HitColoringAndAlignmentOptions (JChem Base API documentation (c) 1998-2017 ChemAxon Ltd.)

java.lang.Object
- chemaxon.util.HitColoringAndAlignmentOptions

All Implemented Interfaces:

Cloneable
```
public final class HitColoringAndAlignmentOptions
extends Object
implements Cloneable
```
Class for specifying coloring and alignment options.

Since:

JChem 5.0

Author:

Szilard Dorant, Vencel Bors Date: Nov 04, 2010

Field Summary

Fields
Modifier and Type	Field and Description
`static int`	`ALIGNMENT_OFF` The structure is displayed with the original coordinates.
`static int`	`ALIGNMENT_PARTIAL_CLEAN` The substructure part of the target will get the exact coordinates of the query, and new coordinates will be generated for the remainder of the structure.
`static int`	`ALIGNMENT_ROTATE` The structure is rotated according to the substructure.
`int`	`alignmentMode` Deprecated. as of JChem 5.10, use `setAlignmentMode(int)` and `getAlignmentMode()` to access this field.
`boolean`	`coloring` Deprecated. as of JChem 5.10, use `setColoringEnabled(boolean)` and `isColoringEnabled()` to access this field.
`static int`	`DISSIMILARITY` The dissimilarity score is shown and stored in the MPropertyContainer of the Molecule.
`boolean`	`enumerateMarkush` Deprecated. as of JChem 5.12, use `setEnumerateMarkush(boolean)` and `getEnumerateMarkush()` to access this field.
`Color`	`hitColor` Deprecated. as of JChem 5.10, use `setHitColor(Color)` and `getHitColor()` to access this field.
`Color`	`hitHomologyColor` Deprecated. as of JChem 5.10, use `setHitHomologyColor(Color)` and `getHitHomologyColor()` to access this field.
`static int`	`MARKUSH_REDUCTION` Constant value specifying, that in case of markush searching the markush structure is expanded according to the query structure.
`static int`	`MARKUSH_REDUCTION_HGEXPANSION` Constant value specifying, that in case of markush searching the markush structure is expanded according to the query structure and homology groups are also replaced by the query structure matching on them.
`int`	`markushDisplayMode` Deprecated. as of JChem 5.10, use `setMarkushDisplayMode(int)` and `getMarkushDisplayMode()` to access this field.
`Color`	`nonHitColor` Deprecated. as of JChem 5.10, use `setNonHitColor(Color)` and `getNonHitColor()` to access this field.
`Color`	`nonHitColor3D` Deprecated. as of JChem 5.10, use `setNonHitColor3D(Color)` and `getNonHitColor3D()` to access this field.
`static int`	`ORIGINAL_MARKUSH` Constant value specifying, that in case of markush searching hit is displayed on the markush structure.
`static String`	`QUERY_LABEL` Label for the query part of a similarity hit.
`static int`	`SIMILARITY` The similarity score is shown and stored in the MPropertyContainer of the Molecule.
`static String`	`SIMILARITY_LABEL` Label for the similarity score part of the hit.
`static int`	`SIMILARITY_OFF` The similarity score is neither shown nor stored in the MPropertyContainer of the Molecule.
`int`	`similarityScoreDisplay` Deprecated. as of JChem 5.10, use `setSimilarityScoreDisplay(int)` and `getSimilarityScoreDisplay()` to access this field.
`static String`	`TARGET_LABEL` Label for the target part of the similarity hit.

Constructor Summary

Constructors
Constructor and Description

HitColoringAndAlignmentOptions()

Constructors
Constructor and Description
`HitColoringAndAlignmentOptions()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`Object`	`clone()` Makes an identical copy of the Options
`int`	`getAlignmentMode()` Returns the alignment mode.
`boolean`	`getEnumerateMarkush()` Returns `true` if markush structures should be hit enumerated according to the query structure.
`Color`	`getHitColor()` Returns the color to be used when coloring the substructure hit.
`Color`	`getHitHomologyColor()` Returns the color used for highlighting user defined homologies in a substructure hit.
`int`	`getMarkushDisplayMode()` Returns the Markush display mode.
`Color`	`getNonHitColor()` Returns the color to be used when coloring the part of the target which is not matching to the query.
`Color`	`getNonHitColor3D()` Returns the color to be used when coloring the part of the 3D target which is not matching to the query.
`int`	`getSimilarityScoreDisplay()` Returns the mode of similarity score display.
`static boolean`	`isAcceptedOptionName(String optionName)` Checks if the given option name can be a hit coloring and alignment option.
`boolean`	`isColoringEnabled()` Specifies if substructure hit coloring should be used.
`boolean`	`isDisplayLabelsAndBoxes()` Gets whether bounding boxes and labels are to be displayed for the components of the search.
`boolean`	`isQueryDisplay()` Gets whether the query should be displayed in the upper left corner along with the hit.
`boolean`	`isRemoveUnusedDefitions()` Gets whether unused definitions should be removed or not.
`void`	`setAlignmentMode(int alignmentMode)` Sets the alignment mode.
`void`	`setColoringEnabled(boolean coloringEnabled)` Sets whether substructure hit coloring should be used.
`void`	`setDisplayLabelsAndBoxes(boolean value)` Set the option to show labels and bounding boxes for the parts of the result: target, query, score.
`void`	`setEnumerateMarkush(boolean enumerateMarkush)` Sets whether markush structures should be hit enumerated according to the query structure.
`void`	`setHitColor(Color hitColor)` Sets the color to be used when coloring the substructure hit.
`void`	`setHitHomologyColor(Color hitHomologyColor)` Set the color of user defined homologies in a substructure hit.
`void`	`setMarkushDisplayMode(int markushDisplayMode)` Sets the Markush display mode.
`void`	`setNonHitColor(Color nonHitColor)` Sets the color to be used when coloring the part of the target which is not matching to the query.
`void`	`setNonHitColor3D(Color nonHitColor3D)` Sets the color to be used when coloring the part of the 3D target which is not matching to the query.
`static void`	`setOptions(HitColoringAndAlignmentOptions hcaaOptions, String hitColorAndAlignOptionList)` Parses the option list given while updating a HitColoringAndAlignmentOptions object.
`void`	`setQueryDisplay(boolean value)` Set query display option
`void`	`setRemoveUnusedDefinitions(boolean value)` Sets the remove unused definitions option.
`void`	`setSimilarityScoreDisplay(int similarityScoreDisplay)` Sets the mode of similarity score display.
`String`	`toString()` Returns a String representation of this object, which can be used in `setOptions(HitColoringAndAlignmentOptions, String)` to fill another HitColoringAndAlignmentOptions object with parameters.
`String`	`toString(String optionSeparator)` Returns a String representation of this object, which can be used in `setOptions(HitColoringAndAlignmentOptions, String)` to fill another HitColoringAndAlignmentOptions object with parameters.

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

- Field Detail
  - ALIGNMENT_OFF
```
public static final int ALIGNMENT_OFF
```
    The structure is displayed with the original coordinates.
    
    See Also:
    
    getAlignmentMode(), setAlignmentMode(int), Constant Field Values
  - ALIGNMENT_ROTATE
```
public static final int ALIGNMENT_ROTATE
```
    The structure is rotated according to the substructure.
    
    See Also:
    
    getAlignmentMode(), setAlignmentMode(int), Constant Field Values
  - ALIGNMENT_PARTIAL_CLEAN
```
public static final int ALIGNMENT_PARTIAL_CLEAN
```
    The substructure part of the target will get the exact coordinates of the query, and new coordinates will be generated for the remainder of the structure.
    
    See Also:
    
    getAlignmentMode(), setAlignmentMode(int), Constant Field Values
  - ORIGINAL_MARKUSH
```
public static final int ORIGINAL_MARKUSH
```
    Constant value specifying, that in case of markush searching hit is displayed on the markush structure.
    
