com.pacbio.secondary.vis.gui.app

Class VioletApp

java.lang.Object

com.pacbio.secondary.vis.gui.app.VioletAppBase

com.pacbio.secondary.vis.gui.app.VioletApp

Direct Known Subclasses:

DesktopApp, LocalTestApp, WebStartApp

public class VioletApp
extends VioletAppBase

Author:

mmilletti

Nested Class Summary

Nested classes/interfaces inherited from class com.pacbio.secondary.vis.gui.app.VioletAppBase

VioletAppBase.APP_TYPE

Field Summary

Fields inherited from class com.pacbio.secondary.vis.gui.app.VioletAppBase

app_options, app_type, cmd_options, data_storage, last_busy, last_data, last_message, last_progress, main_frame, OPEN_REMOTEDATA_NO_ERROR, rois_storage

Constructor Summary

Constructors

Constructor and Description
VioletApp(java.lang.String[] args, VioletAppBase.APP_TYPE type)

Method Summary

Methods

Modifier and Type	Method and Description
int	createAndLoadDataStorage(boolean showProgress)
protected boolean	createAndShowGUI()
protected int	createCmdOptionsFromRemoteDataSelection(java.lang.String[] cmd_line)
boolean	importConsensusSequence(WsFastaSequenceInfo data, GenomicViewDetails view, boolean update)
void	importDataFile(java.io.File file)
void	importDataFromInputStream(java.io.InputStream stream, TrackDataInfo info)
boolean	importGZippedHDFResults(WsResults data, TrackDataInfo clientData)
boolean	importIPDConsensus(WsIPDConsensusInfo data, GenomicViewDetails view, boolean update)
boolean	importReferenceSequence(WsFastaSequenceInfo data, GenomicViewDetails view, boolean update)
void	launchHelpTopicInWebBrowser(java.lang.String topic)
void	launchPanelHelpInWebBrowser(java.lang.String context)
void	launchWebSiteInWebBrowser(java.lang.String site_url)
boolean	loadDefaultWorkspace()
protected void	loadROIsFromProject() load bookmarks if present in same directory as project.jnlp
boolean	loadWorkspaceFromBase64String(java.lang.String layout)
boolean	loadWorkspaceFromResource(java.lang.String res_file)
boolean	loadWorkspaceFromServer()
boolean	saveWorkspaceToServer()
int	selectRemoteData()
void	setLogScaling(boolean b) call to turn visual filtering on or off updates region and whole genome view as needed
void	setViewFilter(boolean b, java.lang.String filter) call to turn visual filtering on or off updates region and details view as needed
void	setVisibleLocusDetailsPanel(Locus locus, boolean updateTablePanel) selects a new locus in details panel
void	setVisibleLocusGenomePanel(Locus locus, boolean updateTablePanel, boolean isGoTo) selects a new locus in genome panel, eventually updates region and details
void	setVisibleLocusRegionPanel(Locus locus, boolean updateTablePanel) selects a new locus in region panel, eventually updates details

Methods inherited from class com.pacbio.secondary.vis.gui.app.VioletAppBase

getAppOptions, getAppTitle, getAppType, getCommandLineOptions, getDataStorage, getDetailsOptions, getGeneDB, getHDFServiceURL, getHostCodebaseHttpPort, getHostName, getIdeogramDB, getJNLPServiceURL, getReferenceInfo, getRegionsOfInterestStorage, getSlots, getSMRTPortalHomeURL, getSMRTViewHomeURL, getVioletFrame, getVisServiceURL, isScreenResolutionMaximizable, isScreenResolutionValid, isServerInWhiteList, isStandAlone, setApplicationLookAndFeel, setApplicationLookAndFeelOld, setAppOptions, setCurrentContig, setDetailsOptions, setRegionsOfInterestStorage, setStatusBarBusy, setStatusBarDataInfoText, setStatusBarProgress, setStatusBarText, setVioletFrame, showErrorMessageOnDataLoadFailure, updateLockedPanels

Methods inherited from class java.lang.Object

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

Constructor Detail

VioletApp

public VioletApp(java.lang.String[] args,
         VioletAppBase.APP_TYPE type)

Method Detail

createAndShowGUI

protected boolean createAndShowGUI()

createAndLoadDataStorage

public int createAndLoadDataStorage(boolean showProgress)

loadROIsFromProject

protected void loadROIsFromProject()

load bookmarks if present in same directory as project.jnlp

selectRemoteData

public int selectRemoteData()

createCmdOptionsFromRemoteDataSelection

protected int createCmdOptionsFromRemoteDataSelection(java.lang.String[] cmd_line)

importDataFromInputStream

public void importDataFromInputStream(java.io.InputStream stream,
                             TrackDataInfo info)

importReferenceSequence

public boolean importReferenceSequence(WsFastaSequenceInfo data,
                              GenomicViewDetails view,
                              boolean update)

importConsensusSequence

public boolean importConsensusSequence(WsFastaSequenceInfo data,
                              GenomicViewDetails view,
                              boolean update)

importIPDConsensus

public boolean importIPDConsensus(WsIPDConsensusInfo data,
                         GenomicViewDetails view,
                         boolean update)

importGZippedHDFResults

public boolean importGZippedHDFResults(WsResults data,
                              TrackDataInfo clientData)

importDataFile

public void importDataFile(java.io.File file)

setVisibleLocusGenomePanel

public void setVisibleLocusGenomePanel(Locus locus,
                              boolean updateTablePanel,
                              boolean isGoTo)

selects a new locus in genome panel, eventually updates region and details

Parameters:

locus -

updateTablePanel -

isGoTo -

setVisibleLocusRegionPanel

public void setVisibleLocusRegionPanel(Locus locus,
                              boolean updateTablePanel)

selects a new locus in region panel, eventually updates details

Parameters:

locus -

updateTablePanel -

setVisibleLocusDetailsPanel

public void setVisibleLocusDetailsPanel(Locus locus,
                               boolean updateTablePanel)

selects a new locus in details panel

Parameters:

locus -

updateTablePanel -

launchPanelHelpInWebBrowser

public void launchPanelHelpInWebBrowser(java.lang.String context)

launchHelpTopicInWebBrowser

public void launchHelpTopicInWebBrowser(java.lang.String topic)

launchWebSiteInWebBrowser

public void launchWebSiteInWebBrowser(java.lang.String site_url)

loadDefaultWorkspace

public boolean loadDefaultWorkspace()

loadWorkspaceFromResource

public boolean loadWorkspaceFromResource(java.lang.String res_file)

loadWorkspaceFromBase64String

public boolean loadWorkspaceFromBase64String(java.lang.String layout)

loadWorkspaceFromServer

public boolean loadWorkspaceFromServer()

saveWorkspaceToServer

public boolean saveWorkspaceToServer()

setViewFilter

public void setViewFilter(boolean b,
                 java.lang.String filter)

call to turn visual filtering on or off updates region and details view as needed

Parameters:

b -

setLogScaling

public void setLogScaling(boolean b)

call to turn visual filtering on or off updates region and whole genome view as needed

Parameters:

b -