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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.
Created by IntelliJ IDEA. User: Marc Date: Jun 18, 2010 Time: 8:56:40 AM
Constructor Summary | |
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Peptide()
Constructor for the peptide |
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Peptide(String aSequence,
ArrayList<String> parentProteins,
ArrayList<ModificationMatch> modifications)
Constructor for the peptide |
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Peptide(String aSequence,
Double mass,
ArrayList<String> parentProteins,
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 |
String |
getCTerminal()
Returns the C-terminal of the peptide as a String. |
String |
getKey()
Returns the index of a peptide. index = SEQUENCE_mod1_mod2 with modifications ordered alphabetically. |
Double |
getMass()
getter for the mass |
static int |
getModificationCount(String peptideKey,
String modification)
Returns how many of the given modification was found in the given peptide |
static ArrayList<String> |
getModificationFamily(String peptideKey)
Returns a list of names of the variable modifications found in the key of a peptide |
ArrayList<ModificationMatch> |
getModificationMatches()
getter for the modifications carried by this peptide |
String |
getModifiedSequenceAsHtml(HashMap<String,Color> colors,
boolean includeHtmlStartEndTag)
Returns the modified sequence as an HTML string with modification color coding |
static String |
getModifiedSequenceAsHtml(HashMap<String,Color> colors,
boolean includeHtmlStartEndTag,
Peptide peptide,
HashMap<Integer,ArrayList<String>> mainModificationSites,
HashMap<Integer,ArrayList<String>> secondaryModificationSites)
Returns the modified sequence as an HTML string with potential modification sites color coding |
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(String sequence,
Enzyme enzyme)
Returns the amount of missed cleavages using the specified enzyme for the given sequence |
String |
getNTerminal()
Returns the N-terminal of the peptide as a String. |
ArrayList<String> |
getParentProteins()
Getter for the parent proteins |
static ArrayList<Integer> |
getPotentialModificationSites(String sequence,
PTM ptm)
returns the potential modification sites as an ordered list of string. 0 is the first aa. |
HashMap<String,Color> |
getPTMShortNameColorMap(HashMap<String,Color> ptmColors)
Returns a map of the ptm short names to the ptm colors. |
HashMap<String,String> |
getPTMShortNameMap()
Returns a map of the ptm short names to the ptm long names for the modification in this peptide. |
String |
getSequence()
getter for the sequence |
static String |
getSequence(String peptideKey)
Returns the sequence of the peptide indexed by the given key |
static boolean |
isModified(String peptideKey)
Returns a boolean indicating whether the peptide has variable modifications based on its key |
static boolean |
isModified(String peptideKey,
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(ArrayList<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(String aSequence, ArrayList<String> parentProteins, ArrayList<ModificationMatch> modifications) throws IllegalArgumentException
aSequence
- The peptide sequenceparentProteins
- The parent proteinsmodifications
- The PTM of this peptide
IllegalArgumentException
- Thrown if the peptide sequence contains unknown amino acidspublic Peptide(String aSequence, Double mass, ArrayList<String> parentProteins, ArrayList<ModificationMatch> modifications)
aSequence
- The peptide sequencemass
- The peptide massparentProteins
- The parent proteinsmodifications
- The PTM of this peptideMethod Detail |
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public Double getMass()
public ArrayList<ModificationMatch> getModificationMatches()
public void clearModificationMAtches()
public void addModificationMatch(ModificationMatch modificationMatch)
modificationMatch
- the modification match to addpublic String getSequence()
public int getNMissedCleavages(Enzyme enzyme)
enzyme
- the enzyme used
public static int getNMissedCleavages(String sequence, Enzyme enzyme)
sequence
- the peptide sequenceenzyme
- the enzyme used
public ArrayList<String> getParentProteins()
public void setParentProteins(ArrayList<String> parentProteins)
parentProteins
- the parent proteins as listpublic String getKey()
public static boolean isModified(String peptideKey)
peptideKey
- the peptide key
public static boolean isModified(String peptideKey, String modification)
peptideKey
- the peptide keymodification
- the name of the modification
public static int getModificationCount(String peptideKey, String modification)
peptideKey
- the peptide keymodification
- the name of the modification
public static String getSequence(String peptideKey)
peptideKey
- the peptide key
public static ArrayList<String> getModificationFamily(String peptideKey)
peptideKey
- the key of a peptide
public static ArrayList<Integer> getPotentialModificationSites(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 String getNTerminal()
public String getCTerminal()
public static String getModifiedSequenceAsHtml(HashMap<String,Color> colors, boolean includeHtmlStartEndTag, Peptide peptide, HashMap<Integer,ArrayList<String>> mainModificationSites, HashMap<Integer,ArrayList<String>> secondaryModificationSites)
colors
- the ptm name to color mappingincludeHtmlStartEndTag
- if true, start and end html tags are addedpeptide
- mainModificationSites
- secondaryModificationSites
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public String getModifiedSequenceAsHtml(HashMap<String,Color> colors, boolean includeHtmlStartEndTag)
colors
- the ptm name to color mappingincludeHtmlStartEndTag
- if true, start and end html tags are added
public HashMap<String,Color> getPTMShortNameColorMap(HashMap<String,Color> ptmColors)
ptmColors
- the ptm color map
public HashMap<String,String> getPTMShortNameMap()
public String getModifiedSequenceAsString(boolean includeTerminals)
includeTerminals
- if true, the terminals are included
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