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

A

AA_CODES - Static variable in class util.Constants
 
AA_PER_LINE - Static variable in class util.Constants
 
AAMap - Class in util
This class represents a default map for the 3-letter to 1-letter amino acid coding.
AAMap() - Constructor for class util.AAMap
Constructor for the simple amino acid map.
accept(File) - Method in class util.FastaFileFilter
Accept all directories, *.fasta files.
accept(File) - Method in class util.PngFileFilter
Accept all directories, *.png files.
actionPerformed(ActionEvent) - Method in class view.LoadAlignFrame.OpenFileAction
 
actionPerformed(ActionEvent) - Method in class view.LoadMethodFrame.OpenFileAction
 
actionPerformed(ActionEvent) - Method in class view.LoadS3DetFrame.OpenFileAction
 
actionPerformed(ActionEvent) - Method in class view.LoadStructureFrame.OpenFileAction
 
actionPerformed(ActionEvent) - Method in class view.LoadXDetFrame.OpenFileAction
 
addGradualScheme(HashMap<Character, Double>, String) - Static method in class util.ColorScheme
Function to add a new numeric color scheme.
addResidueByPosition(int) - Static method in class util.ResidueSelectionManager
 
addSequence(SequenceImpl) - Method in class model.ClusterGroup
This method adds another sequence to the cluster group.
addSequence(String) - Static method in class util.SequenceManager
 
addSequenceByPosition(int) - Static method in class util.SelectionManager
 
addSequenceByPosition(int) - Static method in class util.SequenceManager
 
addToCurrentSelection(FuncResidueImpl) - Static method in class util.ResidueSelectionManager
Adds an element to the current selection.
addToCurrentSelection(int) - Static method in class util.SelectionManager
Adds an element to the current selection.
addUdmObject(UDMObject) - Method in class model.Methods
Adds another UDM object to the UDM Object array.
adjustmentValueChanged(AdjustmentEvent) - Method in class util.SequenceLogo.LogoScrollAdjuster
 
adjustmentValueChanged(AdjustmentEvent) - Method in class view.AlignPanel.ScrollAdjuster
 
adjustmentValueChanged(AdjustmentEvent) - Method in class view.SelectionFrame.SelectionScrollAdjuster
 
AlignFrame - Class in view
This class represents the main user interface containing the different panels, such as the alignment panel.
AlignFrame() - Constructor for class view.AlignFrame
 
AlignFrame(AlignObject, Methods, int, int, boolean) - Constructor for class view.AlignFrame
Constructor for a given AlignObject.
Alignment - Class in util
This class does a simple alignment by using a dot plot matrix for the PDB and the given alignment sequence.
Alignment(String, String) - Constructor for class util.Alignment
Constructor of the DotPlotMatrix
AlignmentExporter - Class in util
 
AlignmentExporter() - Constructor for class util.AlignmentExporter
 
AlignObject - Class in model
This class does the representation of an alignment object.
AlignObject() - Constructor for class model.AlignObject
Default constructor.
AlignObject(SequenceImpl[]) - Constructor for class model.AlignObject
Constructor for AlignObject with sequences as parameter.
AlignPanel - Class in view
Represents the whole alignment panel.
AlignPanel(AlignFrame) - Constructor for class view.AlignPanel
Default constructor for the alignpanel.
AlignPanel(AlignFrame, AlignViewProps) - Constructor for class view.AlignPanel
Constructor of the alignment panel.
AlignPanel.ScrollAdjuster - Class in view
 
AlignPanel.ScrollAdjuster() - Constructor for class view.AlignPanel.ScrollAdjuster
 
ALIGNPANEL_HEIGHT - Static variable in class util.Constants
 
ALIGNPANEL_WIDTH - Static variable in class util.Constants
 
alignSequenceToStructure() - Method in class util.Alignment
Initializes the alignment by the condition of matching the first four amino acids and aligns the two sequences by starting at the first four matching positions and going diagonal (down-to-the-right) in the matrix.
ALIGNVIEW_FONT - Static variable in class util.Constants
 
ALIGNVIEW_FONTSIZE - Static variable in class util.Constants
 
ALIGNVIEW_FONTSTYLE - Static variable in class util.Constants
 
AlignViewProps - Class in view
Defines the view properties for the alignment.
AlignViewProps(AlignObject) - Constructor for class view.AlignViewProps
Constructor for the alignment view properties
AlignViewTest - Class in test
 
AlignViewTest() - Constructor for class test.AlignViewTest
 
APPNAME - Static variable in class util.Constants
 
APPTITLE - Static variable in class util.Constants
 
AXESFRAME_HEIGHT - Static variable in class util.Constants
 
AXESFRAME_WIDTH - Static variable in class util.Constants
 
AXISFRAME_MAX - Static variable in class util.Constants
 

B

BlastPDB - Class in util
 
BlastPDB() - Constructor for class util.BlastPDB
 
blastThePDB(String, double) - Static method in class util.BlastPDB
 

C

calculateFittingFont() - Method in class util.SequenceLogo.LogoPosition
 
centerInComponent(Component, Component) - Static method in class util.ScreenConfig
Center the given component in the given parent.
centerInScreen(Component) - Static method in class util.ScreenConfig
Center the given component in the visible screen.
checkAlignment() - Method in class util.Alignment
Checks sequence converage and shows a warning if it is under the specified threshold
clearGaps() - Method in class model.AlignObject
 
clone() - Method in class view.AlignViewProps
 
close() - Method in class view.AlignFrame
This method is called when the frame is closed.
closeOtherWindows() - Method in class view.AlignFrame
Close all dependant windows
closeRegisteredWindows(String) - Method in class view.SequencePainter
Close all registered windows
CLUSTAL_X - Static variable in class util.ColorScheme
 
Cluster3DFrame - Class in view
This class draws a window containing a graphical representation of clusters defined by S3Det.
Cluster3DFrame(S3DetObject, AlignViewProps, SequencePainter) - Constructor for class view.Cluster3DFrame
 
CLUSTER_POINT_SIZE - Static variable in class util.Constants
 
CLUSTER_SHAPE_NAME - Static variable in class util.Constants
 
ClusterCoordinates - Class in model
This class represents the cluster coordinates.
ClusterCoordinates() - Constructor for class model.ClusterCoordinates
 
ClusterGroup - Class in model
This class defines a cluster group which stands for a subfamily of proteins.
ClusterGroup() - Constructor for class model.ClusterGroup
 
CLUSTERSETTINGSFRM_HEIGHT - Static variable in class util.Constants
 
CLUSTERSETTINGSFRM_WIDTH - Static variable in class util.Constants
 
ClusterWindowListener - Class in view
Default StructureWindowListener class, handles what happens when the Structure3DFrame is closed.
ClusterWindowListener(Cluster3DFrame, SequencePainter) - Constructor for class view.ClusterWindowListener
 
colorColumn(Color, int, int) - Method in class view.SequencePainter
This method colors the columns
ColorParser - Class in parser
This is the parser class for the color scheme files.
ColorParser() - Constructor for class parser.ColorParser
General constructor.
ColorScheme - Class in util
This class represents the color scheme for the amino acids in the alignment.
ColorScheme() - Constructor for class util.ColorScheme
Constructor of the color scheme hash map.
ColorSchemeInfo - Class in view
 
ColorSchemeInfo(double, double) - Constructor for class view.ColorSchemeInfo
 
ColorSchemeInfo(String) - Constructor for class view.ColorSchemeInfo
 
compareTo(FuncResidueImpl) - Method in class model.FuncResidueImpl
Compare function
compareTo(SequenceLogo.FrequencyImage) - Method in class util.SequenceLogo.FrequencyImage
 
CONFIG_DIR - Static variable in class util.Constants
 
Constants - Class in util
This class defines some constants for the whole software.
Constants() - Constructor for class util.Constants
 
contains(FuncResidueImpl) - Static method in class util.ResidueSelectionManager
 
contains(int, char) - Static method in class util.ResidueSelectionManager
 
contains(int) - Static method in class util.ResidueSelectionManager
 
contains(int) - Static method in class util.SelectionManager
Checks if an element is selected
contains(String) - Static method in class util.SequenceManager
Checks if a sequenceis selected
containsKey(Character) - Static method in class util.ColorScheme
 
CONVERSION_PLUGINS_DIR - Static variable in class util.Constants
 
CONVERSION_PLUGINS_PACKAGE - Static variable in class util.Constants
 
Coordinates - Interface in interfaces
Interface as a representation for the coordinates.
createSceneGraph() - Method in class view.Cluster3DFrame
This method receives a protein name and gets his assigned color from s3det algorithm and defined constants.

