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java.lang.Object O2Plib.db.DbBaseSpot
public class DbBaseSpot
Class DbBaseSpot is the base class used to define a spot. It is used as the base class for both DbSpot and DbPspot. It supports a spot data structure for spot features in Open2Dprot programs.
This file is derived from GELLAB-II cmpgl2.c as of "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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static int |
AP
Ambiguous Pair - pairing program generated label |
static java.awt.Color |
APCOLOR
Ambiguous Pair spot label |
DbBaseSpot |
bestPairedSpot
ptr to best paired spot for spot-pairing, if not null |
static int |
BF_DISPLAY_SPOT
Bit feature to display spot |
static int |
BF_FAILED_SXSYR1RANGE
Bit feature failed sX/Sy range lower bound |
static int |
BF_FAILED_SXSYR2RANGE
Bit feature failed sX/Sy range upper bound |
static int |
BF_FAILED_T1AREA
Bit feature failed T1 area lower bound |
static int |
BF_FAILED_T1DENSITY
Bit feature failed T1 density lower bound |
static int |
BF_FAILED_T1DENSRANGE
Bit feature failed T1 density range lower bound |
static int |
BF_FAILED_T2AREA
Bit feature failed T2 area upper bound |
static int |
BF_FAILED_T2DENSITY
Bit feature failed T2 density upper bound |
static int |
BF_FAILED_T2DENSRANGE
Bit feature failed T2 density range upper bound |
static int |
BF_ISVALIDSPOT
Bit feature of a spot |
int |
bitFeatures
bit features of a spot is the OR of BF_xxxx bits |
int |
code
Spot Pairing code DbLM.(SP,PP,AP,US,CP,EP,LM,GS) |
static int |
CP
Composite Sample Database spot pair. |
static java.awt.Color |
CPCOLOR
Composite (averaged) spot label |
DbSample |
dbRsample
|
DbSample |
dbSample
|
float |
dL
distance from spot pair to their landmark |
float |
dP
distance between spots in a pair |
static int |
EP
Extrapolated Pair - by CSD database program |
static java.awt.Color |
EPCOLOR
Extrapolated spot label |
static int |
GS
Garbage Spot - generated by CSD database or editing programs |
int |
idxRsample
index of Rsample this spot is paired with. |
int |
idxSample
Index of Sample for this spot. |
static int |
LM
LandMark spot [could be virtual landmark] - by CSD database program. |
static java.awt.Color |
LMCOLOR
Landmark spot label |
int |
lmNbrI
Landmark number as int index [0:51]. |
java.lang.String |
lmNbrS
Landmark number String as index [0:51] encoded as a name character "A" : "Z or "a" : "z". |
static java.awt.Color |
LMSETCOLOR
Color of spots in the landmark set |
static int |
MAX_SPOT_SUBLIST_SIZE
max size of spot sublist when they are created locally |
DbBaseSpot |
nextLMspot
ptr to Next LM-set spot if not null |
DbBaseSpot |
nextSpot
ptr to Next spot instance in spot list if not null |
int |
nSample
Sample# (RSAMPLE or SAMPLE) to identify type of sample |
static int |
PP
Possible Pair - pairing program generated label |
static java.awt.Color |
PPCOLOR
Possible Pair spot label |
DbBaseSpot |
prevSpot
ptr to Previous spot instance in spot list if not null |
static int |
RSAMPLE
The index for the Rsample (Reference Sample) |
static java.awt.Color |
RSPOTCOLOR
Color of the Rspots |
DbBaseSpot |
rSpotNext
Next instance for CSD database Rspot linked list |
static int |
SAMPLE
The index for the Sample to be paired with the Rsample |
static int |
SP
Sure Pair - pairing program generated label |
static java.awt.Color |
SPCOLOR
Sure Pair spot label |
static int |
SPOT_FEATURE_AREA
Spot area feature index |
static int |
SPOT_FEATURE_DENS_PCT
Spot percent density feature index |
static int |
SPOT_FEATURE_DENS_PRIME
Spot density' feature index |
static int |
SPOT_FEATURE_DENSITY
Spot density feature index |
static int |
SPOT_FEATURE_MAX_DENS
Spot mean density feature index |
static int |
SPOT_FEATURE_MEAN_DENSITY
Spot mean density feature index |
static int |
SPOT_FEATURE_MIN_DENS
Spot max density feature index |
static int |
SPOT_FEATURE_VOLUME
Spot volume feature index |
static java.awt.Color |
SPOTBOXCOLOR
Color of the selected spot indicated by a spot box |
int |
spotNumber
Unique sequential spot number. |
boolean |
swappedRsampleAndSampleFlag
Set if swap the Rsample and Sample fields |
static int |
US
