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| Interface Summary | |
| GeneProductPredictor | |
| ResidueExchangeMatrix | |
| ScoreEngine | Implemented by engines that calculate a score given two sequences. |
| TmPredictor | Engine to predict trans-membrane domains of protein sequences. |
| Class Summary | |
| AlignmentReader | Class to read the sequences in a two-sequence alignment, and then find pairs of residues that are conserved or switched between them. |
| cd2ps | This application reads a CustomizedDiagram in its serialized form and generates a PostScript file. |
| ChunkIterator | Uses MultiplePartFileIterator to split a file into chunks containing a predefined number of sections from the input file. |
| cleanAlignment | |
| CodonTable | |
| CommandLineOptions | Support for command line options a la UNIX. |
| CompareSeqSets | Scans a set of sequences, taken from a file, for potential TM segments. |
| DayhoffMatrix | |
| extract | Extracts a subsequence from chromosome long fasta sequence files. |
| FastaFormat | |
| FetchURL | This bean fetches the text document pointed to by an URL. |
| FragmentIdentityScoreEngine | |
| GenScan | This implementation wraps around GenScan. |
| GetCeleraSeq | Queries the Celera database for a sequence and writes it to a file. |
| Inspect | Inspect a class with the reflection API. |
| MotifFinder | |
| MultiplePartFileIterator | Divides a multiple XML BlastOutput into several single BlastResults. |
| MutationsToURLs | Converts mutation annotations to URL annotations (bean). |
| MutationToUrlConverter | Converts mutation annotations to URL annotations. |
| NCBISequences | Accesses NCBI formatted sequence databases. |
| NotAVisualBean | A bean which is not intended to represent anything graphic. |
| PhdHtmTM | Should Implements the TmPredictor interface. |
| RemoveHTMLTags | |
| ScanForTms | Scans a set of sequences, taken from a file, for potential TM segments. |
| SequenceChunkIterator | Uses MultiplePartFileIterator to split a file into chunks containing a predefined number of sections from the input file. |
| sid | Scans a set of sequences, taken from a file, for potential TM segments. |
| SimpleTM | Implements the TmPredictor interface. |
| smask | |
| SosuiResult | |
| splitfile | Command line tool to splits a file on lines beginning with boundary-prefix. |
| strim | |
| tidyHD | |
| tidySeq | |
| Exception Summary | |
| InvalidMotifException | |
| UnsupportedOrganism | |
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