D

DATA_FLAVOR - Static variable in class util.FileDrop.TransferableObject
The default DataFlavor for FileDrop.TransferableObject has the representation class net.iharder.dnd.TransferableObject.class and the MIME type application/x-net.iharder.dnd.TransferableObject.
DEFAULT_AXIS_COLOR - Static variable in class util.Constants
 
DEFAULT_CLUSTER_COLOR - Static variable in class util.Constants
 
DEFAULT_CLUSTER_COLOR_NAME - Static variable in class util.Constants
 
DEFAULT_HEIGHT - Static variable in class util.Constants
 
DEFAULT_RESIDUE_COLOR - Static variable in class util.Constants
 
DEFAULT_RESIDUE_COLOR_NAME - Static variable in class util.Constants
 
DEFAULT_WIDTH - Static variable in class util.Constants
 
defScheme - Static variable in class util.ColorScheme
Default Clustal X color scheme.
deregister(Observer) - Method in interface interfaces.Observable
 
deregister(Observer) - Method in class view.SequencePainter
Deregisters the observer.
DESCBOXPNL_BGCOLOR - Static variable in class util.Constants
 
disableDoubleBuffering(Component) - Static method in class util.PrintUtilities
 
drawBackground(int, int, int) - Method in class view.SequencePainter
This methods draws the background.
drawBlackName(Graphics2D, SequenceImpl, int) - Method in class view.NamePainter
Draws the name marked as black.
drawComponent(Graphics2D, int, int, int, int) - Method in class view.NamePainter
Draw component method.
drawHorizontal(SequenceImpl, int, int, int, Color) - Method in class view.SequencePainter
This methods draws an horizontal line (used for the group boxes).
drawIndex(Graphics, int, int, int, int) - Method in class view.IndexPanel
Draws the index.
drawName(Graphics2D, SequenceImpl, int, int, Color) - Method in class view.NamePainter
Draws the name.
drawPanel(Graphics, int, int, int, int, int) - Method in class view.SequencePainter
This methods draws the panel.
drawPanel(Graphics, int, int, int, int) - Method in class view.SliderPanel
Draws the method data.
drawSelectedIndex(Graphics, int, int, int, int) - Method in class view.IndexPanel
Draws the index of selected columns.
drawSelectedName(Graphics2D, SequenceImpl, int) - Method in class view.NamePainter
Draws the name marked as selected.
drawSelectionSeq(SequenceImpl, int, int, int) - Method in class view.SequencePainter
This methods actually draws the sequence.
drawSeq(SequenceImpl, int, int, int) - Method in class view.SequencePainter
This methods actually draws the sequence.
drawSquares(Graphics, int, int, int, int) - Method in class view.MethodPanel
Draws the index.
drawVertical(SequenceImpl, int, int, int, Color) - Method in class view.SequencePainter
This methods draws an vertical line (used for the group boxes).
dS - Static variable in class util.Constants
 

E

emptyCurrentSelection() - Static method in class util.ResidueSelectionManager
Clear the current selection
emptyCurrentSelection() - Static method in class util.SelectionManager
Delete all elements from the current selection.
emptySelectedSequences() - Static method in class util.SequenceManager
 
enableDoubleBuffering(Component) - Static method in class util.PrintUtilities
 
enablePicking(Node) - Method in class view.Cluster3DFrame
 
endPrimaryStructureSection() - Method in class util.PDBFile
This part is needed to get the primary sequence out of the PDB file.
ENTROPYCUTOFF_DEFAULT - Static variable in class util.Constants
 
ENTROPYSLIDER_TOOLTIP - Static variable in class util.Constants
 
evaluateBestHit(String) - Static method in class util.BlastPDB
Check PDB result against the specified threshold
exportFasta(AlignFrame, AlignViewProps, ActionEvent, boolean) - Static method in class util.AlignmentExporter
This method manages the Fasta File export of current selection.
exportMethodFile(AlignFrame, ActionEvent, String) - Static method in class util.AlignmentExporter
Create a copy of the original input file on a new location
exportPNGFile(AlignFrame, ActionEvent) - Static method in class util.AlignmentExporter
This method manages the PNG File export.
exportPNGFile(File) - Method in class view.AlignPanel
 

F

FastaFileFilter - Class in util
File filter for *.mfa files.
FastaFileFilter() - Constructor for class util.FastaFileFilter
 
FILE_PREFIX - Static variable in class util.Constants
 
FileDrop - Class in util
This class makes it easy to drag and drop files from the operating system to a Java program.
FileDrop(Component, FileDrop.Listener) - Constructor for class util.FileDrop
Constructs a FileDrop with a default light-blue border and, if c is a Container, recursively sets all elements contained within as drop targets, though only the top level container will change borders.
FileDrop(Component, boolean, FileDrop.Listener) - Constructor for class util.FileDrop
Constructor with a default border and the option to recursively set drop targets.
FileDrop(PrintStream, Component, FileDrop.Listener) - Constructor for class util.FileDrop
Constructor with a default border and debugging optionally turned on.
FileDrop(PrintStream, Component, boolean, FileDrop.Listener) - Constructor for class util.FileDrop
Constructor with a default border, debugging optionally turned on and the option to recursively set drop targets.
FileDrop(Component, Border, FileDrop.Listener) - Constructor for class util.FileDrop
Constructor with a specified border
FileDrop(Component, Border, boolean, FileDrop.Listener) - Constructor for class util.FileDrop
Constructor with a specified border and the option to recursively set drop targets.
FileDrop(PrintStream, Component, Border, FileDrop.Listener) - Constructor for class util.FileDrop
Constructor with a specified border and debugging optionally turned on.
FileDrop(PrintStream, Component, Border, boolean, FileDrop.Listener) - Constructor for class util.FileDrop
Full constructor with a specified border and debugging optionally turned on.
FileDrop.Event - Class in util
This is the event that is passed to the filesDropped(...) method in your FileDropListener when files are dropped onto a registered drop target.
FileDrop.Event(File[], Object) - Constructor for class util.FileDrop.Event
Constructs an FileDrop.Event with the array of files that were dropped and the FileDrop that initiated the event.
FileDrop.Listener - Interface in util
Implement this inner interface to listen for when files are dropped.
FileDrop.TransferableObject - Class in util
At last an easy way to encapsulate your custom objects for dragging and dropping in your Java programs!
FileDrop.TransferableObject(Object) - Constructor for class util.FileDrop.TransferableObject
Creates a new FileDrop.TransferableObject that wraps data.
FileDrop.TransferableObject(FileDrop.TransferableObject.Fetcher) - Constructor for class util.FileDrop.TransferableObject
Creates a new FileDrop.TransferableObject that will return the object that is returned by fetcher.
FileDrop.TransferableObject(Class<?>, FileDrop.TransferableObject.Fetcher) - Constructor for class util.FileDrop.TransferableObject
Creates a new FileDrop.TransferableObject that will return the object that is returned by fetcher.
FileDrop.TransferableObject.Fetcher - Interface in util
Instead of passing your data directly to the FileDrop.TransferableObject constructor, you may want to know exactly when your data was received in case you need to remove it from its source (or do anyting else to it).
filesDropped(File[]) - Method in interface util.FileDrop.Listener
This method is called when files have been successfully dropped.
FILTER_PRESETS_FILE - Static variable in class util.Constants
 
FilterAlignment - Class in util
 
FilterAlignment() - Constructor for class util.FilterAlignment
 
FilterAlignment(AlignFrame, AlignViewProps) - Constructor for class util.FilterAlignment
LoadFrame with a given parent frame.
filterAlignment(AlignFrame, AlignViewProps, ActionEvent, String, String, String, String, boolean) - Method in class util.FilterAlignment
 
FilterAlignment.StreamGobbler - Class in util
 
FilterAlignment.StreamGobbler(String, InputStream, String) - Constructor for class util.FilterAlignment.StreamGobbler
 
findBestHit(String) - Static method in class util.BlastPDB
Gets best PDB hit
findPosition(int) - Method in class model.SequenceImpl
Finds the i'th position in the sequence, skipping the gaps.
FTPSERVER - Static variable in class util.Constants
 
FuncResidue - Interface in interfaces
Interface as a representation for the functional residue.
FuncResidueImpl - Class in model
Implementation of the FuncResidue Interface.
FuncResidueImpl() - Constructor for class model.FuncResidueImpl
Constructors
FuncResidueImpl(int, char) - Constructor for class model.FuncResidueImpl
 

