1gray 9.663D1gray 14.365D'1 0.876D'2 12.723V'1 7.212V'2 1.164Maxd1 0.376Maxd2 0.480MinD1 0.122MinD2 1.570sX1 1.650sX2 0.981sY1 1.639sY2 0.00sdMX,0.00sdMY,0.00sdMD0.00sdMA,0#G,0.044MnBk1 0.237MnBk2

. . .

#A R:278 d(xy)LM1[6,13] (xy)C1[233.0,189.0]  MER1[212:221,203:213] S:1111 d(xy)LM2[9,18] (xy)C2[216.0,208.0]  MER2[229:238,185:193]A dP=5.8,dL=20.161area1 64area2 56.456D1gray 15.077D1gray 34.708D'1 10.568D'2 50.597V'1 12.561V'2 1.700Maxd1 0.396Maxd2 0.174MinD1 0.077MinD2 2.089sX1 1.835sX2 2.009sY1 2.441sY2 0.00sdMX,0.00sdMY,0.00sdMD0.00sdMA,0#G,0.357MnBk1 0.070MnBk2
#A R:223 d(xy)LM1[0,-12] (xy)C1[227.0,164.0]  MER1[224:229,160:165] S:223 d(xy)LM2[20,-26] (xy)C2[227.0,164.0]  MER2[224:229,160:165]A dP=5.8,dL=12.016area1 16area2 6.412D1gray 6.412D1gray 2.112D'1 2.112D'2 7.021V'1 7.021V'2 0.540Maxd1 0.540Maxd2 0.225MinD1 0.225MinD2 1.435sX1 1.435sX2 1.278sY1 1.278sY2 0.00sdMX,0.00sdMY,0.00sdMD0.00sdMA,0#G,0.269MnBk1 0.269MnBk2
#A R:266 d(xy)LM1[23,4] (xy)C1[250.0,180.0]  MER1[246:252,177:183] S:266 d(xy)LM2[43,-10] (xy)C2[250.0,180.0]  MER2[246:252,177:183]A dP=7.8,dL=23.338area1 38area2 32.619D1gray 32.619D1gray 21.457D'1 21.457D'2 27.195V'1 27.195V'2 1.392Maxd1 1.392Maxd2 0.480MinD1 0.480MinD2 1.636sX1 1.636sX2 1.685sY1 1.685sY2 0.00sdMX,0.00sdMY,0.00sdMD0.00sdMA,0#G,0.294MnBk1 0.294MnBk2
#B R:1 d(xy)LM1[0,-82] (xy)C1[208.0,71.0]  MER1[204:210,69:73] S:0 d(xy)LM2[31,0] (xy)C2[0.0,0.0]  MER2[0:0,0:0]U dL=10.0,dL=87.324area1 0area2 0.971D1gray 0.000D1gray 0.971D'1 0.000D'2 0.995V'1 0.000V'2 0.070Maxd1 0.000Maxd2 0.027MinD1 0.000MinD2 1.572sX1 0.000sX2 1.283sY1 0.000sY2 0.00sdMX,0.00sdMY,0.00sdMD0.00sdMA,0#G,0.000MnBk1 0.000MnBk2
#B R:26 d(xy)LM1[0,-77] (xy)C1[158.0,76.0]  MER1[155:162,73:78] S:0 d(xy)LM2[-17,0] (xy)C2[0.0,0.0]  MER2[0:0,0:0]U dL=10.4,dL=79.634area1 0area2 14.270D1gray 0.000D1gray 13.703D'1 0.000D'2 11.852V'1 0.000V'2 0.915Maxd1 0.000Maxd2 0.027MinD1 0.000MinD2 1.840sX1 0.000sX2 0.993sY1 0.000sY2 0.00sdMX,0.00sdMY,0.00sdMD0.00sdMA,0#G,0.017MnBk1 0.000MnBk2
#B R:27 d(xy)LM1[0,-77] (xy)C1[165.0,76.0]  MER1[163:167,73:78] S:0 d(xy)LM2[-17,0] (xy)C2[0.0,0.0]  MER2[0:0,0:0]U dL=10.8,dL=78.119area1 0area2 6.880D1gray 0.000D1gray 6.598D'1 0.000D'2 5.253V'1 0.000V'2 0.667Maxd1 0.000Maxd2 0.027MinD1 0.000MinD2 1.187sX1 0.000sX2 0.936sY1 0.000sY2 0.00sdMX,0.00sdMY,0.00sdMD0.00sdMA,0#G,0.015MnBk1 0.000MnBk2
#B R:28 d(xy)LM1[0,-77] (xy)C1[170.0,76.0]  MER1[168:171,73:78] S:0 d(xy)LM2[-17,0] (xy)C2[0.0,0.0]  MER2[0:0,0:0]U dL=13.5,dL=77.416area1 0area2 2.850D1gray 0.000D1gray 2.613D'1 0.000D'2 2.701V'1 0.000V'2 0.428Maxd1 0.000Maxd2 0.027MinD1 0.000MinD2 0.925sX1 0.000sX2 0.962sY1 0.000sY2 0.00sdMX,0.00sdMY,0.00sdMD0.00sdMA,0#G,0.015MnBk1 0.000MnBk2

