Serialized Form
|
Package org.peace_tools.core |
serialVersionUID: 7642494335728910205L
cp
CustomPanel cp
- A custom panel that actually has the PEACE logo as the
background image. This panel is used to hold all the
components just to make this dialog look nice.
AuthorList
java.lang.String[] AuthorList
- The list of authors and their information to be loaded from
text files in PEACE install directory.
AuthorImages
java.util.ArrayList<E> AuthorImages
- The icons to be displayed for each author to make the about
dialog a bit more fancy.
serialVersionUID: -4658096968134590995L
mainFrame
MainFrame mainFrame
- A convenient reference to the main frame that logically owns
this dialog.
wsEntry
java.lang.Object wsEntry
- The actual work space entry to be removed by this dialog. This
object is a valid work space entry such as: Job, Server,
MSTClusterData, MSTData, or DataSet. However, different actions
and messages are generated depending on the entry being deleted.
deleteFiles
javax.swing.JCheckBox deleteFiles
- A check box to determine if the user wants the physical file to
be deleted as well. If this check box is checked, the physical
files associated with the entry are deleted first before the
entry is deleted.
icon
javax.swing.JLabel icon
- The icon that is displayed in this dialog box to the left.
The icon is stored separately to provide the option of
changing it at a later date.
progressBar
javax.swing.JProgressBar progressBar
- The progress bar that is placed in indeterminate mode when
deleting remote entries and directories.
bottomPanel
javax.swing.JPanel bottomPanel
- The bottom panel in the dialog box that contains both the
OK/Cancel buttons and the progress bar. Only one of them
is shown as this panel is set to use a CardLayout manager.
delPath
javax.swing.JLabel delPath
- This label is used to display the actual path being deleted
when physical file deletion is requested. Initially it is
set to being empty.
mainMessage
javax.swing.JLabel mainMessage
- This label contains the main message displayed in this dialog.
This label's message is updated when the deletion process starts
to make it appear disabled.
serialVersionUID: 5397447232688023756L
job
Job job
- The job entry for which the files are to be copied from the
server (on which the job was run) to the local machine on
which the GUI is running.
fileInfo
javax.swing.JLabel[] fileInfo
- These labels are created in the constructor for each file to
be copied. The labels provide visual information about the
files to the user.
progressInfo
javax.swing.JLabel progressInfo
- Label displayed on top of the progress bar indicating the
file being currently copied.
progressBar
javax.swing.JProgressBar progressBar
- The progress bar that is displayed at the bottom of the
dialog box to indicate the progress made in copying
files.
session
ServerSession session
- The server session to be used for copying the necessary files.
This session is created in the run() method once the dialog
is displayed.
targetFileNames
java.lang.String[] targetFileNames
- The names of the files (with absolute path on local machine)
to be copied from the remote machine to the local machine.
This list is populated in the constructor.
mainFrame
MainFrame mainFrame
- A convenient reference to the main frame that logically owns
this dialog.
serialVersionUID: 1414403952944170343L
centerPane
DnDTabbedPane centerPane
- The permanent tab that is always present in in the main frame.
This pane is created in the constructor and is never changed.
desktop
javax.swing.JPanel desktop
- This is the parent component of all the tabs and tabbed panes
that constitute the visual layout of the main frame. This
component is always present and is never removed from the
main frame.
defaultViewFactory
MainFrame.DefaultViewFactory defaultViewFactory
- The default view factory that is used to create all the
views associated with this main frame.
menuHelpers
java.util.HashMap<K,V> menuHelpers
- The list of menu helpers associated with this main frame.
This hash map is used to maintain and rapidly access various
menu helpers associated with the main frame. The list is
populated in the createMenus() method.
toolbar
javax.swing.JToolBar toolbar
- A reference to the toolbar associated with this main frame. The
tool bar may be visible or invisible at any given time.
serialVersionUID: 5779507970297217323L
firstLaunch
boolean firstLaunch
- Flag to indicate if this is the first time ever the user is running
PEACE GUI. In this situation the user is forced to accept our
license before proceeding further.
showFirstTimeMsg
boolean showFirstTimeMsg
- Flag that tracks if the first time welcome message has already
been displayed or now.
tabs
javax.swing.JTabbedPane tabs
- The set of tabs that are displayed in this dialog for the user
to work with.
wsList
javax.swing.JComboBox wsList
- The list of work spaces that the user can choose from or edit
to start up the GUI session.
workspace
java.lang.String workspace
- The selected work space that is set after the user successfully
chooses a work space.
peace
PEACE peace
- Reference to the main PEACE class. The reference is used to
create the main frame after the user has selected a valid
work space.
cp
CustomPanel cp
- A custom panel that actually has the PEACE logo as the
background image. This panel is used to hold all the
components just to make the GUI look nice.
|
Package org.peace_tools.core.dataset |
serialVersionUID: 804993573751301886L
dataSet
DataSet dataSet
- This is the server entry that is being currently edited via
this wizard. This object is accessed by the various pages
in this wizard and updated as the user navigates through
the wizard pages.
estList
ESTList estList
- The list of ESTs associated with this data set. This object
is set whenever one of the pages loads the EST data.
serialVersionUID: 8538523942750752144L
wizard
DataSetWizard wizard
- A reference to the wizard dialog that logically owns this
page. This reference is used to enable and disable
buttons on this wizard appropriately.
dataSet
DataSet dataSet
- Information about the actual data set entry being edited. This
reference is set when this class is instantiated and is never
changed during the life time.
estFile
javax.swing.JTextField estFile
- Field to read/display the install path where PEACE is (or has
been) installed on the given server.
description
javax.swing.JTextArea description
- Field to read and edit a brief description about the server.