G

getAa() - Method in interface interfaces.FuncResidue
 
getAa() - Method in interface interfaces.Residue
 
getAa() - Method in class model.FuncResidueImpl
Returns the letter of the amino acid.
getAa() - Method in class model.ResidueImpl
Returns the letter of the amino acid.
getAAPosition(MouseEvent) - Method in class view.SequencePainter
Returns the position of a amino acid for a mouse event.
getAlign2PDBPositionMap() - Method in class util.Alignment
Returns the alignment to PDB position hash map.
getAlignFrame() - Method in class view.AlignPanel
 
getAlignPanel() - Method in class view.AlignFrame
Returns the alignment panel.
getAlignPanel() - Method in class view.SequencePainter
Returns the alignment panel.
getAlignPos(int) - Method in class util.Alignment
Receives an aminoacid position on the pdb chain and returns its position on the alignment sequence
getAlObj() - Method in class view.AlignFrame
Returns the alignment object.
getAlObj() - Method in class view.AlignViewProps
Returns the alignment object
getAverageRank() - Method in class model.PredictedPosition
Returns the average rank.
getCanvas3D() - Method in class view.Cluster3DFrame
 
getCharHeight() - Method in class view.AlignViewProps
Returns the char height.
getCharWidth() - Method in class view.AlignViewProps
Returns the char width.
getClusterColor() - Method in class model.SequenceImpl
Returns the cluster sequence color.
getClusterCoords() - Method in class model.S3DetObject
Returns the cluster coordinates.
getClusterGroups() - Method in class util.SequenceOrderer
Retrieve the cluster groups from the sequences and the S3Det method.
getClusterIndex() - Method in class model.SequenceCluster
Returns the value of the cluster index.
getClusterSequences() - Method in class util.SequenceOrderer
Returns all the sequences in the clustered order
getColor() - Method in class model.ClusterGroup
Returns the cluster color.
getColor(Character) - Static method in class util.ColorScheme
Get the color associated to residue on current color scheme
getColorFromValue(double, double, double, double, int) - Static method in class util.ColorScheme
Function to get the color associated to value in the specified range and palette.
getColorPalette() - Static method in class util.ColorScheme
Getter for colorPallete
getColorPalette() - Method in class view.StatusPanel
 
getColorScheme() - Static method in class util.ColorScheme
Getter for new color scheme
getColorSchemeNames() - Static method in class util.ColorScheme
 
getConservedPositions() - Method in class model.S3DetObject
Returns the conserved positions.
getCoords() - Method in interface interfaces.Coordinates
 
getCoords() - Method in class model.ClusterCoordinates
Returns the array of the coordinates.
getCoords() - Method in class model.ResidueCoordinates
Returns the array of the coordinates.
getCoords() - Method in class model.SequenceCoordinates
Returns the array of the coordinates.
getCorrelation() - Method in interface interfaces.FuncResidue
 
getCorrelation() - Method in class model.FuncResidueImpl
Returns the correlation factor.
getCurrentEntropyCutoff() - Method in class model.Methods
 
getCurrentPosition() - Method in class view.SequencePainter
Returns the current position.
getCurrentS3DetCutoff() - Method in class model.Methods
 
getCurrentScoreCutoff() - Method in class model.UDMObject
 
getCurrentSelection() - Static method in class util.ResidueSelectionManager
 
getCurrentSelection() - Static method in class util.SelectionManager
 
getCurrentXDetCutoff() - Method in class model.Methods
 
getCustomDataFlavor() - Method in class util.FileDrop.TransferableObject
Returns the custom DataFlavor associated with the encapsulated object or null if the FileDrop.TransferableObject.Fetcher constructor was used without passing a Class.
getDescription() - Method in class util.FastaFileFilter
The description of this filter
getDescription() - Method in class util.PngFileFilter
The description of this filter
getDownloaded() - Method in class util.PdbFileOpener
Get this download's progress.
getEnd() - Method in interface interfaces.Sequence
 
getEnd() - Method in class model.SequenceImpl
Returns the end position of the sequence.
getEntropy() - Method in interface interfaces.FuncResidue
 
getEntropy() - Method in class model.FuncResidueImpl
Returns the sequence entropy factor.
getEntropyCutoff() - Method in class model.Methods
Returns the entropy cutoff for the XDet method.
getExtension(File) - Static method in class util.FastaFileFilter
Get the extension of a file.
getExtension(File) - Static method in class util.PngFileFilter
Get the extension of a file.
getFilename() - Method in class model.AlignObject
Returns the filename.an
getFilename() - Method in class model.S3DetObject
Returns the file name.
getFilename() - Method in class model.UDMObject
Returns the name of the file.
getFilename() - Method in class model.XDetObject
Returns the name of the XDet file.
getFilename() - Method in class view.LoadStructureFrame
Getter-method for the filename.
getFiles() - Method in class util.FileDrop.Event
Returns an array of files that were dropped on a registered drop target.
getFont() - Method in class view.AlignViewProps
Returns the font object
getFrequency() - Method in class util.SequenceLogo.FrequencyImage
 
getFullSelection() - Static method in class util.SelectionManager
Creates a combination vector of positions from SelectionManager and ResidueSelectionManager
getFuncResidues() - Method in class model.XDetObject
Returns the functional residues as an array.
getGraphics() - Method in class util.ImageExporter
 
getGroupNumber() - Method in class model.PredictedPosition
Returns the group number.
getHeight() - Method in class model.AlignObject
Returns the height of the alignment through the number of Sequences.
getHorizontalScrollbar() - Method in class view.AlignPanel
 
getImage() - Method in class util.SequenceLogo.FrequencyImage
 
getImageIcon(String) - Static method in class view.AlignFrame
Loads an image from icon directory
getIndex() - Method in class model.ClusterGroup
Returns the cluster index.
getIndexPanel() - Method in class view.AlignPanel
 
getLastSelected() - Static method in class util.SequenceManager
 
getLastSelection() - Static method in class util.SelectionManager
 
getLength() - Method in interface interfaces.Sequence
 
getLength() - Method in class model.SequenceImpl
Returns the sequence length.
getLetter() - Method in class model.ResidueCoordinates
Returns the letter of the residue.
getLetterAt(int) - Method in interface interfaces.Sequence
 
getLetterAt(int) - Method in class model.SequenceImpl
Returns the letter (amino acid) at a certain position.
getMarkedSequenceName() - Static method in class util.SequenceManager
Returns the marked sequence name.
getMaxValue() - Method in class model.UDMObject
 
getMethodName() - Method in class model.UDMObject
 
getMethodNumber() - Method in class model.Methods
Returns the total number of the used methods.
getMethodPanel() - Method in class view.AlignPanel
 
getMethods() - Method in class view.AlignFrame
Returns the methods
getMinValue() - Method in class model.UDMObject
 
getName() - Method in interface interfaces.Sequence
 
getName() - Method in class model.ClusterCoordinates
Returns the name of the cluster.
getName() - Method in class model.SequenceCluster
Returns the name of the sequence.
getName() - Method in class model.SequenceCoordinates
Returns the name of the sequence.
getName() - Method in class model.SequenceImpl
Returns the sequence name.
getName2ClusterIndex() - Method in class model.S3DetObject
Returns the name-to-clusterIndex HashMap.
getNamePanel() - Method in class view.AlignPanel
 
getNameRenderer() - Method in class view.NamePanel
 
getNumberOfSelectedAxes() - Method in class model.S3DetObject
Returns the total number of selected axes.
getNumCols() - Method in class util.Alignment
Returns the number of columns of the matrix;
getNumRows() - Method in class util.Alignment
Returns the number of rows of the matrix;
getObject() - Method in interface util.FileDrop.TransferableObject.Fetcher
Return the object being encapsulated in the FileDrop.TransferableObject.
getPaletteImage() - Static method in class util.ColorScheme
Function which shows an image of the current palette
getPdb2alignPositionMap() - Method in class util.Alignment
 
getPdbFile() - Method in class util.PdbFileOpener
Returns the string of the PDB file.
getPDBPos(int) - Method in class util.Alignment
Receives an aminoacid position on the alignment sequence chain and returns its position on the pdb chain
getPdbSequence() - Method in class util.PDBFile
Returns the (build) PDB sequence as a string.
getPluginName(int, int) - Static method in class util.PluginLoader
 
getPlugins(int) - Static method in class util.PluginLoader
 
getPos2PredPosition() - Method in class model.S3DetObject
Returns the Position-To-PredictedPosition HashMap.
getPos2ResMap() - Method in class model.UDMObject
Returns the Position-To-Residue HashMap.
getPos2ResMap() - Method in class model.XDetObject
Returns the Position-To-Residue HashMap.
getPosition() - Method in interface interfaces.FuncResidue
 
getPosition() - Method in interface interfaces.Residue
 
getPosition() - Method in class model.FuncResidueImpl
Returns the position of the amino acid.
getPosition() - Method in class model.ResidueCoordinates
Returns the position of the residue.
getPosition() - Method in class model.ResidueImpl
Returns the position of the amino acid.
getPositionRes() - Method in class model.PredictedPosition
Returns the position of the residue.
getPredictedPositions() - Method in class model.S3DetObject
Returns the predicted positions.
getProteinNumber() - Method in class model.AlignObject
Returns the number of protein.
getResCoords() - Method in class model.S3DetObject
Returns the residue coordinates.
getResidues() - Method in class model.UDMObject
Returns the residues as an array.
getResNumber() - Method in class model.UDMObject
Returns the residue number.
getResNumber() - Method in class model.XDetObject
Returns the residue number.
getS3DetCutoff() - Method in class model.Methods
Returns the average rank cutoff for the S3Det method.
getS3detobj() - Static method in class util.ResidueSelectionManager
 
getS3detobj() - Static method in class util.SelectionManager
 
getS3detobj() - Static method in class util.SequenceManager
 
getS3DetObject() - Method in class model.Methods
Returns the S3DetObject.
getScore() - Method in interface interfaces.Residue
 
