A B C D F G H I J M O P Q R S T U V W

G

generateNewTmpRMainFile() - Method in class IMPACT.Utilities

Generates a new copy of main R script file, ignoring options and replacing source("_file_") lines with lines where the _file_ has absolute path and that matches main file absolute path i.e.

GenericJarTask - Class in IMPACT

Implementation of background task to run any java (jar) program file.
Used for A Tree Viewer (ATV) and Jmol programs.

getAAindex1PropertyName() - Method in class IMPACT.Utilities

Get AAIndex1 property name.
This is obtained from AAIndex1 file field D [property name] (ref).
File must first have been read (successfully).

getAAindex1URL() - Method in class IMPACT.Utilities

Get URL for AAindex1 DB download file.

getBR(String) - Method in class IMPACT.Utilities

Get Buffered Reader for file reading.

getChosenOptions() - Method in class IMPACT.GUIPhyMLOptions

Get selected options.
These are prepared for phyml executable.

getChosenOptionsArray() - Method in class IMPACT.GUIPhyMLOptions

Get selected options as an array and without spaces.

getColumnClass(int) - Method in class IMPACT.CSVTableModel

Get column type, given column index.

getColumnClass(int) - Method in class IMPACT.MSATableModel

Get column type, given column index.

getColumnCount() - Method in class IMPACT.CSVTableModel

Get number of columns.

getColumnCount() - Method in class IMPACT.MSATableModel

Get number of columns.

getColumnCount() - Method in class IMPACT.ResultsView

Get number of columns for active file.

getColumnName(int) - Method in class IMPACT.CSVTableModel

Get column name for column index.

getColumnName(int) - Method in class IMPACT.MSATableModel

Get column name for column index.

getCurrent() - Method in class IMPACT.ConTestTask

Get current value for display progress bar and/or monitor.

getCurrent() - Method in class IMPACT.PhyMLTask

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.RSoftwareTask

Get current value representing status of task.
It returns only the value that is bigger than the previous one.

getDataValues() - Method in class IMPACT.CSVTableModel

Get data values;

getDataValues() - Method in class IMPACT.MSATableModel

Get data values;

getDirectoryOpen() - Method in class IMPACT.GUIFileChooser

Presents dialog to open/select directory.
Returns selected directory name

getExt(String) - Method in class IMPACT.Utilities

Get filename extension.

getFileContent(InputStream) - Method in class IMPACT.Utilities

Get content of file, by input stream.

getFileNameOpen(String) - Method in class IMPACT.GUIFileChooser

Presents dialog to open/select file.
Returns selected file name

getFilePathByValue(String) - Method in class IMPACT.Utilities

Get Property file path given value of same file.

getFormatByExt(String) - Method in class IMPACT.Utilities

Get format of file based on its extension.

getFullPathDir() - Method in class IMPACT.GUIFileChooser

Gets full path with inclusion of the chosen directory name.

getFullPathFile() - Method in class IMPACT.GUIFileChooser

Gets full path with inclusion of the chosen file name.

getHashTableValueByIndex(char, int) - Method in class IMPACT.Utilities

Get value given specific hashtable and index.

getHashTableValueByKey(char, String) - Method in class IMPACT.Utilities

Get value given specific hashtable and key.

getInternalParameters() - Method in class IMPACT.Utilities

Get internal values to print.

getLocation(String) - Method in class IMPACT.Utilities

Get location (hashtable value) path, given key from.

getMaxColumnSize(int) - Method in class IMPACT.ResultsView

Get maximum column size (for active file), between name of column and maximum length of its values.

getMaxColumnValueSize(int) - Method in class IMPACT.ResultsView

Get maximum size between values of specific column, for active file.

getMaxTaxaNameSize() - Method in class IMPACT.AlignmentEditor

Get maximum size for taxa name of input file read.

getMaxTaxaNameSize(String[]) - Method in class IMPACT.FileFormatConverter

Get maximum size for given taxa names.

