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

M

main(String[]) - Static method in class org.peace_tools.core.PEACE

The main method launches the core dialogs in the system to start up on the swing thread.

mainFrame - Variable in class org.peace_tools.core.AbstractMenuHelper

A convenience reference to the main frame that logically owns this menu helper.

mainFrame - Variable in class org.peace_tools.core.DeleteDialog

A convenient reference to the main frame that logically owns this dialog.

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

A convenient reference to the main frame that logically owns this dialog.

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

The main frame that logically owns this job.

MainFrame - Class in org.peace_tools.core

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

Sets up the default layout for the main frame.

mainFrame - Variable in class org.peace_tools.core.ViewFactory

A convenient reference to the main frame that logically owns this view factory.

mainFrame - Variable in class org.peace_tools.views.ClusterSummaryView

Convenient reference to the main frame class that logically owns this component.

mainFrame - Variable in class org.peace_tools.views.ClusterTreeTableView

Convenient reference to the main frame class that logically owns this component.

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

Convenient reference to the main frame class that logically owns this menu in its JMenuBar.

mainFrame - Variable in class org.peace_tools.views.DataSetPopupMenu

Convenient reference to the main frame class that logically owns this menu.

mainFrame - Variable in class org.peace_tools.views.DataSetTreeView

Convenient reference to the main frame class that logically owns this view in its frame.

mainFrame - Variable in class org.peace_tools.views.DBClassifierEditor

Convenient reference to the main frame class that contains this dialog box.

mainFrame - Variable in class org.peace_tools.views.ESTTableView

Convenient reference to the main frame class that logically owns this component.

mainFrame - Variable in class org.peace_tools.views.GenericHTMLView

Convenient reference to the main frame class that logically owns this menu in its JMenuBar.

mainFrame - Variable in class org.peace_tools.views.JobListView

The main frame that logically owns this job list view.

mainFrame - Variable in class org.peace_tools.views.MSTFileView

Convenient reference to the main frame class that logically owns this menu in its JMenuBar.

mainFrame - Variable in class org.peace_tools.views.overlap.OverlapView

Convenient reference to the main frame class that logically owns this component.

mainFrame - Variable in class org.peace_tools.views.ServerListView

The main frame that logically owns this job list view.

MainFrame.DefaultViewFactory - Class in org.peace_tools.core

A default implementation for a view factory.

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

The constructor.

mainMessage - Variable in class org.peace_tools.core.DeleteDialog

This label contains the main message displayed in this dialog.

makeAnalyzerProperties(FWAnalyzer) - Static method in class org.peace_tools.views.PropertiesTreeMaker

Helper method to create a properties node for a given analyzer entry.

makeClusterNode(ArrayList<ClusterNode>, String) - Static method in class org.peace_tools.data.ClusterFile

Helper method to process a comma separated set of values representing a cluster node.

makeDataSetProperties(DataSet, Component) - Static method in class org.peace_tools.views.PropertiesTreeMaker

Helper method to create a properties node for a given data set entry.

makeFileProperties(String, String) - Static method in class org.peace_tools.views.PropertiesTreeMaker

Helper method to create a properties node for a given file.

makeFilterProperties(Filter) - Static method in class org.peace_tools.views.PropertiesTreeMaker

Helper method to create a properties node for a given data set entry.

makeHeuristicProperties(Heuristic) - Static method in class org.peace_tools.views.PropertiesTreeMaker

Helper method to create a properties node for a given data set entry.

makeJobProperties(JobSummary) - Static method in class org.peace_tools.views.PropertiesTreeMaker

Helper method to create a properties node for a given job summary node.

makeJobProperties(Job) - Static method in class org.peace_tools.views.PropertiesTreeMaker

Helper method to create a properties node for a given MST entry.

makeMetadataEntry(String) - Static method in class org.peace_tools.data.ClusterFile

This is a helper method that is used to parse a line of meta data entry (line starts with a '#' character) and convert it to a a Pair containing a name, value pair and returns the meta data as a pair.

makeMetadataEntry(String) - Static method in class org.peace_tools.data.MST

This is a helper method that is used to parse a line of meta data entry (line starts with a '#' character) and convert it to a a Pair containing a name, value pair and returns the meta data as a pair.