    See Also:
    
    getMarkushDisplayMode(), setMarkushDisplayMode(int), Constant Field Values
  - MARKUSH_REDUCTION
```
public static final int MARKUSH_REDUCTION
```
    Constant value specifying, that in case of markush searching the markush structure is expanded according to the query structure.
    
    See Also:
    
    getMarkushDisplayMode(), setMarkushDisplayMode(int), Constant Field Values
  - MARKUSH_REDUCTION_HGEXPANSION
```
public static final int MARKUSH_REDUCTION_HGEXPANSION
```
    Constant value specifying, that in case of markush searching the markush structure is expanded according to the query structure and homology groups are also replaced by the query structure matching on them.
    
    See Also:
    
    getMarkushDisplayMode(), setMarkushDisplayMode(int), Constant Field Values
  - coloring
```
@Deprecated
public boolean coloring
```
    Deprecated. as of JChem 5.10, use setColoringEnabled(boolean) and isColoringEnabled() to access this field.
    
    Specifies if substructure hit coloring should be used.
  - enumerateMarkush
```
@Deprecated
public boolean enumerateMarkush
```
    Deprecated. as of JChem 5.12, use setEnumerateMarkush(boolean) and getEnumerateMarkush() to access this field.
    
    Specifies if markush structures should be hit enumerated according to the query structure. (Markush reduction to the hit.)
  - markushDisplayMode
```
@Deprecated
public int markushDisplayMode
```
    Deprecated. as of JChem 5.10, use setMarkushDisplayMode(int) and getMarkushDisplayMode() to access this field.
    Specifies the display of markush hits. Possible values:
    Since:
    
    version 5.3
  - alignmentMode
```
@Deprecated
public int alignmentMode
```
    Deprecated. as of JChem 5.10, use setAlignmentMode(int) and getAlignmentMode() to access this field.
    Specifies what form of alignment to use for hit display. The following values are accepted:
    - ALIGNMENT_OFF (default)
    - ALIGNMENT_ROTATE
    - ALIGNMENT_PARTIAL_CLEAN
  - hitColor
```
@Deprecated
public Color hitColor
```
    Deprecated. as of JChem 5.10, use setHitColor(Color) and getHitColor() to access this field.
    
    Determines the color of the substructure hit. The default value is Color.blue
  - hitHomologyColor
```
@Deprecated
public Color hitHomologyColor
```
    Deprecated. as of JChem 5.10, use setHitHomologyColor(Color) and getHitHomologyColor() to access this field.
    
    Determines the color of the user defined homologies in a substructure hit. The default value is Color.green
  - nonHitColor
```
@Deprecated
public Color nonHitColor
```
    Deprecated. as of JChem 5.10, use setNonHitColor(Color) and getNonHitColor() to access this field.
    
    Determines the color of the target which is not part of the substructure. The default value is Color.black
    
    See Also:
    
    setNonHitColor3D(Color), getNonHitColor3D()
  - nonHitColor3D
```
@Deprecated
public Color nonHitColor3D
```
    Deprecated. as of JChem 5.10, use setNonHitColor3D(Color) and getNonHitColor3D() to access this field.
    
    Determines the color of the 3D target which is not part of the substructure. The default value is Color.gray
    
    See Also:
    
    setNonHitColor(Color), getNonHitColor()
  - SIMILARITY_OFF
```
public static final int SIMILARITY_OFF
```
    The similarity score is neither shown nor stored in the MPropertyContainer of the Molecule.
    
    See Also:
    
    getSimilarityScoreDisplay(), setSimilarityScoreDisplay(int), Constant Field Values
  - DISSIMILARITY
```
public static final int DISSIMILARITY
```
    The dissimilarity score is shown and stored in the MPropertyContainer of the Molecule.
    
    See Also:
    
    getSimilarityScoreDisplay(), setSimilarityScoreDisplay(int), Constant Field Values
  - SIMILARITY
```
public static final int SIMILARITY
```
    The similarity score is shown and stored in the MPropertyContainer of the Molecule.
    