getMessage(int) - Method in class IMPACT.ConTestTask

Get message that shows task status.

getMessage() - Method in class IMPACT.PhyMLTask

Get formated message of elapsed time since beginning of execution.

getMessage() - Method in class IMPACT.RSoftwareTask

Get message show task status.

getMSATaxaNames() - Method in class IMPACT.ResultsSummary

Get taxa names for table model deselected.

getName(String) - Method in class IMPACT.Utilities

Get name of file given absolute path.
For opposite see also.

getNameDir() - Method in class IMPACT.GUIFileChooser

Gets the field value directory name, does not present dialog.
fileDir must have been already instantiated.

getNameFile() - Method in class IMPACT.GUIFileChooser

Gets the field value file name, does not present dialog.
fileName must have been already instantiated.

getNameNoExt(String) - Method in class IMPACT.Utilities

Remove extension from filename with extension, given absolute path to filename.

getNewGenFile(String, String) - Method in class IMPACT.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.GUIAlignmentEditor

Get MSA file used to run PhyML.

getNewTree() - Method in class IMPACT.GUIAlignmentEditor

Get path for new generated tree file by PhyML execution.

getNewTreeStatFl() - Method in class IMPACT.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.

getNumOfProp() - Method in class IMPACT.Utilities

Get number of properties found in file.

getOutput() - Method in class IMPACT.ConTestTask

Get output from terminated execution.

getOutput() - Method in class IMPACT.PhyMLTask

Get output resulting from terminated execution.

getOutput() - Method in class IMPACT.RSoftwareTask

Get output resulting from terminated execution.

getPathNoName(String) - Method in class IMPACT.Utilities

Get path without directory name, given absolute path.
For opposite see also.

getPropIndexByPath(String) - Method in class IMPACT.Utilities

Get Index for property contained in given file path.

getPropIndexByValue(String) - Method in class IMPACT.Utilities

Get Index for property matching given value.

getPropNameByIndex(int) - Method in class IMPACT.Utilities

Get property name given index.

getPropNames() - Method in class IMPACT.Utilities

Get list of properties names.

getROption(String) - Method in class IMPACT.Utilities

Get option for specified key.

getRowCount() - Method in class IMPACT.CSVTableModel

Get number of rows.

getRowCount() - Method in class IMPACT.MSATableModel

Get number of rows.

getRowCount() - Method in class IMPACT.ResultsView

Get number of rows for active file.

getRSColorizeCount() - Method in class IMPACT.ResultsView

Get number of sequential columns to colorize.
This is obtained from information in a ResultsSummary file.

getRScriptVarNames() - Method in class IMPACT.Utilities

Read options section and get variables names.
Only executes completely for the first time, when names are no set.
Variable names are returned in same order that appear in the script.

getSelectedValue(int) - Method in class IMPACT.MSATableModel

Get selection value for row.

getSequenceCount() - Method in class IMPACT.AlignmentEditor

Get number of sequences for file loaded.

getSequenceCount() - Method in class IMPACT.FileFormatConverter

Get number of sequences, possibly if file loaded.

getSequences() - Method in class IMPACT.FileFormatConverter

Get sequences.

getSiteCount() - Method in class IMPACT.AlignmentEditor

Get number of sites for file loaded.

getSiteCount() - Method in class IMPACT.FileFormatConverter

Get number of sites, possibly if file loaded.

getSubstrChopFst(String) - Method in class IMPACT.Utilities

Get substring without first character.

getSubstrChopLast(String) - Method in class IMPACT.Utilities

Get substring without last charater.

getSubstringByChar(String, String) - Method in class IMPACT.Utilities

Get substring from text given char.
The final string consists of all characters between 0 and index of that character.

getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class IMPACT.MSAColumnColorRenderer

getTableColNames() - Method in class IMPACT.AlignmentEditor

Get column names for table.
These consist of numbered sites.

getTableColNamesRev() - Method in class IMPACT.AlignmentEditor

Get column names for table.
These consist of taxa names.

