Align

class Align
extends java.lang.Object

Utility for helping to perform alignments with BioJava Simple usage of the form:

 Align.global('AATTAATTAA','AATTCATAA').profile
 AATTAATTAA
 AATTCAT-AA

Or for a more readable base by base comparison, use profile:

 Align.profile('AATTAATTAA','AATTCATAA')
 AATTAATTAA
     |     
 AATTCAT-AA

Properties
Type	Name and description
`static java.util.Map`	`ALIGNMENT_DEFAULTS`
`static org.biojava.nbio.core.sequence.location.template.Location`	`l`

Constructors
Constructor and description
`Align ()`

Methods
Type Params	Return Type	Name and description
	`static org.biojava.nbio.alignment.template.Aligner`	`global(java.lang.String queryString, java.lang.String referenceString)` Returns a BioJava aligner with profile computed.
	`static org.biojava.nbio.alignment.template.Aligner`	`global(java.util.Map params, java.lang.String queryString, java.lang.String referenceString)` Returns a BioJava aligner with profile computed.
	`static java.lang.String`	`profile(java.lang.String queryString, java.lang.String referenceString)` Returns a formatted string representing the comparison between the two sequences with '-' representing gaps and '\|' joining mismatches.

Inherited Methods
Methods inherited from class	Name
`class java.lang.Object`	`java.lang.Object#wait(long), java.lang.Object#wait(long, int), java.lang.Object#wait(), java.lang.Object#equals(java.lang.Object), java.lang.Object#toString(), java.lang.Object#hashCode(), java.lang.Object#getClass(), java.lang.Object#notify(), java.lang.Object#notifyAll()`

Groovy Documentation

[Groovy] Class Align