This information can be anything the user desires and is
meaningful only to the user.
lockPath
boolean lockPath
- If this flag is set to true, then this wizard permits the
user only to change the install path on the server.
browse
javax.swing.JButton browse
- The browse button to be enabled only for local installs.
serialVersionUID: 8538523942750752144L
STANDARD_MSG
java.lang.String STANDARD_MSG
- A simple standard message to be displayed at the top of this page.
INFO_MSG
java.lang.String INFO_MSG
- A simple standard message to be displayed at the bottom of this
page.
STATS_STR
java.lang.String STATS_STR
- A simple standard message to be displayed at the bottom of this
page.
wizard
DataSetWizard wizard
- A reference to the wizard dialog that logically owns this
page. This reference is used to enable and disable
buttons on this wizard appropriately.
dataSet
DataSet dataSet
- Information about the actual data set entry being edited. This
reference is set when this class is instantiated and is never
changed during the life time.
infoFields
javax.swing.text.JTextComponent[] infoFields
- Field to be displayed to the user in this wizard pane. The
first field contains the name of the EST data file and the
second field is a multi-line text area that contains some
details about the EST file.
|
Package org.peace_tools.core.job |
serialVersionUID: 8538523942750752144L
wizard
JobWizard wizard
- A reference to the wizard dialog that logically owns this
page. This reference is used to enable and disable
buttons on this wizard appropriately.
analyzerList
javax.swing.JComboBox analyzerList
- A combo-box to select the type of frame/word algorithm to
be used for computing similarity metric.
frameSize
javax.swing.JSpinner frameSize
- Formatted field to read the frame size to be used for
analysis.
frameSizeAuto
javax.swing.JLabel frameSizeAuto
- 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.
wordSize
javax.swing.JComboBox wordSize
- This combo box is provided to permit the user to select a
suitable word size to be used for analysis. Currently the
word size is locked to 6.
cacheList
javax.swing.JComboBox cacheList
- A combo-box to select the type of caching that must be used
to cache intermediate values to improve performance of
the analyzer.
cacheSize
javax.swing.JSpinner cacheSize
- The size of the cache (number of entries maintained in the
cache) to be used for analysis.
serialVersionUID: -1193172876744546755L
wizard
JobWizard wizard
- A reference to the wizard dialog that logically owns this
page. This reference is used to enable and disable
buttons on this wizard appropriately.
clusterFile
javax.swing.JTextField clusterFile
- Field to read/display the install path where the MST file
will be saved after it is generated on the server.
browse
javax.swing.JButton browse
- The browse button to be enabled the user to choose the
directory where the file is to be stored.
threshold
javax.swing.JSpinner threshold
- The spinner for setting the threshold.
description
javax.swing.JTextArea description
- A brief description about the cluster file. This information
is meaningful only to the user.
infoLabels
javax.swing.JLabel[] infoLabels
- This array contains three informational labels containing the
information in
ClusterWizardPage.THRESHOLD_INFO, ClusterWizardPage.TWO_PASS_INFO, and
ClusterWizardPage.CLU_INFO respectively in that order. The labels are
created in ClusterWizardPage.createNotesPanel() method and are
suitably displayed by the ClusterWizardPage.pageChanged(WizardDialog, int, int)
method.
serialVersionUID: 6691921082180723745L
wizard
JobWizard wizard
- A reference to the wizard dialog that logically owns this
page. This reference is used to enable and disable
buttons on this wizard appropriately.
enableLenFilter
javax.swing.JCheckBox enableLenFilter
- Check box to indicate if the length filter must be enabled
for this job.
minLen
javax.swing.JSpinner minLen
- The minimum length of the EST associated with the length filter.
ESTs below this length are filtered out by the length filter
(if it is enabled).
enableLCFilter
javax.swing.JCheckBox enableLCFilter
- Check box to indicate if the Low Complexity (LC) filter must
be enabled for this job.
filterList
javax.swing.JTextField filterList
- 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.
serialVersionUID: 8538523942750752144L
heuristicPanel
javax.swing.JPanel heuristicPanel
- This panel actually contains all the controls for setting up the
necessary heuristics and their parameters required by certain
analyzers. Some of the analyzers currently do not permit setting or
modifications of heuristics. In this case this panel is not displayed
to the user. Instead a simple message indicating that there are no
heuristics to be configured is displayed to the user.
wizard
JobWizard wizard
- A reference to the wizard dialog that logically owns this
page. This reference is used to enable and disable
buttons on this wizard appropriately.
awp
AnalyzerWizardPage awp
- A reference to the analyzer wizard page from where the the
frame size set for the analyzer is obtained and used to
seed the frame size for the t/v heuristic.
enableUV
javax.swing.JCheckBox enableUV
- Check box to indicate if the u/v sample heuristic is to be
used for this job.
enableTV
javax.swing.JCheckBox enableTV
- Check box to indicate if the t/v heuristic is to be
used for this job. Note that t/v heuristic needs u/v
heuristic to be enabled.