makeMSTNode(HashMap<Integer, MSTNode>, String) - Static method in class org.peace_tools.data.MST

Helper method to process a comma separated set of values representing a MST node.

makeMSTProperties(MSTData, boolean, boolean, Component) - Static method in class org.peace_tools.views.PropertiesTreeMaker

Helper method to create a properties node for a given MST entry.

makeProperties(MSTData, Component) - Static method in class org.peace_tools.views.PropertiesTreeMaker

Build a property tree with MST file as the main entry.

makeProperties(MSTClusterData, Component) - Static method in class org.peace_tools.views.PropertiesTreeMaker

Build a property tree with cluster file as the main entry.

makeServerProperties(String) - Static method in class org.peace_tools.views.PropertiesTreeMaker

Helper method to create a properties node for a given server entry.

makeSummaryProperties(MSTClusterData, Component) - Static method in class org.peace_tools.views.PropertiesTreeMaker

Helper method to create a summary node for a given clustering.

makeToolBarButton(AbstractButton, boolean) - Static method in class org.peace_tools.generic.Utilities

Method to add mouse adapter to make button like a tool bar button.

marshall(Element) - Method in class org.peace_tools.workspace.ClassifierList

Method to marshall the data stored in this object to become part of a DOM tree element passed in.

marshall(PrintWriter) - Method in class org.peace_tools.workspace.ClassifierList

Method to marshall the data stored in this object directly to a XML fragement.

marshall(Element) - Method in class org.peace_tools.workspace.DataSet

Method to marshall the data stored in this object to become part of a DOM tree element passed in.

marshall(PrintWriter) - Method in class org.peace_tools.workspace.DataSet

Method to marshall the data stored in this object directly to a XML fragment.

marshall(Element) - Method in class org.peace_tools.workspace.DBClassifier

Method to marshall the data stored in this object to become part of a DOM tree element passed in.

marshall(PrintWriter) - Method in class org.peace_tools.workspace.DBClassifier

Method to marshall the data stored in this object directly to a XML fragment.

marshall(Element) - Method in class org.peace_tools.workspace.Filter

Method to marshall the data stored in this object to become part of a DOM tree element passed in.

marshall(PrintWriter) - Method in class org.peace_tools.workspace.Filter

Method to marshall the data stored in this object directly to a XML fragment.

marshall(Element) - Method in class org.peace_tools.workspace.FWAnalyzer

Method to marshall the data stored in this object to become part of a DOM tree element passed in.

marshall(PrintWriter) - Method in class org.peace_tools.workspace.FWAnalyzer

Method to marshall the data stored in this object directly to a XML fragment.

marshall(Element) - Method in class org.peace_tools.workspace.Heuristic

Method to marshall the data stored in this object to become part of a DOM tree element passed in.

marshall(PrintWriter) - Method in class org.peace_tools.workspace.Heuristic

Method to marshall the data stored in this object directly to a XML fragment.

marshall(Element) - Method in class org.peace_tools.workspace.Job

Method to marshall the data stored in this object to become part of a DOM tree element passed in.

marshall(PrintWriter) - Method in class org.peace_tools.workspace.Job

Method to marshall the data stored in this object directly to a XML fragment.

marshall(Element) - Method in class org.peace_tools.workspace.JobList

Method to marshall the data stored in this object to become part of a DOM tree element passed in.

marshall(PrintWriter) - Method in class org.peace_tools.workspace.JobList

Method to marshall the data stored in this object directly to a XML fragment.

marshall(Element) - Method in class org.peace_tools.workspace.JobSummary

Method to marshall the data stored in this object to become part of a DOM tree element passed in.

marshall(PrintWriter) - Method in class org.peace_tools.workspace.JobSummary

Method to marshall the data stored in this object directly to a XML fragment.

marshall(Element) - Method in class org.peace_tools.workspace.MSTClusterData

Method to marshall the data stored in this object to become part of a DOM tree element passed in.

marshall(PrintWriter) - Method in class org.peace_tools.workspace.MSTClusterData

Method to marshall the data stored in this object directly to a XML fragment.

marshall(Element) - Method in class org.peace_tools.workspace.MSTData

Method to marshall the data stored in this object to become part of a DOM tree element passed in.

