GUIColorSchemes

java.lang.Object
- java.awt.Component
- - java.awt.Container
  - - java.awt.Window
    - - java.awt.Frame
      - javax.swing.JFrame
        
        IMPACT_S.GUIColorSchemes

All Implemented Interfaces:

java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants
```
public class GUIColorSchemes
extends javax.swing.JFrame
```
Class to permit visual understanding of scheme colors (working like in a legend) and to allow color selection in the selected scheme.

Author:

Emanuel Maldonado

See Also:

GUI, ResultsN3DTP, Serialized Form

Nested Class Summary
- Nested classes/interfaces inherited from class javax.swing.JFrame
  javax.swing.JFrame.AccessibleJFrame
- Nested classes/interfaces inherited from class java.awt.Frame
  java.awt.Frame.AccessibleAWTFrame
- Nested classes/interfaces inherited from class java.awt.Window
  java.awt.Window.AccessibleAWTWindow, java.awt.Window.Type
- Nested classes/interfaces inherited from class java.awt.Container
  java.awt.Container.AccessibleAWTContainer
- Nested classes/interfaces inherited from class java.awt.Component
  java.awt.Component.AccessibleAWTComponent, java.awt.Component.BaselineResizeBehavior, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy

Field Summary

Fields
Modifier and Type	Field and Description
`static java.lang.String`	`AAAminoJKey` (Amino-Acid) Color Scheme Key for Amino scheme from Jmol (predefined colors)
`static java.lang.String`	`AADMSitesKey` (Amino-Acid) Color Scheme Key for Datamonkey Sites file
`static java.lang.String`	`AAPAMLBEBM282Key` (Amino-Acid) Color Scheme Key for AAPAMLBEB BEB file (For Both Model 2 and Model 8: Common and Uncommon Sites)
`static java.lang.String`	`AAPAMLBEBM283Key` (Amino-Acid) Color Scheme Key for AAPAMLBEB BEB file (For Both Model 2 and Model 8: All Common Sites; Model 2 Uncommon Sites ; Model 8 Uncommon Sites)
`static java.lang.String`	`AAPAMLBEBM28Key` (Amino-Acid) Color Scheme Key for AACodeml BEB file (For Model 2 or Model 8)
`static java.lang.String`	`AASeaviewKey` (Amino-Acid) Color Scheme Key for Seaview scheme (predefined colors)
`static java.lang.String`	`AAShapelyJKey` (Amino-Acid) Color Scheme Key for Shapely scheme from Jmol (predefined colors)
`static java.lang.String`	`AASideChainsKey` (Amino-Acid) Color Scheme Key for Side Chains scheme (predefined colors)
`static java.lang.String`	`AATSCMLMRKey` (Amino-Acid) Color Scheme Key for Merged ResulAATS file (for Both TreeSAAP PBR and BEB files)
`static java.lang.String`	`AATSType123Key` (Amino-Acid) Color Scheme Key for TreeSAAP PBR/PBS file (All Type I,II,III schemes at once)
`static java.lang.String`	`AATSTypeIIIKey` (Amino-Acid) Color Scheme Key for TreeSAAP PBR/PBS file (Six properties or more)
`static java.lang.String`	`AATSTypeIIIUKey` (Amino-Acid) Color Scheme Key for TreeSAAP PBR/PBS file (N properties or more)
`static java.lang.String`	`AATSTypeIIKey` (Amino-Acid) Color Scheme Key for TreeSAAP PBR/PBS file (Two-Five properties)
`static java.lang.String`	`AATSTypeIKey` (Amino-Acid) Color Scheme Key for TreeSAAP PBR/PBS file (One property at most)
`static java.lang.String`	`DRNAIMPACTKey` (DNA/RNA) Color Scheme Key for IMPACT scheme (predefined colors)
`static java.lang.String`	`DRNAJalviewKey` (DNA/RNA) Color Scheme Key for Jalview scheme (predefined colors)
`static java.lang.String`	`DRNAMEGAKey` (DNA/RNA) Color Scheme Key for MEGA scheme (predefined colors)
`static java.lang.String`	`DRNASeaviewKey` (DNA/RNA) Color Scheme Key for Seaview scheme (predefined colors)
`static int`	`IndexAAAminoJ` Index of the (Amino-Acid) Amino Color Scheme
`static int`	`IndexAADatamonkeySites` Index of the (Amino-Acid) Datamonkey Sites Color Scheme
`static int`	`IndexAAMR` Index of the (Amino-Acid) Merged Results Color Scheme
`static int`	`IndexAAPAMLBEBM28` Index of the (Amino-Acid) PAMLBEB BEB M2 or M8 Color Scheme
`static int`	`IndexAAPAMLBEBM282` Index of the (Amino-Acid) PAMLBEB BEB M2 and M8: (2 Colors) Color Scheme
`static int`	`IndexAAPAMLBEBM283` Index of the (Amino-Acid) PAMLBEB BEB M2 and M8: (3 Colors) Color Scheme
`static int`	`IndexAASeaview` Index of the (Amino-Acid) Seaview Color Scheme
`static int`	`IndexAAShapelyJ` Index of the (Amino-Acid) Shapely Color Scheme
`static int`	`IndexAASideChains` Index of the (Amino-Acid) Side Chains Color Scheme
`static int`	`IndexAATSType123` Index of the (Amino-Acid) All Type I,II,III Color Schemes
`static int`	`IndexAATSTypeI` Index of the (Amino-Acid) Type I Color Scheme
`static int`	`IndexAATSTypeII` Index of the (Amino-Acid) Type II Color Scheme
`static int`	`IndexAATSTypeIII` Index of the (Amino-Acid) Type III Color Scheme
`static int`	`IndexAATSTypeIIIU` Index of the (Amino-Acid) Type III User Color Scheme
`static int`	`IndexDRNAIMPACT` Index of the (DNA/RNA) Amino Color Scheme
`static int`	`IndexDRNAJalview` Index of the (DNA/RNA) Jalview Color Scheme
`static int`	`IndexDRNAMEGA` Index of the (DNA/RNA) MEGA Color Scheme
`static int`	`IndexDRNASeaview` Index of the (DNA/RNA) Seaview Color Scheme