uvParams
javax.swing.JSpinner[] uvParams
- The array of three configuration values for the u/v
heuristic. The first entry is v (the length of common words
to search for), the second entry is u (number of v-word matches)
and word shift (number of words to shift by)
tvParams
javax.swing.JSpinner[] tvParams
- The array of two configuration parameter values for the t/v
heuristic. The first entry is frame size (it is fixed based on
frame size of analyzer), the second entry is t (number of
v-word matches).
serialVersionUID: 8538523942750752144L
wizard
JobWizard wizard
- A reference to the wizard dialog that logically owns this
page. This reference is used to enable and disable
buttons on this wizard appropriately.
dataSetList
javax.swing.JComboBox dataSetList
- A combo-box to select the data set to be used for this job.
This field is created and populated in the constructor.
description
javax.swing.JTextArea description
- Field to read and edit a brief description about the job.
This information can be anything the user desires and is
meaningful only to the user.
maskBases
javax.swing.JCheckBox maskBases
- Check box to permit user to mask out or process nucleotides in
low-case characters. If this check box is un-checked then
"--no-mask-bases" is added to PEACE command line.
serialVersionUID: 804993573751301886L
jiwp
JobInfoWizardPage jiwp
- The job information wizard page that contains the description
of the job.
awp
AnalyzerWizardPage awp
- The analyzer wizard page contains the analyzer information to
be used for constructing the MST for this job.
hwp
HeuristicsWizardPage hwp
- The analyzer wizard page contains the heuristic information to
be used for constructing the MST for this job.
fwp
FiltersWizardPage fwp
- 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.
mwp
MSTWizardPage mwp
- The wizard page that collects information about the MST file
and the server on which the job is to be run.
cwp
ClusterWizardPage cwp
- The wizard page that collects information about the cluster
file in which clustering information is to be stored.
job
Job job
- The job entry that is finally created by this job wizard
when the final wizard page is displayed. This entry is
used by the final wizard page to perform its operations.
mstData
MSTData mstData
- The MST data entry that is finally created by this job wizard
when the final wizard page is displayed. This entry is
used by the final wizard page to perform its operations.
clusterData
MSTClusterData clusterData
- The cluster entry that is finally created by this job wizard
when the final wizard page is displayed. This entry is
used by the final wizard page to perform its operations.
mainFrame
MainFrame mainFrame
- The main frame that logically owns this job. This value is
used to create a job monitor if a job is successfully
submitted to run on a server.
serialVersionUID: -1193172876744546755L
wizard
JobWizard wizard
- A reference to the wizard dialog that logically owns this
page. This reference is used to enable and disable
buttons on this wizard appropriately.
mstFile
javax.swing.JTextField mstFile
- Field to read/display the install path where the MST file
will be saved after it is generated on the server.
browse
javax.swing.JButton browse
- The browse button to be enabled the user to choose the
directory where the file is to be stored.
serverList
javax.swing.JComboBox serverList
- The combo box that permits the user to select the server
to be used for running the job.
nodeInfo
javax.swing.JSpinner[] nodeInfo
- The array of two configuration parameter values for the CPUs
and nodes per CPU on the server. The last two spinners are
used for memory and run time values.
serialVersionUID: 8643291107936550834L
wizard
JobWizard wizard
- A reference to the wizard dialog that logically owns this
page. This reference is used to enable and disable
buttons on this wizard appropriately.
log
javax.swing.JTextArea log
- Field to read and edit a brief description about the job.
This information can be anything the user desires and is
meaningful only to the user.
stepInfo
javax.swing.JLabel[] stepInfo
- The step information labels to display information about
the steps to be done and those that have been completed.
These labels are created in the constructor and updated
periodically.
server
ServerSession server
- The session to the server on which the job is to be submitted.
The connection is used throughout the process of job submission
by various methods. It is created in the startSession() method.
serialVersionUID: 8538523942750752144L
wizard
JobWizard wizard
- A reference to the wizard dialog that logically owns this
page. This reference is used to enable and disable
buttons on this wizard appropriately.
summary
javax.swing.JTextArea summary
- Field to read and edit a brief description about the job.
This information can be anything the user desires and is
meaningful only to the user.
|
Package org.peace_tools.core.server |
serialVersionUID: 8538523942750752144L
STANDARD_MSG
java.lang.String STANDARD_MSG
- A simple standard message to be displayed at the top of this page.
wizard
WizardDialog wizard
- A reference to the wizard dialog that logically owns this
page. This reference is used to enable and disable
buttons on this wizard appropriately.
server
Server server
- Information about the actual server entry being edited. This
reference is set when this class is instantiated and is never
changed during the life time.
infoFields
javax.swing.JTextField[] infoFields
- Field to be displayed to the user in this wizard pane.
serialVersionUID: 8538523942750752144L
wizard
WizardDialog wizard
- A reference to the wizard dialog that logically owns this
page. This reference is used to enable and disable
buttons on this wizard appropriately.
server
Server server
- Information about the actual server entry being edited. This
reference is set when this class is instantiated and is never
changed during the life time.
installPath
javax.swing.JTextField installPath
- Field to read/display the install path where PEACE is (or has
been) installed on the given server.
description
javax.swing.JTextArea description
- Field to read and edit a brief description about the server.