    See Also:
    
    getSimilarityScoreDisplay(), setSimilarityScoreDisplay(int), Constant Field Values
  - similarityScoreDisplay
```
@Deprecated
public int similarityScoreDisplay
```
    Deprecated. as of JChem 5.10, use setSimilarityScoreDisplay(int) and getSimilarityScoreDisplay() to access this field.
    Mode of similarity score display. The following values are accepted:
    - SIMILARITY (default)
    - DISSIMILARITY
    - SIMILARITY_OFF
  - QUERY_LABEL
```
public static final String QUERY_LABEL
```
    Label for the query part of a similarity hit.
    
    See Also:
    
    Constant Field Values
  - TARGET_LABEL
```
public static final String TARGET_LABEL
```
    Label for the target part of the similarity hit.
    
    See Also:
    
    Constant Field Values
  - SIMILARITY_LABEL
```
public static final String SIMILARITY_LABEL
```
    Label for the similarity score part of the hit.
    
    See Also:
    
    Constant Field Values
- Constructor Detail
  - HitColoringAndAlignmentOptions
```
public HitColoringAndAlignmentOptions()
```
- Method Detail
  - getEnumerateMarkush
```
public boolean getEnumerateMarkush()
```
    Returns true if markush structures should be hit enumerated according to the query structure. (Markush reduction to the hit.)
    
    Returns:
    
    true if markush structures should be hit enumerated according to the query structure. (Markush reduction to the hit.)
    
    Since:
    
    JChem 5.12
  - setEnumerateMarkush
```
public void setEnumerateMarkush(boolean enumerateMarkush)
```
    Sets whether markush structures should be hit enumerated according to the query structure. (Markush reduction to the hit.)
    
    Parameters:
    
    enumerateMarkush - true if markush structures should be hit enumerated according to the query structure. (Markush reduction to the hit.)
    
    Since:
    
    JChem 5.12
  - isQueryDisplay
```
public boolean isQueryDisplay()
```
    Gets whether the query should be displayed in the upper left corner along with the hit. Default is false .
    
    Returns:
    
    true if query is to be shown, false if not.
  - setQueryDisplay
```
public void setQueryDisplay(boolean value)
```
    Set query display option
    Parameters:
    value - true if query is to be displayed false if not. See:
    
    QUERY_LABEL
    
    TARGET_LABEL
    
    SIMILARITY_LABEL
  - isRemoveUnusedDefitions
```
public boolean isRemoveUnusedDefitions()
```
    Gets whether unused definitions should be removed or not. Default value is true
    
    Returns:
    
    true if definitions are to be removed false if not.
    
    See Also:
    
    setRemoveUnusedDefinitions(boolean)
  - setRemoveUnusedDefinitions
```
public void setRemoveUnusedDefinitions(boolean value)
```
    Sets the remove unused definitions option. By removing unused definitions readability is increased.
    Default value is true
    
    Parameters:
    
    value - true if definitions are to be removed false if not.
    
    See Also:
    
    isRemoveUnusedDefitions()
  - isDisplayLabelsAndBoxes
```
public boolean isDisplayLabelsAndBoxes()
```
    Gets whether bounding boxes and labels are to be displayed for the components of the search. Used only in case of similarity.
    
    Returns:
    
    true for boxes and labels to be displayed, false if no labels or boxes displayed.
  - setHitHomologyColor
```
public void setHitHomologyColor(Color hitHomologyColor)
```
    Set the color of user defined homologies in a substructure hit. Default: Color.green.
    
    Parameters:
    
    hitHomologyColor - color used for highlighting homolgies in a hit
  - getHitHomologyColor
```
public Color getHitHomologyColor()
```
    Returns the color used for highlighting user defined homologies in a substructure hit. Default: Color.green.
    
    Returns:
    
    the color used for highlighting
  - setDisplayLabelsAndBoxes
```
public void setDisplayLabelsAndBoxes(boolean value)
```
    Set the option to show labels and bounding boxes for the parts of the result: target, query, score. Default is false.
    
    Parameters:
    
    value - true if labels and boxes to be displayed false otherwise.
  - isAcceptedOptionName
```
public static boolean isAcceptedOptionName(String optionName)
```
    Checks if the given option name can be a hit coloring and alignment option. The option value is not checked for validity.
    