getScore() - Method in class model.ResidueImpl
Returns the score value
getScoreCutoff() - Method in class model.UDMObject
Returns the score cutoff.
getScoreCutoffs() - Method in class model.Methods
Returns the score cutoff double array.
getSelectedSequence() - Method in class view.SequencePainter
Returns the selected sequence.
getSelectedSequences() - Static method in class util.SequenceManager
 
getSeqClusters() - Method in class model.S3DetObject
Returns the sequence clusters.
getSeqCoords() - Method in class model.S3DetObject
Returns the sequence coordinates.
getSeqPainter() - Static method in class util.ResidueSelectionManager
 
getSeqPainter() - Static method in class util.SelectionManager
 
getSeqPainter() - Method in class view.SequencePanel
Returns the SeqPainter.
getSeqPanel() - Method in class view.AlignPanel
 
getSequence() - Method in interface interfaces.Sequence
 
getSequence(int, int) - Method in interface interfaces.Sequence
 
getSequence(int, int) - Method in class model.SequenceImpl
Returns the sequence (for start and end position) as char array.
getSequence() - Method in class model.SequenceImpl
Returns the sequence as char array.
getSequence(String, AlignObject) - Static method in class util.SequenceManager
Gets the sequence related with the specified name on the alignment
getSequence(MouseEvent) - Method in class view.SequencePainter
Returns the sequence for a mouse event.
getSequenceAsString() - Method in interface interfaces.Sequence
 
getSequenceAsString() - Method in class model.SequenceImpl
Returns the sequence as a string.
getSequenceAt(int) - Method in class model.AlignObject
Returns the sequence for a certain parameter index.
getSequences() - Method in class model.AlignObject
Returns the array of sequence objects.
getSequences() - Method in class model.ClusterGroup
Returns the sequences.
getSourceName() - Method in class view.LoadAlignFrame.OpenFileAction
 
getSourceName() - Method in class view.LoadMethodFrame.OpenFileAction
 
getSourceName() - Method in class view.LoadS3DetFrame.OpenFileAction
 
getSourceName() - Method in class view.LoadStructureFrame.OpenFileAction
 
getSourceName() - Method in class view.LoadXDetFrame.OpenFileAction
 
getStart() - Method in interface interfaces.Sequence
 
getStart() - Method in class model.SequenceImpl
Returns the sequence start position of the sequence.
getSumScrollX() - Method in class view.SequencePainter
 
getThread() - Method in class util.PdbFileOpener
Returns the thread.
getTransferData(DataFlavor) - Method in class util.FileDrop.TransferableObject
Returns the data encapsulated in this FileDrop.TransferableObject.
getTransferDataFlavors() - Method in class util.FileDrop.TransferableObject
Returns a two- or three-element array containing first the custom data flavor, if one was created in the constructors, second the default FileDrop.TransferableObject.DATA_FLAVOR associated with FileDrop.TransferableObject, and third the java.awt.datatransfer.DataFlavor.stringFlavor.
getUdmNumber() - Method in class model.Methods
Returns the number of user defined methods.
getUdmObjects() - Method in class model.Methods
Returns all the UDM objects.
getVerticalScrollbar() - Method in class view.AlignPanel
 
getViewer() - Method in class view.Structure3DFrame
Returns the viewer from the panel.
getViewProps() - Method in class view.SequencePainter
 
getWidth() - Method in class model.AlignObject
Returns the width through the maximum of the longest sequence.
getxDetCutoff() - Method in class model.Methods
Returns the correlation cutoff for the XDet method.
getxDetObject() - Method in class model.Methods
Returns the XDetObject.
getXEnd() - Method in class view.AlignViewProps
Returns the x end position.
getXStart() - Method in class view.AlignViewProps
Returns the x start position.
getYEnd() - Method in class view.AlignViewProps
Returns the y end position.
getYStart() - Method in class view.AlignViewProps
Returns the y start position.
GREEN - Static variable in class util.Constants
 
GROUPCOLORS - Static variable in class util.Constants
 

H

hasKey(String) - Method in class util.PDBFile
Has-key boolean method.
HDF - Static variable in class util.ColorScheme
 
hdfScheme - Static variable in class util.ColorScheme
Hdf color scheme.

I

ImageExporter - Class in util
With this class the alignment panel can be exported to a PNG file.
ImageExporter(AlignPanel, String, int, int, File) - Constructor for class util.ImageExporter
Constructor of the image exporter.
IndexPanel - Class in view
This class represents the index of the sequence alignment.
IndexPanel() - Constructor for class view.IndexPanel
Default constructor.
IndexPanel(AlignViewProps, SequencePainter) - Constructor for class view.IndexPanel
Constructor of the IndexPanel.
IndexPanel(AlignViewProps) - Constructor for class view.IndexPanel
Constructor of the IndexPanel.
INDEXPANEL_BGCOLOR - Static variable in class util.Constants
 
INDEXPANEL_HEIGHT - Static variable in class util.Constants
 
INDEXPANEL_WIDTH - Static variable in class util.Constants
 
INFOPANEL_HEIGHT - Static variable in class util.Constants
 
INFOPANEL_WIDTH - Static variable in class util.Constants
 
init() - Static method in class util.ColorScheme
 
init() - Method in class view.AlignViewProps
Initializes the alignment view propierties.
init(Graphics) - Method in class view.SequencePainter
Initializes the graphics object.
initialize() - Method in class view.PickPointsBehavior
 
interfaces - package interfaces
 
isClusterEnd() - Method in class model.SequenceImpl
is cluster end boolean.
isClusterStart() - Method in class model.SequenceImpl
Is cluster start boolean.
isDataFlavorSupported(DataFlavor) - Method in class util.FileDrop.TransferableObject
Returns true if flavor is one of the supported flavors.
isEmpty() - Static method in class util.ResidueSelectionManager
Checks if the selection is empty
isEmpty() - Static method in class util.SelectionManager
Checks if the selection is empty
isEmpty() - Static method in class util.SequenceManager
Checks if the selection is empty
isEnabled() - Static method in class util.SelectionManager
 
isEntropyUsed() - Method in class model.Methods
Returns whether entropy method was used or not.
isGap(char) - Static method in class util.Constants
 
isIncreasingScore() - Method in class model.UDMObject
 
isS3DetUsed() - Method in class model.Methods
Returns whether S3Det was used or not.
isSelected(String) - Static method in class util.SequenceManager
 
isUpperSelectionOn() - Static method in class util.SelectionManager
 
isxDetUsed() - Method in class model.Methods
Returns whether xDet was used or not.
itemStateChanged(ItemEvent) - Method in class view.Cluster3DFrame
This method gets called when the user changes the value of a combobox.

J

jarMode - Static variable in class view.AlignFrame
 
JAVA3DFRAME_HEIGHT - Static variable in class util.Constants
 
JAVA3DFRAME_WIDTH - Static variable in class util.Constants
 
JDET_URL - Static variable in class util.Constants
 
JMOLPANEL_HEIGHT - Static variable in class util.Constants
 
JMOLPANEL_WIDTH - Static variable in class util.Constants
 

K

keyReleased(KeyEvent) - Method in class view.SliderKeyAdapter
 

L

LABEL_FONT_SIZE - Static variable in class util.Constants
 
LETTER_WIDTH - Static variable in class util.Constants
 
LoadAlignFrame - Class in view
This the main entry point to the application.
LoadAlignFrame(JFrame) - Constructor for class view.LoadAlignFrame
LoadFrame with a given parent frame.
LoadAlignFrame.OpenFileAction - Class in view
 
loadColorScheme(AlignFrame) - Static method in class util.ColorScheme
Function which shows a file dialog to load a new color schema
loadConversionPlugin(String, AlignObject, AlignFrame) - Static method in class util.PluginLoader
 
LOADFRAME_HEIGHT - Static variable in class util.Constants
 
LOADFRAME_WIDTH - Static variable in class util.Constants
 
LoadMethodFrame - Class in view
This is the load frame for a user-defined method.
LoadMethodFrame(AlignFrame) - Constructor for class view.LoadMethodFrame
LoadFrame with a given parent frame.
LoadMethodFrame.OpenFileAction - Class in view
 
loadMethodPlugin(String, AlignObject, AlignFrame) - Static method in class util.PluginLoader
 
loadPlugins() - Static method in class util.PluginLoader
 
loadPresets(HashMap<String, FilterAlignment.PresetItem>, JComboBox) - Method in class util.FilterAlignment
 
LoadS3DetFrame - Class in view
This the load frame for the S3Det method.
LoadS3DetFrame(AlignFrame) - Constructor for class view.LoadS3DetFrame
LoadXDetFrame with a given parent frame.
LoadS3DetFrame.OpenFileAction - Class in view
 
LoadStructureFrame - Class in view
This class is the loading frame for the JMolViewer.
LoadStructureFrame(AlignViewProps, SequencePainter, NamePainter, AlignPanel, AlignFrame) - Constructor for class view.LoadStructureFrame
Constructor of the LoadJMolFrame
LoadStructureFrame.OpenFileAction - Class in view
Inner action class that creates and show an open-file dialog.
LoadXDetFrame - Class in view
This the load frame for the XDet method.
LoadXDetFrame(AlignFrame) - Constructor for class view.LoadXDetFrame
LoadXDetFrame with a given parent frame.
LoadXDetFrame.OpenFileAction - Class in view
 