This information can be anything the user desires and is
meaningful only to the user.
pollTime
javax.swing.JSpinner pollTime
- Field to read/display the polling time.
fixedMsgs
javax.swing.JComponent[] fixedMsgs
- These labels are created in the constructor but one of them
remains hidden. The visibility of the labels is swapped
just before and after the verification process. The idea is
let the user know that the wizard is doing some operation.
progressBar
javax.swing.JProgressBar progressBar
- A roving progress bar to show the user we are doing
some work. We really can't tell how much progress has
happened but we can say we are doing something so that
the user understands the GUI is not hanging.
lockPath
boolean lockPath
- If this flag is set to true, then this wizard permits the
user only to change the install path on the server.
serverSession
ServerSession serverSession
- This instance variable is used to manage the connection to
the server just for testing purposes. Possibly this
connection can be centralized into the ServerWizard for use
throughout the wizard.
browse
javax.swing.JButton browse
- The browse button to be enabled only for local installs.
serialVersionUID: 8538523942750752144L
wizard
WizardDialog wizard
- A reference to the wizard dialog that logically owns this
page. This reference is used to enable and disable
buttons on this wizard appropriately.
server
Server server
- Information about the actual server entry being edited. This
reference is set when this class is instantiated and is never
changed during the life time.
serverTypes
javax.swing.JComboBox serverTypes
- The combo box that permits the user to choose between a local
and remote server setting.
remoteSrvrInfo
javax.swing.JPanel remoteSrvrInfo
- The panel that contains the data entry fields related to a
remote server entry. This panel contains all the fields so
that they can be enabled and disabled in one big swoop whenever
the user changes between local and remote server settings.
hostName
javax.swing.JTextField hostName
- Field to read/display the host name to the user. The host name
maybe the FQN or the IP address of the host.
userName
javax.swing.JTextField userName
- Field to read/display the user/login ID. This information is
meaningful for remote servers.
password
javax.swing.JTextField password
- Field to read/display the password ID. This information is
meaningful for remote servers.
fixedMsgs
javax.swing.JComponent[] fixedMsgs
- These labels are created in the constructor but one of them
remains hidden. The visibility of the labels is swapped
just before and after the verification process. The idea is
let the user know that the wizard is doing some operation.
progressBar
javax.swing.JProgressBar progressBar
- A roving progress bar to show the user we are doing
some work. We really can't tell how much progress has
happened but we can say we are doing something so that
the user understands the GUI is not hanging.
changeCredentialsOnly
boolean changeCredentialsOnly
- If this flag is set to true, then this wizard permits the
user only to change the credentials associated with a remote
server.
srvrSession
ServerSession srvrSession
- This instance variable is used to manage the connection to
the remote server just for testing purposes. Possibly this
connection can be centralized into the ServerWizard for use
throughout the wizard.
serialVersionUID: -369000313738268902L
server
Server server
- This is the server entry that is being currently edited via
this wizard. This object is accessed by the various pages
in this wizard and updated as the user navigates through
the wizard pages.
center
DnDTabbedPane center
- The DnDTabbedPane to which the actual PEACE installer tab
must be added. This value is set in the constructor.
|
Package org.peace_tools.data |
serialVersionUID: -5174610250739852226L
serialVersionUID: -3412623208152260577L
estList
ESTList estList
- Reference to the list of fragments that is actually exposed by this
table model. This value is set in the constructor and is never changed
during the life time of this class.
maxESTLen
int maxESTLen
- The maximum length of an EST sequence to be adapted by this model.
This value along with the basesPerCol determines the total number of
columns that are logically represented by this model.
basesPerCol
int basesPerCol
- The number of base pairs per column. This value along with the
maxESTLen determines the total number of columns that are logically
represented by this model.
sortedIndexs
java.lang.Integer[] sortedIndexs
- This array contains a sorted list of indexes of fragments if a sorting
scheme has been applied to the data set. If this array is not null then
this table model returns entries using the order specified in this
array. The entries in this array are indexes into the original set of
fragments contained in the estList instance variable.
clusters in the root. This list changes depending on the order of
sorting requested by the user.
serialVersionUID: -5174610250739852226L
serialVersionUID: 5033361156599458567L
serialVersionUID: -5174610250739852226L
|
Package org.peace_tools.generic |
serialVersionUID: 3100922135406430414L
colorCodes
java.lang.String colorCodes
- Create a custom border using 4 character codes for
top, left, bottom, right. The character codes are
"d" for darker and "l" for lighter. Any other
characters result in a null color and a border is not
drawn.
colors
java.awt.Color[] colors
- An array of four colors corresponding to top, left, bottom,
right borders
serialVersionUID: 1L
useImageWidth
boolean useImageWidth
- Flag to indicate if the size of the image should be used
as the preferred size for this panel.
useImageHeight
boolean useImageHeight
- Flag to indicate if the size of the image should be used
as the preferred size for this panel.
backgroundImage
javax.swing.ImageIcon backgroundImage
- The image used for the background
This member object is used to maintain the image that is used as the
background for this panel.
serialVersionUID: -9111663142182703629L
title
java.lang.String title
- The title to be set for this wizard page. This value is set
via the setTitle method and is returned via the getTitle
method.
subTitle
java.lang.String subTitle
- The subtitle to be set for this wizard page. This value is set
via the setTitle method and is returned via the getSubTitle
method.
