Package com.chemaxon.calculations.cli

Class CalculatorPluginOutput<P extends CalculatorPlugin>

java.lang.Object

chemaxon.marvin.plugin.CalculatorPluginService<P>

com.chemaxon.calculations.cli.CalculatorPluginOutput<P>

All Implemented Interfaces:

com.chemaxon.calculations.cli.CalculatorResultAccess

Direct Known Subclasses:

CalculatorPluginOutput

@PublicAPI
public class CalculatorPluginOutput<P extends CalculatorPlugin>
extends CalculatorPluginService<P>
implements com.chemaxon.calculations.cli.CalculatorResultAccess

Class providing plugin output in table form. The default implementation provides the following output:

id	<type1>	<type2>	<type3>	...
<id1>	<result11>	<result12>	<result13>	...
<id2>	<result21>	<result22>	<result23>	...
...	...	...	...	...

where type1, type2, ... are the result types, id1, id2, ... are the molecule ID-s fetched from the given ID tag of the input SDF file or molecule indices if no such tag is given, the resultij is the result string for the i-th molecule and the j-th result type. Other output formats can be implemented by subclassing this class and returning the class name in the plugin-specific implementation of chemaxon.plugin.CalculatorPlugin.getOutputClassName().

Since:

Marvin 3.0

Field Summary

Fields

Modifier and Type	Field	Description
protected Properties	params	The plugin parameter table.
protected P	plugin	The CalculatorPlugin object.
protected String	separator	The separator string separating the results for different result types.

Constructor Summary

Constructors

Constructor	Description
CalculatorPluginOutput()	Default constructor.
CalculatorPluginOutput(CalculatorPlugin plugin)	Constructor that sets plugin.

Method Summary

Modifier and Type	Method	Description
void	close()	Closes the output.
void	close(int opts)	Closes the output.
com.chemaxon.calculations.cli.CalculatorPluginCachedResults	getCachedResults(Molecule target, boolean stringResult)	Returns cached results, separated from the plugin object, so that no further enqueries needed to the plugin to get the result.
String	getHeader()	Returns the table header.
P	getPlugin()	Returns the calculator plugin object.
Properties	getPluginParameters()	Returns the plugin parameter table (this should be set in the plugin).
String	getRemark()	Returns the calculation remark.
String	getResult(Molecule target)	Returns the result string for the given molecule.
int	getResultDomain()	Returns the domain for the first result type.
String	getResultMessage()	Returns the plugin calculation error message, error or warning.
Molecule	getResultMolecule(Molecule target)	Returns the decorated result molecule for the given target molecule.
Molecule[]	getResultMolecules(Molecule target)	Returns the result molecules for the given target molecule.
protected String	getResults(Object type)	Returns result items for the given result type.
double	getSpecResult(Molecule target, String arg)	Returns a specific plugin result corresponding to the given molecule and argument string.
Throwable	getThrowable()	Returns the throwable object.
boolean	isMolecular()	Returns true if molecule output.
boolean	isOK()	Returns true if the calculation has run without error.
boolean	isStreamOutput()	Returns true if stream output.
void	setOutputParameters(Object[] types)	Prepares the output based on the result type string.
void	setOutputStream(OutputStream os)	Sets the output stream.
void	setParameters(Properties params)	Sets the parameter table.
void	setPlugin(CalculatorPlugin plugin)	Deprecated. use setPluginChecked(CalculatorPlugin) instead
void	setPluginChecked(P plugin)	Sets the calculator plugin object.
void	setSeparator(String separator)	Sets the separator string.
void	setThrowable(Throwable throwable)	Sets the throwable object.

Methods inherited from class java.lang.Object

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

Field Detail

plugin

protected P extends CalculatorPlugin plugin

The CalculatorPlugin object.

params

protected Properties params

The plugin parameter table.

separator

protected String separator

The separator string separating the results for different result types.

Constructor Detail

CalculatorPluginOutput

public CalculatorPluginOutput()

Default constructor.

CalculatorPluginOutput

public CalculatorPluginOutput(CalculatorPlugin plugin)

Constructor that sets plugin.

Parameters:

plugin - is the plugin

Method Detail

setPlugin

@Deprecated
public final void setPlugin(CalculatorPlugin plugin)

Deprecated.

use setPluginChecked(CalculatorPlugin) instead

Sets the calculator plugin object.

Parameters:

plugin - is the CalculatorPlugin object

setPluginChecked

public final void setPluginChecked(P plugin)

Sets the calculator plugin object.

Parameters:

plugin - is the CalculatorPlugin object

getPlugin

public final P getPlugin()

Description copied from class: CalculatorPluginService

Returns the calculator plugin object.

Specified by:

getPlugin in class CalculatorPluginService<P extends CalculatorPlugin>

Returns:

the calculator plugin object

setThrowable

public final void setThrowable(Throwable throwable)

Sets the throwable object.

Parameters:

throwable - is the CalculatorPlugin object

getThrowable

public final Throwable getThrowable()

Returns the throwable object.