LOGO_HEIGHT - Static variable in class util.Constants
 
LOGOHEADER_FONT - Static variable in class util.Constants
 
LOGOHEADER_FONT_SIZE - Static variable in class util.Constants
 
LOGOHEADER_FONTSIZE - Static variable in class util.Constants
 
LOGOHEADER_FONTSTYLE - Static variable in class util.Constants
 
LOGOHEADER_HEIGHT - Static variable in class util.Constants
 
LOGOHEADER_MARGIN - Static variable in class util.Constants
 

M

main(String[]) - Static method in class test.AlignViewTest
 
main(String[]) - Static method in class test.S3DetParserTest
 
main(String[]) - Static method in class test.UDMParserTest
 
main(String[]) - Static method in class test.XDetParserTest
 
main(String[]) - Static method in class view.AlignFrame
Main method ==> Entry point to the application.
MANUAL_PATH - Static variable in class util.Constants
 
MANUAL_URL - Static variable in class util.Constants
 
MAX_LABEL_LENGTH - Static variable in class util.Constants
 
MAX_UDM_METHODS - Static variable in class util.Constants
 
METHOD_METRICS_FILE - Static variable in class util.Constants
 
METHOD_OFFSET - Static variable in class util.Constants
 
METHOD_PLUGINS_DIR - Static variable in class util.Constants
 
METHOD_PLUGINS_PACKAGE - Static variable in class util.Constants
 
METHODDESCPNL_BGCOLOR - Static variable in class util.Constants
 
METHODDESCPNL_HEIGHT - Static variable in class util.Constants
 
METHODDESCPNL_WIDTH - Static variable in class util.Constants
 
MethodPanel - Class in view
This class represents the panel where the methods are applied.
MethodPanel() - Constructor for class view.MethodPanel
 
MethodPanel(AlignViewProps, AlignPanel, SequencePainter) - Constructor for class view.MethodPanel
Constructor of the MethodPanel.
METHODPANEL_BGCOLOR - Static variable in class util.Constants
 
METHODPANEL_HEIGHT - Static variable in class util.Constants
 
METHODPANEL_WIDTH - Static variable in class util.Constants
 
Methods - Class in model
The object of that class is mainly used for passing information which methods are used for the application.
Methods() - Constructor for class model.Methods
 
METHODS_DIR - Static variable in class util.Constants
 
MfaParser - Class in parser
This is the parser class for the MFA or FASTA files.
MfaParser() - Constructor for class parser.MfaParser
 
MIME_TYPE - Static variable in class util.FileDrop.TransferableObject
The MIME type for FileDrop.TransferableObject.DATA_FLAVOR is application/x-net.iharder.dnd.TransferableObject.
MIN_PDB_SEQ_ALIGNMENT - Static variable in class util.Constants
 
model - package model
 
mouseClicked(MouseEvent) - Method in class model.MouseSequenceListener
 
mouseEntered(MouseEvent) - Method in class model.MouseSequenceListener
 
mouseExited(MouseEvent) - Method in class model.MouseSequenceListener
 
mousePressed(MouseEvent) - Method in class model.MouseSequenceListener
 
mouseReleased(MouseEvent) - Method in class model.MouseSequenceListener
 
MouseSequenceListener - Class in model
MouseSequenceListener for listening on the mouse event from the alignment panel.
MouseSequenceListener() - Constructor for class model.MouseSequenceListener
 
MW - Static variable in class util.ColorScheme
 
mwScheme - Static variable in class util.ColorScheme
MW color scheme.
MyCallbackListener - Class in view
 
MyCallbackListener(Structure3DFrame.JmolPanel) - Constructor for class view.MyCallbackListener
 

N

NamePainter - Class in view
Represents the painter class for the protein names.
NamePainter(AlignViewProps, AlignPanel, S3DetObject, SequencePainter) - Constructor for class view.NamePainter
Constructor of the namePainter class.
NamePainter(AlignViewProps, S3DetObject) - Constructor for class view.NamePainter
Constructor of the namePainter class without register, used for paint window without interactions.
NamePanel - Class in view
This panel class is mainly uses by the NameRenderer for the proteinID aka. name strings.
NamePanel() - Constructor for class view.NamePanel
Default constructor
NamePanel(AlignViewProps, AlignPanel, SequencePainter) - Constructor for class view.NamePanel
Constructor of the NamePanel.
NamePanel(AlignViewProps, S3DetObject) - Constructor for class view.NamePanel
Constructor of the NamePanel.
NAMEPANEL_HEIGHT - Static variable in class util.Constants
 
NAMEPANEL_SELECTED_BGSEQUENCE - Static variable in class util.Constants
 
NAMEPANEL_SELECTED_FGSEQUENCE - Static variable in class util.Constants
 
NAMEPANEL_WIDTH - Static variable in class util.Constants
 
NO_SELECTION - Static variable in class util.SelectionManager
Constant for marking no selection.
notifyCallback(int, Object[]) - Method in class view.MyCallbackListener
 
notifyEnabled(int) - Method in class view.MyCallbackListener
 
notifyObservers() - Method in interface interfaces.Observable
 
notifyObservers() - Method in class view.SequencePainter
Notify the observer.
notifyOnMouseClick(MouseEvent) - Method in class view.IndexPanel
 
notifyOnMouseClick(MouseEvent) - Method in class view.MethodPanel
 
notifyOnMouseClick(MouseEvent) - Method in class view.SequencePainter
Notifies the observers on a mouse click.
notifyUpperPanels() - Method in class view.SequencePainter
 

O

Observable - Interface in interfaces
This interface depicts the object which gets observed by an observer. --> Gang-of-four behavioral design pattern
Observer - Interface in interfaces
This interface depicts the observer who listens to some observed object. --> Gang-of-four behavioral design pattern
ORANGE - Static variable in class util.Constants
 
OTHERCUTOFF_DEFAULT - Static variable in class util.Constants
 
OTHERSLIDER_DEFAULT - Static variable in class util.Constants
 
OTHERSLIDER_TOOLTIP - Static variable in class util.Constants
 

P

paint(Graphics) - Method in class util.SequenceLogo.LogoPosition
 
paint(Graphics) - Method in class util.SequenceLogo
Draws visible portion of logo, based on scroll and window size
paint(Graphics) - Method in class view.ColorSchemeInfo
 
paint(Graphics) - Method in class view.SelectionFrame
 
paintComponent(Graphics) - Method in class view.AlignPanel
 
paintComponent(Graphics) - Method in class view.IndexPanel
Overriding the paintComponent-method.
paintComponent(Graphics) - Method in class view.MethodPanel
Overriding the paintComponent-method.
paintComponent(Graphics) - Method in class view.NamePainter
paintComponent is overwritten.
paintComponent(Graphics) - Method in class view.SeparatorPanel
 
paintComponent(Graphics) - Method in class view.SequencePainter
 
paintComponent(Graphics) - Method in class view.StatusPanel
 
PAL_RED_BLUE - Static variable in class util.ColorScheme
 
PAL_RED_GREEN_BLUE - Static variable in class util.ColorScheme
 
PALETTE_HEIGHT - Static variable in class util.ColorScheme
 
PALETTE_STEPS - Static variable in class util.ColorScheme
 
PALETTE_TEXT_MARGIN - Static variable in class util.ColorScheme
 
PALETTE_WIDTH - Static variable in class util.ColorScheme
 
PANEL_LOGO_MARGIN - Static variable in class util.Constants
 
PANEL_LOGO_WIDTH - Static variable in class util.Constants
 
parser - package parser
 
PDB_EVALUE_THRESHOLD - Static variable in class util.Constants
 
PDB_IDENTITIES_THRESHOLD - Static variable in class util.Constants
 
PDB_WSDLSERVER - Static variable in class util.Constants
 
PDBFile - Class in util
This class uses the PDB library.
PDBFile(String, String) - Constructor for class util.PDBFile
Constructor for the PDB File menu.
PdbFileOpener - Class in util
This class is for loading an compressed PDB file from the FTP Server and uncompressing it.
PdbFileOpener(String) - Constructor for class util.PdbFileOpener
Constructor of the PdbFileOpener.
PdbFileOpener(String, JTextArea) - Constructor for class util.PdbFileOpener
Constructor of the PdbFileOpener.
PICK_AREA_COLOR - Static variable in class util.Constants
 
PickPointsBehavior - Class in view
This class defines the behavior needed for selecting items on Cluster3DFrame
PickPointsBehavior(Canvas3D, BranchGroup) - Constructor for class view.PickPointsBehavior
 
PLUGIN_TYPE_CONVERSION - Static variable in class util.Constants
 
PLUGIN_TYPE_METHOD - Static variable in class util.Constants
 
PluginLoader - Class in util
 
PluginLoader() - Constructor for class util.PluginLoader
 
plugins - package plugins
 
PngFileFilter - Class in util
File filter for *.png files.
PngFileFilter() - Constructor for class util.PngFileFilter
 
