- GenericJarTask - Class in IMPACT_S
-
Implementation of background task to run any java (jar) program file.
Used for java based programs.
- getAA(String) - Method in class IMPACT_S.SequenceTranslator
-
Get matching AA for given codon.
- getAAColorMap() - Method in class IMPACT_S.GUIColorSchemes
-
Get a map of AA codes to associated colors, from the loaded scheme.
- getAAList(boolean) - Method in class IMPACT_S.SequenceTranslator
-
Get list of all AminoAcids names, by the standard table.
- getAAMatchingList(int) - Method in class IMPACT_S.GUIColorSchemes
-
Get AA name list.
- getAANamesMap(boolean) - Method in class IMPACT_S.SequenceTranslator
-
Get Amino-Acid names table.
- getAllPropsSignifRanges() - Method in class IMPACT_S.TreeSAAPTP
-
For each and every extracted property, get its location (in SlidingWindow) and extract from the
corresponding file, all the rows that have columns 6,7 or 8 with values higher
than 3.090232
Builds an HashMap having properties absolute paths as keys and a linked list
of selected rows as values.
- getArrayObjectToStr(Object[]) - Method in class IMPACT_S.Utilities
-
Produce an String array from an Object array.
- getBR() - Method in class IMPACT_S.FileFormat
-
Get file reader.
- getBR(String) - Method in class IMPACT_S.Utilities
-
Get Buffered Reader for file reading.
- getBW() - Method in class IMPACT_S.FileFormat
-
Get file writer.
- getCDLocation(String) - Method in class IMPACT_S.CodemlTP
-
Get location for Codeml Panel, given key.
- getChiSquare2DF() - Method in class IMPACT_S.CodemlTP
-
Get the Chi Square Critical Values for 2 Degrees of Freedom and significance of 0.05, 0.01 and 0.001 respectively.
- getChiSquare2DFtoStr(int) - Method in class IMPACT_S.CodemlTP
-
Get the Chi Square Critical Values as strings.
- getChiSquare4DF() - Method in class IMPACT_S.CodemlTP
-
Get the Chi Square Critical Values for 4 Degrees of Freedom and significance of
0.05, 0.01 and 0.001 respectively.
- getChiSquare4DFtoStr(int) - Method in class IMPACT_S.CodemlTP
-
Get the Chi Square Critical Values as strings.
- getChosenColors() - Method in class IMPACT_S.GUIColorSchemes
-
Get colors selected or not by user.
- getChosenOptions() - Method in class IMPACT_S.GUIPhyMLOptions
-
Get selected options.
These are prepared for phyml executable.
- getChosenOptionsArray() - Method in class IMPACT_S.GUIPhyMLOptions
-
Get selected options as an array and without spaces.
- getCodemlCtlFileCtt() - Method in class IMPACT_S.CodemlOptions
-
Get content for codeml control file to be viewed by user.
- getCodemlDir() - Method in class IMPACT_S.Utilities
-
Get codeml directory.
- getCOLocation(String) - Method in class IMPACT_S.CodemlOptions
-
Get codeml location of files.
- getColumnClass(int) - Method in class IMPACT_S.CSVTableModel
-
Get column type, given column index.
- getColumnClass(int) - Method in class IMPACT_S.MSATableModel
-
Get column type, given column index.
- getColumnClass(int) - Method in class IMPACT_S.PDBSeqTableModel
-
Get column type, given column index.
- getColumnCount() - Method in class IMPACT_S.CSVTableModel
-
Get number of columns.
- getColumnCount() - Method in class IMPACT_S.MSATableModel
-
Get number of columns.
- getColumnCount() - Method in class IMPACT_S.PDBSeqTableModel
-
Get number of columns.
- getColumnCount() - Method in class IMPACT_S.ResultsView
-
Get number of columns for active file.
- getColumnName(int) - Method in class IMPACT_S.CSVTableModel
-
Get column name for column index.
- getColumnName(int) - Method in class IMPACT_S.MSATableModel
-
Get column name for column index.
- getColumnName(int) - Method in class IMPACT_S.PDBSeqTableModel
-
Get column name for column index.
- getCommand() - Method in class IMPACT_S.PhyMLTask
-
Get complete command previously initialized in constructor, to string.
