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Constant Field Values

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org.peace_tools.*

org.peace_tools.core.AboutDialog
private static final long serialVersionUID 7642494335728910205L

org.peace_tools.core.DeleteDialog
private static final java.lang.String CANT_FIND_SERVER "<html>The server entry for job <i>%s</i> could not be located.<br>The files associated with this job cannot be deleted.<br>(there is no point in keeping this job entry in the workspace)<br>Do you still wish to proceed with removing this job entry?</html>"
private static final java.lang.String DATASET_ERROR "<html>Error occured when attempting to remove entry:<br>%s<br><i>See details below for more information.<br><br>Do you want to continue removing the data set?</html>"
private static final java.lang.String FILE_DEL_ERROR "<html>An error occured when attempting to delete the file(s) for<br>workspace entry: <i>%s</i><br>Click on details below for additional information.<br><br>Do you want to proceed with removing this entry from the workspace?</html>"
private static final long serialVersionUID -4658096968134590995L

org.peace_tools.core.FileCopyDialog
private static final long serialVersionUID 5397447232688023756L

org.peace_tools.core.FileInfo
public static final int DIR_ATTRIB 1
public static final int EXEC_ATTRIB 16
public static final int FILE_ATTRIB 2
public static final int READ_ATTRIB 4
public static final int WRITE_ATTRIB 8

org.peace_tools.core.HelpMenuHelper
private static final java.lang.String ABOUT_ERROR "<html>Unable to create the About dialog box with the necessary information.<br>Possibly your install of PEACE is incomplete or corrupted.<br>You will need to reinstall a recent copy of PEACE to resolve this issue.</html>"

org.peace_tools.core.JobMenuHelper
private static final java.lang.String CANT_ABORT_JOB "<html>Unable to abort the job with Job ID %s<br>that is running on server: %s.<br>because an error occured. Refer to the details below<br>for additional information about the error.</html>"
private static final java.lang.String CANT_FIND_SERVER "<html>Unable to find entry for server ID %s<br>in workspace. Without server entry the job ID: %s<br>cannot be really aborted. If a server entry was not<br>found, there is not a whole lot you can do with this job.<br><br>Do you want to simply flag it as aborted?<br></html>"
private static final java.lang.String SESSION_PURPOSE "<html>Attempting to abort the Job with ID %s<br>that is running on server: %s.</html>"
private static final java.lang.String SUCCESS_MSG "<html>The job with job ID %s that was running on<br>server %s has been aborted.</html>"
private static final java.lang.String SURE_ABORT_JOB "<html>Are you sure you want to abort the job with Job ID %s<br>that is running on server: %s?<br><br><i>Note that if the job is aborted work done by the job<br>will be lost and no data files will be generated.</html>"

org.peace_tools.core.JobMonitor
private static final java.lang.String PURPOSE_MSG "<html>This session is being used to monitor a Job<br>(<i>Job ID: %s</i>) running on the server named<br><i>%s</i>.<br>The session will be closed once the job is complete.<br>You may stop the monitor via the Job table.</html>"

org.peace_tools.core.MainFrame
private static final java.lang.String JOB_DONE_MSG "<html>The job (ID: %1$s) that was scheduled to run on<br>server: %2$s<br>has completed successfully. The generated data files<br>need to copied to be viewed in the GUI. <br><br><b>Would you like to copy the generated file(s) now?</b></html>"
private static final java.lang.String JOB_ERR_MSG "<html>The job (ID: %1$s) that was scheduled to run on<br>server: %2$s<br>did not complete successfully. You can review the outputs<br>from the job to determine the root cause of failure.</html>"
private static final java.lang.String SAVING_ERROR "<html>The workspace file could not be saved. This is a serious issue.<br>Plese refer to the details to identify the root cause. You may try<br>to save the workspace via the menus.</html>"
private static final long serialVersionUID 1414403952944170343L
private static final java.lang.String SERVER_IN_BAD_STATUS "<html>The server <b>%1$s</b> is in an unexpected state.<br>This can occur if PEACE GUI was closed during installation or uninstallation.<br>The status of this server entry will be updated and you may delete this entry<br>from this workspace.</html>"

