JAnnot

JAnnot is a Java library to handle biological sequence data. It is underlying GenomeView. It makes sure that files, websites, data bases, etc. can be used by GenomeView. Since the functionality of reading, writing and parsing data has more applications that just GenomeView, JAnnot is available as a separate package.

Maven Dependency

You can use this from maven with the following dependency.

  <dependency>
	<groupId>net.sf</groupId>
	<artifactId>jannot</artifactId>
	<version>2.0.0</version> 
  </dependency>

and with the following repository

    <repositories>
        <repository>
            <id>artifactory.ewi.tudelft.nl</id>
            <url>https://artifactory.ewi.tudelft.nl/artifactory/libs-release</url>
            <snapshots>
                <enabled>false</enabled>
            </snapshots>
        </repository>
    </repositories>

Supported data types

JAnnot supports several data types:

Wiggle tracks

Wiggle tracks (continuous valued data), with some parsers and an internal representation

Multiple alignment data, with some parsers and internal representation

syntenic block representation