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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 | |
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static String |
CHARGE_ESTIMATION
Deprecated. use the SearchParameters class instead |
static String |
DATABASE_FILE
Deprecated. use the SearchParameters class instead Reference for the database file |
static String |
ENZYME
Deprecated. use the SearchParameters class instead Reference for the enzyme |
static String |
EVALUE_CUTOFF
Deprecated. use the SearchParameters class instead |
static String |
FIXED_MODIFICATIONS
Deprecated. use the SearchParameters class instead |
static String |
FRAGMENT_ION_MASS_ACCURACY
Deprecated. use the SearchParameters class instead |
static String |
FRAGMENT_ION_TYPE_1
Deprecated. use the SearchParameters class instead |
static String |
FRAGMENT_ION_TYPE_2
Deprecated. use the SearchParameters class instead |
static String |
MAX_PEPTIDE_SIZE
Deprecated. use the SearchParameters class instead |
static String |
MAXIMUM_HITLIST_LENGTH
Deprecated. use the SearchParameters class instead |
static String |
MIN_PEPTIDE_SIZE
Deprecated. use the SearchParameters class instead |
static String |
MISSED_CLEAVAGES
Deprecated. use the SearchParameters class instead |
static String |
MODIFICATION_SEPARATOR
Deprecated. use the SearchParameters class instead |
static String |
MODIFICATION_USE_SEPARATOR
Deprecated. use the SearchParameters class instead |
static String |
PRECURSOR_CHARGE_LOWER_BOUND
Deprecated. use the SearchParameters class instead |
static String |
PRECURSOR_CHARGE_TO_CONSIDER_MULTIPLY_CHARGED_FRAGMENTS
Deprecated. use the SearchParameters class instead |
static String |
PRECURSOR_CHARGE_UPPER_BOUND
Deprecated. use the SearchParameters class instead |
static String |
PRECURSOR_ELIMINATION
Deprecated. use the SearchParameters class instead |
static String |
PRECURSOR_MASS_ACCURACY_UNIT
Deprecated. use the SearchParameters class instead |
static String |
PRECURSOR_MASS_TOLERANCE
Deprecated. use the SearchParameters class instead |
static String |
PRECURSOR_SCALING
Deprecated. use the SearchParameters class instead |
static String |
VARIABLE_MODIFICATIONS
Deprecated. use the SearchParameters class instead |
Constructor Summary | |
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IdentificationParametersReader()
Deprecated. |
Method Summary | |
---|---|
static SearchParameters |
getSearchParameters(Properties aProps)
Deprecated. Conversion methods which converts an old school set of identification properties into a SearchParameters instance. |
static Properties |
loadProperties(File aFile)
Deprecated. use the SearchParameters class instead |
static ArrayList<String> |
parseModificationLine(String aLine)
Deprecated. use the SearchParameters class instead |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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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 |
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public IdentificationParametersReader()
Method Detail |
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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.
public static SearchParameters getSearchParameters(Properties aProps)
aProps
- the identification properties
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