org.peace_tools.core.ServerConnectionTester
private static final java.lang.String ERROR_MSG "<html>Unable to establish an independent connection<br>to server: %s<br>because an error Occured. Refer to the detailed information<br>below for additional information about the error that occured.</html>"
private static final java.lang.String INFO_MSG "<html>Attempting to establish an independent connection<br>to server: %s<br><br><i>Please wait...</i></html>"
private static final java.lang.String PURPOSE_MSG "<html>Attempting to connect to the<br>server: %s<br>to verify connectability status.</html>"

org.peace_tools.core.Version
public static final java.lang.String COPYRIGHT "Copyright (C) Miami University, 2009-"
public static final java.lang.String DISCLAIMER "Miami University (MU), Oxford, OHIO makes no representations\nor warranties about the suitability of the software, either \nexpress or implied, including but not limited to the implied\nwarranties of merchantability, fitness for a particular purpose\nor non-infringement. MU shall not be liable for any damages\nsuffered by licensee as a result of using, result of using,\nmodifying or distributing this software or its derivatives.\n\n\nBy using or copying this Software, Licensee agrees to abide by\nthe intellectual property laws, and all other applicable laws\nof the U.S., and the terms of this license."
public static final java.lang.String GUI_VERSION "Version 0.95 (Beta)\n(March 20 2010)"

org.peace_tools.core.ViewFactory
private static final java.lang.String CANT_MAKE_VIEW "<html>Unable to open a view for the specified item.<br>Refer to the details below for additional information.</html>"

org.peace_tools.core.WorkspaceChooser
private static final long serialVersionUID 5779507970297217323L

org.peace_tools.core.dataset.DataSetWizard
private static final java.lang.String OVERVIEW_MSG "<html>This wizard guides you through the process of adding a data<br>set to this workspace. A data set is a collection of a related<br>set of data data files that provide the following information: <br><ul><li>A EST file (in FASTA format) containing EST data</li><li>MST file(s) generated by PEACE for the above EST file</li><li>Clustering file(s) generated from the above MST file</li></ul>Once a basic data set containing just an EST sequence<br>file (in FASTA format) is added to the workspace, the data set<br>can be used to perform clustering (generates MST and clusters)<br>on a server by scheduling a suitable job via other wizards.<br><br><b>Note</b>: Existing MST and cluster files can be added to the data<br>set or can be generated after a basic data set containing just an<br>EST data file (in FASTA format) has been added to the workspace.<br></html>"
private static final long serialVersionUID 804993573751301886L

org.peace_tools.core.dataset.ESTInfoWizardPage
private static final java.lang.String INVALID_FASTA_MSG "<html>The specified EST file is not a valid FASTA file.<br/>Please choose a different EST file.</html>"
private static final long serialVersionUID 8538523942750752144L

org.peace_tools.core.dataset.SummaryWizardPage
private final java.lang.String INFO_MSG "Click the Finish button to add the new data set."
private static final long serialVersionUID 8538523942750752144L
private final java.lang.String STANDARD_MSG "<html>A new data set will be created with using the<br>following EST data file:</html>"
private final java.lang.String STATS_STR " Number of ESTs : %1$d\n Average EST length: %2$d bp (SD: %3$f)\n Shortest EST length: %4$d bp\n Longest EST length: %5$d bp"

org.peace_tools.core.job.AnalyzerWizardPage
private static final java.lang.String INFO_MSG "<html>Configure the analyzer to be used to generate metrics<br>(distance or similarity) for clustering.</html>"
private static final long serialVersionUID 8538523942750752144L

org.peace_tools.core.job.ClusterWizardPage
private static final java.lang.String CLU_INFO "<html>The CLU analyzer automatically computes threshold based on mean.<br>and variance of similarity values. Thefore the threshold is set to<br>-1 as a sentinel value. See help for more details</html>"
private static final java.lang.String INVALID_CLR_MSG "<html>The cluster file does not meet the following criteria:<ul><li>Path to cluster file must be valid</li><li>The file must not exist</li><li>The file must be creatable</li></ul></html>"
private static final long serialVersionUID -1193172876744546755L
private static final java.lang.String THRESHOLD_INFO "<html>This is an <b>important</b> value. Small values discriminate<br>ESTs more making more clusters. Larger thresholds make larger clusters.<br>Optional threshold value is important for best results.<br>See help for more details.</html>"
private static final java.lang.String TWO_PASS_INFO "<html>Two Pass D2 analyzer is adaptive and normalizes thresholds.<br>This value must be set to 1 (one) for Two Pass D2 (and it <br>cannot be changed). See help for more details.</html>"