Fields inherited from class javax.swing.JFrame
accessibleContext, EXIT_ON_CLOSE, rootPane, rootPaneCheckingEnabled

Fields inherited from class java.awt.Frame
CROSSHAIR_CURSOR, DEFAULT_CURSOR, E_RESIZE_CURSOR, HAND_CURSOR, ICONIFIED, MAXIMIZED_BOTH, MAXIMIZED_HORIZ, MAXIMIZED_VERT, MOVE_CURSOR, N_RESIZE_CURSOR, NE_RESIZE_CURSOR, NORMAL, NW_RESIZE_CURSOR, S_RESIZE_CURSOR, SE_RESIZE_CURSOR, SW_RESIZE_CURSOR, TEXT_CURSOR, W_RESIZE_CURSOR, WAIT_CURSOR

Fields inherited from class java.awt.Component
BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface javax.swing.WindowConstants
DISPOSE_ON_CLOSE, DO_NOTHING_ON_CLOSE, HIDE_ON_CLOSE

Fields inherited from interface java.awt.image.ImageObserver
ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Constructor Summary

Constructors
Constructor and Description

GUIColorSchemes(boolean visible)
Creates new form GUIJmolSchemes

Constructors
Constructor and Description
`GUIColorSchemes(boolean visible)` Creates new form GUIJmolSchemes

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`java.util.HashMap<java.lang.String,java.awt.Color>`	`getAAColorMap()` Get a map of AA codes to associated colors, from the loaded scheme.
`java.lang.String[]`	`getAAMatchingList(int namecase)` Get AA name list.
`java.awt.Color[]`	`getChosenColors()` Get colors selected or not by user.
`java.util.HashMap<java.lang.String,java.awt.Color>`	`getDRNAColorMap()` Get a map of DNA/RNA codes to associated colors, from the loaded scheme.
`int`	`getSchemeIndex(java.lang.String key)` Get Color Scheme Index, given key.
`void`	`loadScheme(int loadscheme)` Load user selected scheme of colors.
`boolean`	`schemeChanged()` Tell whether user has changed colors on scheme.
`void`	`setTreeSAAPSchemeOption(int lowerlimit)` Set the Lower limit as the user selected value for the User TreeSAAP coloring scheme.

