Field Detail

• vwr

  private Viewer vwr

• GRAY

  private static final int GRAY

  See Also:

  Constant Field Values

• BYELEMENT_PREFIX

  public static final java.lang.String BYELEMENT_PREFIX

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• BYRESIDUE_PREFIX

  public static final java.lang.String BYRESIDUE_PREFIX

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• BYELEMENT_JMOL

  private static final java.lang.String BYELEMENT_JMOL

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• BYELEMENT_RASMOL

  private static final java.lang.String BYELEMENT_RASMOL

  See Also:

  Constant Field Values

• BYRESIDUE_SHAPELY

  private static final java.lang.String BYRESIDUE_SHAPELY

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• BYRESIDUE_AMINO

  private static final java.lang.String BYRESIDUE_AMINO

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  Constant Field Values

• CUSTOM

  public static final int CUSTOM

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• ROYGB

  public static final int ROYGB

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  Constant Field Values

• BGYOR

  public static final int BGYOR

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  Constant Field Values

• JMOL

  public static final int JMOL

  See Also:

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• RASMOL

  public static final int RASMOL

  See Also:

  Constant Field Values

• SHAPELY

  public static final int SHAPELY

  See Also:

  Constant Field Values

• AMINO

  public static final int AMINO

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• RWB

  public static final int RWB

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• BWR

  public static final int BWR

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• LOW

  public static final int LOW

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• HIGH

  public static final int HIGH

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• BW

  public static final int BW

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  Constant Field Values

• WB

  public static final int WB

  See Also:

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• FRIENDLY

  public static final int FRIENDLY

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• USER

  public static final int USER

  See Also:

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• RESU

  public static final int RESU

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• INHERIT

  public static final int INHERIT

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• ALT

  public static final int ALT

  See Also:

  Constant Field Values

• colorSchemes

  private static final java.lang.String[] colorSchemes

• paletteBW

  private int[] paletteBW

• paletteWB

  private int[] paletteWB

• paletteFriendly

  private int[] paletteFriendly

• argbsCpk

  private int[] argbsCpk

• argbsRoygb

  private int[] argbsRoygb

• argbsRwb

  private int[] argbsRwb

• argbsShapely

  private int[] argbsShapely

• argbsAmino

  private int[] argbsAmino

• ihalf

  private int ihalf

• rasmolScale

  private static int[] rasmolScale

• schemes

  public java.util.Map<java.lang.String,​int[]> schemes

• currentPalette

  public int currentPalette

• currentSegmentCount

  public int currentSegmentCount

• isTranslucent

  public boolean isTranslucent

• lo

  public float lo

• hi

  public float hi

• isReversed

  public boolean isReversed

• userScale

  int[] userScale

• thisScale

  int[] thisScale

• thisName

  java.lang.String thisName

• isColorIndex

  boolean isColorIndex

• ce

  ColorEncoder ce

• argbsChainAtom

  public static int[] argbsChainAtom

• argbsChainHetero

  public static int[] argbsChainHetero

Constructor Detail

• ColorEncoder

  public ColorEncoder​(ColorEncoder ce,
                      Viewer vwr)

Method Detail

• getSchemeIndex

  private static final int getSchemeIndex​(java.lang.String colorScheme)

• fixName

  private static final java.lang.String fixName​(java.lang.String name)

• makeColorScheme

  private int makeColorScheme​(java.lang.String name,
                              int[] scale,
                              boolean isOverloaded)

  Parameters:

  name -

  scale - if null, then this is a reset.

  isOverloaded - if TRUE,

  Returns:

  >= 0 for a default color scheme

• getShapely

  private int[] getShapely()

• getAmino

  private int[] getAmino()

• createColorScheme

  public int createColorScheme​(java.lang.String colorScheme,
                               boolean defaultToRoygb,
                               boolean isOverloaded)

  Parameters:

  colorScheme - name or name= or name=[x......] [x......] ....

  defaultToRoygb -

  isOverloaded -

  Returns:

  paletteID

• setUserScale

  public void setUserScale​(int[] scale)

• getColorSchemeArray

  public int[] getColorSchemeArray​(int palette)

• getColorIndexFromPalette

  public short getColorIndexFromPalette​(float val,
                                        float lo,
                                        float hi,
                                        int palette,
                                        boolean isTranslucent)

• getPaletteColorCount

  private int getPaletteColorCount​(int palette)

• getArgbFromPalette

  public int getArgbFromPalette​(float val,
                                float lo,
                                float hi,
                                int palette)

• setThisScheme

  private void setThisScheme​(java.lang.String name,
                             int[] scale)

• getArgb

  public int getArgb​(float val)

• getArgbMinMax

  public int getArgbMinMax​(float val,
                           float min,
                           float max)

• getColorIndex

  public short getColorIndex​(float val)

• getColorKey

  public java.util.Map<java.lang.String,​java.lang.Object> getColorKey()

• getColorScheme

  public java.lang.String getColorScheme()

• setColorScheme

  public void setColorScheme​(java.lang.String colorScheme,
                             boolean isTranslucent)

  Parameters:

  colorScheme -

  isTranslucent -

• setRange

  public void setRange​(float lo,
                       float hi,
                       boolean isReversed)

• getCurrentColorSchemeName

  public java.lang.String getCurrentColorSchemeName()

• getColorSchemeName

  public java.lang.String getColorSchemeName​(int i)

• getColorSchemeList

  public static final java.lang.String getColorSchemeList​(int[] scheme)

• getRasmolScale

  public static final int[] getRasmolScale()

• getPaletteAC

  private int[] getPaletteAC()

• getPaletteWB

  private int[] getPaletteWB()

• getPaletteAtoB

  public static int[] getPaletteAtoB​(int color1,
                                     int color2,
                                     int n)

• getPaletteBW

  private int[] getPaletteBW()

• quantize

  public float quantize​(float x,
                        boolean isLowEnd)

  gets the value at the color boundary for this color range fraction

  Parameters:

  x -

  isLowEnd -

  Returns:

  quantized value

• quantize4

  public static final int quantize4​(float val,
                                    float lo,
                                    float hi,
                                    int segmentCount)

• colorIndex

  private static final int colorIndex​(float q,
                                      int segmentCount)

• colorIndexRepeat

  private static final int colorIndexRepeat​(float q,
                                            int segmentCount)