| Name | Description | Type | Package | Framework |
| StockholmFileAnnotation | Stores all the content parsed from the #=GF linesSince:3. | Class | org.biojava.nbio.alignment.io | BioJava |
| StockholmFileAnnotation .StockholmFileAnnotationReference | Class | org.biojava.nbio.alignment.io | BioJava | |
| StockholmFileParser | Stockholm file parser. | Class | org.biojava.nbio.alignment.io | BioJava |
| StockholmStructure | Stores all the content of a Stockholm file. | Class | org.biojava.nbio.alignment.io | BioJava |
| StockholmStructure .DatabaseReference | Class | org.biojava.nbio.alignment.io | BioJava | |