Methods inherited from class javax.swing.JFrame
addImpl, createRootPane, frameInit, getAccessibleContext, getContentPane, getDefaultCloseOperation, getGlassPane, getGraphics, getJMenuBar, getLayeredPane, getRootPane, getTransferHandler, isDefaultLookAndFeelDecorated, isRootPaneCheckingEnabled, paramString, processWindowEvent, remove, repaint, setContentPane, setDefaultCloseOperation, setDefaultLookAndFeelDecorated, setGlassPane, setIconImage, setJMenuBar, setLayeredPane, setLayout, setRootPane, setRootPaneCheckingEnabled, setTransferHandler, update

Methods inherited from class java.awt.Frame
addNotify, getCursorType, getExtendedState, getFrames, getIconImage, getMaximizedBounds, getMenuBar, getState, getTitle, isResizable, isUndecorated, remove, removeNotify, setBackground, setCursor, setExtendedState, setMaximizedBounds, setMenuBar, setOpacity, setResizable, setShape, setState, setTitle, setUndecorated

Methods inherited from class java.awt.Window
addPropertyChangeListener, addPropertyChangeListener, addWindowFocusListener, addWindowListener, addWindowStateListener, applyResourceBundle, applyResourceBundle, createBufferStrategy, createBufferStrategy, dispose, getBackground, getBufferStrategy, getFocusableWindowState, getFocusCycleRootAncestor, getFocusOwner, getFocusTraversalKeys, getIconImages, getInputContext, getListeners, getLocale, getModalExclusionType, getMostRecentFocusOwner, getOpacity, getOwnedWindows, getOwner, getOwnerlessWindows, getShape, getToolkit, getType, getWarningString, getWindowFocusListeners, getWindowListeners, getWindows, getWindowStateListeners, hide, isActive, isAlwaysOnTop, isAlwaysOnTopSupported, isAutoRequestFocus, isFocusableWindow, isFocusCycleRoot, isFocused, isLocationByPlatform, isOpaque, isShowing, isValidateRoot, pack, paint, postEvent, processEvent, processWindowFocusEvent, processWindowStateEvent, removeWindowFocusListener, removeWindowListener, removeWindowStateListener, reshape, setAlwaysOnTop, setAutoRequestFocus, setBounds, setBounds, setCursor, setFocusableWindowState, setFocusCycleRoot, setIconImages, setLocation, setLocation, setLocationByPlatform, setLocationRelativeTo, setMinimumSize, setModalExclusionType, setSize, setSize, setType, setVisible, show, toBack, toFront

Methods inherited from class java.awt.Container
add, add, add, add, add, addContainerListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalPolicy, getInsets, getLayout, getMaximumSize, getMinimumSize, getMousePosition, getPreferredSize, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, print, printComponents, processContainerEvent, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusTraversalKeys, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setFont, transferFocusDownCycle, validate, validateTree

Methods inherited from class java.awt.Component
action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, contains, createImage, createImage, createVolatileImage, createVolatileImage, disable, disableEvents, dispatchEvent, enable, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBaseline, getBaselineResizeBehavior, getBounds, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphicsConfiguration, getHeight, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocation, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getSize, getTreeLock, getWidth, getX, getY, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isDoubleBuffered, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, prepareImage, prepareImage, printAll, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processKeyEvent, processMouseEvent, processMouseMotionEvent, processMouseWheelEvent, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resize, resize, revalidate, setComponentOrientation, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setMaximumSize, setName, setPreferredSize, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCycle

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.awt.MenuContainer
getFont, postEvent

- Field Detail
  - AATSTypeIKey
```
public static final java.lang.String AATSTypeIKey
```
    (Amino-Acid) Color Scheme Key for TreeSAAP PBR/PBS file (One property at most)
    
    See Also:
    
    Constant Field Values
  - AATSTypeIIKey
```
public static final java.lang.String AATSTypeIIKey
```
    (Amino-Acid) Color Scheme Key for TreeSAAP PBR/PBS file (Two-Five properties)
    
    See Also:
    
    Constant Field Values
  - AATSTypeIIIKey
```
public static final java.lang.String AATSTypeIIIKey
```
    (Amino-Acid) Color Scheme Key for TreeSAAP PBR/PBS file (Six properties or more)
    
    See Also:
    
    Constant Field Values
  - AATSTypeIIIUKey
```
public static final java.lang.String AATSTypeIIIUKey
```
    (Amino-Acid) Color Scheme Key for TreeSAAP PBR/PBS file (N properties or more)
    