getTableColumnNames() - Method in class IMPACT.ResultsView

Get table column names for active file.

getTableDataValues() - Method in class IMPACT.ResultsView

Get table values for active file.

getTableElements() - Method in class IMPACT.AlignmentEditor

Get table values for table.
These consist of sequences presented in rows.

getTableElementsRev() - Method in class IMPACT.AlignmentEditor

Get table values for table.
These consist of sequences presented in columns.

getTaxaNames() - Method in class IMPACT.FileFormatConverter

Get taxa names.

getUtil() - Method in class IMPACT.GUIConfPreferences

Get updated utilities.

getValueAt(int, int) - Method in class IMPACT.CSVTableModel

Get value of table at specified cell.

getValueAt(int, int) - Method in class IMPACT.MSATableModel

Get value of table at specified cell.

gotError() - Method in class IMPACT.ConTestTask

Verify if task terminated with error.

gotError() - Method in class IMPACT.PhyMLTask

Verify if execution terminated with an error.

gotError() - Method in class IMPACT.RSoftwareTask

Verify if execution terminated with an error.

GUI - Class in IMPACT

Implementation of IMPACT, main.

GUI() - Constructor for class IMPACT.GUI

Creates and initializes GUI for ConTest.

GUIAboutBox - Class in IMPACT

Implementation of an About box for menu Help.

GUIAboutBox(Utilities) - Constructor for class IMPACT.GUIAboutBox

Creates new form GUIAboutBox

GUIAlignmentEditor - Class in IMPACT

Implementation of MSA Editor / Viewer, also topology (re)estimation through PhyML.

GUIAlignmentEditor(File, String, String, Utilities) - Constructor for class IMPACT.GUIAlignmentEditor

Creates new form GUIAlignmentEditor

GUIConfPreferences - Class in IMPACT

Implementation of IMPACT Preferences.
Configuration and management of several paths.

GUIConfPreferences(Utilities) - Constructor for class IMPACT.GUIConfPreferences

Creates new form GUIConfPreferences

GUIDialogs - Class in IMPACT

Implementation of several dialog messages.

GUIDialogs() - Constructor for class IMPACT.GUIDialogs

General case.

GUIDialogs(Component) - Constructor for class IMPACT.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

Implementation of a File Chooser.

GUIFileChooser(int, char, String) - Constructor for class IMPACT.GUIFileChooser

Creates new form GUIFileChooser

GUIFileFormatConverter - Class in IMPACT

Implementation of MSA File Format Converter.
Supports conversion between formats like Mase, Fasta, Clustal and Phylip

GUIFileFormatConverter(Utilities) - Constructor for class IMPACT.GUIFileFormatConverter

Creates new form GUIFileFormatConverter

GUIInitializationBox - Class in IMPACT

Implementation of a user debbuging box, for GUI initialization.

GUIInitializationBox(String, int) - Constructor for class IMPACT.GUIInitializationBox

Creates new form GUIInitializationBox.

GUIPATH_KEY - Static variable in class IMPACT.Utilities

Key for access GUI directory location

GUIPhyMLOptions - Class in IMPACT

Implementation of PhyML Options selection.

GUIPhyMLOptions(Utilities) - Constructor for class IMPACT.GUIPhyMLOptions

Creates new form GUIPhyMLOptions

GUIProgExecOutput - Class in IMPACT

Implementation of external program execution output viewer.

GUIProgExecOutput(String, String) - Constructor for class IMPACT.GUIProgExecOutput

Creates new form GUIProgExecOutput

GUIResultsSummary - Class in IMPACT

Implementation of options to provide for producing summary of results.

GUIResultsSummary(String, String, String, String, Utilities) - Constructor for class IMPACT.GUIResultsSummary

Creates new form GUIResultsSummary

GUIResultsView - Class in IMPACT

Implementation of Comma Separated Values (CSV) format files viewer.

GUIResultsView(String, String, String, Utilities) - Constructor for class IMPACT.GUIResultsView

Creates new form GUIResultsView