 . . .

#U R:0 d(xy)LM1[0,0] (xy)C1[0.0,0.0]  MER1[0:0,0:0] S:862 d(xy)LM2[20,65] (xy)C2[256.0,498.0]  MER2[252:259,494:501]U dL=68.0,dL=68.00area1 52area2 0.000D1gray 36.111D1gray 34.904D'1 34.904D'2 30.105V'1 30.105V'2 0.000Maxd1 1.392Maxd2 0.000MinD1 0.070MinD2 0.000sX1 1.777sX2 0.000sY1 1.716sY2 0.00sdMX,0.00sdMY,0.00sdMD0.00sdMA,0#G,0.000MnBk1 0.023MnBk2
#U R:0 d(xy)LM1[0,0] (xy)C1[0.0,0.0]  MER1[0:0,0:0] S:863 d(xy)LM2[-68,67] (xy)C2[168.0,500.0]  MER2[164:171,497:502]U dL=95.5,dL=95.50area1 38area2 0.000D1gray 10.867D1gray 9.917D'1 9.917D'2 9.453V'1 9.453V'2 0.000Maxd1 0.540Maxd2 0.000MinD1 0.070MinD2 0.000sX1 1.789sX2 0.000sY1 1.380sY2 0.00sdMX,0.00sdMY,0.00sdMD0.00sdMA,0#G,0.000MnBk1 0.025MnBk2
#U R:0 d(xy)LM1[0,0] (xy)C1[0.0,0.0]  MER1[0:0,0:0] S:864 d(xy)LM2[-86,68] (xy)C2[150.0,501.0]  MER2[147:153,499:502]U dL=99.0,dL=109.60area1 19area2 0.000D1gray 0.975D1gray 0.534D'1 0.534D'2 1.143V'1 1.143V'2 0.000Maxd1 0.122Maxd2 0.000MinD1 0.027MinD2 0.000sX1 1.457sX2 0.000sY1 0.909sY2 0.00sdMX,0.00sdMY,0.00sdMD0.00sdMA,0#G,0.000MnBk1 0.023MnBk2
#V R:1510 d(xy)LM1[-46,13] (xy)C1[241.0,431.0]  MER1[238:244,427:435] S:757 d(xy)LM2[-40,8] (xy)C2[276.0,400.0]  MER2[272:280,396:404]P dP=7.8,dL=47.846area1 50area2 11.915D1gray 36.901D1gray 10.297D'1 34.401D'2 9.979V'1 32.682V'2 0.500Maxd1 1.392Maxd2 0.043MinD1 0.174MinD2 1.649sX1 1.809sX2 1.707sY1 1.830sY2 0.00sdMX,0.00sdMY,0.00sdMD0.00sdMA,0#G,0.035MnBk1 0.050MnBk2
#V R:658 d(xy)LM1[0,-63] (xy)C1[322.0,355.0]  MER1[318:326,351:360] S:0 d(xy)LM2[29,0] (xy)C2[0.0,0.0]  MER2[0:0,0:0]U dL=13.4,dL=72.157area1 0area2 42.779D1gray 0.000D1gray 41.829D'1 0.000D'2 38.131V'1 0.000V'2 1.700Maxd1 0.000Maxd2 0.070MinD1 0.000MinD2 1.887sX1 0.000sX2 1.677sY1 0.000sY2 0.00sdMX,0.00sdMY,0.00sdMD0.00sdMA,0#G,0.017MnBk1 0.000MnBk2
#V R:671 d(xy)LM1[0,-56] (xy)C1[371.0,362.0]  MER1[368:376,359:365] S:0 d(xy)LM2[55,0] (xy)C2[0.0,0.0]  MER2[0:0,0:0]U dL=38.9,dL=101.043area1 0area2 1.887D1gray 0.000D1gray 1.569D'1 0.000D'2 2.180V'1 0.000V'2 0.122Maxd1 0.000Maxd2 0.000MinD1 0.000MinD2 1.740sX1 0.000sX2 1.452sY1 0.000sY2 0.00sdMX,0.00sdMY,0.00sdMD0.00sdMA,0#G,0.007MnBk1 0.000MnBk2
#V R:660 d(xy)LM1[37,-47] (xy)C1[353.0,345.0]  MER1[326:334,359:366] S:674 d(xy)LM2[43,-55] (xy)C2[330.0,363.0]  MER2[351:356,341:349]A dP=10.0,dL=69.828area1 49area2 1.416D1gray 20.034D1gray 1.016D'1 19.490D'2 1.828V'1 16.801V'2 0.122Maxd1 0.723Maxd2 0.027MinD1 0.122MinD2 1.398sX1 1.922sX2 1.514sY1 1.705sY2 0.00sdMX,0.00sdMY,0.00sdMD0.00sdMA,0#G,0.014MnBk1 0.011MnBk2