- getCommonSites(String, boolean, String) - Method in class IMPACT_S.DatamonkeyTP
-
Get all common sites among all selected models.
- getControlFilename() - Method in class IMPACT_S.CodemlOptions
-
Get current codeml file name used.
- getCurrent() - Method in class IMPACT_S.CodemlTask
-
Get current value for display progress bar and/or monitor.
It returns only the value that is greater than the previous one.
- getCurrent() - Method in class IMPACT_S.GnuplotTask
-
Get current value for display progress bar and/or monitor.
It returns only the value that is greater than the previous one.
- getCurrent() - Method in class IMPACT_S.PhyMLTask
-
Get current value for display progress bar and/or monitor.
It returns only the value that is greater than the previous one.
- getCurrText() - Method in class IMPACT_S.GUIProgExecOutput
-
Get current text from text area.
Used for text area updates.
- getDataValues() - Method in class IMPACT_S.CSVTableModel
-
Get data values;
- getDataValues() - Method in class IMPACT_S.MSATableModel
-
Get data values;
- getDataValues() - Method in class IMPACT_S.PDBSeqTableModel
-
Get data values;
- getDirectoryOpen() - Method in class IMPACT_S.GUIFileChooser
-
Presents dialog to open/select directory.
Returns selected directory name
- getDLocation(String) - Method in class IMPACT_S.DatamonkeyTP
-
Get Datamonkey location.
- getDRNAColorMap() - Method in class IMPACT_S.GUIColorSchemes
-
Get a map of DNA/RNA codes to associated colors, from the loaded scheme.
- getExt(String) - Method in class IMPACT_S.Utilities
-
Get filename extension.
- getExtractedBEB() - Method in class IMPACT_S.CodemlTP
-
Get extracted BEB rows.
- getExtractedBEBAsTable() - Method in class IMPACT_S.CodemlTP
-
Get BEB results as hashtable.
- getFallBackLocation(String) - Method in class IMPACT_S.Utilities
-
Get location given associated key.
- getFFC() - Method in class IMPACT_S.AlignmentEditor
-
Get File Format Converter.
- getFileContent(InputStream) - Method in class IMPACT_S.Utilities
-
Get content of file, by input stream.
- getFileContent(String) - Method in class IMPACT_S.Utilities
-
Get file content for specified file.
- getFileNameOpen(String) - Method in class IMPACT_S.GUIFileChooser
-
Presents dialog to open/select file.
Returns selected file name
- getFileSavedPR() - Method in class IMPACT_S.GUIResultsView
-
Get new file path if any table was saved as different name/location.
- getFullPathDir() - Method in class IMPACT_S.GUIFileChooser
-
Gets full path with inclusion of the chosen directory name.
- getFullPathFile() - Method in class IMPACT_S.GUIFileChooser
-
Gets full path with inclusion of the chosen file name.
- getGnuplotOptions() - Method in class IMPACT_S.GUIGnuplotOptions
-
Build and create Gnuplot options for further plotting.
- getIntegerFromStr(String) - Method in class IMPACT_S.Utilities
-
Given a string comprised by text and numbers, get the first number found in string.
- getIntegersFrom(String[], boolean, boolean) - Method in class IMPACT_S.Utilities
-
Get array of integers from array of strings consisting of only integers.
- getLikelihoodValues() - Method in class IMPACT_S.CodemlTP
-
Get the likelihood values found in codeml results, in specified or searched models.
- getLnlTable(String) - Method in class IMPACT_S.CodemlTP
-
Create CSV file from collected information.
- getLocation(String) - Method in class IMPACT_S.Utilities
-
Get location given associated key.
- getMaxColumnSize(int) - Method in class IMPACT_S.ResultsView
-
Get maximum column size (for active file), between name of column and maximum length of its values.
- getMaxColumnValueSize(int) - Method in class IMPACT_S.ResultsView
-
Get maximum size between values of specific column, for active file.
- getMaxTaxaNameSize() - Method in class IMPACT_S.AlignmentEditor
-
Get maximum size for taxa name of input file read.
- getMaxTaxaNameSize(String[]) - Method in class IMPACT_S.FileFormatConverter
-
Get maximum size for given taxa names.
- getMessage() - Method in class IMPACT_S.CodemlTask
-
Get formated message of elapsed time since beginning of execution.
