chemaxon.util
Class HitColoringAndAlignmentOptions

java.lang.Object
  chemaxon.util.HitColoringAndAlignmentOptions

All Implemented Interfaces:

java.lang.Cloneable

public class HitColoringAndAlignmentOptions
extends java.lang.Object
implements java.lang.Cloneable

Class for specifying coloring and alignment options.

Since:

JChem 5.0

Author:

Szilard Dorant, Vencel Bors Date: Nov 04, 2010

See Also:

VisualizationExample.java

Field Summary

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 Specifies what form of alignment to use for hit display.
boolean	coloring Specifies if substructure hit coloring should be used.
static int	DISSIMILARITY The dissimilarity score is shown and stored in the MPropertyContainer of the Molecule.
boolean	enumerateMarkush Deprecated. use markushDisplayMode
java.awt.Color	hitColor Determines the color of the substructure hit.
java.awt.Color	hitHomologyColor Determines the color of the user defined homologies in a substructure hit.
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 Specifies the display of markush hits.
java.awt.Color	nonHitColor Determines the color of the target which is not part of the substructure.
java.awt.Color	nonHitColor3D Determines the color of the 3D target which is not part of the substructure.
static int	ORIGINAL_MARKUSH Constant value specifying, that in case of markush searching hit is displayed on the markush structure.
static java.lang.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 java.lang.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 Mode of similarity score display.
static java.lang.String	TARGET_LABEL Label for the target part of the similarity hit.

Constructor Summary

HitColoringAndAlignmentOptions()

Method Summary

java.lang.Object	clone() Makes an identical copy of the Options
java.awt.Color	getHitHomologyColor() Get the color used for highlighting user defined homologies in a substructure hit
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	setDisplayLabelsAndBoxes(boolean value) Set the option to show labels and bounding boxes for the parts of the result: target, query, score.
void	setHitHomologyColor(java.awt.Color hitHomologyColor) Set the color of user defined homologies in a substructure hit
static void	setOptions(HitColoringAndAlignmentOptions hcaaOptions, java.lang.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.

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

ALIGNMENT_OFF

public static final int ALIGNMENT_OFF

The structure is displayed with the original coordinates.

See Also:

Constant Field Values

ALIGNMENT_ROTATE

public static final int ALIGNMENT_ROTATE

The structure is rotated according to the substructure.

See Also:

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:

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:

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:

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:

Constant Field Values

coloring

public boolean coloring

Specifies if substructure hit coloring should be used.

enumerateMarkush

public boolean enumerateMarkush

Deprecated. use markushDisplayMode

Specifies if markush structures should be hit enumerated according to the query structure. (Markush reduction to the hit.)

Since:

version 5.3

markushDisplayMode

public int markushDisplayMode

Specifies the display of markush hits.

Since:

version 5.3

See Also:

ORIGINAL_MARKUSH, MARKUSH_REDUCTION, MARKUSH_REDUCTION_HGEXPANSION

alignmentMode

public int alignmentMode

Specifies what form of alignment to use for hit display. The following values are accepted:

• ALIGNMENT_OFF (default)
• ALIGNMENT_ROTATE
• ALIGNMENT_PARTIAL_CLEAN

hitColor

public java.awt.Color hitColor

Determines the color of the substructure hit. The default value is Color.blue

hitHomologyColor

public java.awt.Color hitHomologyColor

Determines the color of the user defined homologies in a substructure hit. The default value is Color.green

nonHitColor

public java.awt.Color nonHitColor

Determines the color of the target which is not part of the substructure. The default value is Color.black

See Also:

nonHitColor3D

nonHitColor3D

public java.awt.Color nonHitColor3D

Determines the color of the 3D target which is not part of the substructure. The default value is Color.gray

See Also:

nonHitColor

SIMILARITY_OFF

public static final int SIMILARITY_OFF

The similarity score is neither shown nor stored in the MPropertyContainer of the Molecule.

See Also:

similarityScoreDisplay, Constant Field Values

DISSIMILARITY

public static final int DISSIMILARITY

The dissimilarity score is shown and stored in the MPropertyContainer of the Molecule.

See Also:

similarityScoreDisplay, Constant Field Values

SIMILARITY

public static final int SIMILARITY

The similarity score is shown and stored in the MPropertyContainer of the Molecule.

See Also:

similarityScoreDisplay, Constant Field Values

similarityScoreDisplay

public int similarityScoreDisplay

Mode of similarity score display. The following values are accepted:

• SIMILARITY (default)
• DISSIMILARITY
• SIMILARITY_OFF

QUERY_LABEL

public static final java.lang.String QUERY_LABEL

Label for the query part of a similarity hit.

See Also:

Constant Field Values

TARGET_LABEL

public static final java.lang.String TARGET_LABEL

Label for the target part of the similarity hit.

See Also:

Constant Field Values

SIMILARITY_LABEL

public static final java.lang.String SIMILARITY_LABEL

Label for the similarity score part of the hit.

See Also:

Constant Field Values

Constructor Detail

HitColoringAndAlignmentOptions

public HitColoringAndAlignmentOptions()

Method Detail

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(java.awt.Color hitHomologyColor)

Set the color of user defined homologies in a substructure hit

Parameters:

hitHomologyColor - color used for highlighting homolgies in a hit

getHitHomologyColor

public java.awt.Color getHitHomologyColor()

Get the color used for highlighting user defined homologies in a substructure hit

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.

setOptions

public static void setOptions(HitColoringAndAlignmentOptions hcaaOptions,
                              java.lang.String hitColorAndAlignOptionList)
                       throws java.lang.Exception

Parses the option list given while updating a HitColoringAndAlignmentOptions object.

Parameters:

hcaaOptions - HitColoringAndAlignmentOptions to be updated based on option list provided

hitColorAndAlignOptionList - options list to be parsed

Throws:

java.lang.Exception

clone

public java.lang.Object clone()

Makes an identical copy of the Options

Overrides:

clone in class java.lang.Object

Returns:

the copy