serialVersionUID: 6654295035253838886L
icon
javax.swing.Icon icon
- The icon to be used for this mutable tree node. This value
is typically set in the constructor.
serialVersionUID: -3960338752571957543L
pagePanel
CustomPanel pagePanel
- A custom panel that is used to hold all the pages of this wizard. This
panel is added to the center of the wizard and uses a CardLayout
to display one wizard page at a time.
titlePanel
CustomPanel titlePanel
- A custom panel that is used as the title panel for this wizard. The
title panel is displayed on top of the wizard.
titles
javax.swing.JLabel[] titles
- The array of two titles that are displayed at the top of this
wizard dialog. These values are automatically set whenever a new page
is displayed by this wizard. The labels are created when the
showWizard() method is invoked.
seqTitles
javax.swing.JLabel[] seqTitles
- The array of sequence titles that are displayed to the left of the
wizard dialog. These values are automatically updated whenever a
new page is displayed by this wizard. The labels are created when
the showWizard() method is invoked.
prevButton
javax.swing.JButton prevButton
- The "Prev" button that is displayed at the bottom of the wizard
in a separate panel. This button is created in the constructor
but are organized into a panel only when the showWizard() method
is called.
nextButton
javax.swing.JButton nextButton
- The "Next" button that is displayed at the bottom of the wizard
in a separate panel. This button is created in the constructor
but are organized into a panel only when the showWizard() method
is called.
cancelButton
javax.swing.JButton cancelButton
- The "Cancel" button that is displayed at the bottom of the wizard
in a separate panel. This button is created in the constructor
but is organized into a panel only when the showWizard() method
is called.
finishButton
javax.swing.JButton finishButton
- The "Finish" button that is displayed at the bottom of the wizard
in a separate panel. This button is created in the constructor
but are organized into a panel only when the showWizard() method
is called. By default this button is hidden and is displayed
only when the last panel is shown (instead of the next button).
helpButton
javax.swing.JButton helpButton
- The "Help" button that is displayed at the bottom of the wizard
in a separate panel. This button is created in the constructor
but are organized into a panel only when the showWizard() method
is called. By default this button is hidden and is displayed
only if a valid help URL is specified.
sequencePanel
CustomPanel sequencePanel
- A custom column panel that is displayed to the left of the wizard.
This panel displays the sequence of configuration steps associated
with this wizard.
pages
java.util.ArrayList<E> pages
- The array list containing the set of pages to be displayed by
this wizard in the same sequence as they are to be displayed.
Entries are appended to this list via the addPage() method.
currentPage
int currentPage
- The current page that is being displayed by this wizard. This
value is set to zero and works it way up to the last page
in this wizard.
helpURL
java.lang.String helpURL
- The URL to the online help page associated with this wizard.
This value is set via the showWizard() method. If the Help
URL is set then the "Help" button is displayed.
workerThreads
java.util.ArrayList<E> workerThreads
- The list of worker threads that various pages may have spawned.
This list is maintained so that the threads can be killed when
this wizard exits. Various pages may add and remove threads
as they are created and destroyed.
|
Package org.peace_tools.generic.dndTabs |
serialVersionUID: 1414403952944170345L
permanent
boolean permanent
- A boolean variable that indicates if this tab is permanent and should not
be deleted even if it is empty. This flag is set via call to
setPermanent() method. This value is used by the TabDnDHanlder to decide
if this tab should be removed when empty or not. It access's this property
via the isPermanent() method.
dockCue
DnDTabbedPane.Location dockCue
- This instance variable is used to track if this DndTabbedPane should
paint a outline on itself to indicate where a tab being dragged
will be docked with respect to this window. This outline provides a
visual cue to the user as to where a tab being dragged will end up.
The visual cue is setup by the TabDnDHandler's methods.
serialVersionUID: -6226717869585754033L
pane
DnDTabbedPane pane
- The tab pane which which this tab button is logically
associated. This value is set in the constructor when the
button is created.
button
javax.swing.JButton button
- The close button that is visible on the currently active
tab. The close button simply has icons that are displayed
at different times.
|
Package org.peace_tools.views |
serialVersionUID: 4287833783594312723L
TickFontSize
int TickFontSize
- This is a constant that provides the maximum font size we
would like to use for the ticks on the graph.
axisScale
javax.swing.JSlider[] axisScale
- The x and y axis scale controllers.
The following array holds two sliders that can be used to
control the scale of the x-axis and y-axis in the graph. The
sliders are created in the setupToolBar() method. The sliders
are set such that the scale of the graph cannot be set to a
value which reduces the dimension of the graph below 100x100.
yLabel
javax.swing.JLabel yLabel
- The main y-axis label is drawn separately so that it can be
rotated and drawn vertically in the paintGraph() method.
Consequently, it is maintained as a separate instance
variable (unlike other labels).
area
java.awt.Rectangle area
- The area in the graph pane where the actual graph is drawn. This
area is set by the various method to ensure that the graph drawn
does not interfere with the axis and borders etc.
borderSize
int borderSize
- Empty white space around the core graph to make things look
good.
graph
javax.swing.JPanel graph
- The panel that is used to draw the cluster graph. The panel
is created in the setupGraph() method. The paintComponent
call-back is intercepted by this component to draw the
graph.
toolbar
javax.swing.JToolBar toolbar
- The tool bar that contains some commonly used tools with
the summary view and for modifying the graph size / info.
logScale
javax.swing.JToggleButton logScale
- A toggle button which when checked (or depressed) indicates
that the y-axis must be drawn on a logarithmic scale rather
than on a linear scale.
classify
javax.swing.JToggleButton classify
- A toggle button which when checked (or depressed) indicates
that the bars must also include the classification information
for each cluster displayed in the graph.
maxClusterSize
int maxClusterSize
- The largest cluster in the set of clusters that we are working with.
This information is set once and reused to draw the graphs.
clusterFile
ClusterFile clusterFile
- The set of clusters that we are working with. The cluster
data is set when this class is instantiated.
estList
ESTList estList
- The set of ESTs that the clusters correspond to. This data is
actually used only for classification.
LogStartValue
float LogStartValue
- A convenience constant to set the smallest y-axis value when the
data is displayed on a log scale.
mainFrame
MainFrame mainFrame
- Convenient reference to the main frame class that logically owns
this component. This value is set in the constructor
and is never changed.
serialVersionUID: 80617431851108817L
toolbar
javax.swing.JToolBar toolbar
- The toolbar that contains some commonly used tools with
the jobs.
clusterTable
org.netbeans.swing.outline.Outline clusterTable
- The actual Tree-table that provides a graphical view of the
list of clusters in a given cluster file.
model
ClusterTreeTableModel model
- The table-tree model that is being used to display information
in this view. This value is set in the constructor and is
never changed.
mainFrame
MainFrame mainFrame
- Convenient reference to the main frame class that logically owns
this component. This value is set in the constructor
and is never changed.
sortOrder
javax.swing.JComboBox sortOrder
- Various options on how the clusters in the cluster tree table view
are to be sorted. The options are populated when this combo box is
created in the createToolbar() method.
contentPane
javax.swing.JSplitPane contentPane
- The main content pane that contains the summary pane along
with the tree table. The summary pane may or may not be displayed
depending on the current user settings.
SELECT_EST_MSG
java.lang.String SELECT_EST_MSG
- A simple message that is displayed to the user.
serialVersionUID: -9175031053323866144L
monoFont
java.awt.Font monoFont
- The mono-spaced font used to render the EST sequences in
the tree view.
highlightForeground
boolean highlightForeground
Flag to indicate if base pairs in sequences must be highlighted.
This feature increases time for rendering data but can be useful
to luckily identify patterns.
Note: Currently this feature does not operate correctly.
highlightBackground
boolean highlightBackground
- Flag to indicate if background for the base pairs in sequences
must be colored differently for different base pairs.
This feature increases time for rendering data but can be useful
to quickly identify patterns.
Note: Currently this feature does not operate correctly.
serialVersionUID: 80617431851108817L
toolbar
javax.swing.JToolBar toolbar
- The tool bar that contains some commonly used tools with
the servers.
fileTable
javax.swing.JTable fileTable
- The actual JTable that provides a graphical view of the
list of servers currently configured on this work space.
tableModel
DataSetTableModel tableModel
- The table model that provides the data for display in the
file table. This object is used to directly obtain the
object at a given row.
popupMenu
DataSetPopupMenu popupMenu
- This is a pop-up menu that is displayed whenever the user clicks
the left mouse button on a table entry. This menu is created
with a static set of menu items and appropriate entries are
enabled and disabled.
mainFrame
MainFrame mainFrame
- Convenient reference to the main frame class that logically owns
this menu in its JMenuBar. This value is set in the constructor
and is never changed.
FileNameRenderer
DataSetFileListView.ServerNameStatusRenderer FileNameRenderer
- An instance of the cell renderer that is used to render the
first column in the table with a suitable status icon.
treeView
DataSetTreeView treeView
- The actual tree view that provides a graphical view of the
data sets in the form of a tree. This reference is used
to synchronize the selected entries in the tree and
this tabular view.
serialVersionUID: -4789513083096044919L
mainFrame
MainFrame mainFrame
- Convenient reference to the main frame class that logically owns
this menu. This value is set in the constructor
and is never changed.
entry
java.lang.Object entry
- This instance variable tracks the currently selected
work space entry. This value is set via call to the
updateItems method in this class.
isTreeView
boolean isTreeView
- Instance variable that tracks if this pop-up menu is being
used with a tree view or with a table view.
serialVersionUID: 3010633830928489342L
popupMenu
DataSetPopupMenu popupMenu
- This is a pop-up menu that is displayed whenever the user clicks
the left mouse button on a menu item. This menu is created
with a static set of menu items and appropriate entries are
enabled and disabled.
mainFrame
MainFrame mainFrame
- Convenient reference to the main frame class that logically owns
this view in its frame. This value is set in the constructor
and is never changed.
treeModel
DataSetTreeModel treeModel
- The data model that provides the various branches and leaves
to be displayed in the tree. The tree model obtains the
necessary data from the currently active workspace.
toolbar
javax.swing.JToolBar toolbar
- The tool bar that contains some commonly used tools with
the data set tree view.
dataSetTree
javax.swing.JTree dataSetTree
- The actual JTree that provides a hierarchical view of the
data files currently configured on this work space.
listView
DataSetFileListView listView
- The actual JTable that provides a graphical view of the
data sets in the form of a list. This reference is used
to synchronize the selected entries in the tree and
the table.
serialVersionUID: -6093428974800271396L
ColorColumnRenderer
DBClassifierEditor.ColorRenderer ColorColumnRenderer
- An instance of the color renderer that is used to render the
third column in the table with a suitable colored label.
