A B C D E F G H I J K L M N O P R S T U V W X Y

F

FILE_ATTRIB - Static variable in class org.peace_tools.core.FileInfo

Bit value indicating if this entry is a regular file.

FILE_DEL_ERROR - Static variable in class org.peace_tools.core.DeleteDialog

A message that is formatted and displayed to the user when an error occurs when deleting files or directories corresponding to a given entry in the work space.

FILE_ICON - Static variable in class org.peace_tools.views.PropertiesTreeMaker

A static constant to refer to the file icon position in the PropertiesTreeMaker.CustomIcons array.

FILE_MISMATCH - Static variable in class org.peace_tools.core.job.SubmitJobWizardPage

A generic informational message that is displayed to the user when EST file mismatch is detected

FileCopyDialog - Class in org.peace_tools.core

This is a dialog class for copying generated files.

FileCopyDialog(MainFrame, Job) - Constructor for class org.peace_tools.core.FileCopyDialog

The constructor for creating and configuring this dialog.

fileInfo - Variable in class org.peace_tools.core.FileCopyDialog

These labels are created in the constructor for each file to be copied.

FileInfo - Class in org.peace_tools.core

This is a simple class that is used to encapsulate information about a given file.

FileInfo(String, long, long, int) - Constructor for class org.peace_tools.core.FileInfo

Create a complete file information class with all the information.

FileMenuHelper - Class in org.peace_tools.core

The file menu helper for the application.

FileMenuHelper(MainFrame) - Constructor for class org.peace_tools.core.FileMenuHelper

The constructor.

fileName - Variable in class org.peace_tools.data.ClusterFile

The file name from where the data has been read.

fileName - Variable in class org.peace_tools.data.MST

The file name from where the data has been read.

fileNameDisplay - Variable in class org.peace_tools.views.LogPane

This is an internal text field that is used to display the file to which the logs are being currently written.

FileNameRenderer - Variable in class org.peace_tools.views.DataSetFileListView

An instance of the cell renderer that is used to render the first column in the table with a suitable status icon.

fileTable - Variable in class org.peace_tools.views.DataSetFileListView

The actual JTable that provides a graphical view of the list of servers currently configured on this work space.

FileTypeIcons - Static variable in class org.peace_tools.views.DataSetFileListView

The list of icons that are used by this table cell renderer to provide visual cues about the current status of this server.

Filter - Class in org.peace_tools.workspace

This class is meant to encapsulate the information and parameters for various filters used to filter out ESTs that may negatively impact clustering.

Filter(Filter.FilterType) - Constructor for class org.peace_tools.workspace.Filter

The only constructor for this class.

Filter.FilterType - Enum in org.peace_tools.workspace

Different enumerations defining the different types of Filters that are currently supported.

Filter.FilterType() - Constructor for enum org.peace_tools.workspace.Filter.FilterType

FILTER_LIST_MSG - Static variable in class org.peace_tools.core.job.FiltersWizardPage

A generic informational message that is displayed to the user if the string list in filterList is invalid.

filterList - Variable in class org.peace_tools.core.job.FiltersWizardPage

A list of comma separated strings (over ATCG) that are used to generate dummy low complexity sequences for filtering out ESTs that have low complexity regions.

filters - Variable in class org.peace_tools.workspace.Job

The list of filters configured by the user for this job.

FILTERS_ICON - Static variable in class org.peace_tools.views.PropertiesTreeMaker

A static constant to refer to the filters icon position in the PropertiesTreeMaker.CustomIcons array.

filtersSummary - Variable in class org.peace_tools.workspace.JobSummary

A string that contains summary of filters run as a part of the job used to generate the associated data.

FiltersWizardPage - Class in org.peace_tools.core.job

This class serves as an interactive page in a JobWizard.

