chemaxon.util
Class HitDisplayTool

java.lang.Object
  chemaxon.util.HitDisplayTool

All Implemented Interfaces:

SearchConstants

public class HitDisplayTool

extends java.lang.Object

implements SearchConstants

Class for displaying hit results with hit coloring, alignment, partial clean, etc.

Since:

JChem 5.0

Author:

Szilard Dorant

Field Summary

Fields inherited from interface chemaxon.sss.SearchConstants

ABS_STEREO_ALWAYS_ON, ABS_STEREO_CHIRAL_FLAG, ABS_STEREO_TABLE_OPTION, CHARGE_MATCHING_DEFAULT, CHARGE_MATCHING_EXACT, CHARGE_MATCHING_IGNORE, DEFAULT_DISSIMILARITY_THRESHOLD, DEFAULT_SIMILARITY_THRESHOLD, DISSIMILARITY, EXACT, EXACT_FRAGMENT, EXACT_FRAGMENT_OFF, EXACT_FRAGMENT_ON, HCOUNT_MATCHING_AUTO, HCOUNT_MATCHING_EQUAL, HCOUNT_MATCHING_GREATER_OR_EQUAL, IMPLICIT_H_MATCHING_DEFAULT, IMPLICIT_H_MATCHING_DISABLED, IMPLICIT_H_MATCHING_ENABLED, ISOTOPE_MATCHING_DEFAULT, ISOTOPE_MATCHING_EXACT, ISOTOPE_MATCHING_IGNORE, KEEP_QUERY_ORDER, MARKUSH_AROM_FINAL_CHECK, MARKUSH_AROM_NO_FINAL_CHECK, MARKUSH_AROM_OFF, MARKUSH_DISABLED, MARKUSH_ENABLED, MARKUSH_HIT_ORIGINAL, MARKUSH_HIT_SUPERGRAPH, MATCH_COUNT_BETWEEN, MATCH_COUNT_RELATION, MIX_SGROUP_MATCHING_OFF, MIX_SGROUP_MATCHING_ON, NO_ABAS, NO_SCREEN, OPTION_CHARGE_MATCHING, OPTION_EXACT_FRAGMENT, OPTION_ISOTOPE_MATCHING, OPTION_KEEP_QUERY_ORDER, OPTION_MARKUSH_AROM, OPTION_MARKUSH_ENABLED, OPTION_MARKUSH_HIT, OPTION_MIX_SGROUP_MATCHING, OPTION_RADICAL_MATCHING, OPTION_STEREO_MODEL, OPTION_TAUTOMER_SEARCH, OPTION_VAGUE_BOND, OPTION_VALENCE_MATCHING, PERFECT, R_NODE_PLACEHOLDER, RADICAL_MATCHING_DEFAULT, RADICAL_MATCHING_EXACT, RADICAL_MATCHING_IGNORE, REARRANGE_QUERY, REGULAR_SEARCH, SEARCH_MODE_NAMES, SEARCH_OPTIONS_LENGTH, SIMILARITY, STEREO_MODEL_COMPREHENSIVE, STEREO_MODEL_DEFAULT, STEREO_MODEL_GLOBAL, STEREO_MODEL_LOCAL, SUBSTRUCTURE, SUPERSTRUCTURE, TAUTOMER_SEARCH_OFF, TAUTOMER_SEARCH_ON, VAGUE_BOND_DEFAULT, VAGUE_BOND_LEVEL1, VAGUE_BOND_LEVEL2, VAGUE_BOND_LEVEL3, VAGUE_BOND_LEVEL4, VAGUE_BOND_OFF, VALENCE_MATCHING_IGNORE, VALENCE_MATCHING_ON

Constructor Summary

HitDisplayTool(HitColoringAndAlignmentOptions options, MolSearchOptions searchOptions, Standardizer standardizer, Molecule query)
Constructor.

Method Summary

Molecule	getHit(Molecule target) Processes the next target structure.
java.util.ArrayList	getHitIndexes() Returns the hit indexes for the last target.
Molecule[]	getHits(Molecule target, chemaxon.enumeration.supergraph.Supergraph markushSupergraph, int maxHitCount) Processes the next target structure.

Methods inherited from class java.lang.Object

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

Constructor Detail

HitDisplayTool

public HitDisplayTool(HitColoringAndAlignmentOptions options,
                      MolSearchOptions searchOptions,
                      Standardizer standardizer,
                      Molecule query)

Constructor.

Parameters:

options - options for coloring and alignment

searchOptions - search options

standardizer - this Standardizer will be used during the search process, or null for only aromatization.

query - the query structure

Method Detail

getHit

public Molecule getHit(Molecule target)
                throws chemaxon.sss.search.SearchException,
                       chemaxon.enumeration.supergraph.SupergraphException

Processes the next target structure.

Parameters:

target - the target

Returns:

the structure to be displayed, or null if there was no hit

Throws:

chemaxon.sss.search.SearchException

chemaxon.enumeration.supergraph.SupergraphException

getHits

public Molecule[] getHits(Molecule target,
                          chemaxon.enumeration.supergraph.Supergraph markushSupergraph,
                          int maxHitCount)
                   throws chemaxon.sss.search.SearchException,
                          chemaxon.enumeration.supergraph.SupergraphException

Processes the next target structure.

Parameters:

target - the target

markushSupergraph - a standardized markush supergraph can be specified here if present, or null

maxHitCount - specify 0 to get back all the hits found, or an arbitrary limit.
Specify -1 to get back only a single hit, the best fitting is returned in case of alignment (default).

Returns:

the structures to be displayed, or a zero sized array if there were no hits

Throws:

chemaxon.sss.search.SearchException

chemaxon.enumeration.supergraph.SupergraphException

getHitIndexes

public java.util.ArrayList getHitIndexes()

Returns the hit indexes for the last target. Can be called after getHit(chemaxon.struc.Molecule) or getHits(chemaxon.struc.Molecule, chemaxon.enumeration.supergraph.Supergraph, int)

Returns:

the hit indexes in an ArrayList, containing int[] elements.