POL_G - Static variable in class util.ColorScheme
 
polScheme - Static variable in class util.ColorScheme
Pol G color scheme.
PredictedPosition - Class in model
This class holds information about the predicted positions (SDPs) from the S3Det Output.
PredictedPosition() - Constructor for class model.PredictedPosition
 
print() - Method in class util.PrintUtilities
 
print(Graphics, PageFormat, int) - Method in class util.PrintUtilities
 
print(Graphics, PageFormat, int) - Method in class view.AlignPanel
Overrides the print Method of Component.
printComponent(Component) - Static method in class util.PrintUtilities
 
printPanel(Graphics, int, int, int) - Method in class view.AlignPanel
 
PrintUtilities - Class in util
 
PrintUtilities(Component) - Constructor for class util.PrintUtilities
 
processDroppedFile(String) - Method in class view.AlignFrame
 
processStimulus(Enumeration) - Method in class view.PickPointsBehavior
 

R

read(String) - Method in class parser.ColorParser
This method parses aminoacid and color value associated, separated by tabs
read(String) - Method in class parser.MfaParser
This method parses protein name and sequence of the MFA or FASTA file.
read(String, AlignObject) - Method in class parser.S3DetParser
This method reads the s3detfile.
read(String) - Method in class parser.UDMParser
This method parses position, amino acid, entropy and correlation of the xdet file.
read(String, AlignObject) - Method in class parser.XDetParser
This method parses position, amino acid, entropy and correlation of the xdet file.
read() - Method in class util.PDBFile
Reads and parses the input file.
readLine() - Method in class util.PDBFile
Read one line of the file.
RED - Static variable in class util.Constants
 
register(Observer) - Method in interface interfaces.Observable
 
register(Observer) - Method in class view.SequencePainter
Registers the observer.
reloadOnlyAlignment(AlignFrame) - Method in class model.AlignObject
 
remove(Component) - Static method in class util.FileDrop
Removes the drag-and-drop hooks from the component and optionally from the all children.
remove(PrintStream, Component, boolean) - Static method in class util.FileDrop
Removes the drag-and-drop hooks from the component and optionally from the all children.
repaintClusters(BranchGroup) - Method in class view.Cluster3DFrame
This method repaints the clusters and its points, without recreating them to conserve rotation.
Residue - Interface in interfaces
The interface describes a general residue object used for the user defined method: position - amino acid - score
RESIDUE_POINT_SIZE - Static variable in class util.Constants
 
RESIDUE_SHAPE_NAME - Static variable in class util.Constants
 
ResidueCoordinates - Class in model
This class represents the residue coordinates.
ResidueCoordinates() - Constructor for class model.ResidueCoordinates
 
ResidueImpl - Class in model
Implementation of the Residue Interface.
ResidueImpl() - Constructor for class model.ResidueImpl
 
ResidueSelectionManager - Class in util
 
ResidueSelectionManager() - Constructor for class util.ResidueSelectionManager
 
run() - Method in class util.FilterAlignment.StreamGobbler
 
run() - Method in class util.PdbFileOpener
Runs the thread: Downloading + Uncompressing the PDB file.
run() - Method in class util.RunMethods.StreamGobbler
 
runMethod(AlignFrame, AlignViewProps, ActionEvent, String, String, String) - Method in class util.RunMethods
 
RunMethods - Class in util
 
RunMethods() - Constructor for class util.RunMethods
 
RunMethods(AlignFrame, AlignViewProps, String) - Constructor for class util.RunMethods
LoadFrame with a given parent frame.
RunMethods.StreamGobbler - Class in util
 
RunMethods.StreamGobbler(String, InputStream, String) - Constructor for class util.RunMethods.StreamGobbler
 

S

S3DETCUTOFF_DEFAULT - Static variable in class util.Constants
 
S3DetObject - Class in model
This class represents an object of the S3Det information.
S3DetObject() - Constructor for class model.S3DetObject
 
S3DetParser - Class in parser
This is the parser for the S3Det files.
S3DetParser() - Constructor for class parser.S3DetParser
General constructor.
S3DetParserTest - Class in test
 
S3DetParserTest() - Constructor for class test.S3DetParserTest
 
S3DETSLIDER_TOOLTIP - Static variable in class util.Constants
 
saveFasta(AlignViewProps, File, boolean) - Static method in class util.AlignmentExporter
 
saveFile(String, File) - Static method in class util.AlignmentExporter
Sets the name-to-clusterIndex HashMap.
ScreenConfig - Class in util
Provides some helper routines for screen configuration.
ScreenConfig() - Constructor for class util.ScreenConfig
 
scrollPainting(int, int) - Method in class view.NamePainter
This methods simplifies the drawing of the sequence.
scrollPainting(int, int) - Method in class view.SequencePainter
This method does the scroll painting.
SELECTED_PROTEIN_COLOR - Static variable in class util.Constants
 
SELECTED_RESIDUE_COLOR - Static variable in class util.Constants
 
SELECTED_RESIDUE_POINT_SIZE - Static variable in class util.Constants
 
SELECTED_RESIDUE_SHAPE_NAME - Static variable in class util.Constants
 
selectEntropyItems(int) - Method in class view.AlignFrame
 
SELECTION_AND - Static variable in class util.Constants
 
SELECTION_ONLY - Static variable in class util.Constants
 
SELECTION_OR - Static variable in class util.Constants
 
SELECTION_PRECISION - Static variable in class util.Constants
 
SelectionFrame - Class in view
 
SelectionFrame(AlignViewProps, S3DetObject) - Constructor for class view.SelectionFrame
This class draws a window containing an graphical representation of a selection from the current alignment.
SelectionFrame.SelectionScrollAdjuster - Class in view
 
SelectionFrame.SelectionScrollAdjuster() - Constructor for class view.SelectionFrame.SelectionScrollAdjuster
 
SelectionManager - Class in util
This manager class handles the selections made by the user.
SelectionManager() - Constructor for class util.SelectionManager
 
selectS3DetItems(int) - Method in class view.AlignFrame
 
selectUserDefItems(String, int) - Method in class view.AlignFrame
 
selectXDetItems(int) - Method in class view.AlignFrame
 
SeparatorPanel - Class in view
Used to separate the sections of the StatusPanel.
SeparatorPanel(Color, Color) - Constructor for class view.SeparatorPanel
 
SEQPANEL_HEIGHT - Static variable in class util.Constants
 
SEQPANEL_WIDTH - Static variable in class util.Constants
 
Sequence - Interface in interfaces
Interface as a representation for the protein sequence.
SEQUENCE_POINT_SIZE - Static variable in class util.Constants
 
SEQUENCE_SHAPE_NAME - Static variable in class util.Constants
 
sequenceClicked(MouseEvent) - Method in class view.NamePainter
 
SequenceCluster - Class in model
This class provides information about which sequence belongs to which cluster from the S3Det.
SequenceCluster() - Constructor for class model.SequenceCluster
 
SequenceCoordinates - Class in model
This class contains information about the sequence coordinates from the S3Det.
SequenceCoordinates() - Constructor for class model.SequenceCoordinates
 
SequenceImpl - Class in model
Implementation of the Sequence Interface.
SequenceImpl(SequenceImpl) - Constructor for class model.SequenceImpl
Copy Constructor
SequenceImpl(String, String, int, int) - Constructor for class model.SequenceImpl
Constructor for the sequence implementation, where sequence is given as string
SequenceImpl(String, String) - Constructor for class model.SequenceImpl
Constructor for the sequence implementation.
SequenceLogo - Class in util
This class draws a sequence logo from the current selection
SequenceLogo(AlignViewProps) - Constructor for class util.SequenceLogo
Constructor for a sequence logo from all selected sequences
SequenceLogo(AlignViewProps, boolean) - Constructor for class util.SequenceLogo
Constructor for two sequence logo from selected and vs no selected sequences
SequenceLogo(AlignViewProps, S3DetObject) - Constructor for class util.SequenceLogo
Constructor for a sequence logo from selected sequences of each cluster
SequenceLogo.FrequencyImage - Class in util
This class contains a graphic representation of a residue the alignment and its frequency
SequenceLogo.FrequencyImage(Image, double) - Constructor for class util.SequenceLogo.FrequencyImage
 
SequenceLogo.LogoPosition - Class in util
This class draws a graphic representation of a position in the alignment
SequenceLogo.LogoPosition(double[], int, Color) - Constructor for class util.SequenceLogo.LogoPosition
 
SequenceLogo.LogoScrollAdjuster - Class in util
 
SequenceLogo.LogoScrollAdjuster() - Constructor for class util.SequenceLogo.LogoScrollAdjuster
 
SequenceManager - Class in util
This class handles marking a sequence for the alignment.
SequenceManager() - Constructor for class util.SequenceManager
 
