com.chemaxon.overlap.wui.res

Class MolsRes

java.lang.Object

com.chemaxon.overlap.wui.res.MolsRes

All Implemented Interfaces:

Described, HasSizeinfo

public class MolsRes
extends Object
implements Described, HasSizeinfo

Implementation for mols.

Constructor Summary

Constructors

Constructor and Description
MolsRes(String description, long time, MasterMoleculeStorage mms, MasterStorage<String> id, Map<String,MolProp<?>> propsOrNull) Construct.

Method Summary

Modifier and Type	Method and Description
int	findId(String id_to_find) Find ID.
String	forceSmilesWithId(int index)
static byte[]	generatePlaceholderPng(int w, int h) Generate a placeholder image.
Set<String>	getAllPropNames() Return all property names.
String	getDescription() Human readable description of the instance.
Optional<String>	getId(int index) Get ID.
Optional<Molecule>	getMol(int index) Get molecule.
MoleculeInfo	getMolInfo(String setUrl, int index, boolean smiles) Fill single molecule info.
MoleculeInfo	getMolInfo(String setUrl, int index, boolean smiles, boolean props) Fill single molecule info.
Optional<byte[]>	getPng(int index, int w, int h) Get PNG of molecule if present.
Optional<byte[]>	getPng(int index, Sink<Molecule> preprocessOrNull, int w, int h) Get PNG of molecule if present.
MolProp<?>	getProp(String name) Get an additional property container.
MoleculeSetInfo	getSetInfo(String setUrl, String setName) Fill molecule set info.
long	getSize() Size of the represented resource.
SizeInfoDto	getSizeInfo(Function<Object,Long> sizeof, Function<Object,Long> sizeof2) Invoke size calculation.
Optional<String>	getSmiles(int index) Get SMILES source.
long	getTime() Init/load/prepare time of the represented resource.
int	size() Size of storages.

Methods inherited from class java.lang.Object

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

Constructor Detail

MolsRes

public MolsRes(String description,
               long time,
               MasterMoleculeStorage mms,
               MasterStorage<String> id,
               Map<String,MolProp<?>> propsOrNull)

Construct.

Parameters:

description - Description of the current instance

time - Associated init/create/load time

mms - Exposed master molecule storage

id - Exposed master ID storage

propsOrNull - Additional properties or null

Method Detail

getSizeInfo

public SizeInfoDto getSizeInfo(Function<Object,Long> sizeof,
                               Function<Object,Long> sizeof2)

Description copied from interface: HasSizeinfo

Invoke size calculation.

Specified by:

getSizeInfo in interface HasSizeinfo

Parameters:

sizeof - Function for deep size calculation, expected to handle NoSize annotations.

sizeof2 - Function for deep size calculation of the large storages

Returns:

Size description

size

public int size()

Size of storages.

Returns:

Size

getAllPropNames

public Set<String> getAllPropNames()

Return all property names.

Returns:

Property names

getProp

public MolProp<?> getProp(String name)

Get an additional property container.

Parameters:

name - Property name

Returns:

Property container or null when the given property is not present

getId

public Optional<String> getId(int index)
                       throws WuiNotFoundException

Get ID.

Parameters:

index - Index

Returns:

Associated IDlua

Throws:

WuiNotFoundException

findId

public int findId(String id_to_find)
           throws WuiNotFoundException

Find ID.

Parameters:

id_to_find - ID to find

Returns:

Index of the found ID

Throws:

WuiNotFoundException - When ID not found

getMol

public Optional<Molecule> getMol(int index)

Get molecule.

Parameters:

index - Index

Returns:

Molecule

getSmiles

public Optional<String> getSmiles(int index)

Get SMILES source.

Parameters:

index - Index

Returns:

Smiles source when present

generatePlaceholderPng

public static byte[] generatePlaceholderPng(int w,
                                            int h)

Generate a placeholder image.

Parameters:

w - Image width

h - Image height

getPng

public Optional<byte[]> getPng(int index,
                               Sink<Molecule> preprocessOrNull,
                               int w,
                               int h)

Get PNG of molecule if present.

Parameters:

index - Molecule index

preprocessOrNull - Optional preprocess of the sturcture

w - Image width

h - Image height

Returns:

Image if molecule is present

getPng

public Optional<byte[]> getPng(int index,
                               int w,
                               int h)

Get PNG of molecule if present.

Parameters:

index - Molecule index

w - Image width

h - Image height

Returns:

Image if molecule is present

forceSmilesWithId

public String forceSmilesWithId(int index)
                         throws WuiNotFoundException

Throws:

WuiNotFoundException

getDescription

public String getDescription()

Description copied from interface: Described

Human readable description of the instance.

Specified by:

getDescription in interface Described

Returns:

description

getSetInfo

public MoleculeSetInfo getSetInfo(String setUrl,
                                  String setName)

Fill molecule set info.

Parameters:

setUrl - URL of this molecule set resource.

setName - Name of this molecule set resource.

Returns:

Set info

getMolInfo

public MoleculeInfo getMolInfo(String setUrl,
                               int index,
                               boolean smiles)
                        throws WuiNotFoundException

Fill single molecule info.

Parameters:

setUrl - URL of this molecule set resource

index - Index of the structure

smiles - If false no smiles lookup will be made

Returns:

Single molecule info

Throws:

WuiNotFoundException

getMolInfo

public MoleculeInfo getMolInfo(String setUrl,
                               int index,
                               boolean smiles,
                               boolean props)
                        throws WuiNotFoundException

Fill single molecule info.

Parameters:

setUrl - URL of this molecule set resource

index - Index of the structure

smiles - If false no smiles lookup will be made

props - If no properties will be included

Returns:

Single molecule info

Throws:

WuiNotFoundException

getSize

public long getSize()

Description copied from interface: Described

Size of the represented resource.

Specified by:

getSize in interface Described

Returns:

Size in units described by the associated ResourceInfo.sizeDescription()

getTime

public long getTime()

Description copied from interface: Described

Init/load/prepare time of the represented resource.

Specified by:

getTime in interface Described

Returns:

Associated time