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java.lang.Object O2Plib.db.CSD.CSDglb O2Plib.db.CSD.CSDlms
public class CSDlms
Class CSDlms contains lists of LMset landmark database for the Composite Samples Database (CSD).
This file is derived from Open2Dprot, MAExplorer, Flicker and GELLAB-II code.
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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DbLM |
dbLM
landmark database if it exists |
java.lang.String |
landmarkFile
Landmark file name |
LMset[] |
lmSetsList
list of LMsets [0:nLMsetsList-1] |
java.lang.String[] |
lmSetsNames
Names of the LMsets [0:nLMsetsList-1] |
int |
maxLMS
the actual number of LMS used if any. |
int |
nLMsetsList
Size of list of LMsets |
static java.lang.String |
VERSION
Version for this module |
Constructor Summary | |
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CSDlms()
CSDlms() - Constructor for new CSDlms. |
Method Summary | |
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boolean |
addLMS(LMset lms)
addLMS() - add LMset to list of LMsets. |
boolean |
addLMS(LMset lms,
java.lang.String sName)
addLMS() - add LMset to list of LMsets. |
void |
clear()
clear() - clear condition. |
void |
computeAllLMSradii()
computeAllLMSradii() -compute the LMS radii for a sample pairs. |
boolean |
createLMsetListFromDbLMtable(DbLM dbLM)
createLMsetListFromDbLMtable() - build LM set list from DbLM table |
LMset[] |
getListOfLMSlists()
getListOfLMSlists() - get the list of LMset objects |
java.lang.String |
getLMsetsDBradiiReport(int dBugLMset)
getLMsetsDBradiiReport() - get LMset half-radii report for all (sample, Rsample) landmarks for all CSDlms LMsets. |
java.lang.String |
getLMsetsDBxyValuesReport(int dBugLMset)
getLMsetsDBxyValuesReport() - get LMset(x,y) values report for all (sample, Rsample) landmarks for all CSDlms LMsets. |
java.lang.String[] |
getLMSlistsNames()
getLMSlistsNames() - get the list of LMset names |
int |
getRsample_xLM(int idxSample,
int lmNbr)
getRsample_xLM() - get the Rsample's nbrLM landmark X value |
int |
getRsample_yLM(int idxSample,
int lmNbr)
getRsample_yLM() - get the Rsample's nbrLM landmark Y value |
int |
getSample_xLM(int idxSample,
int lmNbr)
getSample_xLM() - get the Sample's nbrLM landmark X value |
int |
getSample_yLM(int idxSample,
int lmNbr)
getSample_yLM() - get the Sample's nbrLM landmark Y value |
int |
getSampleSpotNbr(int idxSample,
int lmNbr)
getSampleSpotNbr() - get the Sample's nbrLM landmark spotNumber value [TODO- REFACTORE] since dbLM list not in CSD with DbSpots. |
boolean |
getSampleUseLMflag(int idxSample,
int lmNbr)
getSampleUseLMflag() - get the sample's useLM flag |
boolean |
isLandmarkSpot(DbPspot ps)
isLandmarkSpot() - test if sample's ccNbr spot is a landmark spot. |
int |
lookupIdxByLMS(LMset lms)
lookupIdxByLMS() - lookup index of LMset name in list of LMsets. |
int |
lookupIdxByLMS(java.lang.String sName)
lookupIdxByLMS() - lookup index of LMset name in list of LMsets. |
boolean |
regrowLMS(int newSize)
regrowLMS() - grow the condition. |
boolean |
rmvLMS(java.lang.String sName)
rmvLMS() - remove LMset name from list of LMsets. |
DbLM |
setLandmarkDB(DbLM dbLM,
java.lang.String landmarkFile,
int lmsFormatMode)
setLandmarkDB() - assign the landmark DB. |
java.lang.String |
toString()
toString() - get a pretty-print string representation of this instance |
java.lang.String |
toTabDelimitedData()
toTabDelimitedData() - get a string representation of this instance as tab-delimited data values |
java.lang.String |
toTabDelimitedFields()
toTabDelimitedFields() - get a string representation of this instance as tab-delimited data fields |
java.lang.String |
toXML()
toXML() - get a string representation of this instance as XML |
int |
updateLMsetsFromDbLM(java.lang.String rsampleName,
java.lang.String[] sampleNames)
updateLMsetsFromDbLM() - update the LMset database from the DbLM that was previously setup. |
Methods inherited from class O2Plib.db.CSD.CSDglb |
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initGlb |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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public static final java.lang.String VERSION
public java.lang.String landmarkFile
public DbLM dbLM
public int maxLMS
public int nLMsetsList
public java.lang.String[] lmSetsNames
public LMset[] lmSetsList
Constructor Detail |
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public CSDlms()
Method Detail |
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public void clear()
public DbLM setLandmarkDB(DbLM dbLM, java.lang.String landmarkFile, int lmsFormatMode)
dbLM
- to use if it is already opened.landmarkFile
- is landmark database filelmsFormatMode
- is the LMS DB formatpublic int updateLMsetsFromDbLM(java.lang.String rsampleName, java.lang.String[] sampleNames)
rSampleName
- to look forsampleNames
- is a list of SPF samples paired with the Rsample
public void computeAllLMSradii()
public boolean regrowLMS(int newSize)
newSize
- of the condition list
public boolean addLMS(LMset lms, java.lang.String sName)
lms
- is LMset objectsName
- is LMset name
public boolean addLMS(LMset lms)
lms
- is LMset object
public int lookupIdxByLMS(java.lang.String sName)
sName
- is LMset name
public int lookupIdxByLMS(LMset lms)
lms
- is LMset object
public boolean rmvLMS(java.lang.String sName)
sName
- is LMset name
public java.lang.String[] getLMSlistsNames()
public LMset[] getListOfLMSlists()
public boolean createLMsetListFromDbLMtable(DbLM dbLM)
public java.lang.String getLMsetsDBxyValuesReport(int dBugLMset)
dBugLMset
- is -1 to report all landmarks, else just specified one
public java.lang.String getLMsetsDBradiiReport(int dBugLMset)
dBugLMset
- is -1 to report all landmarks, else just specified one
public boolean getSampleUseLMflag(int idxSample, int lmNbr)
idxSample
- index of sample to uselmNbr
- to get
public int getSampleSpotNbr(int idxSample, int lmNbr)
idxSample
- index of sample to uselmNbr
- to get
public int getSample_xLM(int idxSample, int lmNbr)
idxSample
- index of sample to uselmNbr
- to get
public int getSample_yLM(int idxSample, int lmNbr)
idxSample
- index of sample to uselmNbr
- to get
public int getRsample_xLM(int idxSample, int lmNbr)
idxSample
- index of sample to uselmNbr
- to get
public int getRsample_yLM(int idxSample, int lmNbr)
idxSample
- index of sample to uselmNbr
- to get
public boolean isLandmarkSpot(DbPspot ps)
ps
- is DbPspot to test
public java.lang.String toString()
toString
in class java.lang.Object
public java.lang.String toTabDelimitedFields()
public java.lang.String toTabDelimitedData()
public java.lang.String toXML()
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