public class IdentificationParametersReader extends Object
Modifier and Type | Field and Description |
---|---|
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 and Description |
---|
IdentificationParametersReader()
Deprecated.
|
Modifier and Type | Method and Description |
---|---|
static SearchParameters |
getSearchParameters(Properties aProps,
File userModsFile)
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
|
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
public IdentificationParametersReader()
public static Properties loadProperties(File aFile) throws FileNotFoundException, IOException
aFile
- a searchGUI properties fileFileNotFoundException
- exception thrown if the file is not foundIOException
- 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, File userModsFile) throws org.xmlpull.v1.XmlPullParserException, FileNotFoundException, IOException
aProps
- the identification propertiesuserModsFile
- if there are user modifications, provide the user
modification file (usermods.xml)org.xmlpull.v1.XmlPullParserException
FileNotFoundException
IOException
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