chemaxon.struc.sgroup

Class DataSgroup

java.lang.Object

chemaxon.struc.Sgroup

chemaxon.struc.sgroup.DataSgroup

All Implemented Interfaces:

Serializable

public class DataSgroup
extends Sgroup

Data Sgroup.

Since:

Marvin 4.0, 1/07/2005

Version:

Marvin 5.0.2, 03/07/2008

Author:

Szabolcs Csepregi Date: Jan 7, 2005

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static int	DT_FORMATTED Field type: formatted.
static int	DT_NUMERIC Field type: numeric.
static int	DT_TEXT Field type: text.
static int	DT_UNSPEC Field type: unspecified.
static int	DT_URL Field type: url.
static int	HIDDEN Specifies that the data sgroup is hidden.

Fields inherited from class chemaxon.struc.Sgroup

atomSet, brackets, CHARGE_ON_ATOMS, CHARGE_ON_GROUP, parentSgroup, PR_ATSYMS, RA_IN_EXPAND, RA_REMOVE_EXCEPT_RU, SCN_EITHER_UNKNOWN, SCN_HEAD_TO_HEAD, SCN_HEAD_TO_TAIL, SGROUP_TYPE_COUNT, sgroupGraph, sgroupType, SORT_CHILD_PARENT, SORT_PARENT_CHILD, SST_ALTERNATING, SST_BLOCK, SST_RANDOM, ST_AMINOACID, ST_ANY, ST_COMPONENT, ST_COPOLYMER, ST_CROSSLINK, ST_DATA, ST_FORMULATION, ST_GENERIC, ST_GRAFT, ST_MER, ST_MIXTURE, ST_MODIFICATION, ST_MONOMER, ST_MULTICENTER, ST_MULTIPLE, ST_SRU, ST_SUPERATOM, XSTATE_C, XSTATE_NONE, XSTATE_X, XSTATE_XC

Constructor Summary

Constructors

Constructor and Description
DataSgroup(DataSgroup sg, Molecule mol, Sgroup psg) Copy constructor.
DataSgroup(DataSgroup sg, Molecule mol, Sgroup psg, int[] atomIndexMap) Copy constructor.
DataSgroup(Molecule parent) Creates a Data S-group with the specified parent.

