public class Tools
extends java.lang.Object
Constructor and Description |
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Tools() |
Modifier and Type | Method and Description |
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static java.lang.String |
buildListIdentifier(BiomoleculeGroup aBG)
Building a list identifier for this BiomoleculeGroup
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static int |
calcMaxNumberPeptids(BiomoleculeList aBL)
Calculates the maximum number of peptides that are assigned to a protein within the given BiomoleculeList.
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static int |
calculateExternalGaps(java.lang.String alignmentRes)
Calculates the number of terminal gaps for the given string that represents the result of a pairwise sequence alignment.
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int |
calculateNumberGaps(java.lang.String seq)
The method calculates the number of gaps for a given sequence obtained for an alignment algorithm
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static Enzyme |
createEnzyme(java.lang.String enzymeFeatures)
This method creates an instance of Enzyme from the information specified in the Enzymes section of the configuration file.
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static java.util.List<java.util.regex.MatchResult> |
findMatches(java.lang.String pattern,
java.lang.CharSequence s)
This method returns a list of matched subsequences according to the regular expression pattern specified as parameter of the method.
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static java.lang.String |
getCurrentDate()
Gives a formatted string representation of the current date and time.
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static java.lang.String |
getFileExtension(java.lang.String filename)
Gets the extension from the specified name of the file.
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static java.lang.String |
removeModifications(java.lang.String sequence,
java.lang.String modificationNotation)
Removes the modification information from a given sequence with respect to the applied notation of modifications.
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static java.util.ArrayList<Peptide> |
removeModificationsFromPeptideSet(java.util.ArrayList<Peptide> aPeptSet,
java.lang.String regExPTM)
Removes the modification information from all peptides in a given peptide set.
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static java.lang.String |
removePTMs(java.lang.String sequence,
java.lang.String regExPTM)
Removes the modification information from a given sequence.
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static java.lang.String |
trimFileExtension(java.lang.String filename)
Trims the file extension and returns the remaining name of the file.
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public static java.lang.String trimFileExtension(java.lang.String filename)
filename
- public static java.lang.String getFileExtension(java.lang.String filename)
filename
- public static java.lang.String removeModifications(java.lang.String sequence, java.lang.String modificationNotation) throws WrongProLiCSettingException
sequence
- modificationNotation
- WrongProLiCSettingException
public static java.lang.String removePTMs(java.lang.String sequence, java.lang.String regExPTM)
sequence
- regExPTM
- public static java.util.ArrayList<Peptide> removeModificationsFromPeptideSet(java.util.ArrayList<Peptide> aPeptSet, java.lang.String regExPTM)
public static int calculateExternalGaps(java.lang.String alignmentRes)
alignmentRes
- public int calculateNumberGaps(java.lang.String seq)
seq
- public static int calcMaxNumberPeptids(BiomoleculeList aBL)
public static Enzyme createEnzyme(java.lang.String enzymeFeatures) throws WrongProLiCSettingException
enzymeFeatures
- WrongProLiCSettingException
public static java.util.List<java.util.regex.MatchResult> findMatches(java.lang.String pattern, java.lang.CharSequence s)
pattern
- s
- public static java.lang.String buildListIdentifier(BiomoleculeGroup aBG)
aBG
- public static java.lang.String getCurrentDate()