java.lang.Object
- org.intermine.bio.web.logic.GenomicRegionSearchUtil

```
public final class GenomicRegionSearchUtil
extends java.lang.Object
```
This utility class instance a GenomicRegionSearchService object based on mine's setting.

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method	Description
`static java.util.List<GenomicRegion>`	`createGenomicRegionsFromString(java.util.Collection<java.lang.String> regionStringList, java.lang.String organism, java.lang.Integer extendedRegionSize, java.lang.Boolean isInterBaseCoordinate)`	Create a list of GenomicRegion objects from a collection of region strings
`static java.util.Map<GenomicRegion,org.intermine.objectstore.query.Query>`	`createQueryList(java.util.Collection<GenomicRegion> genomicRegions, int extension, java.lang.String organismName, java.util.Set<java.lang.Class<?>> featureTypes, boolean strandSpecific)`	Create a list of queries from user regions.
`static java.util.Map<GenomicRegion,org.intermine.objectstore.query.Query>`	`createRegionListQueries(java.util.Collection<GenomicRegion> genomicRegions, int extension, java.util.Map<java.lang.String,ChromosomeInfo> chromInfo, java.lang.String organismName, java.util.Set<java.lang.Class<?>> featureTypes, boolean strandSpecific)`	Create a list of queries from user regions.
`static java.util.List<GenomicRegion>`	`generateGenomicRegions(java.util.Collection<java.lang.String> genomicRegionStringCollection)`	Generate a GenomicRegion object from region strings and relevant information
`static GenomicRegionSearchService`	`getGenomicRegionSearchService(javax.servlet.http.HttpServletRequest request)`	Generate GenomicRegionSearchService object by using Java reflection
`static java.util.List<GenomicRegion>`	`groupGenomicRegionByInterval(java.lang.String interval, java.util.Set<GenomicRegion> regionSet)`	Look for genomic regions within or overlap an interval.
`static GenomicRegion`	`parseRegion(java.lang.String span, boolean isInterbase, java.util.Map<java.lang.String,ChromosomeInfo> chromsForOrg)`	Parse region from string to GenomicRegion object

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

getGenomicRegionSearchService
```
public static GenomicRegionSearchService getGenomicRegionSearchService(javax.servlet.http.HttpServletRequest request)
```
Generate GenomicRegionSearchService object by using Java reflection

Parameters:

request - HttpServletRequest

Returns:

the current mine's GenomicRegionSearchService object

parseRegion

public static GenomicRegion parseRegion(java.lang.String span,
                                        boolean isInterbase,
                                        java.util.Map<java.lang.String,ChromosomeInfo> chromsForOrg)
                                 throws RegionParseException

Parse region from string to GenomicRegion object

Parameters:: span - a region string; isInterbase - 0/1-based; chromsForOrg - chr-organism info map
Returns:: GenomicRegion object
Throws:: RegionParseException - a RegionParseException

createQueryList

public static java.util.Map<GenomicRegion,org.intermine.objectstore.query.Query> createQueryList(java.util.Collection<GenomicRegion> genomicRegions,
                                                                                                       int extension,
                                                                                                       java.lang.String organismName,
                                                                                                       java.util.Set<java.lang.Class<?>> featureTypes,
                                                                                                       boolean strandSpecific)

Create a list of queries from user regions.

Parameters:: genomicRegions - list of gr; extension - the flanking; organismName - org short name; featureTypes - ft; strandSpecific - flag
Returns:: map of gr-query

createRegionListQueries

public static java.util.Map<GenomicRegion,org.intermine.objectstore.query.Query> createRegionListQueries(java.util.Collection<GenomicRegion> genomicRegions,
                                                                                                               int extension,
                                                                                                               java.util.Map<java.lang.String,ChromosomeInfo> chromInfo,
                                                                                                               java.lang.String organismName,
                                                                                                               java.util.Set<java.lang.Class<?>> featureTypes,
                                                                                                               boolean strandSpecific)

Create a list of queries from user regions.

Parameters:: genomicRegions - list of gr; extension - the flanking; chromInfo - chr info map; organismName - org short name; featureTypes - ft; strandSpecific - flag
Returns:: map of gr-query

generateGenomicRegions
```
public static java.util.List<GenomicRegion> generateGenomicRegions(java.util.Collection<java.lang.String> genomicRegionStringCollection)
                                                            throws java.lang.Exception
```
Generate a GenomicRegion object from region strings and relevant information

Parameters:

genomicRegionStringCollection - a list of string such as 2L:14615455..14619002|0|D. melanogaster or 2L:14615456..14619003|2L:14615455..14619002|1|D. melanogaster

Returns:

a GenomicRegion object

Throws:

java.lang.Exception - with error message

createGenomicRegionsFromString

public static java.util.List<GenomicRegion> createGenomicRegionsFromString(java.util.Collection<java.lang.String> regionStringList,
                                                                           java.lang.String organism,
                                                                           java.lang.Integer extendedRegionSize,
                                                                           java.lang.Boolean isInterBaseCoordinate)

Create a list of GenomicRegion objects from a collection of region strings

Parameters:: regionStringList - list of region strings; organism - short name; extendedRegionSize - flanking; isInterBaseCoordinate - inter base
Returns:: a list of GenomicRegion objects

groupGenomicRegionByInterval

public static java.util.List<GenomicRegion> groupGenomicRegionByInterval(java.lang.String interval,
                                                                         java.util.Set<GenomicRegion> regionSet)
                                                                  throws java.lang.Exception

Look for genomic regions within or overlap an interval.

Parameters:: interval - the given interval; regionSet - a set of regions
Returns:: a list of genomic region objects
Throws:: java.lang.Exception - with error message

Class GenomicRegionSearchUtil