Method Summary

Methods

Modifier and Type	Method and Description
void	addDataLine(String line) Adds a line to the data stored in the field.
protected Sgroup	cloneSgroup(Molecule mol, Sgroup psg, int[] atomIndexMap) Gets a new DataSgroup instance.
DPoint3	getAbsoluteXY() Gets the X and Y coordinates of the data label in the molecule's coordinate system, considering absolute/relative placement.
String	getContext() Gets the context of the data sgroup.
int	getContextId() Gets the id of the context of the data sgroup.
String	getData() Gets the data value to be set.
String	getDataLine(int i) Gets a line of data.
int	getDataLineCount() Gets the number of data lines.
int	getDisplayedChars() Gets the number of characters to be displayed(1...999 or 0 for all)
int	getDisplayedLines() Gets the number of lines to be displayed (0: show all)
String	getFieldName() Gets the data field name.
int	getFieldType() Gets the field type.
String	getLineOnScreen(int i) Returns the i-th row of the data sgroup label, as displayed on the screen (with tag, query operator, units etc.)
void	getObjectsMiddle(DPoint3 p) Calculates the middle point of the coordinates of objects this sgroup is associated to.
void	getPlacementOrigin(DPoint3 p) If isAbsolutePlacement is false it calculates the middle point of the coordinates of atoms this S-group is associated to.
int	getPos() Gets the data display DASP position (0...9).
String	getQueryCode() Gets the program code of the query option.
String	getQueryOp() Gets the data query operator.
String	getSubscript() Gets the subscript for non-superatom S-groups.
char	getTag() Gets the tag character for footnote display (or space if blank).
String	getUnits() Gets the unit of this data field.
double	getX() Gets the X coordinate.
double	getY() Gets the Y coordinate.
boolean	hasBrackets() Brackets are painted if mouse runs over sgroup atoms.
boolean	isAbsolutePlacement() Gets whether the placement of this attached data is absolute or relative to the objects it is attached.
boolean	isDataDetached() Gets whether the data should be displayed close to the objects or separately (detached).
boolean	isUnitDisplayed() Gets whether the units string should be displayed.
void	setAbsolutePlacement(boolean b) Sets whether the placement of this attached data is absolute or relative to the objects it is attached.
void	setAbsoluteXY(double x, double y) Sets the X and Y coordinates of the data label in the molecule's coordinate system, considering absolute/relative placement.
void	setAbsoluteXY(DPoint3 p) Sets the X and Y coordinates of the data label in the molecule's coordinate system, considering absolute/relative placement.
void	setContext(int id) Sets the context of this data sgroup.
void	setContext(String context) Sets the context of this data sgroup.
void	setData(String s) Sets the data value to be set.
void	setDataDetached(boolean b) Sets whether the data should be displayed close to the objects or separately (detached).
void	setDataLine(int i, String line) Sets a line of data.
void	setDisplayedChars(int chars) Sets the number of characters to be displayed (1...999 or 0 for no restriction)
void	setDisplayedLines(int lines) Sets the number of lines to be displayed (0: show all)
void	setFieldName(String nameP) Sets the data field name.
void	setFieldType(int typeP) Sets the field type.
void	setFieldType(String ft) Sets the field type from string representation.
void	setPos(int p) Sets the data display DASP position (0...9).
void	setQueryCode(String queryCodeP) Sets the program code for the query option.
void	setQueryOp(String queryOpP) Sets the data query operator.
void	setTag(char c) Sets the tag character for the footnote display.
void	setUnitDisplayed(boolean b) Sets whether the units string should be displayed.
void	setUnits(String unitsP) Sets the unit of this data field.
void	setX(double x) Sets the X coordinate.
void	setY(double y) Sets the Y coordinate.
protected void	transformByParent(CTransform3D t, boolean incg) Applies a transformation matrix to the Data Sgroup coordinates.

Methods inherited from class chemaxon.struc.Sgroup

add, addBracket, addChildSgroup, areChildSgroupsVisible, checkBondConsistency, checkBonds, checkConsistencyInEmbeddings, checkSgroupGraphConsistency, clearObjects, cloneSgroup, cloneStructure, contains, containsAllAtomsOf, contract, countAllAtoms, createMolecule, createMolecule, expand, findCrossingBonds, findSmallestSgroupContaining, findSmallestSgroupOf, getAtom, getAtomArray, getAtomCount, getAtomSymbolListAsString, getAttach, getBondArray, getBracketCount, getBrackets, getChargeLocation, getChildSgroup, getChildSgroupCount, getChildSgroups, getConnectivity, getCrossingAtoms, getParentMolecule, getParentSgroup, getSgroupGraph, getSgroupType, getSubType, getSuperscript, getTotalCharge, getType, getXState, hasAtom, indexOf, indexOf, initBrackets, isBracketCrossingBond, isBracketVisible, isDescendantOf, isEmpty, isOrderedComponentSgroup, isPartSelected, isRemovable, isSelected, isTotalSelected, isVisible, removeAtom, removeAtom, removeAtom, removeBond, removeBonds, removeChildSgroup, removeGroupedAtom, removeObject, replaceAtom, replaceAtom, selectAllObjects, setAtom, setChargeLocation, setConnectivity, setGUIStateRecursively, setGUIStateRecursively, setParentMolecule, setSgroupGraph, setSubscript, setSubType, setXState, setXState, setXState0, sort, toString, toString

Methods inherited from class java.lang.Object

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

Field Detail

DT_UNSPEC

public static final int DT_UNSPEC

Field type: unspecified.

See Also:

Constant Field Values

DT_FORMATTED

public static final int DT_FORMATTED

Field type: formatted.

See Also:

Constant Field Values

DT_NUMERIC

public static final int DT_NUMERIC

Field type: numeric.

