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SUMMARY: INNER | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Object | +--MJAbase | +--MJAnormalization
MAExplorer Open Java API class to access MJAnormalization methods and data structures. Access normalization data and methods.
List of methods available to Plugin-writers
getNormMethod() - name of current normalization method getNormMethodDisplayName() - display name of current normalization method recalcNorms() - recalculate normalizations of all samples computeWorkingGeneList() - run data Filter and recompute working gene list madeChanges() - set the madeChangesFlag since state changed. setPosQuantModeState() - Positive Quantified Intensity state
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 MAExplorer Mozilla and Legal files are available on http://maexplorer.sourceforge.net/.
Method Summary | |
void |
computeWorkingGeneList()
computeWorkingGeneList() - run the data Filter and compute the working gene list. |
java.lang.String |
getNormMethod()
getNormMethod() - get name of current normalization method |
java.lang.String |
getNormMethodDisplayName()
getNormMethodDisplayName() - get display name of current normalization method |
void |
madeChanges()
madeChanges() - set the madeChangesFlag since state changed. |
void |
recalcNorms(java.lang.String msg,
boolean flag)
recalcNorms() - recalculate normalizations of all samples |
void |
setPosQuantModeState(boolean flag)
setPosQuantModeState() - set Positive Quantified Intensity state [MAEPlugin] forced implementation via MAEStub. |
Methods inherited from class MJAbase |
cvtHashtable2SimpleTable, cvtTable2Hashtable |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Method Detail |
public final java.lang.String getNormMethod()
null
if not found.public final java.lang.String getNormMethodDisplayName()
null
if not found.public final void recalcNorms(java.lang.String msg, boolean flag)
msg
- title stringflag
- flag passed to recalcNorms (????)...public final void computeWorkingGeneList()
public final void madeChanges()
public final void setPosQuantModeState(boolean flag)
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