Uses of Class
uk.ac.ebi.pridemod.io.slimmod.model.SlimModCollection

Packages that use SlimModCollection

Package	Description
uk.ac.ebi.pridemod.io
uk.ac.ebi.pridemod.io.pridemod.xml
uk.ac.ebi.pridemod.io.slimmod.model
uk.ac.ebi.pridemod.io.slimmod.tab

Uses of SlimModCollection in uk.ac.ebi.pridemod.io

Methods in uk.ac.ebi.pridemod.io that return SlimModCollection

Modifier and Type	Method and Description
static SlimModCollection	PrideModController.parseSlimModCollection()

Uses of SlimModCollection in uk.ac.ebi.pridemod.io.pridemod.xml

Methods in uk.ac.ebi.pridemod.io.pridemod.xml that return SlimModCollection

Modifier and Type	Method and Description
SlimModCollection	PrideModReader.getSlimModCollection()

Uses of SlimModCollection in uk.ac.ebi.pridemod.io.slimmod.model

Methods in uk.ac.ebi.pridemod.io.slimmod.model that return SlimModCollection

Modifier and Type	Method and Description
SlimModCollection	SlimModCollection.getbyDelta(double deltaMass, double difference) This method return an object of SlimCollection with a list of the slim modifications by a given mass and small windows or error between the delta mass of the modifications and the parameter deltaMass.
SlimModCollection	SlimModCollection.getbySpecificity(Specificity.AminoAcid specificity) This method return an SlimModCollection object, a list of the slim modifications that contain an specific specificity in the list of possible specificities.
SlimModCollection	SlimModCollection.getbySpecificity(Specificity.AminoAcid specificity, double mass, double difference) This method allow users to obtain the slim modification filtering with a delta mass a possible error (difference) and one specificity in the list of the possible specificities for each modification.
SlimModCollection	SlimModCollection.getbySpecificity(String nameSpecificity) This method return an SlimModCollection object, a list of the slim modifications that contain an specific specificity in the list of possible specificities.
SlimModCollection	SlimModCollection.getbySpecificity(String nameSpecificity, double mass, double difference) This method allow users to obtain the slim modification filtering with a delta mass a possible error (difference) and one specificity in the list of the possible specificities for each modification.

Uses of SlimModCollection in uk.ac.ebi.pridemod.io.slimmod.tab

Methods in uk.ac.ebi.pridemod.io.slimmod.tab that return SlimModCollection

Modifier and Type	Method and Description
static SlimModCollection	ReadTabSlim.parseSlimModification(Scanner scanner)
static SlimModCollection	ReadTabSlim.parseSlimModification(String fileName)
static SlimModCollection	ReadTabSlim.parseSlimModification(URL url) Template method that calls ReadTabSlim.processLine(String).