org.peace_tools.core.job.FiltersWizardPage
private static final java.lang.String FILTER_LIST_MSG "<html>The filter list you provided is not valid.<br><br>This filter requires a comma separated list of substrings<br>that are repeated (to required length) to detect low complexity<br>regions in fragments. Example: <i>A,C</i> or <i>AG,A,C,TC</i>.</html>"
private static final java.lang.String INFO_MSG "It is best to use both filters for high quality clustering."
private static final long serialVersionUID 6691921082180723745L

org.peace_tools.core.job.HeuristicsWizardPage
private static final java.lang.String CLU_INFO "<html>This analyzer currently does not use any heuristics.<br>Therefore there are no heuristics to configure on this page.</html>"
private static final java.lang.String INFO_MSG "It is best to use both heuristics for maximum performance."
private static final long serialVersionUID 8538523942750752144L
private static final java.lang.String TWO_PASS_INFO "<html>Two Pass D2 analyzer is adaptive and uses several different ranges<br>of window (aka frame) sizes that are most suitable to analyze<br>a given pair of fragments. In addition, the analyzer suitably<br>sets the values and thresholds for the <i>u/v</i> and the <i>t/v</i><br>heuristics. Consequently, there is no additional heuristic setup or<br>configuration needed for this analyzer. PEACE will automatically<br>default to the best, adaptive choices.</html>"
private static final java.lang.String UV_INFO_MSG "<html>This heursitc requires: <i>v</i> (#common words), <i>u</i> (# v-word<br>matches) and <i>shift</i> (# of bases to shift/skip)</html>"

org.peace_tools.core.job.JobInfoWizardPage
private static final java.lang.String INFO_MSG "<html>Select the data set that contains the EST file to be<br>processed by this job. Subsequent wizard pages will<br>permit setting up additional information for the job."
private static final java.lang.String INVALID_ENTRY "<html>The FASTA file %s<br>associated with the currently selected data set is not valid<br>(Either the file does not exist anymore or is a zero byte file)<br><br>Please choose a different data set.</html>"
private static final java.lang.String MASK_MSG "<htmL>Mask out nucleotides in lower case letters (atcg).<br><font size=\"-2\">If unchecked then lower case and upper case nucleotides<br>are processed in the same manner.</font></html>"
private static final long serialVersionUID 8538523942750752144L

org.peace_tools.core.job.JobWizard
private static final java.lang.String OVERVIEW_MSG "<html>This wizard guides you through the process of creating a job.<br>A job runs on a selected server (in parallel is so configured)<br>and computes Minimum Spanning Tree (MST) data as well as<br>clustering information for a given EST file. The EST file is<br>chosen from a data set added to the workspace.<br><br>The time taken to compute MST data is O(<i>n</i><sup>2</sup>), where <i>n</i><br>is the number of EST sequences in the EST file. It is best to<br>run even medium (more than 25,0000) sets of ESTs in parallel<br>to obtain the results quickly.<br><br><b>Note</b>: Existing MST and cluster files can be added to the data<br>set and do not have to be generated.<br></html>"
private static final long serialVersionUID 804993573751301886L

org.peace_tools.core.job.MSTWizardPage
private static final java.lang.String CPU_INFO_MSG "<html>The CPUs selected and nodes per CPU must match<br>the configuration of the server.</html>"
private static final java.lang.String INVALID_MST_MSG "<html>The EST file does not meet the following criteria:<ul><li>Path to MST file must be valid</li><li>The file must not exist</li><li>The file must be creatable</li></ul></html>"
private static final long serialVersionUID -1193172876744546755L

