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java.lang.Objectcom.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.experiment.identification.matches.ModificationMatch
public class ModificationMatch
This class models the match between theoretic ptm and identification results.
Constructor Summary | |
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ModificationMatch(java.lang.String theoreticPtm,
boolean variable,
int modifiedSite)
Constructor for a modification match. |
Method Summary | |
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int |
getModificationSite()
Getter for the modification site, 1 is the first amino acid. |
java.lang.String |
getTheoreticPtm()
Getter for the theoretic PTM name. |
boolean |
isConfident()
Returns a boolean indicating whether the modification is confidently localized on the sequence. |
boolean |
isInferred()
Returns a boolean indicating whether the modification is inferred from another peptide. |
boolean |
isVariable()
Returns a boolean indicating if the modification is variable. |
void |
setConfident(boolean confident)
Sets whether the modification is confidently localized on the sequence. |
void |
setInferred(boolean inferred)
Sets whether the modification is inferred from another peptide. |
void |
setModificationSite(int site)
Setter for the modification site, 1 is the first amino acid. |
void |
setTheoreticPtm(java.lang.String ptm)
Sets the theoretic PTM. |
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 |
Constructor Detail |
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public ModificationMatch(java.lang.String theoreticPtm, boolean variable, int modifiedSite)
theoreticPtm
- the theoretic PTMvariable
- true for variable modifications, false otherwisemodifiedSite
- the position of the modification in the sequence, 1
is the first residueMethod Detail |
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public boolean isVariable()
public java.lang.String getTheoreticPtm()
public void setTheoreticPtm(java.lang.String ptm)
ptm
- the theoretic PTM namepublic int getModificationSite()
public void setModificationSite(int site)
site
- the index of the modification in the sequencepublic boolean isConfident()
public void setConfident(boolean confident)
confident
- a boolean indicating whether the modification is
confidently localized on the sequencepublic boolean isInferred()
public void setInferred(boolean inferred)
inferred
- a boolean indicating whether the modification is
inferred from another peptide
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