Package | Description |
---|---|
de.mpc.prolic.misc | |
de.mpc.prolic.model |
Modifier and Type | Method and Description |
---|---|
static java.lang.String |
IO.writeBMIdentifier(Biomolecule aBM,
java.lang.String outStringData_,
java.lang.String columnDelim_)
Auxiliary method used to write the identifier of the biomolecule
|
static java.lang.String |
IO.writeBMOrigin(Biomolecule aBM,
java.lang.String outStringData_,
java.lang.String columnDelim_)
Auxiliary method used to write the origin of the biomolecule (i.e. the list where the biomolecule originate from)
|
static java.lang.String |
IO.writeBMSequence(Biomolecule aBM,
java.lang.String outStringData_,
java.lang.String columnDelim_)
Auxiliary method used to write the sequence of the biomolecule (either amino acid or nucleotide sequences)
|
static java.lang.String |
IO.writeGeneName(Biomolecule aB_,
java.lang.String outStringData_,
java.lang.String columnDelim_,
java.lang.String BiomoleculeType_)
Auxiliary method used to ensure correct output format of the ProLiC result file even in case of wrong user settings, i.e. enabling writing
of gene name information in case of missing availability of such information.
|
static java.lang.String |
IO.writePeptideInformations(Biomolecule aB_,
java.lang.String outStringData_,
java.lang.String columnDelim_,
java.lang.String BiomoleculeType_)
Auxiliary method used to ensure correct output format of the ProLiC result file even in case of wrong user settings, i.e. enabling writing
of peptide information in case of missing availability of such information.
|
static java.lang.String |
IO.writeProteinName(Biomolecule aB_,
java.lang.String outStringData_,
java.lang.String columnDelim_,
java.lang.String BiomoleculeType_)
Auxiliary method used to ensure correct output format of the ProLiC result file even in case of wrong user settings, i.e. enabling writing
of protein name information in case of missing information.
|
static java.lang.String |
IO.writeRepresentative(Biomolecule bgRepr,
java.lang.String outStringData_,
java.lang.String columnDelim_)
Auxiliary method used to write group representative information
|
Modifier and Type | Class and Description |
---|---|
class |
Gene
Representation of a Gene.
|
class |
Peptide
Representation of a peptide, usually created by means of protein digestion.
|
class |
Probe
A Probe instance is the representation of a small DNA reporter molecule that is used to measure expression levels of related transcripts and
subsequently genes by use of DNA microarray experiments.
|
class |
Protein
Representation of a protein.
|
class |
Transcript
Representation of a Transcript (i.e. the processed messenger mRNA that arise from the precursor mRNA).
|
Modifier and Type | Method and Description |
---|---|
Biomolecule |
BiomoleculeGroup.getRepresentative() |
Modifier and Type | Method and Description |
---|---|
java.util.ArrayList<Biomolecule> |
BiomoleculeGroup.getBiomoleculeGroup() |
java.util.Vector<Biomolecule> |
BiomoleculePair.getBiomoleculePair()
Setter and Getter
|
java.util.ArrayList<Biomolecule> |
BiomoleculeList.getBiomolecules() |
Modifier and Type | Method and Description |
---|---|
void |
BiomoleculeGroup.addBiomolecule(Biomolecule aBiomolecule_)
The method adds a Biomolecule to this biomolecule group.
|
void |
BiomoleculePair.addBiomolecule(Biomolecule aBM) |
void |
BiomoleculeList.addBiomolecules(Biomolecule aBiomolecule)
Adds a Biomolecule to the existing ArrayList biomolecules.
|
void |
BiomoleculeGroup.setRepresentative(Biomolecule representative_) |
Modifier and Type | Method and Description |
---|---|
void |
BiomoleculeGroup.addBiomolecules(java.util.Set<Biomolecule> bmSet)
Adding all at once the biomolecules that belong to this group.
|
void |
BiomoleculeGroup.setBiomoleculeGroup(java.util.ArrayList<Biomolecule> biomoleculeGroup_) |
void |
BiomoleculePair.setBiomoleculePair(java.util.Vector<Biomolecule> biomoleculePair_) |
void |
BiomoleculeList.setBiomolecules(java.util.ArrayList<Biomolecule> biomolecules_) |
Constructor and Description |
---|
BiomoleculeList(java.util.ArrayList<Biomolecule> biomolecules_)
Generating a BiomoleculeList instance along with a collection of the related biomolecules.
|
BiomoleculeList(java.util.ArrayList<Biomolecule> biomolecules_,
java.lang.String listName_)
Generating a BiomoleculeList instance along with a collection of the related biomolecules and the list identifier.
|