    Parameters:
    
    optionName - the option in question
    
    Returns:
    
    true if it is an accepted option name.
  - setOptions
```
public static void setOptions(HitColoringAndAlignmentOptions hcaaOptions,
                              String hitColorAndAlignOptionList)
```
    Parses the option list given while updating a HitColoringAndAlignmentOptions object. This can read in the option string returned by toString(String).
    Parameters:
    
    hcaaOptions - HitColoringAndAlignmentOptions to be updated based on option list provided
    hitColorAndAlignOptionList - options list to be parsed Can set multiple options. Name and value of an option should be separated by ":", and different pairs of names/values by spaces. Instead of spaces an alternative option separator string (even more than 1 character) can be specified at the beginning of optionString by the syntax "sep='separator string' ...". After 'separator string' there must be at least 1 space character!)
    E.g.
    
    setOptions("hitColoring:y")
    
    setOptions(" hitColoring:y align:r")
    
    setOptions("sep=*-* align:r*-*markushDisplayMode:rhg")
    Throws:
    
    IllegalArgumentException - in case of wrong option value string
    
    See Also:
    
    toString(String)
  - toString
```
public String toString()
```
    Returns a String representation of this object, which can be used in setOptions(HitColoringAndAlignmentOptions, String) to fill another HitColoringAndAlignmentOptions object with parameters.
    
    Overrides:
    
    toString in class Object
    
    Returns:
    
    a String representation of this object
    
    See Also:
    
    setOptions(HitColoringAndAlignmentOptions, String)
  - toString
```
public String toString(String optionSeparator)
```
    Returns a String representation of this object, which can be used in setOptions(HitColoringAndAlignmentOptions, String) to fill another HitColoringAndAlignmentOptions object with parameters.
    
    Parameters:
    
    optionSeparator - the separator string used between parameters, null means space (" ")
    
    Returns:
    
    a String representation of this object
    
    See Also:
    
    setOptions(HitColoringAndAlignmentOptions, String)
  - clone
```
public Object clone()
```
    Makes an identical copy of the Options
    
    Overrides:
    
    clone in class Object
    
    Returns:
    
    the copy
  - getMarkushDisplayMode
```
public int getMarkushDisplayMode()
```
    Returns the Markush display mode. Possible values:
    - ORIGINAL_MARKUSH (default)
    - MARKUSH_REDUCTION
    - MARKUSH_REDUCTION_HGEXPANSION
    Returns:
    
    the Markush display mode
    
    Since:
    
    JChem 5.10
  - setMarkushDisplayMode
```
public void setMarkushDisplayMode(int markushDisplayMode)
```
    Sets the Markush display mode. Possible values:
    - ORIGINAL_MARKUSH (default)
    - MARKUSH_REDUCTION
    - MARKUSH_REDUCTION_HGEXPANSION
    Parameters:
    
    markushDisplayMode - the Markush display mode
    
    Since:
    
    JChem 5.10
  - getAlignmentMode
```
public int getAlignmentMode()
```
    Returns the alignment mode. Possible values:
    - ALIGNMENT_OFF (default)
    - ALIGNMENT_ROTATE
    - ALIGNMENT_PARTIAL_CLEAN
    Returns:
    
    the alignment mode
    
    Since:
    
    JChem 5.10
  - setAlignmentMode
```
public void setAlignmentMode(int alignmentMode)
```
    Sets the alignment mode. Possible values:
    - ALIGNMENT_OFF (default)
    - ALIGNMENT_ROTATE
    - ALIGNMENT_PARTIAL_CLEAN
    Parameters:
    
    alignmentMode - the alignment mode
    
    Since:
    
    JChem 5.10
  - isColoringEnabled
```
public boolean isColoringEnabled()
```
    Specifies if substructure hit coloring should be used. Default: false.
    
    Returns:
    
    true if substructure hit coloring should be used
    
    Since:
    
    JChem 5.10
  - setColoringEnabled
```
public void setColoringEnabled(boolean coloringEnabled)
```
    Sets whether substructure hit coloring should be used. Default: false.
    