org.peace_tools.core.job.SubmitJobWizardPage
private static final java.lang.String FILE_MISMATCH "<html>Error the remote EST file is not consistent with the local<br>copy of the EST file. Do you want to overwrite the copy on the server?</html>"
private static final java.lang.String INFO_MSG "<html>Please wait while the wizard verifies and submits<br>the job on the remote server...</html>"
private static final java.lang.String JOB_SUBMIT_ERROR "<html>Error occured when attempting to submit the job on<br>the remote server. The job was not successfully started.<br>The necessary MST and cluster data will not be computed.</html>"
private static final long serialVersionUID 8643291107936550834L
private static final java.lang.String SUCCESS_MESSAGE "<html>The job was successfully started on the server.<br>The GUI will periodically check on the status of the job<br>and notify you about the progress. You do not have to keep<br>the GUI open until the job completes. You may exit the GUI<br>and run it again at a later time to check on the status of the job.</html>"

org.peace_tools.core.job.VerifyWizardPage
private static final java.lang.String CAUTION_MSG "<html><b>On clicking the \'Next\' button the job will be submitted!</b><br>You will not be able to backtrack from the next page.</html>"
private static final java.lang.String INFO_MSG "<html>You have provided the following information regarding<br>the job to be scheduled. Please verify the information. Next<br>the wizard will perform the initial job setup.</html>"
private static final long serialVersionUID 8538523942750752144L

org.peace_tools.core.server.ServerAddingEntryWizardPage
private static final java.lang.String INFO_MSG "<html>The install process will be run in the background<br>and the results will be displayed on a separate<br>window in the workpsace.</html>"
private static final long serialVersionUID 8538523942750752144L
private final java.lang.String STANDARD_MSG "<html>You have provided all the necessary information to create a<br>server entry. On clicking the Finish button, a new server<br>entry will be added to the workspace. <br><br>Next, the actual PEACE runtime installation will commence. <br>The installation process will take several (about 5 to 10) <br>minutes depending on the server speed and network bandwidth.</html>"

org.peace_tools.core.server.ServerInfoWizardPage
private static final java.lang.String ErrorMsg "<html>Unable to proceed further with the provided server information.<br/>Either the installation path is not valid or the server does<br/>not have the necessary software tools installed on it.<br/><b>See details below for full details.</b><br>Contact your system administrator to ensure all the necessary<br>software tools are installed and the server is operational.</html>"
private static final java.lang.String NO_MPI_MSG "<html>The MPI C++ compiler (mpicc) was not found in the default path<br>(You need to set path in <b>.bashrc</b> for bash and in <b>.cshrc</b> for tcsh).<br>Either MPI is not installed on the machine or your path is<br>incorrectly setup. You need to contact your system adminstrator<br>to determine if MPI is setup or if your path is not correct. Some<br>clusters require MPI module(s) to be loaded manually, which your<br>administrator can automate so that PEACE finds mpicc correctly.<br><br><b>Note that PEACE uses a non-interactive shell to communicate<br>with remote hosts. Therefore ensure your setup is consistent<br>in both interactive and non-interactive logins/shells.</b><br><br>You may still procceed further with the default non-MPI based C++<br>compiler. <i>However, PEACE will not run in parallel mode.</i><br><br>Do you wish to proceed with default C++ compiler (if available)?</html>"
private static final java.lang.String NO_SPACE_MSG "<html>The installation path has spaces in it. Spaces cause<br>several compatibility problems and are hard to work around.<br>Consequently, in the current version of PEACE spaces cannot<br>be present in the installation path.<br><br><b>Please choose a path without spaces in it.<b></html>"
private static final long serialVersionUID 8538523942750752144L

org.peace_tools.core.server.ServerTypeWizardPage
private static final java.lang.String ErrorMsg "<html>Failed to connect to the remote server. Either your<br>supplied host name and credentials are incorrect or<br>the remote host is not a Linux server compatible with PEACE.<br><br>Please verify that the information you provided is<br>correct and try again.</html>"
private static final long serialVersionUID 8538523942750752144L

org.peace_tools.core.server.ServerWizard
private static final long serialVersionUID -369000313738268902L

org.peace_tools.data.DataSetTableModel
private static final long serialVersionUID -5174610250739852226L