marshall(PrintWriter) - Method in class org.peace_tools.workspace.MSTData

Method to marshall the data stored in this object directly to a XML fragment.

marshall(Element) - Method in class org.peace_tools.workspace.Server

Method to marshall the data stored in this object to become part of a DOM tree element passed in.

marshall(PrintWriter) - Method in class org.peace_tools.workspace.Server

Method to marshall the data stored in this object directly to a XML fragment.

marshall(Element) - Method in class org.peace_tools.workspace.ServerList

Method to marshall the data stored in this object to become part of a DOM tree element passed in.

marshall(PrintWriter) - Method in class org.peace_tools.workspace.ServerList

Method to marshall the data stored in this object directly to a XML fragement.

marshall() - Method in class org.peace_tools.workspace.Workspace

Obtain a new DOM document representing the data associated with the current work space configuration information.

marshall(PrintWriter) - Method in class org.peace_tools.workspace.Workspace

Method to marshall the data stored in this object directly to a XML fragment.

MASK_MSG - Static variable in class org.peace_tools.core.job.JobInfoWizardPage

A generic informational message that is displayed at the top of this wizard page to provide some additional information to the user.

maskBases - Variable in class org.peace_tools.core.job.JobInfoWizardPage

Check box to permit user to mask out or process nucleotides in low-case characters.

maxClusterSize - Variable in class org.peace_tools.views.ClusterSummaryView

The largest cluster in the set of clusters that we are working with.

maxCol - Variable in class org.peace_tools.data.OverlapModel

The widest row in the estEntryTable.

maxESTLen - Variable in class org.peace_tools.data.ClusterTreeTableModel

The maximum length of an EST sequence to be adapted by this model.

maxESTLen - Variable in class org.peace_tools.data.ESTTableModel

The maximum length of an EST sequence to be adapted by this model.

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

The total wall clock run time to be reserved for this job when submitting via a PBS system.

MEM_USAGE - Static variable in class org.peace_tools.data.DataStore

Memory statistics to be displayed to the user after formatting (to fill in the necessary information).

MEM_USAGE_LOG - Static variable in class org.peace_tools.data.DataStore

A simple log message that is cut just before the memory checks are performed by the memoryCheck() method in this class.

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

The peak memory to be reserved for this job when submitting via a PBS system.

memoryCheck(File, Component) - Method in class org.peace_tools.data.DataStore

Helper method to ensure there is sufficient memory to load data.

MENU_ITEM - Static variable in class org.peace_tools.generic.Utilities

Constant that can be supplied to the createMenuItem method

menuHelpers - Variable in class org.peace_tools.core.MainFrame

The list of menu helpers associated with this main frame.

MenuSubTitles - Static variable in class org.peace_tools.core.FileMenuHelper

The various sub menu titles that are used in the main menu.

MenuSubTitles - Static variable in class org.peace_tools.core.HelpMenuHelper

The various sub menu titles that are used in the main menu.

MenuSubTitles - Static variable in class org.peace_tools.core.JobMenuHelper

The various sub menu titles that are used in the main menu.

MenuSubTitles - Static variable in class org.peace_tools.core.ServerMenuHelper

The various sub menu titles that are used in the main menu.

MenuSubTitles - Static variable in class org.peace_tools.core.ViewMenuHelper

The various sub menu titles that are used in the main menu.

MenuTitles - Static variable in class org.peace_tools.core.FileMenuHelper

The strings for each menu title created by this helper.

MenuTitles - Static variable in class org.peace_tools.core.HelpMenuHelper

The strings for each menu title created by this helper.

MenuTitles - Static variable in class org.peace_tools.core.ServerMenuHelper

The strings for each menu title created by this helper.

MenuTitles - Static variable in class org.peace_tools.core.ViewMenuHelper

The strings for each menu title created by this helper.

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

A set of predefined static messages to be displayed to the user indicating the entry to be removed and the implications of removing the entry.

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

The set of meta data that was loaded from the cluster file.

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

The set of meta data that was loaded from the MST file.

metric - Variable in class org.peace_tools.data.MSTNode

The similarity/distance metric generated by a given EST analyzer indicating the relationship between this node and its parent node.

MIN_COL_SCALE_FACTOR - Variable in class org.peace_tools.views.overlap.OverlapView

Factor to determine minimum column scale value.

