|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectcom.compomics.util.experiment.io.identifications.IdentificationParametersReader
public class IdentificationParametersReader
The identification parameters reader returns the parameters used for identification from a searchGUI parameters file
Field Summary | |
---|---|
static String |
CHARGE_ESTIMATION
Reference for the charge estimation |
static String |
DATABASE_FILE
Reference for the database file |
static String |
ENZYME
Reference for the enzyme |
static String |
EVALUE_CUTOFF
Reference for the e-value cutoff |
static String |
FIXED_MODIFICATIONS
Reference for the fixed modifications |
static String |
FRAGMENT_ION_MASS_ACCURACY
Reference for the fragment ion mass tolerance |
static String |
FRAGMENT_ION_TYPE_1
Reference for the type of fragment ion 1 |
static String |
FRAGMENT_ION_TYPE_2
Reference for the type of fragment ion 2 |
static String |
MAX_PEPTIDE_SIZE
Reference for the maximal peptide size |
static String |
MAXIMUM_HITLIST_LENGTH
Reference for the maximum length of the hitlist |
static String |
MIN_PEPTIDE_SIZE
Reference for the minimal peptide size |
static String |
MISSED_CLEAVAGES
Reference for the missed cleavages |
static String |
MODIFICATION_SEPARATOR
Reference for the separation of modifications |
static String |
MODIFICATION_USE_SEPARATOR
Reference for the separation of modification and its frequency |
static String |
PRECURSOR_CHARGE_LOWER_BOUND
Reference for the lower precursor charge |
static String |
PRECURSOR_CHARGE_TO_CONSIDER_MULTIPLY_CHARGED_FRAGMENTS
Reference for the precursor charge to start considering multiply charged fragments |
static String |
PRECURSOR_CHARGE_UPPER_BOUND
Reference for the upper precursor charge |
static String |
PRECURSOR_ELIMINATION
Reference for the precursor elimination option |
static String |
PRECURSOR_MASS_ACCURACY_UNIT
Reference for the precursor mass tolerance unit |
static String |
PRECURSOR_MASS_TOLERANCE
Reference for the precursor mass tolerance |
static String |
PRECURSOR_SCALING
Reference for the precursor scaling option |
static String |
VARIABLE_MODIFICATIONS
Reference for the variable modifications |
Constructor Summary | |
---|---|
IdentificationParametersReader()
|
Method Summary | |
---|---|
static Properties |
loadProperties(File aFile)
Loads the search properties from a SearchGUI properties file. |
static ArrayList<String> |
parseModificationLine(String aLine)
This method parses a modification line from a properties file. |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
---|
public static final String DATABASE_FILE
public static final String ENZYME
public static final String MODIFICATION_SEPARATOR
public static final String MODIFICATION_USE_SEPARATOR
public static final String FIXED_MODIFICATIONS
public static final String VARIABLE_MODIFICATIONS
public static final String MISSED_CLEAVAGES
public static final String PRECURSOR_MASS_TOLERANCE
public static final String PRECURSOR_MASS_ACCURACY_UNIT
public static final String FRAGMENT_ION_MASS_ACCURACY
public static final String PRECURSOR_CHARGE_LOWER_BOUND
public static final String PRECURSOR_CHARGE_UPPER_BOUND
public static final String FRAGMENT_ION_TYPE_1
public static final String FRAGMENT_ION_TYPE_2
public static final String EVALUE_CUTOFF
public static final String MAXIMUM_HITLIST_LENGTH
public static final String PRECURSOR_CHARGE_TO_CONSIDER_MULTIPLY_CHARGED_FRAGMENTS
public static final String PRECURSOR_ELIMINATION
public static final String PRECURSOR_SCALING
public static final String MIN_PEPTIDE_SIZE
public static final String MAX_PEPTIDE_SIZE
public static final String CHARGE_ESTIMATION
Constructor Detail |
---|
public IdentificationParametersReader()
Method Detail |
---|
public static Properties loadProperties(File aFile) throws FileNotFoundException, IOException
aFile
- a searchGUI properties file
FileNotFoundException
- exception thrown if the file is not found
IOException
- exception thrown whenever a problem occurs while reading the filepublic static ArrayList<String> parseModificationLine(String aLine)
aLine
- String with the modification line from the properties file.ptmFactory
-
Exception
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |