Package | Description |
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com.compomics.util.experiment.biology |
This package contains experiement classes related to biological entities.
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com.compomics.util.experiment.identification |
This package contains experiment classes related to identifications.
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com.compomics.util.gui.spectrum |
This package contains GUI classes related to Spectrum and Chromatogram visualization.
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Modifier and Type | Method and Description |
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void |
PTMFactory.checkFixedModifications(ModificationProfile modificationProfile,
Peptide peptide)
Removes the fixed modifications of the peptide and remaps the one
searched for according to the ModificationProfile.
|
HashMap<Integer,ArrayList<String>> |
PTMFactory.getExpectedPTMs(ModificationProfile modificationProfile,
Peptide peptide,
double modificationMass,
double massTolerance)
Returns the expected modifications based on the modification profile, the
peptide found and the modification details.
|
HashMap<Integer,ArrayList<String>> |
PTMFactory.getExpectedPTMs(ModificationProfile modificationProfile,
Peptide peptide,
String ptmName)
Returns the names of the possibly expected modification based on the name
of the expected modification in a map where the PTM names are indexed by
their potential site on the sequence.
|
PTM |
PTMFactory.getPTM(ModificationProfile modificationProfile,
int index)
Get a PTM according to its OMSSA index.
|
String |
Peptide.getTaggedModifiedSequence(ModificationProfile modificationProfile,
boolean useHtmlColorCoding,
boolean includeHtmlStartEndTags,
boolean useShortName)
Returns the modified sequence as an tagged string with potential
modification sites color coded or with ptm tags, e.g, <mox>.
|
static String |
Peptide.getTaggedModifiedSequence(ModificationProfile modificationProfile,
Peptide peptide,
HashMap<Integer,ArrayList<String>> mainModificationSites,
HashMap<Integer,ArrayList<String>> secondaryModificationSites,
HashMap<Integer,ArrayList<String>> fixedModificationSites,
boolean useHtmlColorCoding,
boolean includeHtmlStartEndTags,
boolean useShortName)
Returns the modified sequence as an tagged string with potential
modification sites color coded or with ptm tags, e.g, <mox>.
|
void |
PTMFactory.setSearchedOMSSAIndexes(ModificationProfile modificationProfile)
Set the OMSSA indexes used for this search.
|
Modifier and Type | Method and Description |
---|---|
ModificationProfile |
SearchParameters.getModificationProfile()
Returns the modification profile of the project.
|
Modifier and Type | Method and Description |
---|---|
void |
SearchParameters.setModificationProfile(ModificationProfile modificationProfile)
Sets the modification profile of the project.
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Constructor and Description |
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SequenceFragmentationPanel(String aSequence,
ArrayList<IonMatch> aIonMatches,
boolean boolModifiedSequence,
boolean aHighlightModifications,
ModificationProfile modificationProfile)
Deprecated.
use the panel with ion selection instead
|
SequenceFragmentationPanel(String aSequence,
ArrayList<IonMatch> aIonMatches,
boolean boolModifiedSequence,
boolean aHighlightModifications,
ModificationProfile modificationProfile,
int forwardIon,
int rewindIon)
Creates a new SequenceFragmentationPanel working with B and Y ions.
|
SequenceFragmentationPanel(String taggedModifiedSequence,
ArrayList<IonMatch> aIonMatches,
boolean aHighlightModifications,
ModificationProfile modificationProfile,
int forwardIon,
int rewindIon)
Creates a new SequenceFragmentationPanel working with B and Y ions.
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