 . . .

#V R:0 d(xy)LM1[0,0] (xy)C1[0.0,0.0]  MER1[0:0,0:0] S:827 d(xy)LM2[65,60] (xy)C2[381.0,452.0]  MER2[378:384,449:455]U dL=99.0,dL=101.40area1 27area2 0.000D1gray 0.484D1gray 0.339D'1 0.339D'2 0.474V'1 0.474V'2 0.000Maxd1 0.041Maxd2 0.000MinD1 0.000MinD2 0.000sX1 1.437sX2 0.000sY1 1.134sY2 0.00sdMX,0.00sdMY,0.00sdMD0.00sdMA,0#G,0.000MnBk1 0.005MnBk2
#V R:0 d(xy)LM1[0,0] (xy)C1[0.0,0.0]  MER1[0:0,0:0] S:836 d(xy)LM2[5,70] (xy)C2[321.0,462.0]  MER2[317:324,459:465]U dL=70.2,dL=70.20area1 40area2 0.000D1gray 3.944D1gray 3.444D'1 3.444D'2 3.371V'1 3.371V'2 0.000Maxd1 0.174Maxd2 0.000MinyD1 0.041MinD2 0.000sX1 1.943sX2 0.000sY1 1.408sY2 0.00sdMX,0.00sdMY,0.00sdMD0.00sdMA,0#G,0.000MnBk1 0.013MnBk2
#V R:0 d(xy)LM1[0,0] (xy)C1[0.0,0.0]  MER1[0:0,0:0] S:855 d(xy)LM2[15,96] (xy)C2[331.0,488.0]  MER2[327:333,486:491]U dL=97.2,dL=97.20area1 22area2 0.000D1gray 0.580D1gray 0.462D'1 0.462D'2 0.480V'1 0.480V'2 0.000Maxd1 0.041Maxd2 0.000MinD1 0.000MinD2 0.000sX1 1.330sX2 0.000sY1 1.240sY2 0.00sdMX,0.00sdMY,0.00sdMD0.00sdMA,0#G,0.000MnBk1 0.005MnBk2
#V R:0 d(xy)LM1[0,0] (xy)C1[0.0,0.0]  MER1[0:0,0:0] S:857 d(xy)LM2[37,103] (xy)C2[353.0,495.0]  MER2[349:357,491:498]U dL=99.0,dL=109.40area1 47area2 0.000D1gray 1.691D1gray 1.439D'1 1.439D'2 1.617V'1 1.617V'2 0.000Maxd1 0.070Maxd2 0.000MinD1 0.000MinD2 0.000sX1 1.849sX2 0.000sY1 1.774sY2 0.00sdMX,0.00sdMY,0.00sdMD0.00sdMA,0#G,0.000MnBk1 0.005MnBk2
#V R:0 d(xy)LM1[0,0] (xy)C1[0.0,0.0]  MER1[0:0,0:0] S:859 d(xy)LM2[130,104] (xy)C2[446.0,496.0]  MER2[441:448,493:499]U dL=99.0,dL=177.10area1 33area2 0.000D1gray 0.630D1gray 0.395D'1 0.395D'2 0.601V'1 0.601V'2 0.000Maxd1 0.041Maxd2 0.000MinD1 0.000MinD2 0.000sX1 1.512sX2 0.000sY1 1.365sY2 0.00sdMX,0.00sdMY,0.00sdMD0.00sdMA,0#G,0.000MnBk1 0.007MnBk2