Specified by:

getThrowable in interface com.chemaxon.calculations.cli.CalculatorResultAccess

Returns:

the throwable plugin object

setSeparator

public void setSeparator(String separator)

Sets the separator string.

Parameters:

separator - is the separator string

setParameters

public void setParameters(Properties params)
                   throws PluginException

Sets the parameter table.

Parameters:

params - is the parameter table

Throws:

PluginException - on error

getPluginParameters

public Properties getPluginParameters()
                               throws PluginException

Returns the plugin parameter table (this should be set in the plugin). The default implementation returns the given parameter table itself.

Returns:

the original parameter table if it is the same, a new table with the plugin params otherwise

Throws:

PluginException - on error

setOutputParameters

public void setOutputParameters(Object[] types)
                         throws PluginException

Prepares the output based on the result type string. The default implementation does nothing.

Parameters:

types - the result types

Throws:

PluginException - on error

isMolecular

public boolean isMolecular()

Returns true if molecule output. The default implementation returns false.

Returns:

true if molecule output

isStreamOutput

public boolean isStreamOutput()

Returns true if stream output. The default implementation returns false.

Returns:

true if stream output

setOutputStream

public void setOutputStream(OutputStream os)
                     throws IOException

Sets the output stream. Used for molecule output. The default implementation does nothing.

Parameters:

os - the output stream

Throws:

IOException

close

public void close()
           throws IOException

Closes the output. The default implementation calls close(int) with MolExporter.C_CLOSE_STREAM parameter.

Throws:

IOException

close

public void close(int opts)
           throws IOException

Closes the output. The default implementation does nothing.

Parameters:

opts - closing options, MolExporter.C_CLOSE_STREAM or MolExporter.C_FLUSH_STREAM

Throws:

IOException

Since:

Marvin 5.1.1

getCachedResults

public final com.chemaxon.calculations.cli.CalculatorPluginCachedResults getCachedResults(Molecule target,
                                                                                          boolean stringResult)
                                                                                   throws PluginException

Returns cached results, separated from the plugin object, so that no further enqueries needed to the plugin to get the result.

Parameters:

target - the target molecule

stringResult - is true if string result is needed, false if decorated molecule is needed

Returns:

the cached results

Throws:

PluginException

Since:

Marvin 5.2

getResultMessage

public final String getResultMessage()

Returns the plugin calculation error message, error or warning.

Specified by:

getResultMessage in interface com.chemaxon.calculations.cli.CalculatorResultAccess

Returns:

the plugin calculation error message

getRemark

public String getRemark()

Returns the calculation remark.

Specified by:

getRemark in interface com.chemaxon.calculations.cli.CalculatorResultAccess

Returns:

the calculation remark

isOK

public boolean isOK()

Returns true if the calculation has run without error.

Specified by:

isOK in interface com.chemaxon.calculations.cli.CalculatorResultAccess

Returns:

true if the calculation has run without error

getHeader

public String getHeader()

Returns the table header. The default implementation returns "id" and the result types.

Specified by:

getHeader in interface com.chemaxon.calculations.cli.CalculatorResultAccess

Returns:

the table header

getResult

public String getResult(Molecule target)
                 throws PluginException

Returns the result string for the given molecule. The default implementation returns the result strings corresponding to the result types.

Specified by:

getResult in interface com.chemaxon.calculations.cli.CalculatorResultAccess

Parameters:

target - is the target molecule

Returns:

the result row

Throws:

PluginException - on error

getResults

protected String getResults(Object type)
                     throws PluginException

Returns result items for the given result type.

Parameters:

type - is the result type

Returns:

result items separated by ';'

Throws:

PluginException - on error

getResultMolecule

public Molecule getResultMolecule(Molecule target)
                           throws PluginException

Returns the decorated result molecule for the given target molecule. Used in case of MRV output (-M, --mrv-output).

Specified by:

getResultMolecule in interface com.chemaxon.calculations.cli.CalculatorResultAccess

Parameters:

target - is the target molecule

Returns:

the result molecule

Throws:

PluginException - on error

getResultMolecules

public Molecule[] getResultMolecules(Molecule target)
                              throws PluginException

Returns the result molecules for the given target molecule. The default implementation returns null.

Specified by:

getResultMolecules in interface com.chemaxon.calculations.cli.CalculatorResultAccess

Parameters:

target - is the target molecules

Returns:

the result molecules

Throws:

PluginException - on error

getResultDomain

public int getResultDomain()

Returns the domain for the first result type.

Returns:

the domain for the first result type: CalculatorPlugin.ATOM, CalculatorPlugin.MOLECULE or CalculatorPlugin.MOLECULES

getSpecResult

public double getSpecResult(Molecule target,
                            String arg)
                     throws PluginException

Returns a specific plugin result corresponding to the given molecule and argument string. The default implementation returns the result value returned by CalculatorPlugin.getResult(int index) (converted to double) with index given in the argument string: the argument string format is <result index>.

Parameters:

target - is the target molecule

arg - is the argument string

Returns:

the queried plugin result

Throws:

PluginException - in case of plugin calculation error