    Parameters:
    
    coloringEnabled - true if substructure hit coloring should be used
    
    Since:
    
    JChem 5.10
  - getHitColor
```
public Color getHitColor()
```
    Returns the color to be used when coloring the substructure hit. Default: Color.blue.
    
    Returns:
    
    the hitColor
    
    Since:
    
    JChem 5.10
  - setHitColor
```
public void setHitColor(Color hitColor)
```
    Sets the color to be used when coloring the substructure hit. Default: Color.blue.
    
    Parameters:
    
    hitColor - the hitColor to set
    
    Since:
    
    JChem 5.10
  - getNonHitColor
```
public Color getNonHitColor()
```
    Returns the color to be used when coloring the part of the target which is not matching to the query. Default: Color.black.
    
    Returns:
    
    the nonHitColor
    
    Since:
    
    JChem 5.10
  - setNonHitColor
```
public void setNonHitColor(Color nonHitColor)
```
    Sets the color to be used when coloring the part of the target which is not matching to the query. Default: Color.black.
    
    Parameters:
    
    nonHitColor - the nonHitColor to set
    
    Since:
    
    JChem 5.10
  - getNonHitColor3D
```
public Color getNonHitColor3D()
```
    Returns the color to be used when coloring the part of the 3D target which is not matching to the query. Default: Color.gray.
    
    Returns:
    
    the nonHitColor3D
    
    Since:
    
    JChem 5.10
  - setNonHitColor3D
```
public void setNonHitColor3D(Color nonHitColor3D)
```
    Sets the color to be used when coloring the part of the 3D target which is not matching to the query. Default: Color.gray.
    
    Parameters:
    
    nonHitColor3D - the nonHitColor3D to set
    
    Since:
    
    JChem 5.10
  - getSimilarityScoreDisplay
```
public int getSimilarityScoreDisplay()
```
    Returns the mode of similarity score display. Possible values:
    - SIMILARITY (default)
    - DISSIMILARITY
    - SIMILARITY_OFF
    Returns:
    
    the similarityScoreDisplay
    
    Since:
    
    JChem 5.10
  - setSimilarityScoreDisplay
```
public void setSimilarityScoreDisplay(int similarityScoreDisplay)
```
    Sets the mode of similarity score display. Possible values:
    - SIMILARITY (default)
    - DISSIMILARITY
    - SIMILARITY_OFF
    Parameters:
    
    similarityScoreDisplay - the similarityScoreDisplay to set
    
    Since:
    
    JChem 5.10

Class HitColoringAndAlignmentOptions

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

ALIGNMENT_OFF

ALIGNMENT_ROTATE

ALIGNMENT_PARTIAL_CLEAN

ORIGINAL_MARKUSH

MARKUSH_REDUCTION

MARKUSH_REDUCTION_HGEXPANSION

coloring

enumerateMarkush

markushDisplayMode

alignmentMode

hitColor

hitHomologyColor

nonHitColor

nonHitColor3D

SIMILARITY_OFF

DISSIMILARITY

SIMILARITY

similarityScoreDisplay

QUERY_LABEL

TARGET_LABEL

SIMILARITY_LABEL

Constructor Detail

HitColoringAndAlignmentOptions

Method Detail

getEnumerateMarkush

setEnumerateMarkush

isQueryDisplay

setQueryDisplay

isRemoveUnusedDefitions

setRemoveUnusedDefinitions

isDisplayLabelsAndBoxes

setHitHomologyColor

getHitHomologyColor

setDisplayLabelsAndBoxes

isAcceptedOptionName

setOptions

toString

toString

clone

getMarkushDisplayMode

setMarkushDisplayMode

getAlignmentMode

setAlignmentMode

isColoringEnabled

setColoringEnabled

getHitColor

setHitColor

getNonHitColor

setNonHitColor

getNonHitColor3D

setNonHitColor3D

getSimilarityScoreDisplay

setSimilarityScoreDisplay