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java.lang.Objectcom.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.experiment.biology.Peptide
public class Peptide
This class models a peptide.
Constructor Summary | |
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Peptide()
Constructor for the peptide. |
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Peptide(java.lang.String aSequence,
java.util.ArrayList<java.lang.String> parentProteins,
java.util.ArrayList<ModificationMatch> modifications)
Constructor for the peptide. |
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Peptide(java.lang.String aSequence,
java.lang.Double mass,
java.util.ArrayList<java.lang.String> parentProteins,
java.util.ArrayList<ModificationMatch> modifications)
Constructor for the peptide. |
Method Summary | |
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void |
addModificationMatch(ModificationMatch modificationMatch)
Adds a modification match. |
void |
clearModificationMatches()
Clears the list of imported modification matches. |
java.lang.String |
getCTerminal()
Returns the C-terminal of the peptide as a String. |
java.lang.String |
getKey()
Returns the index of a peptide. |
java.lang.Double |
getMass()
Getter for the mass. |
static int |
getModificationCount(java.lang.String peptideKey,
java.lang.String modification)
Returns how many of the given modification was found in the given peptide. |
static java.util.ArrayList<java.lang.String> |
getModificationFamily(java.lang.String peptideKey)
Returns a list of names of the variable modifications found in the key of a peptide. |
java.util.ArrayList<ModificationMatch> |
getModificationMatches()
Getter for the modifications carried by this peptide. |
java.lang.String |
getModifiedSequenceAsHtml(java.util.HashMap<java.lang.String,java.awt.Color> colors,
boolean includeHtmlStartEndTag)
Returns the modified sequence as an HTML string with modification color coding. |
static java.lang.String |
getModifiedSequenceAsHtml(java.util.HashMap<java.lang.String,java.awt.Color> colors,
boolean includeHtmlStartEndTag,
Peptide peptide,
java.util.HashMap<java.lang.Integer,java.util.ArrayList<java.lang.String>> mainModificationSites,
java.util.HashMap<java.lang.Integer,java.util.ArrayList<java.lang.String>> secondaryModificationSites)
Returns the modified sequence as an HTML string with potential modification sites color coding. |
java.lang.String |
getModifiedSequenceAsString(boolean includeTerminals)
Returns the modified sequence as a string, e.g., NH2-PEP |
int |
getNMissedCleavages(Enzyme enzyme)
Returns the amount of missed cleavages using the specified enzyme. |
static int |
getNMissedCleavages(java.lang.String sequence,
Enzyme enzyme)
Returns the amount of missed cleavages using the specified enzyme for the given sequence. |
java.lang.String |
getNTerminal()
Returns the N-terminal of the peptide as a String. |
java.util.ArrayList<java.lang.String> |
getParentProteins()
Getter for the parent proteins. |
static java.util.ArrayList<java.lang.Integer> |
getPotentialModificationSites(java.lang.String sequence,
PTM ptm)
Returns the potential modification sites as an ordered list of string. |
java.util.HashMap<java.lang.String,java.awt.Color> |
getPTMShortNameColorMap(java.util.HashMap<java.lang.String,java.awt.Color> ptmColors)
Returns a map of the ptm short names to the ptm colors. |
java.util.HashMap<java.lang.String,java.lang.String> |
getPTMShortNameMap()
Returns a map of the ptm short names to the ptm long names for the modification in this peptide. |
java.lang.String |
getSequence()
Getter for the sequence. |
static java.lang.String |
getSequence(java.lang.String peptideKey)
Returns the sequence of the peptide indexed by the given key. |
static boolean |
isModified(java.lang.String peptideKey)
Returns a boolean indicating whether the peptide has variable modifications based on its key. |
static boolean |
isModified(java.lang.String peptideKey,
java.lang.String modification)
Returns a boolean indicating whether the peptide has the given variable modification based on its key. |
boolean |
isSameAs(Peptide anotherPeptide)
A method which compares to peptides. |
