Class ReportPRP

java.lang.Object
  |
  +--ReportPRP

public class ReportPRP

extends java.lang.Object

Class ReportPRP.java - popup various reports. This work was produced by Peter Lemkin of the National Cancer Institute, an agency of the United States Government and Djamel Medjahed (SAIC-Frederick). 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.

Version:

$Date: 2002/10/14 20:17:17 $ $Revision: $

Author:

P. Lemkin (NCI), Djamel Medjahed (SAIC), NCI-Frederick, Frederick, MD

See Also:

ProtPlot Home

This work was derived from MAExplorer under the Mozilla 1.1 Open Source Public License by Peter Lemkin of the National Cancer Institute, an agency of the United States Government subject to the limitations noted in the accompanying LEGAL file. See licence info on http://maexplorer.sourceforge.org/

Field Summary

Filter	fil Instance of Data Filter.
private ProtPlot	prp instance of ProtPlot
StatisticsPRP	stat Instance of StatisticsPRP.
UtilPRP	util Utility instance

Constructor Summary

ReportPRP(ProtPlot prp)
ReportPRP() - constructor

Method Summary

(package private) java.lang.String	getSamplesSubtitle() getSamplesSubtitle() - of samples based on plot mode
boolean	showExprProfilesFilteredReport() showExprProfilesFilteredReport() - show popup of expression profiles of filtered proteins
void	showFilteredReport() showFilteredReport() - show popup report of filtered proteins in the prp.mPidFiltered[0:prp.nMpidFiltered-1] list of mPids [TODO] Sort by expression or by ratioX/Y
void	showListOfExprProfileSamplesReport() showListOfExprProfileSamplesReport() - show popup report of list of samples in the current Protein expression profile.
boolean	showSampleAssignmentsReport() showSampleAssignmentsReport() - list sample assignments in various sets
boolean	showSampleNbrsReport() showSampleNbrsReport() - list the samples and numbers of proteins/sample
boolean	showSimilarProteinReport(Cluster clust) showSimilarProteinReport() - show popup similar-cluster report of similar proteins that were previously clustered.
boolean	showStateReport() showStateReport() - show popup of the state values including slider values
boolean	showXYEPsetsMissingProtFilteredReport() showXYEPsetsMissingProtFilteredReport() - show popup of X&Y or EP sets statistics of missing prot filtered proteins
boolean	updateReport() updateReport() - update the popup report if possible using the rptType.

Methods inherited from class java.lang.Object

, clone, equals, finalize, getClass, hashCode, notify, notifyAll, registerNatives, toString, wait, wait, wait

Field Detail

prp

private ProtPlot prp

instance of ProtPlot

util

public UtilPRP util

Utility instance

fil

public Filter fil

Instance of Data Filter.

stat

public StatisticsPRP stat

Instance of StatisticsPRP.

Constructor Detail

ReportPRP

public ReportPRP(ProtPlot prp)

ReportPRP() - constructor

Parameters:

prp - is instance of ProtPlot

title - of plot

Method Detail

getSamplesSubtitle

java.lang.String getSamplesSubtitle()

getSamplesSubtitle() - of samples based on plot mode

Returns:

subtitles

showListOfExprProfileSamplesReport

public void showListOfExprProfileSamplesReport()

showListOfExprProfileSamplesReport() - show popup report of list of samples in the current Protein expression profile.

showFilteredReport

public void showFilteredReport()

showFilteredReport() - show popup report of filtered proteins in the prp.mPidFiltered[0:prp.nMpidFiltered-1] list of mPids [TODO] Sort by expression or by ratioX/Y

showExprProfilesFilteredReport

public boolean showExprProfilesFilteredReport()

showExprProfilesFilteredReport() - show popup of expression profiles of filtered proteins

Returns:

true if succeed

showXYEPsetsMissingProtFilteredReport

public boolean showXYEPsetsMissingProtFilteredReport()

showXYEPsetsMissingProtFilteredReport() - show popup of X&Y or EP sets statistics of missing prot filtered proteins

Returns:

true if succeed

showStateReport

public boolean showStateReport()

showStateReport() - show popup of the state values including slider values

Returns:

true if succeed

showSimilarProteinReport

public boolean showSimilarProteinReport(Cluster clust)

showSimilarProteinReport() - show popup similar-cluster report of similar proteins that were previously clustered.

Returns:

true if succeed

showSampleAssignmentsReport

public boolean showSampleAssignmentsReport()

showSampleAssignmentsReport() - list sample assignments in various sets

Returns:

true if succeed

showSampleNbrsReport

public boolean showSampleNbrsReport()

showSampleNbrsReport() - list the samples and numbers of proteins/sample

Returns:

true if succeed

updateReport

public boolean updateReport()

updateReport() - update the popup report if possible using the rptType. This may be called when the user changes the samples, changes the current protein, changes the filter selection or changes the slider values. NOTE: since some recomputations take a while, we may only want to update when the user presses an optional "Update" button or the prp.autoUpdateFlag was set.

 Types of reports and action:
  Type                 Action
  ----                 --------
  "Help"               fixed - no updates 
  "FilterRpt"          regenerate the report text
  "EPFilterRpt"        regenerate the report text
  "XYEPmissingRpt"     regenerate the report text
  "EPsamplesRpt"       regenerate the report text
  "StateRpt"           regenerate the report text
  "SampleAssignRpt"    regenerate the report text
  "SampleNbrsRpt"      fixed data for the database - NO updates
  "SimClusterRpt"      NOT done here - it is done in Cluster. NO-OP

Returns:

true if did an update