See Also:

Constant Field Values

DT_TEXT

public static final int DT_TEXT

Field type: text.

See Also:

Constant Field Values

DT_URL

public static final int DT_URL

Field type: url.

See Also:

Constant Field Values

HIDDEN

public static final int HIDDEN

Specifies that the data sgroup is hidden.

Since:

Marvin 4.1.6 01/12/2007

See Also:

setDisplayedLines(int), Constant Field Values

Constructor Detail

DataSgroup

public DataSgroup(Molecule parent)

Creates a Data S-group with the specified parent.

Parameters:

parent - the parent molecule

DataSgroup

public DataSgroup(DataSgroup sg,
          Molecule mol,
          Sgroup psg,
          int[] atomIndexMap)

Copy constructor.

Parameters:

sg - the S-group to copy

mol - the new parent molecule

psg - the new parent S-group or null if no parent S-group exists

atomIndexMap - indices of cloned atoms in the original molecule in the case of partial cloning, or null otherwise

Since:

Marvin 5.3.3 30/03/2010

DataSgroup

public DataSgroup(DataSgroup sg,
          Molecule mol,
          Sgroup psg)

Copy constructor.

Parameters:

sg - the S-group to copy

mol - the new parent molecule

psg - the new parent S-group or null

Since:

Marvin 4.0 1/08/2005

Method Detail

cloneSgroup

protected Sgroup cloneSgroup(Molecule mol,
                 Sgroup psg,
                 int[] atomIndexMap)

Gets a new DataSgroup instance.

Overrides:

cloneSgroup in class Sgroup

Parameters:

mol - the new parent molecule

psg - the new parent S-group

atomIndexMap - indices of cloned atoms in the original molecule or null

Returns:

the new object

getContext

public String getContext()

Gets the context of the data sgroup. Possible context values: Atom, Bond, Single Bond, Double Bond, Fragment, Group (Selection)

Returns:

the context of this DataSgroup

setContext

public void setContext(String context)

Sets the context of this data sgroup. Context play role when displaying the data for this DataSgroup. Possible context values and their meaning: Atom - the data sgroup information should be displayed for any atom in this group separately. Bond - the data sgroup information should be displayed for any bond in this group separately. Single Bond - the data sgroup information should be displayed for any single bond in this group separately. Double Bond - the data sgroup information should be displayed for any double bond in this group separately. Fragment - the data sgroup information should be displayed for any disconnected molecule fragment in this group separately. Group (Selection) - the data sgroup information should be displayed for the whole group once.

Parameters:

context - - the string representation of the context.

getContextId

public int getContextId()

Gets the id of the context of the data sgroup. Ids and the corresponding context values: 0 - Atom 1 - Bond 2 - Single Bond 3 - Double Bond 4 - Fragment 5 - Group (Selection)

Returns:

the id of the context of this DataSgroup

setContext

public void setContext(int id)

Sets the context of this data sgroup.

Parameters:

id - - the id of the context.

See Also:

setContext(String), getContextId()

getFieldName

public String getFieldName()

Gets the data field name. (V2000: the first 30 chars can only be exported.)

Returns:

The data field identifier.

setFieldName

public void setFieldName(String nameP)

Sets the data field name. (V2000: the first 30 chars can only be exported.)

Parameters:

nameP - The data field identifier.

getFieldType

public int getFieldType()

Gets the field type.

Returns:

The type of the field.

See Also:

DT_UNSPEC, DT_FORMATTED, DT_NUMERIC, DT_TEXT, DT_URL

setFieldType

public void setFieldType(int typeP)

Sets the field type.

Parameters:

typeP - The type of the data field.

See Also:

DT_UNSPEC, DT_FORMATTED, DT_NUMERIC, DT_TEXT, DT_URL

setFieldType

public void setFieldType(String ft)

Sets the field type from string representation.

