net.maizegenetics.dna.map

Class GenomeFeatureBuilder

java.lang.Object

net.maizegenetics.dna.map.GenomeFeatureBuilder

public class GenomeFeatureBuilder
extends Object

Created by jgw87 on 7/2/14. Builder class to create a GenomeFeature. All annoations are stored in a HashMap. Any annotation can be added through the addAnnotation() method, but the more common fields have their own convenience methods. Only the feature's own ID is required; all other annotations are optional

Constructor Summary

Constructors

Constructor and Description
GenomeFeatureBuilder() Generic constructor which does nothing special
GenomeFeatureBuilder(GenomeFeature feature) Constructor to build a new feature off of an existing one.

Method Summary

Modifier and Type	Method and Description
GenomeFeatureBuilder	addAnnotation(String key, String value)
GenomeFeature	build() Public accessor method to get a new GenomeFeatureBuilder based off an existing GenomeFeature TODO: Get this matching other getInstance methods better; doesn't seem to fit, so commented out for now //@param feature //@return
GenomeFeatureBuilder	chromosome(Chromosome chr)
GenomeFeatureBuilder	chromosome(int chr)
GenomeFeatureBuilder	chromosome(String chr)
static String	getFeatureIdFromGffAttributes(String attributes) Parse a GFF attribute field to identify the name of the current GenomeFeature.
static String	getParentFromGffAttributes(String attributes) Parse a GFF attribute field to identify the parent of the current GenomeFeature.
GenomeFeatureBuilder	id(String id)
GenomeFeatureBuilder	loadAll(HashMap<String,String> newAnnotations) Load all annotations from a hashmap.
GenomeFeatureBuilder	parentId(String parentId)
GenomeFeatureBuilder	parseGffLine(String line) Create a GenomeFeature from a line of GFF file.
GenomeFeatureBuilder	parseJsonObject(org.json.simple.JSONObject featureData)
GenomeFeatureBuilder	position(int position)
GenomeFeatureBuilder	position(String position)
GenomeFeatureBuilder	start(int start)
GenomeFeatureBuilder	start(String start)
GenomeFeatureBuilder	stop(int stop)
GenomeFeatureBuilder	stop(String stop)
static String	synonymizeKeys(String key) Method that takes common synonyms of annotation types and standardizes them according to the following rules: (1) Make lowercase (2) Standardize according to following rules.
GenomeFeatureBuilder	type(String type)

Methods inherited from class java.lang.Object

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

Constructor Detail

GenomeFeatureBuilder

public GenomeFeatureBuilder()

Generic constructor which does nothing special

GenomeFeatureBuilder

public GenomeFeatureBuilder(GenomeFeature feature)

Constructor to build a new feature off of an existing one.

Parameters:

feature - The genome feature to copy

Method Detail

build

public GenomeFeature build()

Public accessor method to get a new GenomeFeatureBuilder based off an existing GenomeFeature TODO: Get this matching other getInstance methods better; doesn't seem to fit, so commented out for now //@param feature //@return

id

public GenomeFeatureBuilder id(String id)

type

public GenomeFeatureBuilder type(String type)

parentId

public GenomeFeatureBuilder parentId(String parentId)

chromosome

public GenomeFeatureBuilder chromosome(Chromosome chr)

chromosome

public GenomeFeatureBuilder chromosome(String chr)

chromosome

public GenomeFeatureBuilder chromosome(int chr)

start

public GenomeFeatureBuilder start(int start)

start

public GenomeFeatureBuilder start(String start)

stop

public GenomeFeatureBuilder stop(int stop)

stop

public GenomeFeatureBuilder stop(String stop)

position

public GenomeFeatureBuilder position(String position)

position

public GenomeFeatureBuilder position(int position)

addAnnotation

public GenomeFeatureBuilder addAnnotation(String key,
                                          String value)

synonymizeKeys

public static String synonymizeKeys(String key)

Method that takes common synonyms of annotation types and standardizes them according to the following rules: (1) Make lowercase (2) Standardize according to following rules. (Any not on this list are returned as just lowercased) name, id -> id chr, chrom, chromosome -> chromosome stop, end -> stop parentid, parent_id, parent -> parent_id pos, position -> position

Parameters:

key - The key to standardize

Returns:

loadAll

public GenomeFeatureBuilder loadAll(HashMap<String,String> newAnnotations)

Load all annotations from a hashmap. Keys become the annotations, and values the annotation value. Each key-value pair is added individually (instead of using a putAll() method) to allow for key standardization, etc.

Returns:

This builder, with the new data loaded from the hashmap

parseGffLine

public GenomeFeatureBuilder parseGffLine(String line)

Create a GenomeFeature from a line of GFF file. This method is modified from the BioJava source code for the same purpose, in biojava3-genome/src/main/java/org/biojava3/genome/GFF3Reader.java

Parameters:

line - A single line from a GFF file as a string

Returns:

This builder, with the data loaded from the line

getParentFromGffAttributes

public static String getParentFromGffAttributes(String attributes)

Parse a GFF attribute field to identify the parent of the current GenomeFeature. Tricky b/c of the different ways it can be represented. There's a hierarchy of accepted answers, with 'parent_id', 'Parent=', 'transcript_id', and 'gene_id' taken in that order. If nothing is found, returns an empty string ("")

Parameters:

attributes - The string from the attribute field of the GFF file

Returns:

The parent's ID string

getFeatureIdFromGffAttributes

public static String getFeatureIdFromGffAttributes(String attributes)

Parse a GFF attribute field to identify the name of the current GenomeFeature. Looks for 'ID=' and 'Name=' fields

Parameters:

attributes - The string from the attribute field of the GFF file. REturns null if not found

Returns:

The feature's ID string

parseJsonObject

public GenomeFeatureBuilder parseJsonObject(org.json.simple.JSONObject featureData)