ColorColumnEditor
DBClassifierEditor.ColorEditor ColorColumnEditor
- An instance of the color renderer that is used to render the
third column in the table with a suitable colored label.
table
javax.swing.JTable table
- The JTable with the list of DB classifiers that are being
currently edited by the user.
tableData
javax.swing.table.DefaultTableModel tableData
- This instance variable contains the mutable data model that
contains the actual classifier data displayed in the table.
toolbar
javax.swing.JToolBar toolbar
- The tool bar that contains the various buttons/tools with
with the classifier list can be edited and modified.
mainFrame
MainFrame mainFrame
- Convenient reference to the main frame class that contains this
dialog box. This value is set in the constructor
and is never changed. The main frame reference is primarily used
to handle help requests.
REG_EX_ERR_MSG
java.lang.String REG_EX_ERR_MSG
- A simple error message to be displayed to the user whenever
a invalid regular expression is entered.
CANCEL_MSG
java.lang.String CANCEL_MSG
- A conventional message to be displayed to the user prior to
canceling out of this dialog.
CHECK_MSG
java.lang.String CHECK_MSG
- A String.format() style message to be displayed to the
user while prompting to enter data string for validating a given
regular expression. The actual regular expression is substituted
by the testRegExp() method.
CHECK_RESULT_MSG
java.lang.String CHECK_RESULT_MSG
- A String.format() style message to be displayed to the
user after validating a regular expression against a data string
entered by the user. The actual regular expression and data string
is substituted by the testRegExp() method.
serialVersionUID: 6547127105109078286L
toolbar
javax.swing.JToolBar toolbar
- The toolbar that contains some commonly used tools with
the jobs.
clusterTable
javax.swing.JTable clusterTable
- The actual Tree-table that provides a graphical view of the
list of clusters in a given cluster file.
model
ESTTableModel model
- The table model that is being used to display information
in this view. This value is set in the constructor and is
never changed.
mainFrame
MainFrame mainFrame
- Convenient reference to the main frame class that logically owns
this component. This value is set in the constructor
and is never changed.
sortOrder
javax.swing.JComboBox sortOrder
- Various options on how the clusters in the cluster tree table view
are to be sorted. The options are populated when this combo box is
created in the createToolbar() method.
columization
javax.swing.JCheckBox columization
- A checkbox that can be used by the user to enable or disable
column-wise display of nucleotide sequences.
basesPerCol
javax.swing.JSpinner basesPerCol
- A spinner that is displayed in the toolbar. This spinner can be used
by the user to set the number of bases/nucleotides to be displayed
in a single column in the table.
SELECT_EST_MSG
java.lang.String SELECT_EST_MSG
- A simple message that is displayed to the user.
serialVersionUID: -7553639166871732314L
mainFrame
MainFrame mainFrame
- Convenient reference to the main frame class that logically owns
this menu in its JMenuBar. This value is set in the constructor
and is never changed.
serialVersionUID: -20535421438589052L
outputs
javax.swing.text.DefaultStyledDocument[] outputs
- The styled documents that is used to display the output from
the job information.
job
Job job
- The job whose details is being displayed by this panel.
This value is set in the constructor and is never changed
during the lifetime of this class.
serialVersionUID: 80617431851108817L
model
JobListTableModel model
- The model that we are using to render the information in the
tabular view of jobs.
toolbar
javax.swing.JToolBar toolbar
- The toolbar that contains some commonly used tools with
the jobs.
jobTable
javax.swing.JTable jobTable
- The actual JTable that provides a graphical view of the
list of jobs currently configured on this workspace.
popupMenu
javax.swing.JPopupMenu popupMenu
- The pop up menu that is displayed when the user left-clicks
on an item in the job list view.
JobNameRenderer
JobListView.JobNameStatusRenderer JobNameRenderer
- An instance of the cell renderer that is used to render the
first column in the table with a suitable status icon.
StatusRenderer
JobListView.JobStatusRenderer StatusRenderer
- An instance of the cell renderer that is used to render the
second column in the table to display status or progress
information.
mainFrame
MainFrame mainFrame
- The main frame that logically owns this job list view. The
main frame is primarily used as the job listener which
receives notifications on job completion.
serialVersionUID: -2203502234634483701L
FONT_SIZE_CHANGE
int FONT_SIZE_CHANGE
- Constant to make the fonts in the controls in the tool bar a bit
small because they look huge on Linux.
log
Log log
- This instance variable holds a reference to the actual log class
from which this log pane is displaying log entries. This value is
set in the constructor and is never changed during the life time
of this object.
fileNameDisplay
javax.swing.JTextField fileNameDisplay
- This is an internal text field that is used to display the file to which
the logs are being currently written. If the fileName is null, then this
field displays "" and the toggle button to save data to the file
is disabled.
saveLogsButton
javax.swing.JToggleButton saveLogsButton
- A toggle button that can be in "on" or "off" state to indicate if logs
are to be saved to the specified fileName (if it is not null) or not.
This button is disabled until the user chooses a valid log file name.