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

The minimum length of the EST associated with the length filter.

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

Creates a directory on the server.

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

Creates a directory on the server.

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

Creates a directory on the server.

model - Variable in class org.peace_tools.views.ClusterTreeTableView

The table-tree model that is being used to display information in this view.

model - Variable in class org.peace_tools.views.ESTTableView

The table model that is being used to display information in this view.

model - Variable in class org.peace_tools.views.JobListView

The model that we are using to render the information in the tabular view of jobs.

model - Variable in class org.peace_tools.views.ServerListView

The model that we are using to render the information in the tabular view of servers in the workspace.

modelSize - Variable in class org.peace_tools.views.overlap.Ruler

The Dimension that provides the necessary information for rendering the ruler displayed in this class.

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

A transient (not persistent) reference to the monitor thread for this job (if any).

monoFont - Variable in class org.peace_tools.views.CustomTableCellRenderer

The mono-spaced font used to render the EST sequences in the tree view.

MST - Class in org.peace_tools.data

The top-level class that encapsulates all the pertinent information regarding a MST data file.

MST(String) - Constructor for class org.peace_tools.data.MST

The constructor creates an empty MST object.

mst - Variable in class org.peace_tools.data.MSTTreeModel

The MST data file that provides all the necessary information for displaying the MST.

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

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

MSTClusterData - Class in org.peace_tools.workspace

This class encapsulates all the data necessary to use a given clustering information generated from a Spanning Tree (MST) data file.

MSTClusterData(String, String, String, String, int, JobSummary) - Constructor for class org.peace_tools.workspace.MSTClusterData

The constructor to create a fully populated MSTClusterData object that contains all the meta data regarding a MST file that has been generated from a given EST file.

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

The MST data entry that is finally created by this job wizard when the final wizard page is displayed.

MSTData - Class in org.peace_tools.workspace

This class encapsulates all the data necessary to use a given Minimum Spanning Tree (MST) data file.

MSTData(String, MSTData.MSTBuilderType, String, String, FWAnalyzer, JobSummary) - Constructor for class org.peace_tools.workspace.MSTData

The constructor to create a fully populated MSTData object that contains all the meta data regarding a MST file that has been generated from a given EST file.

MSTData.MSTBuilderType - Enum in org.peace_tools.workspace

Different enumerations defining the different approaches that PEACE currently supports for building a MST.

MSTData.MSTBuilderType() - Constructor for enum org.peace_tools.workspace.MSTData.MSTBuilderType

mstFile - Variable in class org.peace_tools.core.job.MSTWizardPage

Field to read/display the install path where the MST file will be saved after it is generated on the server.

MSTFileView - Class in org.peace_tools.views

A simple tree-based view of a Minimum Spanning Tree (MST).

MSTFileView(MainFrame, MSTTreeModel) - Constructor for class org.peace_tools.views.MSTFileView

The constructor creates the tree view using the data from the current work space.

MSTFileView.DataSetRenderer - Class in org.peace_tools.views

A tree cell renderer that essentially provides a better representative set of Icons to make the overall display look a bit prettier.

MSTFileView.DataSetRenderer() - Constructor for class org.peace_tools.views.MSTFileView.DataSetRenderer

mstID - Variable in class org.peace_tools.workspace.MSTClusterData

The unique value for the MSTData entry based on which this cluster data was generated.

mstList - Variable in class org.peace_tools.workspace.DataSet

The optional list of MST data files that are currently associated with this data set.

MSTNode - Class in org.peace_tools.data

A class that represents a single node in a Minimum Spanning Tree (MST).

MSTNode(MSTNode, int, float, int) - Constructor for class org.peace_tools.data.MSTNode

Constructor to create a MSTNode.

mstTree - Variable in class org.peace_tools.views.MSTFileView

The actual JTree that provides a hierarchical view of the data files currently configured on this work space.

MSTTreeModel - Class in org.peace_tools.data

A bridge class between a MST and a JTree.

MSTTreeModel(MST, ESTList, MSTData) - Constructor for class org.peace_tools.data.MSTTreeModel

The default constructor.

MSTWizardPage - Class in org.peace_tools.core.job

This class serves as an interactive page in a JobWizard.

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

The constructor.

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

The wizard page that collects information about the MST file and the server on which the job is to be run.