|
|||||||||
| Home >> All >> [ MAEPlugin overview ] | PREV CLASS NEXT CLASS | ||||||||
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD |
DETAIL: FIELD | CONSTR | METHOD | ||||||||
MAEPlugin
Interface Normalization
- public interface Normalization
| Method Summary | |
float[] |
calcIntensityScaleExtrema(float maxRI,
float minRI,
float maxRaw,
float minRaw,
int sampleNbr)
calcIntensityScaleExtrema() - compute scaled Intensity upper and lower limits of raw data for each sample. |
boolean |
finishPipeline(int optArg)
finishPipeline() - finish filter at end of normalization of all genes (if required). |
java.lang.Object |
getSample()
getSample() - get the sample object |
boolean |
getState()
getState() - get the state of the checkbox |
void |
recalcNormalizationExtrema()
recalcNormalizationExtrema() - set the extreama for all samples for this plugin |
boolean |
resetPipeline(int optArg)
resetPipeline() - reset filter at start of data Normalization. |
float |
scaleIntensityData(float rawData)
scaleIntensityData() - scale raw intensity data as fct of normalization mode. |
float |
scaleIntensityData(float rawIntensity,
float rawBkgrd,
int mid,
int gid,
int sampleIdx)
scaleIntensityData() - the gene normalization operating on gene mid for sampleIdx where the data is ether extracted here or from the resetPipeline pre-analysis. |
float |
scaleIntensityData(float rawData,
int mid,
int gid,
int sampleNbr)
scaleIntensityData() - scale raw intensity data as fct of normalization mode. |
void |
setSample(java.lang.Object o)
setSample() - set the sample object |
void |
setState(boolean flag)
setState() - set the state of the checkbox |
| Method Detail |
calcIntensityScaleExtrema
public float[] calcIntensityScaleExtrema(float maxRI,
float minRI,
float maxRaw,
float minRaw,
int sampleNbr)
- calcIntensityScaleExtrema() - compute scaled Intensity upper
and lower limits of raw data for each sample. It is called
to get extrema for use in scaling displays and other computations
where the limits must be known.
resetPipeline
public boolean resetPipeline(int optArg)
- resetPipeline() - reset filter at start of data Normalization.
We will test for ALL GENES (if required) using the midOK[] boolean
created here to later determine if we actually perform the test.
This sets up the state that may be used during the pipeline operation.
finishPipeline
public boolean finishPipeline(int optArg)
- finishPipeline() - finish filter at end of normalization of all genes (if required).
This may be used to clean up the state after the pipeline operation.
scaleIntensityData
public float scaleIntensityData(float rawData)
- scaleIntensityData() - scale raw intensity data as fct of normalization
mode. This method is called on a per-spot basis.
scaleIntensityData
public float scaleIntensityData(float rawData,
int mid,
int gid,
int sampleNbr)
- scaleIntensityData() - scale raw intensity data as fct of normalization mode.
This method passes the (gid,sampleNbr) in case it is needed.
This method is called on a per-spot basis.
scaleIntensityData
public float scaleIntensityData(float rawIntensity,
float rawBkgrd,
int mid,
int gid,
int sampleIdx)
- scaleIntensityData() - the gene normalization operating on gene mid
for sampleIdx where the data is ether extracted here or from the resetPipeline
pre-analysis.
If the normalization is inoperative, then just return 0.0.
The mid must be >=0 since -1 indicates an illegal gene.
The midOK[mid] must be true, else it indicates an illegal gene.
[NOTE] The plugin writer should try to avoid doing special analyses here that
need to be computed DURING the processing and instead do the computations
during the resetPipeline() operation if possible. That may be able to
optimized and the data cached to avoid constant recomputation.
getState
public boolean getState()
- getState() - get the state of the checkbox
setState
public void setState(boolean flag)
- setState() - set the state of the checkbox
recalcNormalizationExtrema
public void recalcNormalizationExtrema()
- recalcNormalizationExtrema() - set the extreama for all samples for this plugin
setSample
public void setSample(java.lang.Object o)
- setSample() - set the sample object
getSample
public java.lang.Object getSample()
- getSample() - get the sample object
|
|||||||||
| Home >> All >> [ MAEPlugin overview ] | PREV CLASS NEXT CLASS | ||||||||
|
SUMMARY: JAVADOC | SOURCE | DOWNLOAD | NESTED | FIELD | CONSTR | METHOD |
DETAIL: FIELD | CONSTR | METHOD | ||||||||