SequenceOrderer - Class in util
This helper class puts the sequence in order, so that they are put into cluster groups.
SequenceOrderer(AlignObject, S3DetObject) - Constructor for class util.SequenceOrderer
Constructor of the SequenceOrderer.
SequencePainter - Class in view
This class does all the sequence painting, implements Observable, as the structure frame listens to the mouse events on the alignment panel.
SequencePainter(AlignViewProps, AlignPanel, S3DetObject) - Constructor for class view.SequencePainter
Constructor of the SeqRenderer.
SequencePainter(AlignViewProps, S3DetObject) - Constructor for class view.SequencePainter
Constructor of the SequencePainter without observers.
SequencePanel - Class in view
This panel class is mainly uses by the SeqRenderer for the protein sequences.
SequencePanel() - Constructor for class view.SequencePanel
Default constructor.
SequencePanel(AlignViewProps, AlignPanel) - Constructor for class view.SequencePanel
Constructor of the SequencePanel.
SequencePanel(AlignViewProps, S3DetObject) - Constructor for class view.SequencePanel
Constructor of the SequencePanel for showing the current selection.
sequencePressed(MouseEvent) - Method in class view.NamePainter
 
sequenceReleased(MouseEvent) - Method in class view.NamePainter
 
setAa(char) - Method in interface interfaces.FuncResidue
 
setAa(char) - Method in interface interfaces.Residue
 
setAa(char) - Method in class model.FuncResidueImpl
Set the letter of the amino acid.
setAa(char) - Method in class model.ResidueImpl
Set the letter of the amino acid.
setAlObj(AlignObject) - Method in class view.AlignViewProps
Sets the alignment object
setAverageRank(BigDecimal) - Method in class model.PredictedPosition
Sets the average rank.
setCallbackFunction(String, String) - Method in class view.MyCallbackListener
 
setCharHeight(int) - Method in class view.AlignViewProps
Sets the char height.
setCharWidth(int) - Method in class view.AlignViewProps
Sets the char width.
setClusterColor(Color) - Method in class model.SequenceImpl
Sets the cluster sequence color.
setClusterCoords(ClusterCoordinates[]) - Method in class model.S3DetObject
Sets the cluster coordinates.
setClusterEnd(boolean) - Method in class model.SequenceImpl
Set the cluster end boolean.
setClusterIndex(int) - Method in class model.SequenceCluster
Sets the value of the cluster index.
setClusterStart(boolean) - Method in class model.SequenceImpl
Set the cluster start boolean.
setColor(Color) - Method in class model.ClusterGroup
Sets the cluster Color
setColorPalette(int) - Static method in class util.ColorScheme
Changes color pallete and reclacule colors for all numeric color schemes
setColorPalette(ColorSchemeInfo) - Method in class view.StatusPanel
 
setColorScheme(String) - Static method in class util.ColorScheme
Setter for new color scheme
setConservedPositions(int[]) - Method in class model.S3DetObject
Sets the conserved positions.
setCoords(double[]) - Method in interface interfaces.Coordinates
 
setCoords(double[]) - Method in class model.ClusterCoordinates
Sets the array of the coordinates.
setCoords(double[]) - Method in class model.ResidueCoordinates
Sets the array of the coordinates.
setCoords(double[]) - Method in class model.SequenceCoordinates
Sets the array of the coordinates.
setCorrelation(BigDecimal) - Method in interface interfaces.FuncResidue
 
setCorrelation(BigDecimal) - Method in class model.FuncResidueImpl
Sets the correlation factor.
setCurrentEntropyCutoff(double) - Method in class model.Methods
 
setCurrentS3DetCutoff(double) - Method in class model.Methods
 
setCurrentScoreCutoff(double) - Method in class model.UDMObject
 
setCurrentSelection(Vector<FuncResidueImpl>) - Static method in class util.ResidueSelectionManager
 
setCurrentSelection(Vector<Integer>) - Static method in class util.SelectionManager
 
setCurrentXDetCutoff(double) - Method in class model.Methods
 
setEnabled(boolean) - Static method in class util.SelectionManager
 
setEnd(int) - Method in interface interfaces.Sequence
 
setEnd(int) - Method in class model.SequenceImpl
Sets the end position of the sequence.
setEntropy(BigDecimal) - Method in interface interfaces.FuncResidue
 
setEntropy(BigDecimal) - Method in class model.FuncResidueImpl
Set the sequence entropy factor.
setEntropyCutoff(double) - Method in class model.Methods
Sets the entropy cutoff for the XDet method.
setEntropyUsed(boolean) - Method in class model.Methods
Sets the entropyUsed boolean.
setExport(boolean) - Method in class view.SequencePainter
 
setFilename(String) - Method in class model.AlignObject
Sets the filename.
setFilename(String) - Method in class model.S3DetObject
Sets the file name.
setFilename(String) - Method in class model.UDMObject
Sets the name of the file.
setFilename(String) - Method in class model.XDetObject
Sets the name of the Xdet file.
setFilename(String) - Method in class view.LoadStructureFrame
Setter method for the filename.
setFont(Font) - Method in class view.AlignViewProps
Sets the font object and does some font metrics stuff.
setFuncResidues(FuncResidueImpl[]) - Method in class model.XDetObject
Sets the functional residues array.
setGroupNumber(int) - Method in class model.PredictedPosition
Sets the group number.
setHorizontalScrollbar(JScrollBar) - Method in class view.AlignPanel
 
setIncreasingScore(boolean) - Method in class model.UDMObject
 
setIndex(int) - Method in class model.ClusterGroup
Sets the cluster index.
setJmolPanel(Structure3DFrame.JmolPanel) - Method in class view.SequencePainter
Sets the jMolPanel and registers the seqPainter.
setLastSelected(String) - Static method in class util.SequenceManager
 
setLastSelection(int, boolean) - Static method in class util.SelectionManager
 
setLetter(char) - Method in class model.ResidueCoordinates
Sets the letter of the residue.
setMarkedSequenceName(String) - Static method in class util.SequenceManager
Sets the marked sequence name.
setMethodName(String) - Method in class model.UDMObject
 
setMethodNumber(int) - Method in class model.Methods
Sets the total number of the used methods.
setName(String) - Method in interface interfaces.Sequence
 
setName(String) - Method in class model.ClusterCoordinates
Sets the name of the cluster.
setName(String) - Method in class model.SequenceCluster
Sets the name of the sequence.
setName(String) - Method in class model.SequenceCoordinates
Sets the name of the sequence.
setName(String) - Method in class model.SequenceImpl
Sets the sequence name.
setName2ClusterIndex(HashMap<String, Integer>) - Method in class model.S3DetObject
Sets the name-to-clusterIndex HashMap.
setNumberOfSelectedAxes(int) - Method in class model.S3DetObject
Sets the total number of selected axes.
setPaletteName(String) - Method in class view.ColorSchemeInfo
 
setPos2PredPosition(HashMap<Integer, PredictedPosition>) - Method in class model.S3DetObject
Sets the Position-To-PredictedPosition HashMap.
setPos2ResMap(HashMap<Integer, ResidueImpl>) - Method in class model.UDMObject
Sets the Position-To-Residue HashMap.
setPos2ResMap(HashMap<Integer, FuncResidueImpl>) - Method in class model.XDetObject
Sets the Position-To-Residue HashMap.
setPosition(int) - Method in interface interfaces.FuncResidue
 
setPosition(int) - Method in interface interfaces.Residue
 
setPosition(int) - Method in class model.FuncResidueImpl
Sets the position of the amino acid.
setPosition(int) - Method in class model.ResidueCoordinates
Sets the position of the residue.
setPosition(int) - Method in class model.ResidueImpl
Sets the position of the amino acid.
setPositionRes(int) - Method in class model.PredictedPosition
Sets the position of the residue.
setPredictedPositions(PredictedPosition[]) - Method in class model.S3DetObject
Sets the predicted positions.
setProteinNumber(int) - Method in class model.AlignObject
Sets the number of protein.
setResCoords(ResidueCoordinates[]) - Method in class model.S3DetObject
Sets the residue coordinates.
setResidues(ResidueImpl[]) - Method in class model.UDMObject
Sets the functional residues array.
setResNumber(int) - Method in class model.UDMObject
Set the residues number.
setResNumber(int) - Method in class model.XDetObject
Set the residues number.
setS3DetCutoff(double) - Method in class model.Methods
Sets the average rank cutoff for the S3Det method.
setS3detobj(S3DetObject) - Static method in class util.ResidueSelectionManager
 
setS3detobj(S3DetObject) - Static method in class util.SelectionManager
 
setS3detobj(S3DetObject) - Static method in class util.SequenceManager
 
setS3DetObject(S3DetObject) - Method in class model.Methods
Sets the S3DetObject.
setS3DetUsed(boolean) - Method in class model.Methods
Sets the s3DetUsed boolean.
setScore(BigDecimal) - Method in interface interfaces.Residue
 
setScore(BigDecimal) - Method in class model.ResidueImpl
Set the sequence entropy factor.
setScoreCutoff(double) - Method in class model.UDMObject
Sets the score cutoff.
setScrollValues() - Method in class util.SequenceLogo
Calculate scroll values from window size
setScrollValues(int, int) - Method in class view.AlignPanel
 
setScrollValues(int, int) - Method in class view.SelectionFrame
 
setSelectedSequences(Vector<String>) - Static method in class util.SequenceManager
 