Summary: of paired-spot statistics
----------------------------------
Rsample has 1564, Sample 864 spots in all landmark sets.
After Initial pairing:
  US 107
  SP 312
  PP 882
  AP 671
  CP 0
  EP 0
0.5(SP+PP)/(|G1| MIN |G2|)=69.10%

After secondary pairing:
  US 95
  SP 312
  PP 918
  AP 647
  CP 0
  EP 0

After secondary pairing: 0.5(SP+PP)/(|G1| MIN |G2|)=71.2%
mean dP(SP+PP)=1.88, mean dP'((|G1|+|G2|)/(SP+PP))=0.63

List of image files and generated files
---------------------------------------
Input Rsample pix file  [demo\ppx\gel-HM-019.gif]
Input Sample pix file   [demo\ppx\gel-HM-071.gif]
Input Rsample SSF file  [demo\xml\gel-HM-019.xml]
Input Sample SSF file   [demo\xml\gel-HM-071.xml]
Output SPF file         [demo\xml\gel-HM-071.spf]

FINISHED! The Sample Paired-spotlist File (SPF), is demo\xml\gel-HM-071.spf
Run time =0:0:1 (H:M:S) or 1.6 seconds


    

    



    

    8.5 Examples - using command line processing for batch
    

It is possible to run the CmpSpots from the command line in your
operating system. We give two examples doing this. The first example
shows a script for the Microsoft Windows batch (.bat) file demo-CmpSpots.bat file (available on the Files
Mirror.  The second example
shows the same commands in a shell script for a Unix operating system
(Linux, MacOS, Solaris, etc.) that you can download with demo-CmpSpots.sh. 

    

Command line scripts to run the GUI version on one sample are in the 
second example and
forth example. These may be downloaded
from  
demo-CmpSpots.bat and   
demo-CmpSpotsGUI.sh.

    

The data for these scripts is in the demo/ directory available with the
installation. Alternatively, you can download the demo data from the
Files Mirror as Demo.Z.

    

The installation packages are available from the 
Files mirror
under the CmpSpots releases.

    



    

    8.5.1 Examples - batch processing under Microsoft Windows
    

    
REM File: demo-CmpSpots.bat - pair spots to the Reference sample for a list of samples
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 JAR files:  
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 Sample Paired-spot-list Files (SPF) are saved in:
REM      demo/xml/
REM Generated images are saved in:
REM      demo/tmp/
REM
REM P. Lemkin $Date$ 

echo "demo-CmpSpots.bat"

pwd
date /T 

java -Xmx256M -jar CmpSpots.jar -default -project:demo\ -sample:gel-HM-071 -rsample:gel-HM-019
java -Xmx256M -jar CmpSpots.jar -default -project:demo\ -sample:gel-HM-087 -rsample:gel-HM-019
java -Xmx256M -jar CmpSpots.jar -default -project:demo\ -sample:gel-HM-096 -rsample:gel-HM-019

echo "-- Finished pairing the samples ---"

date /T 


    



    

    8.5.1.1 Examples - batch processing with GUI under Microsoft Windows
    

    
REM File: demo-CmpSpots-GUI.bat - pair spots to the Reference sample for a sample using the GUI
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 Sample Paired-spot-list Files (SPF) are saved in::
REM      demo/xml/
REM Generated images are saved in:
REM      demo/tmp/
REM
REM P. Lemkin $Date$ 

echo "demo-CmpSpots-GUI.bat"

pwd
date /T 

java -Xmx256M -jar CmpSpots.jar -demo -project:demo\ -sample:gel-HM-071 -rsample:gel-HM-019

echo "-- Finished pairing the sample ---"

date /T 


    



    

    8.5.2 Examples - batch processing under Unix
    

Because java is relatively operating system independent, the same java
command lines are used with the "\" changed to "/" from Windows to
Unix file path convention.
    