When in the "on" state, new logs are written to the supplied file.
logLevelList
javax.swing.JComboBox logLevelList
- A combo box to permit the user to set the level at which logs are to be
saved by this logger. Typically this facility is used only by the UserLog
and not by the programmer log.
serialVersionUID: 3010633830928489342L
mainFrame
MainFrame mainFrame
- Convenient reference to the main frame class that logically owns
this menu in its JMenuBar. This value is set in the constructor
and is never changed.
treeModel
MSTTreeModel treeModel
- The data model that provides the various branches and leaves
of a MST to be displayed in the tree. The tree model obtains
the necessary data from the currently active work space.
mstTree
javax.swing.JTree mstTree
- The actual JTree that provides a hierarchical view of the
data files currently configured on this work space.
serialVersionUID: 2213371948161753574L
logArea
javax.swing.JTextArea logArea
- The table to which we write our log into. This is the visual component
that provides the necessary display to the user in a tabular form.
serialVersionUID: -20535421438589052L
jobInfo
javax.swing.text.DefaultStyledDocument jobInfo
- The styled documents that is used to display the list of
jobs/processes running on a process.
userID
java.lang.String userID
- The ID of the user whose jobs/processes are to be listed
in this view.
serialVersionUID: 80617431851108817L
model
ServerListTableModel model
- The model that we are using to render the information in the
tabular view of servers in the workspace.
toolbar
javax.swing.JToolBar toolbar
- The toolbar that contains some commonly used tools with
the servers.
serverTable
javax.swing.JTable serverTable
- The actual JTable that provides a graphical view of the
list of servers currently configured on this workspace.
mainFrame
MainFrame mainFrame
- The main frame that logically owns this job list view.
ServerNameRenderer
ServerListView.ServerNameStatusRenderer ServerNameRenderer
- An instance of the cell renderer that is used to render the
first column in the table with a suitable status icon.
popupMenu
javax.swing.JPopupMenu popupMenu
- The pop up menu that is displayed when the user left-clicks
on an item in the server list view.
serialVersionUID: 2213371948161753574L
log
javax.swing.JTable log
- The table to which we write our log into. This is the visual component
that provides the necessary display to the user in a tabular form.
TimeStampRenderer
UserLogPane.StatusTimeStamp TimeStampRenderer
- An instance of the cell renderer that is used to render the
first column in the table with a suitable status icon.
|
Package org.peace_tools.views.overlap |
serialVersionUID: 4287833783594312723L
axisScale
javax.swing.JSlider[] axisScale
- The row and column size scale controllers.
The following array holds two sliders that can be used to
control the scale of the row and column in the graph. The
sliders are created in the setupToolBar() method. The sliders
are set such that the scale for the row cannot be decreased below
1 pixel and the column size cannot drop below 1/4 pixel (four
nucleotides per pixel).
toolbar
javax.swing.JToolBar toolbar
- The tool bar that contains some commonly used tools with
the overlap view and for modifying the scale used to
draw the overlap view.
clusterList
ClusterList clusterList
- The list that displays the list of clusters currently present in
the memory model and permits the user to change colors. This object
is created in the constructor and is added to the tool bar as the
first component.
pam
OverlapModel pam
- The PreAlignmentModel that provides the necessary information
for rendering the core information required for this view.
This instance variable is initialized by the constructor and
it is never changed during the life time of this object.
panel
OverlapPanel panel
- The overlap panel that actual renders the fragments for us.
This instance variable holds an immutable reference to the
overlap panel that actually renders the fragments.
mainFrame
MainFrame mainFrame
- Convenient reference to the main frame class that logically owns
this component. This value is set in the constructor
and is never changed.
horizontalRuler
Ruler horizontalRuler
- The horizontal ruler that is displayed at the top of the overview
panel. This ruler is added to the scroll pane that contains the
OverlapView.panel. The horizontal ruler displays a ruler with
column numbers indicating the relative position of each nucleotide.
verticalRuler
Ruler verticalRuler
- The vertical ruler that is displayed to the left of the overview
panel. This ruler is added to the scroll pane that contains the
OverlapView.panel. The vertical ruler displays a ruler with
row numbers indicating the relative row number where a given
fragment was accomodated.
MIN_COL_SCALE_FACTOR
double MIN_COL_SCALE_FACTOR
- Factor to determine minimum column scale value.
This constant provides a convenient mechanism to quickly change
the minimum scaling factor for columns in the fragment display
panel. The minimum scaling factor is computed as:
1.0 / MIN_COL_SCALE_FACTOR. This value is used in various
spots in the code to configure and work with sliders that requires
integral values to operate (it cannot deal with fractional values
like 0.25)
clusterColorMap
java.util.HashMap<K,V> clusterColorMap
- A hash map to quickly look-up color for a given cluster ID.
This hash map is used when rendering fragments. The hash map is
used to look up the colors set for a given cluster, given its
cluster ID. This hash map is used to implement methods in the
ClusterColorMapper interface.
|
Package org.peace_tools.workspace |
serialVersionUID: -2063315046609995997L
entryType
WorkspaceEvent.EntryType entryType
- This instance variable is used to contain the type of the entry
regarding which a status change is being reported.
operation
WorkspaceEvent.Operation operation
- This instance variable is used to contain the type of status change
being reported via this event.