FiltersWizardPage(JobWizard) - Constructor for class org.peace_tools.core.job.FiltersWizardPage

The constructor.

filterType - Variable in class org.peace_tools.workspace.Filter

The name/type of this filter.

finalize() - Method in class org.peace_tools.views.LogPane

This method overrides the default implementation in the base class to remove the log pane from the list of log listeners to receive updates.

finishButton - Variable in class org.peace_tools.generic.WizardDialog

The "Finish" button that is displayed at the bottom of the wizard in a separate panel.

fireDataChanged() - Method in class org.peace_tools.data.OverlapModel

Helper method to notify listeners whenever data changes.

fireTableStructureChanged() - Method in class org.peace_tools.data.ClusterTreeTableModel

Helper method to broadcast notification to all model listeners.

fireTreeStructureChanged(Object) - Method in class org.peace_tools.data.DataSetTreeModel

The only event raised by this model is TreeStructureChanged with the appropriate entry to be

fireTreeStructureChanged(Object) - Method in class org.peace_tools.data.MSTTreeModel

The only event raised by this model is TreeStructureChanged with the appropriate entry to be

fireWorkspaceChanged(WorkspaceEvent) - Method in class org.peace_tools.workspace.Workspace

Utility method to notify all the listeners about a change to the Workspace.

firstLaunch - Variable in class org.peace_tools.core.WorkspaceChooser

Flag to indicate if this is the first time ever the user is running PEACE GUI.

FirstTimeMsg - Static variable in class org.peace_tools.core.WorkspaceChooser

A static piece of text that is prepended to the license text when PEACE is launched for the first time to provide the user with some additional information.

fixedMsgs - Variable in class org.peace_tools.core.server.ServerInfoWizardPage

These labels are created in the constructor but one of them remains hidden.

fixedMsgs - Variable in class org.peace_tools.core.server.ServerTypeWizardPage

These labels are created in the constructor but one of them remains hidden.

flavors - Variable in class org.peace_tools.generic.dndTabs.DnDTabHandler.TransferableTab

An array of flavours that is supported by this Transferable node.

font - Variable in class org.peace_tools.views.overlap.OverlapPanel

The font being used by this panel to render information for each fragment.

FONT_SIZE_CHANGE - Variable in class org.peace_tools.views.LogPane

Constant to make the fonts in the controls in the tool bar a bit small because they look huge on Linux.

frameSize - Variable in class org.peace_tools.core.job.AnalyzerWizardPage

Formatted field to read the frame size to be used for analysis.

frameSizeAuto - Variable in class org.peace_tools.core.job.AnalyzerWizardPage

A simple JLabel that is used instead of the AnalyzerWizardPage.frameSize spinner whenever the user selected TwoPassD2 to indicate that the frame size is automatically determined.

fstat(String) - Method in class org.peace_tools.core.session.LocalServerSession

Obtain information about a given path on the server.

fstat(String) - Method in class org.peace_tools.core.session.RemoteServerSession

Obtain information about a given path on the remote machine.

fstat(String) - Method in class org.peace_tools.core.session.ServerSession

Obtain information about a given path on the server.

FWAnalyzer - Class in org.peace_tools.workspace

A simple class to encapsulate information about the frame/word analyzer that was used to generate Minimum Spanning Tree (MST) data.

FWAnalyzer(FWAnalyzer.FWAnalyzerType, boolean, int, int, String, int) - Constructor for class org.peace_tools.workspace.FWAnalyzer

The constructor merely initializes the immutable instance variables to their values using appropriate parameters.

FWAnalyzer.FWAnalyzerType - Enum in org.peace_tools.workspace

The different kinds of frame/word analyzers that are currently supported in PEACE.

FWAnalyzer.FWAnalyzerType() - Constructor for enum org.peace_tools.workspace.FWAnalyzer.FWAnalyzerType

fwp - Variable in class org.peace_tools.core.job.JobWizard

The filter wizard page that contains information about the various filters configured by the user to weed out problematic ESTs that could negatively impact the quality of clustering.