boolean |
sameModificationsAs(Peptide anotherPeptide)
Indicates whether another peptide has the same modifications at the same localization as this peptide. |
void |
setParentProteins(java.util.ArrayList<java.lang.String> parentProteins)
Sets the parent proteins. |
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 Peptide()
public Peptide(java.lang.String aSequence, java.util.ArrayList<java.lang.String> parentProteins, java.util.ArrayList<ModificationMatch> modifications) throws java.lang.IllegalArgumentException
aSequence
- The peptide sequenceparentProteins
- The parent proteinsmodifications
- The PTM of this peptide
java.lang.IllegalArgumentException
- Thrown if the peptide sequence contains
unknown amino acidspublic Peptide(java.lang.String aSequence, java.lang.Double mass, java.util.ArrayList<java.lang.String> parentProteins, java.util.ArrayList<ModificationMatch> modifications)
aSequence
- The peptide sequencemass
- The peptide massparentProteins
- The parent proteinsmodifications
- The PTM of this peptideMethod Detail |
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public java.lang.Double getMass()
public java.util.ArrayList<ModificationMatch> getModificationMatches()
public void clearModificationMatches()
public void addModificationMatch(ModificationMatch modificationMatch)
modificationMatch
- the modification match to addpublic java.lang.String getSequence()
public int getNMissedCleavages(Enzyme enzyme)
enzyme
- the enzyme used
public static int getNMissedCleavages(java.lang.String sequence, Enzyme enzyme)
sequence
- the peptide sequenceenzyme
- the enzyme used
public java.util.ArrayList<java.lang.String> getParentProteins()
public void setParentProteins(java.util.ArrayList<java.lang.String> parentProteins)
parentProteins
- the parent proteins as listpublic java.lang.String getKey()
public static boolean isModified(java.lang.String peptideKey)
peptideKey
- the peptide key
public static boolean isModified(java.lang.String peptideKey, java.lang.String modification)
peptideKey
- the peptide keymodification
- the name of the modification
public static int getModificationCount(java.lang.String peptideKey, java.lang.String modification)
peptideKey
- the peptide keymodification
- the name of the modification
public static java.lang.String getSequence(java.lang.String peptideKey)
peptideKey
- the peptide key
public static java.util.ArrayList<java.lang.String> getModificationFamily(java.lang.String peptideKey)
peptideKey
- the key of a peptide
public static java.util.ArrayList<java.lang.Integer> getPotentialModificationSites(java.lang.String sequence, PTM ptm)
sequence
- the sequence of the peptide of interestptm
- the PTM considered
public boolean isSameAs(Peptide anotherPeptide)
anotherPeptide
- another peptide
public boolean sameModificationsAs(Peptide anotherPeptide)
anotherPeptide
- another peptide
public java.lang.String getNTerminal()
public java.lang.String getCTerminal()
public static java.lang.String getModifiedSequenceAsHtml(java.util.HashMap<java.lang.String,java.awt.Color> colors, boolean includeHtmlStartEndTag, Peptide peptide, java.util.HashMap<java.lang.Integer,java.util.ArrayList<java.lang.String>> mainModificationSites, java.util.HashMap<java.lang.Integer,java.util.ArrayList<java.lang.String>> secondaryModificationSites)
colors
- the ptm name to color mappingincludeHtmlStartEndTag
- if true, start and end html tags are addedpeptide
- mainModificationSites
- secondaryModificationSites
-
public java.lang.String getModifiedSequenceAsHtml(java.util.HashMap<java.lang.String,java.awt.Color> colors, boolean includeHtmlStartEndTag)
colors
- the ptm name to color mappingincludeHtmlStartEndTag
- if true, start and end html tags are added
public java.util.HashMap<java.lang.String,java.awt.Color> getPTMShortNameColorMap(java.util.HashMap<java.lang.String,java.awt.Color> ptmColors)
ptmColors
- the ptm color map
public java.util.HashMap<java.lang.String,java.lang.String> getPTMShortNameMap()
public java.lang.String getModifiedSequenceAsString(boolean includeTerminals)
includeTerminals
- if true, the terminals are included
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