    See Also:
    
    Constant Field Values
  - AATSType123Key
```
public static final java.lang.String AATSType123Key
```
    (Amino-Acid) Color Scheme Key for TreeSAAP PBR/PBS file (All Type I,II,III schemes at once)
    
    See Also:
    
    Constant Field Values
  - AADMSitesKey
```
public static final java.lang.String AADMSitesKey
```
    (Amino-Acid) Color Scheme Key for Datamonkey Sites file
    
    See Also:
    
    Constant Field Values
  - AAPAMLBEBM28Key
```
public static final java.lang.String AAPAMLBEBM28Key
```
    (Amino-Acid) Color Scheme Key for AACodeml BEB file (For Model 2 or Model 8)
    
    See Also:
    
    Constant Field Values
  - AAPAMLBEBM282Key
```
public static final java.lang.String AAPAMLBEBM282Key
```
    (Amino-Acid) Color Scheme Key for AAPAMLBEB BEB file (For Both Model 2 and Model 8: Common and Uncommon Sites)
    
    See Also:
    
    Constant Field Values
  - AAPAMLBEBM283Key
```
public static final java.lang.String AAPAMLBEBM283Key
```
    (Amino-Acid) Color Scheme Key for AAPAMLBEB BEB file (For Both Model 2 and Model 8: All Common Sites; Model 2 Uncommon Sites ; Model 8 Uncommon Sites)
    
    See Also:
    
    Constant Field Values
  - AATSCMLMRKey
```
public static final java.lang.String AATSCMLMRKey
```
    (Amino-Acid) Color Scheme Key for Merged ResulAATS file (for Both TreeSAAP PBR and BEB files)
    
    See Also:
    
    Constant Field Values
  - AASideChainsKey
```
public static final java.lang.String AASideChainsKey
```
    (Amino-Acid) Color Scheme Key for Side Chains scheme (predefined colors)
    
    See Also:
    
    Constant Field Values
  - AASeaviewKey
```
public static final java.lang.String AASeaviewKey
```
    (Amino-Acid) Color Scheme Key for Seaview scheme (predefined colors)
    
    See Also:
    
    Constant Field Values
  - AAAminoJKey
```
public static final java.lang.String AAAminoJKey
```
    (Amino-Acid) Color Scheme Key for Amino scheme from Jmol (predefined colors)
    
    See Also:
    
    Constant Field Values
  - AAShapelyJKey
```
public static final java.lang.String AAShapelyJKey
```
    (Amino-Acid) Color Scheme Key for Shapely scheme from Jmol (predefined colors)
    
    See Also:
    
    Constant Field Values
  - DRNAIMPACTKey
```
public static final java.lang.String DRNAIMPACTKey
```
    (DNA/RNA) Color Scheme Key for IMPACT scheme (predefined colors)
    
    See Also:
    
    Constant Field Values
  - DRNASeaviewKey
```
public static final java.lang.String DRNASeaviewKey
```
    (DNA/RNA) Color Scheme Key for Seaview scheme (predefined colors)
    
    See Also:
    
    Constant Field Values
  - DRNAJalviewKey
```
public static final java.lang.String DRNAJalviewKey
```
    (DNA/RNA) Color Scheme Key for Jalview scheme (predefined colors)
    
    See Also:
    
    Constant Field Values
  - DRNAMEGAKey
```
public static final java.lang.String DRNAMEGAKey
```
    (DNA/RNA) Color Scheme Key for MEGA scheme (predefined colors)
    
    See Also:
    
    Constant Field Values
  - IndexAATSTypeI
```
public static final int IndexAATSTypeI
```
    Index of the (Amino-Acid) Type I Color Scheme
    
    See Also:
    
    Constant Field Values
  - IndexAATSTypeII
```
public static final int IndexAATSTypeII
```
    Index of the (Amino-Acid) Type II Color Scheme
    
    See Also:
    
    Constant Field Values
  - IndexAATSTypeIII
```
public static final int IndexAATSTypeIII
```
    Index of the (Amino-Acid) Type III Color Scheme
    
    See Also:
    
    Constant Field Values
  - IndexAATSTypeIIIU
```
public static final int IndexAATSTypeIIIU
```
    Index of the (Amino-Acid) Type III User Color Scheme
    
    See Also:
    
