chemaxon.util
Class HitColoringAndAlignmentOptions

java.lang.Object
  chemaxon.util.HitColoringAndAlignmentOptions

public class HitColoringAndAlignmentOptions
extends java.lang.Object

Class for specifying coloring and alignment options.

Since:

JChem 5.0

Author:

Szilard Dorant

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.
boolean	enumerateMarkush Deprecated. use markushDisplayMode
java.awt.Color	hitColor Determines the color of the 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.

Constructor Summary

HitColoringAndAlignmentOptions()

Method Summary

Methods inherited from class java.lang.Object

clone, 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

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

Constructor Detail

HitColoringAndAlignmentOptions

public HitColoringAndAlignmentOptions()