public class ProteinMatch extends IdentificationMatch
IdentificationMatch.MatchType
Modifier and Type | Field and Description |
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static String |
PROTEIN_KEY_SPLITTER
The splitter in the key between protein accessions.
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Constructor and Description |
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ProteinMatch()
Constructor for the protein match.
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ProteinMatch(Peptide peptide,
String peptideMatchKey)
Constructor for the protein match.
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ProteinMatch(String proteinAccession)
Constructor for the protein match.
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Modifier and Type | Method and Description |
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void |
addPeptideMatchKey(String peptideMatchKey)
Add a subordinated peptide key.
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void |
addTheoreticProtein(String proteinAccession)
Setter for the matching protein.
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static void |
clearCache()
Clears the cache.
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static boolean |
contains(HashSet<String> sharedAccessions,
ArrayList<String> uniqueKeys)
Returns a boolean indicating whether a protein match contains another set
of matches.
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boolean |
contains(ProteinMatch proteinMatch)
Returns a boolean indicating whether the protein match contains another
set of theoretic proteins.
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boolean |
contains(String aProtein)
Returns a boolean indicating whether a protein was found in this protein
match.
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static boolean |
contains(String sharedKey,
String uniqueKey)
Returns a boolean indicating whether a protein match contains another set
of matches.
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static String[] |
getAccessions(String groupKey)
Returns a list of accessions from the given key.
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static ArrayList<String> |
getCommonProteins(String group1,
String group2)
Returns the common proteins between two protein groups.
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String |
getKey()
Returns the key of a match.
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String |
getMainMatch()
Returns the main match accession after protein inference.
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int |
getNProteins()
Returns the number of proteins for this match.
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static int |
getNProteins(String matchKey)
Returns the number of proteins for the match corresponding to the given.
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static ArrayList<String> |
getOtherProteins(String group1,
String group2)
Returns the proteins in a group (group1) which are not in another group
(group2).
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int |
getPeptideCount()
Returns the number of peptides found.
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ArrayList<String> |
getPeptideMatchesKeys()
Getter for the peptide keys.
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static String |
getProteinMatchKey(Peptide peptide)
Convenience method which returns the protein key of a peptide.
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ArrayList<String> |
getTheoreticProteinsAccessions()
Returns the accessions of the possible theoretic proteins.
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IdentificationMatch.MatchType |
getType()
Returns the type of match.
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boolean |
hasEnzymaticPeptide(String accession,
Enzyme enzyme,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether the protein group has an enzymatic peptide when
considering the given accession as main accession.
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boolean |
isDecoy()
Method indicates if the protein match is a decoy one.
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static boolean |
isDecoy(String key)
Convenience method indicating whether a match is decoy based on the match
key.
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void |
setMainMatch(String mainMatch)
Sets the main protein accession after protein inference.
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void |
setPeptideKeys(ArrayList<String> peptideMatchKeys)
Sets the peptide keys for this protein match.
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addUrParam, getParameterKey, getUrParam
public static final String PROTEIN_KEY_SPLITTER
public ProteinMatch()
public ProteinMatch(String proteinAccession) throws IllegalArgumentException
proteinAccession
- the matching proteinIllegalArgumentException
- if an IllegalArgumentException occurspublic ProteinMatch(Peptide peptide, String peptideMatchKey) throws IOException, SQLException, ClassNotFoundException, InterruptedException
peptide
- the corresponding peptide matchpeptideMatchKey
- the key of the peptide matchIOException
- if an IOException occursSQLException
- if an SQLException occursClassNotFoundException
- if a ClassNotFoundException occursInterruptedException
- if an InterruptedException occurspublic 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> getPeptideMatchesKeys()
public void addPeptideMatchKey(String peptideMatchKey)
peptideMatchKey
- a peptide keypublic void setPeptideKeys(ArrayList<String> peptideMatchKeys)
peptideMatchKeys
- the peptide match keyspublic int getPeptideCount()
public boolean isDecoy()
public static boolean isDecoy(String key)
key
- the match keypublic String getKey()
IdentificationMatch
getKey
in class IdentificationMatch
public static String getProteinMatchKey(Peptide peptide) throws IOException, SQLException, ClassNotFoundException, InterruptedException
peptide
- the considered peptideIOException
- if an IOException occursSQLException
- if an SQLException occursClassNotFoundException
- if a ClassNotFoundException occursInterruptedException
- if an InterruptedException occurspublic static int getNProteins(String matchKey)
matchKey
- the given keypublic int getNProteins()
public static boolean contains(String sharedKey, String uniqueKey)
sharedKey
- the key of the protein of interestuniqueKey
- the key of the protein supposedly containedpublic static boolean contains(HashSet<String> sharedAccessions, ArrayList<String> uniqueKeys)
sharedAccessions
- the accessions of the shared protein matchuniqueKeys
- the keys of the unique protein matchpublic static ArrayList<String> getOtherProteins(String group1, String group2)
group1
- the key of the shared groupgroup2
- the key of the unique grouppublic static ArrayList<String> getCommonProteins(String group1, String group2)
group1
- key of the first groupgroup2
- key of the second grouppublic boolean contains(ProteinMatch proteinMatch)
proteinMatch
- another protein matchpublic boolean contains(String aProtein)
aProtein
- the inspected proteinpublic static String[] getAccessions(String groupKey)
groupKey
- the given keypublic static void clearCache()
public boolean hasEnzymaticPeptide(String accession, Enzyme enzyme, SequenceMatchingPreferences sequenceMatchingPreferences) throws IOException, IllegalArgumentException, InterruptedException, FileNotFoundException, ClassNotFoundException
accession
- the candidate main accessionenzyme
- the enzyme usedsequenceMatchingPreferences
- the sequence matching preferencesIOException
- if an IOException occursIllegalArgumentException
- if an IllegalArgumentException occursFileNotFoundException
- if a FileNotFoundException occursClassNotFoundException
- if a ClassNotFoundException occursInterruptedException
- if an InterruptedException occurspublic IdentificationMatch.MatchType getType()
IdentificationMatch
getType
in class IdentificationMatch
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