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java.lang.Object Landmark.Lmsglb Landmark.Landmark
public class Landmark
The Landmarking program for Open2Dprot is used to add and edit landmark data for the landmark database of sets of corresponding pairs of (x,y) landmarks for pairs of Rsample and Samples.
Edited and refactored by Greg Thornwall, SAIC.
This code was derived and refactored other Open2Dprot Java programs and from GELLAB-II landmark C language files "Version November 9, 1999".
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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Landmark()
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Method Summary | |
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boolean |
createNewLandmarkDBfile(java.lang.String lmsDatabaseName,
java.lang.String lmsDBfile)
createNewLandmarkDBfile() - create a new the landmark database file with the header but not the data. |
private boolean |
lookupSampleEntryInAccDB(java.lang.String accNameData,
java.lang.String accFieldName,
java.lang.String accFile,
DbSample dbS)
lookupSampleEntryInAccDB() - lookup the sample image name in the accession DB. |
static void |
main(java.lang.String[] args)
main() - for Landmark 2D spot-landmark program for Open2Dprot. |
boolean |
openLandmarkDBfile(java.lang.String lmsDatabaseName,
boolean tryToSaveCurAccFile)
openLandmarkDBfile() - open the landmark database. |
private int |
processSamples(java.lang.String[] args)
processSamples() - process the two samples. |
private char[] |
readSsfImage(java.lang.String imageFile,
DbSample dbS)
readSsfImage() - read the SSF image and set image status in the dbSample instance |
private static void |
resetResources(boolean fullResetFlag)
resetResources() - reset any resources that must be reset for the next run of the program. |
boolean |
setNewRsampleLMSfromAnotherLMSdbPair(java.lang.String rSample,
java.lang.String sample)
setNewRsampleLMSfromAnotherLMSdbPair() - lookup LMS DB for specified (rsample, sample) pair and set Rsample list of spots into current dbLM LMset. |
boolean |
setRsampleByName(java.lang.String rName)
setRsampleByName() - set and load the Rsample data into dbRsample |
boolean |
setSampleByName(java.lang.String sName)
setSampleByName() - set and load the Sample data into dbSample |
static java.lang.String[] |
setupDebugSwitches(java.lang.String[] argv)
setupDebugSwitches() - setup the debug switches |
static java.lang.String[] |
setupDemoSwitches(java.lang.String[] argv)
setupDemoSwitches() - setup the demo switches for the "gel-HM-019" (HUMAN-AML) and "gel-HM-071" (Human-ALL) samples |
static java.lang.String[] |
setupMinDefaultsSwitches(java.lang.String[] argv)
setupMinDefaultsSwitches() - add the minimum default switches. |
Methods inherited from class Landmark.Lmsglb |
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initGlb, resetGlb, 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 Landmark()
Method Detail |
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public static void main(java.lang.String[] args)
args
- is the argument list of command lineprivate int processSamples(java.lang.String[] args)
private boolean lookupSampleEntryInAccDB(java.lang.String accNameData, java.lang.String accFieldName, java.lang.String accFile, DbSample dbS)
accNameData
- is the sample image name to search for. Do not
specify the file extension.accFieldName
- is the accession field nameaccFile
- is the name of the accession filedbS
- is the SSF instance to use
private char[] readSsfImage(java.lang.String imageFile, DbSample dbS)
imageFile
- to readdbS
- to update
public boolean setRsampleByName(java.lang.String rName)
rName
- - Rsample name to load
public boolean setSampleByName(java.lang.String sName)
sampleName
- - to load
public boolean setNewRsampleLMSfromAnotherLMSdbPair(java.lang.String rSample, java.lang.String sample)
rSample
- to usesample
- to use in pair
private static void resetResources(boolean fullResetFlag)
fullResetFlag
- force new resource allocationpublic boolean openLandmarkDBfile(java.lang.String lmsDatabaseName, boolean tryToSaveCurAccFile)
lmsDatabaseName
- name of new landmark database filetryToSaveCurAccFile
- if needed (i.e., if
the needToSaveAccessionDataFlag flag is set).
public boolean createNewLandmarkDBfile(java.lang.String lmsDatabaseName, java.lang.String lmsDBfile)
lmsDatabaseName
- name of new landmark database filelmsDBfile
- is full path of new landmark database file
public static java.lang.String[] setupMinDefaultsSwitches(java.lang.String[] argv)
argv
- is list of original switches
public static java.lang.String[] setupDemoSwitches(java.lang.String[] argv)
argv
- is list of original switches
public static java.lang.String[] setupDebugSwitches(java.lang.String[] argv)
argv
- list of original switches
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