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| Interface Summary | |
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| AAIndexProvider | |
| Class Summary | |
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| AAindexFactory | Factory class to get Providers for substitution matrices the are provided by the AAINDEX database. |
| AAIndexFileParser | |
| DefaultAAIndexProvider | The default provider for AAINDEX loads substituion matrices from the AAINDEX file in the resources directory |
| ScaledSubstitutionMatrix | The biojava-alignment module represents substitution matrices with short values. |
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