- getMessage() - Method in class IMPACT_S.GnuplotTask
-
Get formated message of elapsed time since beginning of execution.
- getMessage() - Method in class IMPACT_S.PhyMLTask
-
Get formated message of elapsed time since beginning of execution.
- getModelledRange() - Method in class IMPACT_S.ProtToSwissModel
-
Get the modeled range of amino acids modeled among the submitted sequence.
- getModelledRange() - Method in class IMPACT_S.ResultsN3DTP
-
Retrieve the modeled range.
- getModelTable(char, boolean) - Method in class IMPACT_S.DatamonkeyTP
-
Select which positive or negative selection to use, given also the table code.
- getMRCommonSitesTable() - Method in class IMPACT_S.ResultsN3DTP
-
Get Merged Results common sites table.
- getMSignifValue() - Method in class IMPACT_S.TreeSAAPTP
-
Get the most significant value (P = 0.001).
- getMSNSynSubs(String) - Method in class IMPACT_S.TreeSAAPTP
-
Obtain the most significant rows from the NSynSubs file.
- getName(String) - Method in class IMPACT_S.Utilities
-
Get name of file given absolute path.
For opposite see also.
- getNameDir() - Method in class IMPACT_S.GUIFileChooser
-
Gets the field value directory name, does not present dialog.
fileDir must have been already instantiated.
- getNameFile() - Method in class IMPACT_S.GUIFileChooser
-
Gets the field value file name, does not present dialog.
fileName must have been already instantiated.
- getNameNoExt(String) - Method in class IMPACT_S.Utilities
-
Remove extension from filename with extension, given absolute path to filename.
- getNewGenFile(String, String) - Method in class IMPACT_S.Utilities
-
For given file absolute path (with no name),
calculates new name until it is found not to exist.
If it is needed (&99) number of generation IDs may be extended.
- getNewMSAFl() - Method in class IMPACT_S.GUIAlignmentEditor
-
Get MSA file used to run PhyML.
- getNewTree() - Method in class IMPACT_S.GUIAlignmentEditor
-
Get path for new generated tree file by PhyML execution.
- getNewTreeStatFl() - Method in class IMPACT_S.GUIAlignmentEditor
-
Get path for new generated stat file by PhyML execution.
In this case it is the file with the values that is printed together with the tree.
- getNumberParam() - Method in class IMPACT_S.CodemlTP
-
Get the np values found in codeml results, in specified or searched models.
- getOutput() - Method in class IMPACT_S.CodemlTask
-
Get output resulting from terminated execution.
- getOutput() - Method in class IMPACT_S.GnuplotTask
-
Get output resulting from terminated execution.
- getOutput() - Method in class IMPACT_S.PhyMLTask
-
Get output resulting from terminated execution.
- getPaintedSites() - Method in class IMPACT_S.ResultsN3DTP
-
Get all painted sites after Jmol script is created.
- getPathNoName(String) - Method in class IMPACT_S.Utilities
-
Get path without file name, given absolute path.
For opposite see also.
- getPBSTable() - Method in class IMPACT_S.TreeSAAPTP
-
Get NSynSubs Properties by Site table.
- getPDBdownloadlink() - Method in class IMPACT_S.ProtToSwissModel
-
Get direct download link to Template Library (Swiss Model tools).
- getPDBFileResRange() - Method in class IMPACT_S.ResultsN3DTP
-
Obtain start and end of residue range described in PDB file.
- getPDBFileSequence() - Method in class IMPACT_S.ResultsN3DTP
-
Get PDB Sequence from file.
- getPDBLocation() - Method in class IMPACT_S.ProtToSwissModel
-
If there was success downloading file, location is returned.
Otherwise empty is returned.
- getPDBResRange() - Method in class IMPACT_S.ResultsN3DTP
-
Get values previously obtained from PDB file.
- getPDBurl() - Method in class IMPACT_S.ProtToSwissModel
-
Get pdb url of the modelled file.
- getPLocation(String) - Method in class IMPACT_S.TreeSAAPTP
-
Get location of property given its name.
- getPropertiesByRange() - Method in class IMPACT_S.TreeSAAPTP
-
From a range list obtained from a property file, find all
ranges that match to the most significant row (range) for each property.
