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| Interface Summary | |
| ReaderType | ReaderType encapsulates the information about a sequence "file format". |
| SequenceReader | SequenceReader are used by a SequenceReaderFactory. |
| SequenceReaderFactory | Gives access to specialized Sequence readers. |
| Class Summary | |
| ExtendedSwissProtReader | An extended version of the SwissProtReader. |
| FastaReader | The fasta reader is very simple and cannot do a lot of error checking (because the FASTA format does not provide enough information to cross check). |
| FastaReaderType | |
| FortranOutputParser | Parses lines of fortran formated output. |
| PDBReader | The PDB Header Reader. |
| PDBReaderOrigin | |
| PDBReaderType | Describes the PDB reader for the sake of a GUI. |
| PIRReader | Reads BNRF/PIR files as Clustal outputs them. |
| PIRReaderType | |
| SequenceReaderFactoryImpl | This default implementation of SequenceReaderFactory allows to read sequence files in the following formats: FASTA/Pearson PIR SwissProt with some annotations PDB headers with SEQRES and with secondary structure annotations. |
| SeqUtils | Provides methods of common interest to this package, related to sequence operations. |
| SwissProtReader | The SwissProt Reader. |
| SwissProtReaderOrigin | |
| SwissProtReaderType | Information about the SwissProtReader. |
| Exception Summary | |
| InvalidFieldLimits | Thrown when the field limits were incorrectly specified. |
| SyntaxErrorException | |
| UnsupportedFileFormatException | |
| UnsupportedResidueType | |
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