Parameters:

ft - "F", "T" or "N"

See Also:

DT_UNSPEC, DT_FORMATTED, DT_NUMERIC, DT_TEXT, DT_URL

getUnits

public String getUnits()

Gets the unit of this data field. (V2000: The first 20 characters can only be exported.)

Returns:

The unit of the data, e.g. "A^2" or "kJ/cm3"

setUnits

public void setUnits(String unitsP)

Sets the unit of this data field. (V2000: The first 20 characters can only be exported.)

Parameters:

unitsP - The units of the data attached, e.g. "A^2" or "kJ/cm3"

getQueryCode

public String getQueryCode()

Gets the program code of the query option.

• mQ = marvin query
• MQ = MACCS-II query
• IQ = ISIS query
• <P>Q = program name code query

Returns:

the string identifying a program for the query option.

setQueryCode

public void setQueryCode(String queryCodeP)

Sets the program code for the query option.

Parameters:

queryCodeP - the string identifying a program for the query option. mQ = marvin query, MQ = MACCS-II query, IQ = ISIS query, <P>Q = program name code query

getQueryOp

public String getQueryOp()

Gets the data query operator.

Returns:

One of the following: "<", ">", "<=", ">=", "<>", "between", "like", "contains", "=" or null if not set.

setQueryOp

public void setQueryOp(String queryOpP)

Sets the data query operator.

Parameters:

queryOpP - One of the following: "<", ">", "<=", ">=", "<>", "between", "like", "contains", "=" or null if not set.

getX

public double getX()

Gets the X coordinate. This is the label coordinate in case of absolute placement, translation vector coordinate in case of relative placement.

Returns:

The X coordinate in Angstroms.

setX

public void setX(double x)

Sets the X coordinate. This is the label coordinate in case of absolute placement, translation vector coordinate in case of relative placement.

Parameters:

x - The X coordinate in Angstroms.

getY

public double getY()

Gets the Y coordinate. This is the label coordinate in case of absolute placement, translation vector coordinate in case of relative placement.

Returns:

The Y coordinate in Angstroms.

setY

public void setY(double y)

Sets the Y coordinate. This is the label coordinate in case of absolute placement, translation vector coordinate in case of relative placement.

Parameters:

y - The Y coordinate in Angstroms.

setAbsoluteXY

public void setAbsoluteXY(DPoint3 p)

Sets the X and Y coordinates of the data label in the molecule's coordinate system, considering absolute/relative placement.

Parameters:

p - the absolute coordinates.

See Also:

getX(), getY(), isAbsolutePlacement()

setAbsoluteXY

public void setAbsoluteXY(double x,
                 double y)

Sets the X and Y coordinates of the data label in the molecule's coordinate system, considering absolute/relative placement.

Parameters:

x - X absolute coordinate.

y - Y absolute coordinate.

See Also:

getX(), getY(), isAbsolutePlacement()

getAbsoluteXY

public DPoint3 getAbsoluteXY()

Gets the X and Y coordinates of the data label in the molecule's coordinate system, considering absolute/relative placement.

Returns:

the absolute coordinates.

See Also:

getX(), getY(), isAbsolutePlacement()

getPlacementOrigin

public void getPlacementOrigin(DPoint3 p)

If isAbsolutePlacement is false it calculates the middle point of the coordinates of atoms this S-group is associated to. The top right reference point of the parent S-group's bracket is used in the case of empty S-groups as placement of origin. Otherwise it returns an all-zero vector.

Parameters:

p - This point will contain the calculated X and Y coordinates.

See Also:

getObjectsMiddle(chemaxon.struc.DPoint3)

getObjectsMiddle

public void getObjectsMiddle(DPoint3 p)

Calculates the middle point of the coordinates of objects this sgroup is associated to.

Parameters:

p - This point will contain the calculated X and Y coordinates.

isDataDetached

public boolean isDataDetached()

Gets whether the data should be displayed close to the objects or separately (detached).

Returns:

True if the data is detached.

setDataDetached

public void setDataDetached(boolean b)

Sets whether the data should be displayed close to the objects or separately (detached).