- getPropertiesBySite(boolean, boolean) - Method in class IMPACT_S.TreeSAAPTP
-
Find and retrieve all properties for each site.
- getPropertiesFound() - Method in class IMPACT_S.TreeSAAPTP
-
Get listing of properties found in directory Sliding Window.
- getPropertiesFoundCnt() - Method in class IMPACT_S.TreeSAAPTP
-
Get count of properties found in directory Sliding Window.
- getPropertyMostSignif(String) - Method in class IMPACT_S.TreeSAAPTP
-
Get list of most significant ranges (rows) for given property name.
- getPropertyMostSignifToFile(String) - Method in class IMPACT_S.TreeSAAPTP
-
Retrieve and write property containing most significant rows to file.
- getRatioTable(String) - Method in class IMPACT_S.CodemlTP
-
Create ratios (dN/dS) table from collected information.
- getRCSBPDBFastaFileURL() - Method in class IMPACT_S.RCSBTools
-
Get direct download link for PDB Fasta file.
Just append the pdbid at the end.
- getRCSBPDBFileURL() - Method in class IMPACT_S.RCSBTools
-
Get direct download link for PDB file.
Just append the pdbid at the end.
- getRGBColor(String, String) - Method in class IMPACT_S.Utilities
-
Get color given by Color.toString() in format r,g,b only.
- getRLocations(String) - Method in class IMPACT_S.ResultsN3DTP
-
Get value for associated key.
- getRowCount() - Method in class IMPACT_S.CSVTableModel
-
Get number of rows.
- getRowCount() - Method in class IMPACT_S.MSATableModel
-
Get number of rows.
- getRowCount() - Method in class IMPACT_S.PDBSeqTableModel
-
Get number of rows.
- getRowCount() - Method in class IMPACT_S.ResultsView
-
Get number of rows for active file.
- getRSColorizeCount() - Method in class IMPACT_S.ResultsView
-
Get number of sequential columns to colorize.
This is obtained from information in a ResultsSummary file.
- getSchemeIndex(String) - Method in class IMPACT_S.GUIColorSchemes
-
Get Color Scheme Index, given key.
- getSelectedOption() - Method in class IMPACT_S.CodemlOptions
-
Get selected PAML set of options index.
- getSelectedValue(int) - Method in class IMPACT_S.MSATableModel
-
Get selection value for row.
- getSelectedValue(int) - Method in class IMPACT_S.PDBSeqTableModel
-
Get selection value for row.
- getSequence(int) - Method in class IMPACT_S.FileFormatReader
-
Get specific sequence by given index.
- getSequence(int) - Method in class IMPACT_S.SequenceTranslator
-
Get sequence from list of sequences.
- getSequenceCount() - Method in class IMPACT_S.AlignmentEditor
-
Get number of sequences for file loaded.
- getSequenceCount() - Method in class IMPACT_S.FileFormatConverter
-
Get number of sequences, possibly if file loaded.
- getSequences() - Method in class IMPACT_S.AlignmentEditor
-
Get alignment sequences.
- getSequences() - Method in class IMPACT_S.FileFormatConverter
-
Get sequences.
- getSequenceTitle(int) - Method in class IMPACT_S.FileFormatReader
-
Get specific sequence title, given index location.
- getSiteCount() - Method in class IMPACT_S.AlignmentEditor
-
Get number of sites for file loaded.
- getSiteCount() - Method in class IMPACT_S.FileFormatConverter
-
Get number of sites, possibly if file loaded.
- getSMDefaultEmail() - Method in class IMPACT_S.ProtToSwissModel
-
Get default email address.
- getSMDefaultProjTitle() - Method in class IMPACT_S.ProtToSwissModel
-
Get default project title.
- getSubstrChopFst(String) - Method in class IMPACT_S.Utilities
-
Get substring without first character.
- getSubstrChopLast(String) - Method in class IMPACT_S.Utilities
-
Get substring without last character.
- getSubstringByChar(String, String) - Method in class IMPACT_S.Utilities
-
Get substring from text given char.
The final string consists of all characters between 0 and index of that character.
- getSWProperties() - Method in class IMPACT_S.TreeSAAPTP
-
Retrieve all properties found in Sliding Window directory.
Initialize related names and locations.
- getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class IMPACT_S.MSAColumnColorRenderer
-
- getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class IMPACT_S.PDBSeqColClrRenderer
-
- getTableColNames() - Method in class IMPACT_S.AlignmentEditor
-
Get column names for table.
These consist of numbered sites.
- getTableColNamesRev() - Method in class IMPACT_S.AlignmentEditor
-
Get column names for table.
These consist of taxa names.
- getTableColumnNames() - Method in class IMPACT_S.ResultsView
-
Get table column names for active file.
- getTableDataValues() - Method in class IMPACT_S.ResultsView
-
Get table values for active file.
- getTableElements() - Method in class IMPACT_S.AlignmentEditor
-
Get table values for table.
These consist of sequences presented in rows.
- getTableElementsRev() - Method in class IMPACT_S.AlignmentEditor
-
Get table values for table.
These consist of sequences presented in columns.
- getTaxaNames() - Method in class IMPACT_S.AlignmentEditor
-
Get sequence descriptions from alignment.
- getTaxaNames() - Method in class IMPACT_S.FileFormatConverter
-
Get taxa names.
- getTaxaNames() - Method in class IMPACT_S.FileFormatReader
-
Get all sequences titles or names.
- getTSLocation(String) - Method in class IMPACT_S.TreeSAAPTP
-
Get TreeSAAP location given key.
- getUsrSelectedColors() - Method in class IMPACT_S.GUIPDBColorSeq
-
Get the user selected colors for each site.
- getValueAt(int, int) - Method in class IMPACT_S.CSVTableModel
-
Get value of table at specified cell.
- getValueAt(int, int) - Method in class IMPACT_S.MSATableModel
-
Get value of table at specified cell.
- getValueAt(int, int) - Method in class IMPACT_S.PDBSeqTableModel
-
Get value of table at specified cell.
- getZSPPropertiesNames() - Method in class IMPACT_S.TreeSAAPTP
-
Get names of significant properties whose rows have been extracted from Z-SigProp.
- getZSPSignifRows() - Method in class IMPACT_S.TreeSAAPTP
-
Extract lines from the file Z-SigProp which are most singificant.
- GNUPLOTExeKey - Static variable in class IMPACT_S.Utilities
-
Gnuplot program location
- GnuplotTask - Class in IMPACT_S
-
Implementation of a background task for Gnuplot execution.
- GnuplotTask(String, String, int) - Constructor for class IMPACT_S.GnuplotTask
-
Initialize Gnuplot Task.
- gotError() - Method in class IMPACT_S.CodemlTask
-
Verify if execution terminated with an error.
- gotError() - Method in class IMPACT_S.GnuplotTask
-
Verify if execution terminated with an error.
- gotError() - Method in class IMPACT_S.PhyMLTask
-
Verify if execution terminated with an error.
- GUI - Class in IMPACT_S
-
IMPACT_S main class/window.
- GUI() - Constructor for class IMPACT_S.GUI
-
Creates new form GUI
- GUIAboutBox - Class in IMPACT_S
-
GUI About Box.
- GUIAboutBox() - Constructor for class IMPACT_S.GUIAboutBox
-
Creates new form GUIAboutBox
- GUIAlignmentEditor - Class in IMPACT_S
-
Implementation of MSA Editor / Viewer, also topology (re)estimation through PhyML.
- GUIAlignmentEditor(File, String, String, Utilities) - Constructor for class IMPACT_S.GUIAlignmentEditor
-
Creates new form GUIAlignmentEditor
- GUIAlignmentFiltering - Class in IMPACT_S
-
Implementation of alignment filtering operation.
- GUIAlignmentFiltering(String, HashMap<String, String>, Utilities) - Constructor for class IMPACT_S.GUIAlignmentFiltering
-
Creates new form GUIAlignmentFiltering
- GUIAlignmentFiltering(String, String, Utilities) - Constructor for class IMPACT_S.GUIAlignmentFiltering
-
Creates new form GUIAlignmentFiltering
- GUICodemlOptions - Class in IMPACT_S
-
GUI implementing Codeml options for the user.
- GUICodemlOptions(CodemlOptions, Utilities, boolean) - Constructor for class IMPACT_S.GUICodemlOptions
-
Creates new form GUICodemlOptions.
- GUIColorSchemes - Class in IMPACT_S
-
Class to permit visual understanding of scheme colors (working like in a legend) and
to allow color selection in the selected scheme.
- GUIColorSchemes(boolean) - Constructor for class IMPACT_S.GUIColorSchemes
-
Creates new form GUIJmolSchemes
- GUIDialogs - Class in IMPACT_S
-
Implementation of several dialog messages.
- GUIDialogs() - Constructor for class IMPACT_S.GUIDialogs
-
General case.
- GUIDialogs(Component) - Constructor for class IMPACT_S.GUIDialogs
-
Specific case.
Parent component only in dialogs UTIL_BFF, UTIL_FEF and UTIL_FMF,
used in initialization process.
In other dialogs works like in general case constructor.
- GUIFileChooser - Class in IMPACT_S
-
Implementation of a File Chooser.
- GUIFileChooser(int, char, String) - Constructor for class IMPACT_S.GUIFileChooser
-
Creates new form GUIFileChooser
- GUIFileFormatConverter - Class in IMPACT_S
-
Implementation of MSA File Format Converter.
Supports conversion between formats like Mase, Fasta, Clustal and Phylip
- GUIFileFormatConverter(Utilities) - Constructor for class IMPACT_S.GUIFileFormatConverter
-
Creates new form GUIFileFormatConverter
- GUIGnuplotOptions - Class in IMPACT_S
-
Class to allow the creation / visualization of graphs for
TreeSAAP Sliding Window properties files.
- GUIGnuplotOptions(String, boolean, Utilities) - Constructor for class IMPACT_S.GUIGnuplotOptions
-
Creates new form GnuplotOptions
- GUIINFO - Class in IMPACT_S
-
Specific GUI informative window.
- GUIINFO(String) - Constructor for class IMPACT_S.GUIINFO
-
Creates new form GUIINFO
- GUIInitBox - Class in IMPACT_S
-
A simple initialization box.
- GUIInitBox() - Constructor for class IMPACT_S.GUIInitBox
-
Creates new form GUIInitBox
- GUIPDBColorSeq - Class in IMPACT_S
-
GUI to allow user to color/exhibit the PDB file amino-acid sequence.
- GUIPDBColorSeq(String, String[]) - Constructor for class IMPACT_S.GUIPDBColorSeq
-
Creates new form GUIPDBColorSeq
- GUIPDBTool - Class in IMPACT_S
-
Download PDB and FASTA files from RCSB, or
PDB files having only one chain, from Swiss Model - Template Library.
- GUIPDBTool(ResultsN3DTP, Utilities) - Constructor for class IMPACT_S.GUIPDBTool
-
Creates new form GUIPDBTool
- GUIPhyMLOptions - Class in IMPACT_S
-
Implementation of PhyML Options selection.
- GUIPhyMLOptions(Utilities) - Constructor for class IMPACT_S.GUIPhyMLOptions
-
Creates new form GUIPhyMLOptions
- GUIPreferences - Class in IMPACT_S
-
GUI for user preferences.
- GUIPreferences(Utilities) - Constructor for class IMPACT_S.GUIPreferences
-
Creates new form GUIPreferences
- GUIProgExecOutput - Class in IMPACT_S
-
Implementation of external program execution output viewer.
- GUIProgExecOutput(String, String) - Constructor for class IMPACT_S.GUIProgExecOutput
-
Creates new form GUIProgExecOutput
- GUIProtToSwissModel - Class in IMPACT_S
-
GUI to allow submission of data to Swiss Model and obtain modelled PDB.
- GUIProtToSwissModel(FileFormatConverter, ResultsN3DTP, Utilities) - Constructor for class IMPACT_S.GUIProtToSwissModel
-
Creates new form GUIProtToSwissModel
- GUIProtToSwissModel(ResultsN3DTP, Utilities) - Constructor for class IMPACT_S.GUIProtToSwissModel
-
Creates new form GUIProtToSwissModel
Initialization is performed from the window itself.
- GUIResultsView - Class in IMPACT_S
-
Implementation of Comma Separated Values (CSV) format files viewer.
- GUIResultsView(String, String, String, Utilities) - Constructor for class IMPACT_S.GUIResultsView
-
Creates new form GUIResultsView