org.peace_tools.data.DataStore
private static final java.lang.String LOW_MEMORY_MSG "<html>Your Java VM maybe running low on memory and may not be able to open the<br>file: %s (size=%.1f MB). Conservative memory safety threshold: %.1f MB<br>See details below for current memory usage statistics. Bear in mind that <br>java garbage collection is lazy (that is memory may be available but the JVM <br>is yet to garbage collect. This is a Java behavior and has nothing to with PEACE).<br>You can proceed with opening the file (<i>but may experience problems</i>)<br>or try closing open files to freeup some memory and then open this file.<br><br>The best solution would be to exit PEACE and restart it with a larger heap<br>as shown in the command line below (set suitable heap value instead of 2G):<br><b>java -Xmx2G -jar peace.jar<br><br>Proceed opening the selected file?</html>"
private static final java.lang.String MEM_USAGE "Free memory available: %.1f MB\nCurrent memory used: %.1f MB\nMaximum memory available to Java: %.1f MB"
private static final java.lang.String MEM_USAGE_LOG "memCheck: maxMemory: %f, reservedMemory: %f, availMemory: %f, fileSize: %d\n"

org.peace_tools.data.ESTTableModel
private static final long serialVersionUID -3412623208152260577L

org.peace_tools.data.JobListTableModel
private static final long serialVersionUID -5174610250739852226L

org.peace_tools.data.LowMemoryException
private static final long serialVersionUID 5033361156599458567L

org.peace_tools.data.ServerListTableModel
private static final long serialVersionUID -5174610250739852226L

org.peace_tools.generic.CustomBorder
private static final long serialVersionUID 3100922135406430414L

org.peace_tools.generic.CustomPanel
private static final long serialVersionUID 1L

org.peace_tools.generic.GenericWizardPage
private static final long serialVersionUID -9111663142182703629L

org.peace_tools.generic.HelpHandler
private static final java.lang.String HELP_ERROR "<html>The default system browser could not be launched to display help.<br>You may view the help web site directly from your system browser by<br>navigating to the appropriate help section from http://www.peace-tools.org/</html>"

org.peace_tools.generic.IconTreeNode
private static final long serialVersionUID 6654295035253838886L

org.peace_tools.generic.Utilities
public static final int CHECK_BOX_ITEM 2
public static final int MENU_ITEM 1
public static final java.lang.String PATH_PREFIX "../../../"
public static final int RADIO_BUTTON_ITEM 3

org.peace_tools.generic.WizardDialog
private static final long serialVersionUID -3960338752571957543L

org.peace_tools.generic.dndTabs.DnDTabbedPane
private static final double EDGE_PANEL_SIZE 0.25
private static final long serialVersionUID 1414403952944170345L

org.peace_tools.generic.dndTabs.DnDTabButton
private static final long serialVersionUID -6226717869585754033L

org.peace_tools.views.ClusterSummaryView
private final float LogStartValue 0.5f
private static final long serialVersionUID 4287833783594312723L
private final int TickFontSize 10

org.peace_tools.views.org.peace_tools.views.ClusterSummaryView.TickLine
private static final long serialVersionUID 3622568645120048270L

org.peace_tools.views.ClusterTreeTableView
private static final long serialVersionUID 80617431851108817L

org.peace_tools.views.CustomTableCellRenderer
private static final long serialVersionUID -9175031053323866144L

org.peace_tools.views.DataSetFileListView
private static final long serialVersionUID 80617431851108817L

org.peace_tools.views.org.peace_tools.views.DataSetFileListView.ServerNameStatusRenderer
private static final long serialVersionUID 5654108539980884223L

org.peace_tools.views.DataSetPopupMenu
private static final long serialVersionUID -4789513083096044919L

org.peace_tools.views.DataSetTreeView
private static final long serialVersionUID 3010633830928489342L

org.peace_tools.views.org.peace_tools.views.DataSetTreeView.DataSetRenderer
private static final long serialVersionUID -5720888296480938746L

org.peace_tools.views.DBClassifierEditor
private static final long serialVersionUID -6093428974800271396L

org.peace_tools.views.org.peace_tools.views.DBClassifierEditor.ColorEditor
private static final long serialVersionUID 6443184579706912472L

org.peace_tools.views.org.peace_tools.views.DBClassifierEditor.ColorRenderer
private static final long serialVersionUID 5654108539980884223L

org.peace_tools.views.org.peace_tools.views.DetailView
private static final long serialVersionUID 6192661377313095929L

org.peace_tools.views.ESTTableView
private static final long serialVersionUID 6547127105109078286L

org.peace_tools.views.GenericHTMLView
private static final long serialVersionUID -7553639166871732314L