Parameters:

b - true if the data is detached.

isUnitDisplayed

public boolean isUnitDisplayed()

Gets whether the units string should be displayed.

Returns:

True if the units string is displayed.

setUnitDisplayed

public void setUnitDisplayed(boolean b)

Sets whether the units string should be displayed. (Default is false.)

Parameters:

b - True if the units string should be displayed.

isAbsolutePlacement

public boolean isAbsolutePlacement()

Gets whether the placement of this attached data is absolute or relative to the objects it is attached.

Returns:

true when getX() and getY() coordinates refer to absolute placement.

setAbsolutePlacement

public void setAbsolutePlacement(boolean b)

Sets whether the placement of this attached data is absolute or relative to the objects it is attached. It does not modifies the coordinates, just changes the interpretation.

Parameters:

b - true when getX() and getY() coordinates should refer to absolute placement.

getDisplayedChars

public int getDisplayedChars()

Gets the number of characters to be displayed(1...999 or 0 for all)

Returns:

Gets the number of characters to display per line

setDisplayedChars

public void setDisplayedChars(int chars)

Sets the number of characters to be displayed (1...999 or 0 for no restriction)

Parameters:

chars - the number of characters to display per line

getDisplayedLines

public int getDisplayedLines()

Gets the number of lines to be displayed (0: show all)

Returns:

The number of lines to be displayed.

setDisplayedLines

public void setDisplayedLines(int lines)

Sets the number of lines to be displayed (0: show all)

Parameters:

lines - The number of lines to be displayed. 0 means to show all, -1 hides the data, and -2(HIDDEN) hides bracket highlighting as well.

See Also:

HIDDEN

getTag

public char getTag()

Gets the tag character for footnote display (or space if blank).

Returns:

The caracter to use in the footnote for the attached data.

setTag

public void setTag(char c)

Sets the tag character for the footnote display.

Parameters:

c - The character to use in the footnote or space to clear.

getPos

public int getPos()

Gets the data display DASP position (0...9). (MACCS)

Returns:

The above position number (1-9 or 0 if not set.)

setPos

public void setPos(int p)

Sets the data display DASP position (0...9). (MACCS)

Parameters:

p - The position number to be set (1-9) or 0 if not set.

getData

public String getData()

Gets the data value to be set. Can be multiline: '\n' characters separate lines.

Returns:

The value of the attached data.

setData

public void setData(String s)

Sets the data value to be set.

Parameters:

s - The value of the attached data. Can be multiline: '\n' characters separate lines.

getDataLineCount

public int getDataLineCount()

Gets the number of data lines.

getDataLine

public String getDataLine(int i)

Gets a line of data.

Parameters:

i - line index

setDataLine

public void setDataLine(int i,
               String line)

Sets a line of data.

Parameters:

i - line index

addDataLine

public void addDataLine(String line)

Adds a line to the data stored in the field.

Parameters:

line - Next line to add.

getLineOnScreen

public String getLineOnScreen(int i)

Returns the i-th row of the data sgroup label, as displayed on the screen (with tag, query operator, units etc.)

Parameters:

i - number of line

hasBrackets

public boolean hasBrackets()

Brackets are painted if mouse runs over sgroup atoms.

Overrides:

hasBrackets in class Sgroup

Returns:

always true in the default implementation

getSubscript

public String getSubscript()

Gets the subscript for non-superatom S-groups.

Overrides:

getSubscript in class Sgroup

Returns:

the subscript

transformByParent

protected void transformByParent(CTransform3D t,
                     boolean incg)

Applies a transformation matrix to the Data Sgroup coordinates. (Only absolute placement.) This method is called by the parent molecule's Molecule.transform(CTransform3D, boolean) method, thus only those atom coordinates are transformed here that are not handled in MoleculeGraph.transform(CTransform3D, boolean).

Overrides:

transformByParent in class Sgroup

Parameters:

t - the transformation matrix

incg - graph invariants are changed (true) or not (false)

Since:

Marvin 4.0.2, 10/26/2005