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| Class Summary | |
|---|---|
| AcrylamideHydrophobicityAdjuster | This class knows how to adjust normalized hydrophobicities based on the effect of acrylamide, vs. |
| AmtDatabase | A representation of a full AMT database. |
| AmtDatabaseBuilder | Builds AMT databases, in various ways If you want to build an AMT database in some other way, put a method in here to do it your way. |
| AmtDatabaseFeatureSetGenerator | This class Generates FeatureSets based on AMT Database entries. |
| AmtDatabaseManager | Manages AMT databases -- prunes outliers of various kinds |
| AmtDatabaseMatcher | This class performs simple matching between an AMT database and a feature files. |
| AmtDatabaseMatcher.PeptideProphetComparatorDesc | |
| AmtFeatureSetMatcherFactory | Creates instances of particular FeatureSetMatchers |
| AMTFileRestrictor | |
| AmtLabeledQuant | Methods for performing labeled quantitation on AMT data. |
| AmtMatchedProtein | Created by IntelliJ IDEA. |
| AmtMatchedProtein.AmtMatchedPeptide | |
| AmtMatchProbabilityAssigner | This class assigns a probability to every AMT match, based on the distribution of target and decoy mass and H errors. |
| AmtPeptideEntry | Encapsulates everything we need to retrieve from / store into an AMT database. |
| AmtPeptideEntry.AmtPeptideModificationStateEntry | Represents an entry for a specific modification state |
| AmtPeptideEntry.AmtPeptideObservation | Represents a single peptide observation. |
| AmtRunEntry | Encapsulates everything we need to retrieve from / store into an AMT database related to a run. |
| AmtTsvReader | A class for writing AMT TSV files. |
| AmtTsvReader.AmtTsvRow | Used by TabLoader to represent one row. |
| AmtUtilities | Utilities related to AMT |
| AmtUtilities.FeatureMassHydroClusterable | Clusterable for clustering based on feature mass and hydrophobicity. |
| AmtUtilities.FeatureMzHydroClusterable | Clusterable for clustering based on feature mz and hydrophobicity. |
| AmtXmlReader | A restrictive wrapper for reading AmtXml files. |
| AmtXmlWriter | A restrictive wrapper for writing AmtXml files. |
| HydrophobicityNormalizer | Converts hydrophobicity values from various algorithms to normalized values. |
| PeptideMatcher | |
| ProteinDisplay | Methods for HTML display of protein sequences. |
| ProteinMatcher | |
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