    Constant Field Values
  - IndexAATSType123
```
public static final int IndexAATSType123
```
    Index of the (Amino-Acid) All Type I,II,III Color Schemes
    
    See Also:
    
    Constant Field Values
  - IndexAADatamonkeySites
```
public static final int IndexAADatamonkeySites
```
    Index of the (Amino-Acid) Datamonkey Sites Color Scheme
    
    See Also:
    
    Constant Field Values
  - IndexAAPAMLBEBM28
```
public static final int IndexAAPAMLBEBM28
```
    Index of the (Amino-Acid) PAMLBEB BEB M2 or M8 Color Scheme
    
    See Also:
    
    Constant Field Values
  - IndexAAPAMLBEBM282
```
public static final int IndexAAPAMLBEBM282
```
    Index of the (Amino-Acid) PAMLBEB BEB M2 and M8: (2 Colors) Color Scheme
    
    See Also:
    
    Constant Field Values
  - IndexAAPAMLBEBM283
```
public static final int IndexAAPAMLBEBM283
```
    Index of the (Amino-Acid) PAMLBEB BEB M2 and M8: (3 Colors) Color Scheme
    
    See Also:
    
    Constant Field Values
  - IndexAAMR
```
public static final int IndexAAMR
```
    Index of the (Amino-Acid) Merged Results Color Scheme
    
    See Also:
    
    Constant Field Values
  - IndexAASideChains
```
public static final int IndexAASideChains
```
    Index of the (Amino-Acid) Side Chains Color Scheme
    
    See Also:
    
    Constant Field Values
  - IndexAASeaview
```
public static final int IndexAASeaview
```
    Index of the (Amino-Acid) Seaview Color Scheme
    
    See Also:
    
    Constant Field Values
  - IndexAAAminoJ
```
public static final int IndexAAAminoJ
```
    Index of the (Amino-Acid) Amino Color Scheme
    
    See Also:
    
    Constant Field Values
  - IndexAAShapelyJ
```
public static final int IndexAAShapelyJ
```
    Index of the (Amino-Acid) Shapely Color Scheme
    
    See Also:
    
    Constant Field Values
  - IndexDRNAIMPACT
```
public static final int IndexDRNAIMPACT
```
    Index of the (DNA/RNA) Amino Color Scheme
    
    See Also:
    
    Constant Field Values
  - IndexDRNASeaview
```
public static final int IndexDRNASeaview
```
    Index of the (DNA/RNA) Seaview Color Scheme
    
    See Also:
    
    Constant Field Values
  - IndexDRNAJalview
```
public static final int IndexDRNAJalview
```
    Index of the (DNA/RNA) Jalview Color Scheme
    
    See Also:
    
    Constant Field Values
  - IndexDRNAMEGA
```
public static final int IndexDRNAMEGA
```
    Index of the (DNA/RNA) MEGA Color Scheme
    
    See Also:
    
    Constant Field Values
- Constructor Detail
  - GUIColorSchemes
```
public GUIColorSchemes(boolean visible)
```
    Creates new form GUIJmolSchemes
    
    Parameters:
    
    visible - determine the visibility of this window.
- Method Detail
  - setTreeSAAPSchemeOption
```
public void setTreeSAAPSchemeOption(int lowerlimit)
```
    Set the Lower limit as the user selected value for the User TreeSAAP coloring scheme.
    
    Parameters:
    
    lowerlimit - set the user selected value for the coloring scheme.
  - getSchemeIndex
```
public int getSchemeIndex(java.lang.String key)
```
    Get Color Scheme Index, given key.
    
    Parameters:
    
    key - for obtaining corresponding index.
    
    Returns:
    
    the color scheme index.
    
    See Also:
    
    loadScheme(int), AATSTypeIKey, AATSTypeIIKey, AATSTypeIIIKey, AATSTypeIIIUKey, AATSType123Key, AAPAMLBEBM28Key, AAPAMLBEBM282Key, AAPAMLBEBM283Key, AATSCMLMRKey, AASideChainsKey, AASeaviewKey, AAAminoJKey, AAShapelyJKey, DRNAIMPACTKey, DRNASeaviewKey, DRNAJalviewKey, DRNAMEGAKey
  - loadScheme
```
public void loadScheme(int loadscheme)
```
    Load user selected scheme of colors.
    