    
#!/bin/sh
# File: demo-CmpSpots.sh - Unix script to pair spots to the 
# Reference sample for a list of samples
# 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 sample 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 Sample Paired-spot-list Files (SPF) are saved in:
#      demo/xml/
# Generated images are saved in:
#      demo/tmp/
#
# P. Lemkin $Date$ 

echo "demo-CmpSpots.sh"

pwd
date

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

echo "-- Finished pairing the samples ---"

date


    



    

    8.5.2.1 Examples - batch processing with GUI under Unix
    


    
#!/bin/sh
# File: demo-CmpSpots-GUI.sh - Unix script to pair spots to the 
# Reference sample for a sample using the GUI.
# 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 sample image files:
#      demo/ppx/gel-HM-019 (Reference sample)
#      demo/ppx/gel-HM-071
# 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 Sample Paired-spot-list Files (SPF) are saved in:
#      demo/xml/
# Generated images are saved in:
#      demo/tmp/
#
# P. Lemkin $Date$ 

echo "demo-CmpSpots-GUI.sh"

pwd
date

java -Xmx256M -jar CmpSpots.jar -demo -gui -project:demo/ -sample:gel-HM-071 -rsample:gel-HM-019

echo "-- Finished pairing the samples ---"

date


    





    

    

    9. CmpSpots References
    

These papers (a subset of the GELLAB-II papers),
reference the GELLAB-II spot pairing program.  The Open2Dprot
Java-language CmpSpots program was derived from the GELLAB-II
C-language program as well as from code from the MAExplorer and Flicker projects.
New Java code was added as well. Although CmpSpots has been enhanced
in many ways, the basic algorithm is similar so these papers may be
useful for more details on the algorithm.
    


      


    1.  Lipkin, L.E., Lemkin, P.F. (1980) Database techniques for
   multiple PAGE (2D gel) analysis. Clinical Chemistry 26,
   1403-1413.


    2.  Lemkin, P., Lipkin, L. (1981) GELLAB: A computer system for 2D
   gel electrophoresis analysis. I. Segmentation and preliminaries.
   Computers in Biomedical Research 14, 272-297.


    3.  Lemkin, P., Lipkin, L. (1981) GELLAB: A computer system for 2D
   gel electrophoresis analysis. II. Pairing Spots.  Computers in
   Biomedical Research 14, 355-380.


    4.  Lester, E.P., Lemkin, P.F., Lipkin, L.E. (1981) New Dimensions
   in Protein Analysis - 2D Gels Coming of Age Through Image
   Processing, Invited paper, Analytical Chemistry 53,
   390A-397A.


    5.  Lemkin, P.F., Lipkin, L.E. (1983) Database Techniques for 2D
   Electrophoretic Gel Analysis, in Computing in Biological
   Science, Elsevier/North-Holland, M. Geisow, A. Barrett (eds),
   181-226.


    6.  Lemkin, P.F., Lipkin, L.E., Lester, E.P. (1982) Extensions to
   the GELLAB 2D Electrophoresis Gel Analysis System. Paper given at
   "Clinical Applications of 2D Electrophoresis", Mayo Clinic, Nov.
   15-18, 1981. Clinical Chemistry 840-849.


    7.  Lemkin, P.F., Lester, E.P. (1989) Database and Search
   Techniques for 2D Gel Protein Data: A Comparison of Paradigms For
   Exploratory Data Analysis and Prospects for Biological Modeling,
   Electrophoresis 10(2): 122-140.


    8.  Lemkin, P.F. (1989) GELLAB-II, A workstation based 2D
   electrophoresis gel analysis system, in proceedings of
   Two-Dimensional Electrophoresis T. Endler, S.Hanash (Eds),
   Vienna Austria, Nov 8-11, 1988, VCH Press, W.Germany. pp 53-57.


    9.  Lemkin, P.F., Rogan, P. (1991) Automatic Detection of noisy
   spots in two-dimensional Southern Blots, Applied and Theoretical
   Electrophoresis 2, 141-149.


    10.  Myrick, J.E., Lemkin, P.F., Robinson, M.K., Upton, K.M.
   (1993) Comparison of the BioImage Visage(TM) 2,000 and the
   GELLAB-II two-dimensional electrophoretic analysis
   systems. Applied and Theoretical Electrophoresis 3,
   335-346.


    


    


    

    


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open2dprot.sourceforge.net/CmpSpots

    
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Revised: 05/19/2006