com.chemaxon.overlap.cli.util

Class Imports

java.lang.Object

com.chemaxon.overlap.cli.util.Imports

public final class Imports
extends Object

Utilities for importing data for searching.

Method Summary

Modifier and Type	Method and Description
static Optional<Function<StructureRecord,String>>	createIdExtractorWhenSpecified(boolean idName, String idPropOrNull) Create an ID extractor when specified.
static Optional<Iterable<Supplier<InputStream>>>	fromCliArgsOptional(String bothMsg, List<String> inlineArgs, String location) Create InputStream for inline and location specifications.
static Iterable<Supplier<InputStream>>	fromCliArgsPresent(String noneMsg, String bothMsg, List<String> inlineArgs, String location) Create InputStream for inline and location specifications.
static DescriptorsWithIds	generateDescriptors(OverlapAnalysisContext context, Iterable<Supplier<InputStream>> inputs, boolean idName, String idPropOrNull, Supplier<SubProgressObserver> po, ExecutorService ex) Generate descriptors.
static DescriptorsWithMols	generateDescriptorsWithMols(OverlapAnalysisContext context, Iterable<Supplier<InputStream>> inputs, boolean idName, String idPropOrNull, Map<String,PropertyExtractor> additionalPropertiesOrNull, SubProgressObserver po, ExecutorService ex) Generate descriptors, store molecules.
static InputStream	inputStreamFromLocationWithIae(String location) Delegate CmdlineUtils.inputStreamFromLocation(java.lang.String, boolean) with no checked exceptions.
static InputStream	inputStreamFromLocationWithIae(String location, boolean autoGzip) Delegate CmdlineUtils.inputStreamFromLocation(java.lang.String, boolean) with no checked exceptions.
static DescriptorsWithIds	parseCustomDescriptors(OverlapAnalysisContext context, Iterable<Supplier<InputStream>> inputs, String idSplitter, String descSplitter, Supplier<SubProgressObserver> po, ExecutorService ex) Parse custom descriptors.
static DescriptorsWithIds	readSerializedStorages(String descriptors, String ids, Supplier<SubProgressObserver> descpo, Supplier<SubProgressObserver> idpo) Read serialized descriptors and optionally IDs from locations.

Methods inherited from class java.lang.Object

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

Method Detail

inputStreamFromLocationWithIae

public static InputStream inputStreamFromLocationWithIae(String location,
                                                         boolean autoGzip)

Delegate CmdlineUtils.inputStreamFromLocation(java.lang.String, boolean) with no checked exceptions.

Parameters:

location - Location to open

autoGzip - Use{CmdlineUtils.autoGzip(java.io.InputStream)

Returns:

Input stream

Throws:

IllegalArgumentException - from delegated method's IOException.

inputStreamFromLocationWithIae

public static InputStream inputStreamFromLocationWithIae(String location)

Delegate CmdlineUtils.inputStreamFromLocation(java.lang.String, boolean) with no checked exceptions.

Parameters:

location - Location to open

Returns:

Input stream

Throws:

IllegalArgumentException - from delegated method's IOException.

fromCliArgsPresent

@Beta
public static Iterable<Supplier<InputStream>> fromCliArgsPresent(String noneMsg,
                                                                       String bothMsg,
                                                                       List<String> inlineArgs,
                                                                       String location)

Create InputStream for inline and location specifications.

Parameters:

noneMsg - Error message when none of the input sources are specified

bothMsg - Error message when both input sources are specified

inlineArgs - Inline arguments, each will be represented as a separate InputStream

location - Location of input

Returns:

Inputs

Throws:

IllegalArgumentException - when none or both inlines and locations are specified

fromCliArgsOptional

@Beta
public static Optional<Iterable<Supplier<InputStream>>> fromCliArgsOptional(String bothMsg,
                                                                                  List<String> inlineArgs,
                                                                                  String location)

Create InputStream for inline and location specifications.

Parameters:

bothMsg - Error message when both input sources are specified

inlineArgs - Inline arguments, each will be represented as a separate InputStream

location - Location of input

Returns:

Inputs when specified

Throws:

IllegalArgumentException - when both inlines and locations are specified

createIdExtractorWhenSpecified

public static Optional<Function<StructureRecord,String>> createIdExtractorWhenSpecified(boolean idName,
                                                                                        String idPropOrNull)

Create an ID extractor when specified.

Parameters:

idName - Use Molecule name when true

idPropOrNull - SD property to use as IDs when not null

Returns:

ID extractor specification

generateDescriptorsWithMols

public static DescriptorsWithMols generateDescriptorsWithMols(OverlapAnalysisContext context,
                                                              Iterable<Supplier<InputStream>> inputs,
                                                              boolean idName,
                                                              String idPropOrNull,
                                                              Map<String,PropertyExtractor> additionalPropertiesOrNull,
                                                              SubProgressObserver po,
                                                              ExecutorService ex)
                                                       throws IOException

Generate descriptors, store molecules.

Parameters:

context - Context to use

inputs - Inputs to read from

idName - Use Molecule name when true

idPropOrNull - SD property to use as IDs when not null

additionalPropertiesOrNull - Additional properties to store

po - Progress observer to track execution

ex - ExecutorService for concurrent execution

Returns:

Parsed molecules, generated descriptors

Throws:

IOException - propagated

generateDescriptors

public static DescriptorsWithIds generateDescriptors(OverlapAnalysisContext context,
                                                     Iterable<Supplier<InputStream>> inputs,
                                                     boolean idName,
                                                     String idPropOrNull,
                                                     Supplier<SubProgressObserver> po,
                                                     ExecutorService ex)
                                              throws IOException

Generate descriptors.

Parameters:

context - Context to use

inputs - Inputs to read from

idName - Use Molecule name when true

idPropOrNull - SD property to use as IDs when not null

po - Progress observer to track execution

ex - ExecutorService for concurrent execution

Returns:

Parsed descriptors

Throws:

IOException

parseCustomDescriptors

public static DescriptorsWithIds parseCustomDescriptors(OverlapAnalysisContext context,
                                                        Iterable<Supplier<InputStream>> inputs,
                                                        String idSplitter,
                                                        String descSplitter,
                                                        Supplier<SubProgressObserver> po,
                                                        ExecutorService ex)
                                                 throws IOException

Parse custom descriptors.

Parameters:

context - Context to use

inputs - Inputs to read from

idSplitter - Splitter for IDs or null

descSplitter - Splitter for the descriptors part; required

po - Progress observer to track execution

ex - ExecutorService to track execution

Returns:

Parsed custom descriptors

Throws:

IOException - propagated

readSerializedStorages

public static DescriptorsWithIds readSerializedStorages(String descriptors,
                                                        String ids,
                                                        Supplier<SubProgressObserver> descpo,
                                                        Supplier<SubProgressObserver> idpo)
                                                 throws IOException,
                                                        ClassNotFoundException

Read serialized descriptors and optionally IDs from locations.

Parameters:

descriptors - Location for serialized descriptors storage

ids - Optional location of serialized ID storage or null. When null passed a default ID store will be used

descpo - Supplier for ProgressObserver for descriptor deserialization. Method Supplier.get() will be invoked before deserialization, exactly once

idpo - Supplier for ProgressObserver for ID storage deserialization. Method will be invoked when ID store is presented, just before ID storage deserializtion. storage is allocated returning indices.

Returns:

deserialized storages

Throws:

ClassNotFoundException - propagated from SerializationUtil.expect(java.lang.Class, java.io.ObjectInputStream, com.chemaxon.calculations.common.SubProgressObserver)

IOException - propagated