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java.lang.Object Seg2Dgel.Sg2glb Seg2Dgel.Seg2Dgel
public class Seg2Dgel
The Seg2Dgel program is a 2D gel spot segmenter for the Open2Dprot project. Seg2Dgel may be used for segmenting other types of images (such as 2D LC-MS, etc) into spot list files (Sample Spotlist Files or SSF) for Open2Dprot.
This code is derived and refactored from the GELLAB-II sg2gii C files as of "Version November 7, 1992". Seg2Dgel program ----------------- Seg2Dgel is a program that is part of the Open2Dprot project. It is used to segment and quantify 2D electrophoresis gel images. The input is a 2D gel image (TIFF, GIF, JPEG, or PPX). The output is a quantified spot list in various ASCII formats including XML and tab-delimited as well as the historical GELLAB-II SSF formats. Images may be generated (a the user's option) to view the segmented spots and various intermediate images used by Seg2Dgel. More detailed documentation is found in documentation on the Web site.
This work was produced by Peter Lemkin of the National Cancer Institute, an agency of the United States Government. As a work of the United States Government there is no associated copyright. It is offered as open source software under the Mozilla Public License (version 1.1) subject to the limitations noted in the accompanying LEGAL file. This notice must be included with the code. The Open2Dprot Mozilla and Legal files are available on http://open2dprot.sourceforge.net/.
Field Summary |
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Constructor Summary | |
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Seg2Dgel()
Seg2Dgel() - Constructor |
Method Summary | |
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static void |
main(java.lang.String[] args)
main() - for Seg2Dgel 2D Electrophoresis Gel Spot Segmenter. |
void |
popupImageViewer()
popupImageViewer() - popup the image viewer after the images were computed by the segmenter. |
private static void |
resetResources(boolean fullResetFlag)
resetResources() - reset any resources that must be reset for the next run of the segmenter. |
private static int |
segmentSampleImage(java.lang.String[] args)
segmentSampleImage() - segment the sample gel image. |
static java.lang.String[] |
setupDebugSwitches(java.lang.String[] argv)
setupDebugSwitches() - setup the debug switches. |
static java.lang.String[] |
setupDemo_2DLCMS_Switches(java.lang.String[] argv)
setupDemo_2DLCMS_Switches() - setup "demo/ppx/2D-LC-MS-01.gif" for special debug image that is a 868x612 pixel 8-bit/pixel image with some saturated spots. |
static java.lang.String[] |
setupDemo2Kx2KSwitches(java.lang.String[] argv)
setupDemo2Kx2KSwitches() - setup "demo/ppx/testGel-2Kx2K.gif" for special debug image "demo/ppx/testGel-2Kx2K.gif" which is a 2000x2000 pixel 8-bit/pixel image with some saturated spots. |
static java.lang.String[] |
setupDemo3Kx3KSwitches(java.lang.String[] argv)
setupDemo3Kx3KSwitches() - setup "demo/ppx/testGel-3Kx3K.gif" for special debug image "demo/ppx/testGel-3Kx3K.gif" which is a 3100x3100 pixel 8-bit/pixel image with some saturated spots. |
static java.lang.String[] |
setupDemoSwitches(java.lang.String[] argv)
setupDemoSwitches() - setup the demo switches for the demo/ppx/ Human AML leukemia image. |
static java.lang.String[] |
setupMinDefaultsSwitches(java.lang.String[] argv,
int defTypeCode)
setupMinDefaultsSwitches() - add the minimum default switches. |
private static boolean |
setupStdDemoImageCalibDefaults()
setupStdDemoImageCalibDefaults() - setup the debug CW, ND wedge default values and compute the gray to od calibration. |
Methods inherited from class Seg2Dgel.Sg2glb |
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get2D, get2D, getPixLineBuf, getPixLineBuf, initGlb, isDBwindow, isDBwindow, put2Dbuf, resetGlb, set2D, set2D, setPixLineBuf, setPixLineBuf, showReportStatus |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public Seg2Dgel()
Method Detail |
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public static void main(java.lang.String[] args)
args
- is command line arg listprivate static int segmentSampleImage(java.lang.String[] args)
private static void resetResources(boolean fullResetFlag)
fullResetFlag
- force new resource allocationpublic static java.lang.String[] setupDebugSwitches(java.lang.String[] argv)
argv
- list of original switches
public static java.lang.String[] setupMinDefaultsSwitches(java.lang.String[] argv, int defTypeCode)
argv
- is list of original switches
public static java.lang.String[] setupDemoSwitches(java.lang.String[] argv)
argv
- is list of original switches
private static boolean setupStdDemoImageCalibDefaults()
Note that is mapping is NOT accurate or maybe quite inaccurate for gels other than these specific demo gels - although the Gray to OD mappings may look reasonable.
public static java.lang.String[] setupDemo2Kx2KSwitches(java.lang.String[] argv)
argv
- is list of original switches
public static java.lang.String[] setupDemo3Kx3KSwitches(java.lang.String[] argv)
argv
- is list of original switches
public static java.lang.String[] setupDemo_2DLCMS_Switches(java.lang.String[] argv)
argv
- is list of original switches
public void popupImageViewer()
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