org.peace_tools.views.JobDetailsView
private static final java.lang.String INFO_ERR_MSG "<html>Unable to determine all the information about job %s<br>from server %s<br>because an error occured. Only partial information was obtained.<br>See details below for more information.<html>"
private static final long serialVersionUID -20535421438589052L
private static final java.lang.String SERVER_INFO "\tServer: %s\n\tNodes: %d\n\tCPUs per Node: %d\n\tMax Memory (GB): %d\n\tMax run time (hours): %d\n"

org.peace_tools.views.JobListView
private static final long serialVersionUID 80617431851108817L

org.peace_tools.views.org.peace_tools.views.JobListView.JobNameStatusRenderer
private static final long serialVersionUID 5654108539980884223L

org.peace_tools.views.org.peace_tools.views.JobListView.JobStatusRenderer
private static final long serialVersionUID 5654108539980884223L

org.peace_tools.views.LogPane
private static final java.lang.String CHANGE_LOG_FILE_NAME "ChangeLogFileName"
private static final java.lang.String CHANGE_LOG_LEVEL "ChangeLogLevel"
private final int FONT_SIZE_CHANGE -2
private static final long serialVersionUID -2203502234634483701L
private static final java.lang.String TOGGLE_LOG_SAVING "ToggleLogSaving"

org.peace_tools.views.MSTFileView
private static final long serialVersionUID 3010633830928489342L

org.peace_tools.views.org.peace_tools.views.MSTFileView.DataSetRenderer
private static final long serialVersionUID -5720888296480938746L

org.peace_tools.views.ProgrammerLogPane
private static final long serialVersionUID 2213371948161753574L

org.peace_tools.views.PropertiesTreeMaker
private static final int CLUSTER_ICON 1
private static final int DATASET_ICON 2
private static final int ERROR_ICON 8
private static final int FILE_ICON 4
private static final int FILTERS_ICON 7
private static final int HEURISTICS_ICON 6
private static final int JOB_ICON 3
private static final int MST_ICON 0
private static final int SERVER_ICON 5
private static final int STATS_ICON 9

org.peace_tools.views.ServerJobsView
private static final java.lang.String INFO_ERR_MSG "<html>Unable to determine all the information about jobs<br>or processes from server %s<br>because an error occured. Only partial information was<br>obtained. See details below for more information.<html>"
private static final java.lang.String NO_JOB_INFO "\nIt appears that noneof your jobs/process are currently\nrunning on this server. Therefore there is no job/process\ninformation to display at this time."
private static final long serialVersionUID -20535421438589052L

org.peace_tools.views.ServerListView
private static final long serialVersionUID 80617431851108817L

org.peace_tools.views.org.peace_tools.views.ServerListView.ServerNameStatusRenderer
private static final long serialVersionUID 5654108539980884223L

org.peace_tools.views.UserLogPane
private static final long serialVersionUID 2213371948161753574L

org.peace_tools.views.org.peace_tools.views.UserLogPane.StatusTimeStamp
private static final long serialVersionUID 5654108539980884223L

org.peace_tools.views.overlap.org.peace_tools.views.overlap.ClusterList
private static final java.lang.String LOW_COLOR_MSG "<html>The number of default colors used to randomly color the clusters<br>were fewer than the number of clusters. Therefore, two or more<br>clusters have the same color. You may choose clusters from the <br>list and selectively assign different colors to them to suitably<br>distinguish them from each other.<br></html>"
private static final long serialVersionUID 5321838842105746304L

org.peace_tools.views.overlap.org.peace_tools.views.overlap.ClusterListCellRenderer
private static final int ICON_SIZE 12
private static final long serialVersionUID -1180299364821332033L

org.peace_tools.views.overlap.org.peace_tools.views.overlap.OverlapPanel
private static final long serialVersionUID 5321838842105746304L

org.peace_tools.views.overlap.OverlapView
private final double MIN_COL_SCALE_FACTOR 10.0
private static final long serialVersionUID 4287833783594312723L

org.peace_tools.views.overlap.org.peace_tools.views.overlap.Ruler
private static final long serialVersionUID -292125515405864885L

org.peace_tools.workspace.WorkspaceEvent
private static final long serialVersionUID -2063315046609995997L

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