    Parameters:
    
    loadscheme - selected scheme. Possible Values are:
    
    See Also:
    
    AATSTypeIKey, AATSTypeIIKey, AATSTypeIIIKey, AATSTypeIIIUKey, AATSType123Key, AAPAMLBEBM28Key, AAPAMLBEBM282Key, AAPAMLBEBM283Key, AATSCMLMRKey, AASideChainsKey, AASeaviewKey, AAAminoJKey, AAShapelyJKey, DRNAIMPACTKey, DRNASeaviewKey, DRNAJalviewKey, DRNAMEGAKey
  - schemeChanged
```
public boolean schemeChanged()
```
    Tell whether user has changed colors on scheme.
    
    Returns:
    
    true if changed; false, otherwise.
  - getAAColorMap
```
public java.util.HashMap<java.lang.String,java.awt.Color> getAAColorMap()
```
    Get a map of AA codes to associated colors, from the loaded scheme.
    
    Returns:
    
    Map of amino acids codes to colors.
    
    See Also:
    
    SequenceTranslator.getAANamesMap(boolean), getAAMatchingList(int), getChosenColors(), getDRNAColorMap()
  - getDRNAColorMap
```
public java.util.HashMap<java.lang.String,java.awt.Color> getDRNAColorMap()
```
    Get a map of DNA/RNA codes to associated colors, from the loaded scheme.
    
    Returns:
    
    Map of nucleotides codes to colors.
    
    See Also:
    
    getChosenColors(), getAAColorMap()
  - getChosenColors
```
public java.awt.Color[] getChosenColors()
```
    Get colors selected or not by user. These can be the default colors.
    The order of colors is the same as presented in the GUI from top to bottom.
    
    Returns:
    
    array of colors.
  - getAAMatchingList
```
public java.lang.String[] getAAMatchingList(int namecase)
```
    Get AA name list. This is a fixed list which will be in same order as the chosen colors list. This list is obtained from the text of each label from the labels array.
    
    Parameters:
    
    namecase - 0 - normal case; 1 - all lowercase; other - all uppercase
    
    Returns:
    
    names
    
    See Also:
    
    getChosenColors()

Class GUIColorSchemes

Nested Class Summary

Nested classes/interfaces inherited from class javax.swing.JFrame

Nested classes/interfaces inherited from class java.awt.Frame

Nested classes/interfaces inherited from class java.awt.Window

Nested classes/interfaces inherited from class java.awt.Container

Nested classes/interfaces inherited from class java.awt.Component

Field Summary

Fields inherited from class javax.swing.JFrame

Fields inherited from class java.awt.Frame

Fields inherited from class java.awt.Component

Fields inherited from interface javax.swing.WindowConstants

Fields inherited from interface java.awt.image.ImageObserver

Constructor Summary

Method Summary

Methods inherited from class javax.swing.JFrame

Methods inherited from class java.awt.Frame

Methods inherited from class java.awt.Window

Methods inherited from class java.awt.Container

Methods inherited from class java.awt.Component

Methods inherited from class java.lang.Object

Methods inherited from interface java.awt.MenuContainer

Field Detail

AATSTypeIKey

AATSTypeIIKey

AATSTypeIIIKey

AATSTypeIIIUKey

AATSType123Key

AADMSitesKey

AAPAMLBEBM28Key

AAPAMLBEBM282Key

AAPAMLBEBM283Key

AATSCMLMRKey

AASideChainsKey

AASeaviewKey

AAAminoJKey

AAShapelyJKey

DRNAIMPACTKey

DRNASeaviewKey

DRNAJalviewKey

DRNAMEGAKey

IndexAATSTypeI

IndexAATSTypeII

IndexAATSTypeIII

IndexAATSTypeIIIU

IndexAATSType123

IndexAADatamonkeySites

IndexAAPAMLBEBM28

IndexAAPAMLBEBM282

IndexAAPAMLBEBM283

IndexAAMR

IndexAASideChains

IndexAASeaview

IndexAAAminoJ

IndexAAShapelyJ

IndexDRNAIMPACT

IndexDRNASeaview

IndexDRNAJalview

IndexDRNAMEGA

Constructor Detail

GUIColorSchemes

Method Detail

setTreeSAAPSchemeOption

getSchemeIndex

loadScheme

schemeChanged

getAAColorMap

getDRNAColorMap

getChosenColors

getAAMatchingList