Class FASTABioSequenceReader

java.lang.Object
org.episteme.core.io.AbstractResourceReader<List<BioSequence>>
org.episteme.natural.biology.loaders.FASTABioSequenceReader
All Implemented Interfaces:
ResourceIO<List<BioSequence>>, ResourceReader<List<BioSequence>>
public class FASTABioSequenceReader extends AbstractResourceReader<List<BioSequence>>
Parser for FASTA format files.
Since:
1.0
Author:
Silvere Martin-Michiellot, Gemini AI (Google DeepMind)

  • Constructor Details

    • FASTABioSequenceReader

      public FASTABioSequenceReader()

  • Method Details

    • loadFromSource

      protected List<BioSequence> loadFromSource(String resourceId) throws Exception
      Specified by:
      loadFromSource in class AbstractResourceReader<List<BioSequence>>
      Throws:
      Exception

    • getResourcePath

      public String getResourcePath()
      Description copied from interface: ResourceIO
      Returns the base path where this resource is located.

    • getResourceType

      public Class<List<BioSequence>> getResourceType()
      Description copied from interface: ResourceIO
      Returns the type of resource.

    • getSupportedVersions

      public String[] getSupportedVersions()
      Description copied from interface: ResourceIO
      Returns the supported versions of the format this reader/writer handles.

      Each implementation MUST override this method to declare which versions of the underlying format are supported. The returned array should contain version strings in the format's standard notation (e.g., "3.0", "2.1", "Level 3 Version 2").

      Examples:

      • MathML: {"3.0", "2.0"}
      • SBML: {"Level 3 Version 2", "Level 3 Version 1", "Level 2 Version 5"}
      • PhyloXML: {"1.10", "1.00"}

      Returns:
      array of supported version strings, never null (empty array if version-agnostic)

    • parse

      public List<BioSequence> parse(InputStream inputStream) throws IOException
      Parses a FASTA input stream.
      Parameters:
      inputStream - the input stream containing FASTA data
      Returns:
      a list of BioSequence objects
      Throws:
      IOException - if an I/O error occurs

    • getCategory

      public String getCategory()
      Description copied from interface: ResourceIO
      Returns the category for grouping. MUST be implemented with I18N support.
      Returns:
      the category name

    • getName

      public String getName()
      Description copied from interface: ResourceIO
      Returns the display name of this resource handler. MUST be implemented with I18N support.
      Returns:
      the display name

    • getDescription

      public String getDescription()
      Description copied from interface: ResourceIO
      Returns a short description of this resource handler. MUST be implemented with I18N support.
      Returns:
      the description

    • getLongDescription

      public String getLongDescription()
      Description copied from interface: ResourceIO
      Returns a long description of this resource handler. MUST be implemented with I18N support.
      Returns:
      the long description