| Package | Description |
|---|---|
| com.compomics.software.dialogs | |
| com.compomics.util.experiment.biology |
This package contains experiement classes related to biological entities.
|
| com.compomics.util.experiment.identification |
This package contains experiment classes related to identifications.
|
| com.compomics.util.experiment.identification.tags | |
| com.compomics.util.gui.gene_mapping | |
| com.compomics.util.gui.searchsettings.algorithm_settings | |
| com.compomics.util.gui.spectrum |
This package contains GUI classes related to Spectrum and Chromatogram visualization.
|
| com.compomics.util.preferences | |
| com.compomics.util.preferences.gui |
| Class and Description |
|---|
| UtilitiesUserPreferences
Utilities user preferences will be serialized in the user folder and provide
useful information to all compomics software, well as soon as they use it of
course.
|
| Class and Description |
|---|
| ModificationProfile
This class stores the information about the modification preferences (colors,
names) used for the selected project.
|
| Class and Description |
|---|
| ModificationProfile
This class stores the information about the modification preferences (colors,
names) used for the selected project.
|
| Class and Description |
|---|
| ModificationProfile
This class stores the information about the modification preferences (colors,
names) used for the selected project.
|
| Class and Description |
|---|
| GenePreferences
Contains methods for downloading gene and GO mappings.
|
| Class and Description |
|---|
| ModificationProfile
This class stores the information about the modification preferences (colors,
names) used for the selected project.
|
| Class and Description |
|---|
| ModificationProfile
This class stores the information about the modification preferences (colors,
names) used for the selected project.
|
| Class and Description |
|---|
| GenePreferences
Contains methods for downloading gene and GO mappings.
|
| IdFilter
This class achieves a pre-filtering of the identifications for PeptideShaker.
|
| ModificationProfile
This class stores the information about the modification preferences (colors,
names) used for the selected project.
|
| UtilitiesPathPreferences.UtilitiesPathKey
Enum of the paths which can be set in utilities.
|
| UtilitiesUserPreferences
Utilities user preferences will be serialized in the user folder and provide
useful information to all compomics software, well as soon as they use it of
course.
|
| Class and Description |
|---|
| IdFilter
This class achieves a pre-filtering of the identifications for PeptideShaker.
|
| ProcessingPreferences
This class groups the user preferences for the initial PeptideShaker
processing.
|
| PTMScoringPreferences
This class contains the PTM scoring preferences.
|
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