Unresolved Spot - pairing program generated label |
static java.awt.Color |
USCOLOR
Unresolved spot label |
static java.lang.String |
VERSION
Version for this module |
Constructor Summary | |
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DbBaseSpot()
DbBaseSpot() - Constructor for new DbSpot. |
|
DbBaseSpot(DbSample dbSample)
DbBaseSpot() - Constructor for new DbBaseSpot. |
|
DbBaseSpot(DbSample dbRsample,
DbSample dbSample)
DbBaseSpot() - Constructor for new DbBaseSpot. |
Method Summary | |
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boolean |
copyBaseValues(DbBaseSpot sp,
boolean copyPointersFlag)
copyBaseValues() - copy values in spot sp into this spot. |
void |
copyRsampleToSampleBaseValues()
copyRsampleToSampleBaseValues() - copy Rsample base field field values in this Pspot to the Sample base field values. |
void |
setDbSamples(DbSample dbRsample,
DbSample dbSample)
setDbSamples() - set the dbRsample and dbSample objects for this DbBaseSpot. |
void |
swapBaseValues()
swapBaseValues() - swap the Rsample and Sample field values |
boolean |
verifyNotCircularSSFlist(DbBaseSpot p,
java.lang.String msg)
verifyNotCircularSSFlist() - test to see if the spotlist is circular given a pointer into the list. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public static final java.lang.String VERSION
public static final int BF_ISVALIDSPOT
public static final int BF_FAILED_T1AREA
public static final int BF_FAILED_T2AREA
public static final int BF_FAILED_T1DENSITY
public static final int BF_FAILED_T2DENSITY
public static final int BF_FAILED_T1DENSRANGE
public static final int BF_FAILED_T2DENSRANGE
public static final int BF_FAILED_SXSYR1RANGE
public static final int BF_FAILED_SXSYR2RANGE
public static final int BF_DISPLAY_SPOT
public static final int MAX_SPOT_SUBLIST_SIZE
public static java.awt.Color SPCOLOR
public static java.awt.Color PPCOLOR
public static java.awt.Color APCOLOR
public static java.awt.Color USCOLOR
public static java.awt.Color EPCOLOR
public static java.awt.Color CPCOLOR
public static java.awt.Color LMCOLOR
public static java.awt.Color LMSETCOLOR
public static java.awt.Color SPOTBOXCOLOR
public static java.awt.Color RSPOTCOLOR
public static final int SPOT_FEATURE_AREA
public static final int SPOT_FEATURE_DENSITY
public static final int SPOT_FEATURE_DENS_PRIME
public static final int SPOT_FEATURE_DENS_PCT
public static final int SPOT_FEATURE_VOLUME
public static final int SPOT_FEATURE_MEAN_DENSITY
public static final int SPOT_FEATURE_MAX_DENS
public static final int SPOT_FEATURE_MIN_DENS
public static final int RSAMPLE
public static final int SAMPLE
public static final int US
public static final int SP
public static final int PP
public static final int AP
public static final int EP
public static final int CP
public static final int GS
public static final int LM
public int nSample
public int idxSample
public int idxRsample
public DbSample dbRsample
public DbSample dbSample
public int spotNumber
public int bitFeatures
public boolean swappedRsampleAndSampleFlag
public java.lang.String lmNbrS
public int lmNbrI
public int code
public float dP
public float dL
public DbBaseSpot prevSpot
public DbBaseSpot nextSpot
public DbBaseSpot nextLMspot
public DbBaseSpot bestPairedSpot
public DbBaseSpot rSpotNext
Constructor Detail |
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public DbBaseSpot()
public DbBaseSpot(DbSample dbSample)
dbSample
- for this spotpublic DbBaseSpot(DbSample dbRsample, DbSample dbSample)
dbRsample
- is sample for pairing with this spotdbSample
- for this spotMethod Detail |
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public void setDbSamples(DbSample dbRsample, DbSample dbSample)
dbRsample
- is sample for pairing with this spotdbSample
- for this spotpublic boolean copyBaseValues(DbBaseSpot sp, boolean copyPointersFlag)
sp
- is spotcopyPointersFlag
- to copy spot pointers as well
public void swapBaseValues()
public void copyRsampleToSampleBaseValues()
public boolean verifyNotCircularSSFlist(DbBaseSpot p, java.lang.String msg)
p
- is DbBaseSpot pointer to list of spotsmsg
- is the message to print if an error if not null
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