setSeqClusters(SequenceCluster[]) - Method in class model.S3DetObject
Sets the sequence clusters.
setSeqCoords(SequenceCoordinates[]) - Method in class model.S3DetObject
Sets the sequence coordinates.
setSeqPainter(SequencePainter) - Static method in class util.ResidueSelectionManager
 
setSeqPainter(SequencePainter) - Static method in class util.SelectionManager
 
setSequence(String) - Method in interface interfaces.Sequence
 
setSequence(String) - Method in class model.SequenceImpl
Sets the sequence as string.
setSequence(char[]) - Method in class model.SequenceImpl
Sets the sequence as char array.
setSequences(SequenceImpl[]) - Method in class model.AlignObject
Sets the array of sequence objects.
setSequences(SequenceImpl[]) - Method in class model.ClusterGroup
Sets the sequences.
setSourceName(String) - Method in class view.LoadAlignFrame.OpenFileAction
 
setSourceName(String) - Method in class view.LoadMethodFrame.OpenFileAction
 
setSourceName(String) - Method in class view.LoadS3DetFrame.OpenFileAction
 
setSourceName(String) - Method in class view.LoadStructureFrame.OpenFileAction
 
setSourceName(String) - Method in class view.LoadXDetFrame.OpenFileAction
 
setStart(int) - Method in interface interfaces.Sequence
 
setStart(int) - Method in class model.SequenceImpl
Sets the start position of the sequence.
setSumScrollX(int) - Method in class view.SequencePainter
 
setUdmObjects(UDMObject[]) - Method in class model.Methods
 
setUpperSelectionOn(boolean) - Static method in class util.SelectionManager
 
setUserDefSchemeValues(HashMap<Character, Double>) - Static method in class util.ColorScheme
Setter for user defined color scheme
setValues(double, double) - Method in class view.ColorSchemeInfo
 
setVerticalScrollbar(JScrollBar) - Method in class view.AlignPanel
 
setViewProps(AlignViewProps) - Method in class view.SequencePainter
 
setxDetCutoff(double) - Method in class model.Methods
Sets the correlation cutoff for the XDet method.
setxDetObject(XDetObject) - Method in class model.Methods
Sets the XDetObject.
setxDetUsed(boolean) - Method in class model.Methods
Sets the xDetUsed boolean.
setXEnd(int) - Method in class view.AlignViewProps
Sets the x end position.
setXStart(int) - Method in class view.AlignViewProps
Sets the x start position.
setYEnd(int) - Method in class view.AlignViewProps
Sets the y end position.
setYStart(int) - Method in class view.AlignViewProps
Sets the y start position.
showAlignment() - Method in class util.Alignment
Shows a a window with the alignment data
SliderChangeListener - Class in view
This class is an extension to the simple change listener on a JSlider object.
SliderChangeListener(AlignFrame, JSlider, JTextField, int) - Constructor for class view.SliderChangeListener
 
SliderKeyAdapter - Class in view
 
SliderKeyAdapter(JSlider, JTextField, int) - Constructor for class view.SliderKeyAdapter
 
SliderPanel - Class in view
Represents the panel on the upper left corner which contains the threshold panels + sliders.
SliderPanel() - Constructor for class view.SliderPanel
Default constructor.
SliderPanel(AlignFrame) - Constructor for class view.SliderPanel
Constructor of the SliderPanel.
start() - Method in class util.FilterAlignment.StreamGobbler
 
start() - Method in class util.RunMethods.StreamGobbler
 
stateChanged(ChangeEvent) - Method in class view.SliderChangeListener
 
StatusPanel - Class in view
Extended StatusPanel for showing the alignment name, the sequence length and the sequence number.
StatusPanel() - Constructor for class view.StatusPanel
 
StatusPanel(AlignViewProps) - Constructor for class view.StatusPanel
 
Structure3DFrame - Class in view
This class is the viewer for the protein 3D structure.
Structure3DFrame(String, SequencePainter, String, Alignment, NamePainter, AlignPanel) - Constructor for class view.Structure3DFrame
Constructor for the Structure3DFrame
StructureWindowListener - Class in view
Default StructureWindowListener class, handles what happens when the Structure3DFrame is closed.
StructureWindowListener(Structure3DFrame, NamePainter, SequencePainter, MethodPanel, IndexPanel) - Constructor for class view.StructureWindowListener
 

T

test - package test
 
TEXTFIELD_TOOLTIP - Static variable in class util.Constants
 
TMP_DIR - Static variable in class util.Constants
 
toggleResidue(MouseEvent) - Method in class view.SequencePainter
 
toggleSelection(FuncResidueImpl) - Static method in class util.ResidueSelectionManager
Adds an element to the current selection.
toggleSelection(int, boolean) - Static method in class util.SelectionManager
Adds an element to the current selection.
toggleSequence(String) - Static method in class util.SequenceManager
 
TUTORIAL_PATH - Static variable in class util.Constants
 
TUTORIAL_URL - Static variable in class util.Constants
 

U

UDMObject - Class in model
This class represents a user defined method (UDM) object, which should be generic for a any file which gives position, amino acid and score.
UDMObject() - Constructor for class model.UDMObject
 
UDMParser - Class in parser
This represents the parser for the user defined method.
UDMParser() - Constructor for class parser.UDMParser
General constructor.
UDMParserTest - Class in test
 
UDMParserTest() - Constructor for class test.UDMParserTest
 
unsetJmolPanel() - Method in class view.SequencePainter
Unsets the seqPainter.
update(Observable) - Method in interface interfaces.Observer
 
update(Observable) - Method in class view.Cluster3DFrame
Updates the data from the observable object.
update(Observable) - Method in class view.IndexPanel
Updates the data from the observable object.
update(Observable) - Method in class view.MethodPanel
Updates the data from the observable object.
update(Observable) - Method in class view.NamePainter
Updates the data from the observable object.
update(Observable) - Method in class view.SequencePainter
Updates the data from the observable object.
update(Observable) - Method in class view.Structure3DFrame
Updates the data from the observable object.
updateColors(BranchGroup) - Method in class view.Cluster3DFrame
This method change colors of the cluster points, to mark selected points.
updatePaletteImage(ColorSchemeInfo) - Static method in class util.ColorScheme
Function which shows an image of the current palette
updatePanelWithEntropyThreshold(double) - Method in class view.MethodPanel
This updates the panel with the entropy threshold.
updatePanelWithS3detThreshold(double) - Method in class view.MethodPanel
This updates the panel with the s3det threshold.
updatePanelWithScoreThreshold(double, int) - Method in class view.MethodPanel
This updates the panel with the user defined score threshold.
updatePanelWithXdetThreshold(double) - Method in class view.MethodPanel
This updates the panel with the xdet threshold.
updateSeqPainter() - Static method in class util.ResidueSelectionManager
 
updateSeqPainter() - Static method in class util.SelectionManager
 
updateWidth() - Method in class view.StatusPanel
 
USER_DEF - Static variable in class util.ColorScheme
 
util - package util
 

V

VERSION - Static variable in class util.Constants
 
VERSIONDATE - Static variable in class util.Constants
 
view - package view
 

W

windowActivated(WindowEvent) - Method in class view.ClusterWindowListener
 
windowActivated(WindowEvent) - Method in class view.StructureWindowListener
 
windowClosed(WindowEvent) - Method in class view.ClusterWindowListener
 
windowClosed(WindowEvent) - Method in class view.StructureWindowListener
 
windowClosing(WindowEvent) - Method in class view.ClusterWindowListener
When the window is closing, the marking and the selections are canceled.
windowClosing(WindowEvent) - Method in class view.StructureWindowListener
When the window is closing, the marking and the selections are canceled.
windowDeactivated(WindowEvent) - Method in class view.ClusterWindowListener
 
windowDeactivated(WindowEvent) - Method in class view.StructureWindowListener
 
windowDeiconified(WindowEvent) - Method in class view.ClusterWindowListener
 
windowDeiconified(WindowEvent) - Method in class view.StructureWindowListener
 
windowIconified(WindowEvent) - Method in class view.ClusterWindowListener
 
windowIconified(WindowEvent) - Method in class view.StructureWindowListener
 
windowOpened(WindowEvent) - Method in class view.ClusterWindowListener
 
windowOpened(WindowEvent) - Method in class view.StructureWindowListener
 
write() - Method in class util.ImageExporter
Write the image to a PNG file.
writeProgress(String) - Method in class util.RunMethods
 

X

XDETCUTOFF_DEFAULT - Static variable in class util.Constants
 
XDetObject - Class in model
This class does the representation of an XDet object.
XDetObject() - Constructor for class model.XDetObject
 
XDetParser - Class in parser
This is the parser class for the XDet files.
XDetParser() - Constructor for class parser.XDetParser
General constructor.
XDetParserTest - Class in test
 
XDetParserTest() - Constructor for class test.XDetParserTest
 
XDETSLIDER_TOOLTIP - Static variable in class util.Constants
 

Y

YELLOW - Static variable in class util.Constants
 

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