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java.lang.Objectcom.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.experiment.identification.IdentificationMatch
com.compomics.util.experiment.identification.matches.ProteinMatch
public class ProteinMatch
This class models a protein match.
Nested Class Summary | |
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static class |
ProteinMatch.MatchingType
The different types of peptide to protein amino acid matching. |
Nested classes/interfaces inherited from class com.compomics.util.experiment.identification.IdentificationMatch |
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IdentificationMatch.MatchType |
Field Summary | |
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static String |
PROTEIN_KEY_SPLITTER
The splitter in the key between spectrumFile and spectrumTitle. |
Constructor Summary | |
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ProteinMatch()
Constructor for the protein match. |
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ProteinMatch(Peptide peptide)
Constructor for the protein match. |
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ProteinMatch(String proteinAccession)
Constructor for the protein match. |
Method Summary | |
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void |
addPeptideMatch(String peptideMatchKey)
Add a subordinated peptide key. |
void |
addTheoreticProtein(String proteinAccession)
Setter for the matching protein. |
boolean |
contains(ProteinMatch proteinMatch)
Returns a boolean indicating whether the protein match contains another set of theoretic proteins. |
boolean |
contains(String aProtein)
Returns a boolean indicating whether a protein was found in this protein match. |
static boolean |
contains(String sharedKey,
String uniqueKey)
Returns a boolean indicating whether a protein match contains another set of matches. |
static String[] |
getAccessions(String key)
Returns a list of accessions from the given key. |
static ArrayList<String> |
getCommonProteins(String group1,
String group2)
Returns the common proteins between two protein groups. |
String |
getKey()
returns the key of a match. |
String |
getMainMatch()
Returns the main match accession after protein inference. |
int |
getNProteins()
Returns the number of proteins for this match. |
static int |
getNProteins(String matchKey)
Returns the number of proteins for the match corresponding to the given. |
static ArrayList<String> |
getOtherProteins(String group1,
String group2)
Returns the proteins in a group (group1) which are not in another group (group2). |
int |
getPeptideCount()
Returns the number of peptides found. |
ArrayList<String> |
getPeptideMatches()
Getter for the peptide keys. |
static String |
getProteinMatchKey(Peptide peptide)
Convenience method which returns the protein key of a peptide. |
ArrayList<String> |
getTheoreticProteinsAccessions()
Returns the accessions of the possible theoretic proteins. |
IdentificationMatch.MatchType |
getType()
Returns the type of match. |
boolean |
hasEnzymaticPeptide(String accession,
Enzyme enzyme,
ProteinMatch.MatchingType matchingType,
Double massTolerance)
Indicates whether the protein group has an enzymatic peptide when considering the given accession as main accession. |
boolean |
isDecoy()
Method indicates if the protein match is a decoy one. |
static boolean |
isDecoy(String key)
Convenience method indicating whether a match is decoy based on the match key. |
void |
setMainMatch(String mainMatch)
Sets the main protein accession after protein inference. |
Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject |
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addUrParam, getParameterKey, getUrParam |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public static final String PROTEIN_KEY_SPLITTER
Constructor Detail |
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public ProteinMatch()
public ProteinMatch(String proteinAccession) throws IllegalArgumentException
proteinAccession
- the matching protein
IllegalArgumentException
public ProteinMatch(Peptide peptide)
peptide
- the corresponding peptide matchMethod Detail |
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public ArrayList<String> getTheoreticProteinsAccessions()
public void addTheoreticProtein(String proteinAccession)
proteinAccession
- the matching proteinpublic String getMainMatch()
public void setMainMatch(String mainMatch)
mainMatch
- the main matchpublic ArrayList<String> getPeptideMatches()
public void addPeptideMatch(String peptideMatchKey)
peptideMatchKey
- a peptide keypublic int getPeptideCount()
public boolean isDecoy()
public static boolean isDecoy(String key)
key
- the match key
public String getKey()
IdentificationMatch
getKey
in class IdentificationMatch
public static String getProteinMatchKey(Peptide peptide)
peptide
- the considered peptide
public static int getNProteins(String matchKey)
matchKey
- the given key
public int getNProteins()
public static boolean contains(String sharedKey, String uniqueKey)
sharedKey
- the key of the protein of interestuniqueKey
- the key of the protein supposedly contained
public static ArrayList<String> getOtherProteins(String group1, String group2)
group1
- the key of the shared groupgroup2
- the key of the unique group
public static ArrayList<String> getCommonProteins(String group1, String group2)
group1
- key of the first groupgroup2
- key of the second group
public boolean contains(ProteinMatch proteinMatch)
proteinMatch
- another protein match
public boolean contains(String aProtein)
aProtein
- the inspected protein
public static String[] getAccessions(String key)
key
- the given key
public boolean hasEnzymaticPeptide(String accession, Enzyme enzyme, ProteinMatch.MatchingType matchingType, Double massTolerance) throws IOException, IllegalArgumentException, InterruptedException, FileNotFoundException, ClassNotFoundException
accession
- the candidate main accessionenzyme
- the enzyme usedmatchingType
- the matching typemassTolerance
- the mass tolerance for matching type
'indistiguishibleAminoAcids'. Can be null otherwise
IOException
IllegalArgumentException
InterruptedException
FileNotFoundException
ClassNotFoundException
public IdentificationMatch.MatchType getType()
IdentificationMatch
getType
in class IdentificationMatch
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