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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 java.lang.String |
CHARGE_ESTIMATION
Deprecated. use the SearchParameters class instead |
static java.lang.String |
DATABASE_FILE
Deprecated. use the SearchParameters class instead Reference for the database file |
static java.lang.String |
ENZYME
Deprecated. use the SearchParameters class instead Reference for the enzyme |
static java.lang.String |
EVALUE_CUTOFF
Deprecated. use the SearchParameters class instead |
static java.lang.String |
FIXED_MODIFICATIONS
Deprecated. use the SearchParameters class instead |
static java.lang.String |
FRAGMENT_ION_MASS_ACCURACY
Deprecated. use the SearchParameters class instead |
static java.lang.String |
FRAGMENT_ION_TYPE_1
Deprecated. use the SearchParameters class instead |
static java.lang.String |
FRAGMENT_ION_TYPE_2
Deprecated. use the SearchParameters class instead |
static java.lang.String |
MAX_PEPTIDE_SIZE
Deprecated. use the SearchParameters class instead |
static java.lang.String |
MAXIMUM_HITLIST_LENGTH
Deprecated. use the SearchParameters class instead |
static java.lang.String |
MIN_PEPTIDE_SIZE
Deprecated. use the SearchParameters class instead |
static java.lang.String |
MISSED_CLEAVAGES
Deprecated. use the SearchParameters class instead |
static java.lang.String |
MODIFICATION_SEPARATOR
Deprecated. use the SearchParameters class instead |
static java.lang.String |
MODIFICATION_USE_SEPARATOR
Deprecated. use the SearchParameters class instead |
static java.lang.String |
PRECURSOR_CHARGE_LOWER_BOUND
Deprecated. use the SearchParameters class instead |
static java.lang.String |
PRECURSOR_CHARGE_TO_CONSIDER_MULTIPLY_CHARGED_FRAGMENTS
Deprecated. use the SearchParameters class instead |
static java.lang.String |
PRECURSOR_CHARGE_UPPER_BOUND
Deprecated. use the SearchParameters class instead |
static java.lang.String |
PRECURSOR_ELIMINATION
Deprecated. use the SearchParameters class instead |
static java.lang.String |
PRECURSOR_MASS_ACCURACY_UNIT
Deprecated. use the SearchParameters class instead |
static java.lang.String |
PRECURSOR_MASS_TOLERANCE
Deprecated. use the SearchParameters class instead |
static java.lang.String |
PRECURSOR_SCALING
Deprecated. use the SearchParameters class instead |
static java.lang.String |
VARIABLE_MODIFICATIONS
Deprecated. use the SearchParameters class instead |
Constructor Summary | |
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IdentificationParametersReader()
Deprecated. |
Method Summary | |
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static SearchParameters |
getSearchParameters(java.util.Properties aProps,
java.io.File userModsFile)
Deprecated. Conversion methods which converts an old school set of identification properties into a SearchParameters instance. |
static java.util.Properties |
loadProperties(java.io.File aFile)
Deprecated. use the SearchParameters class instead |
static java.util.ArrayList<java.lang.String> |
parseModificationLine(java.lang.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 java.lang.String DATABASE_FILE
public static final java.lang.String ENZYME
public static final java.lang.String MODIFICATION_SEPARATOR
public static final java.lang.String MODIFICATION_USE_SEPARATOR
public static final java.lang.String FIXED_MODIFICATIONS
public static final java.lang.String VARIABLE_MODIFICATIONS
public static final java.lang.String MISSED_CLEAVAGES
public static final java.lang.String PRECURSOR_MASS_TOLERANCE
public static final java.lang.String PRECURSOR_MASS_ACCURACY_UNIT
public static final java.lang.String FRAGMENT_ION_MASS_ACCURACY
public static final java.lang.String PRECURSOR_CHARGE_LOWER_BOUND
public static final java.lang.String PRECURSOR_CHARGE_UPPER_BOUND
public static final java.lang.String FRAGMENT_ION_TYPE_1
public static final java.lang.String FRAGMENT_ION_TYPE_2
public static final java.lang.String EVALUE_CUTOFF
public static final java.lang.String MAXIMUM_HITLIST_LENGTH
public static final java.lang.String PRECURSOR_CHARGE_TO_CONSIDER_MULTIPLY_CHARGED_FRAGMENTS
public static final java.lang.String PRECURSOR_ELIMINATION
public static final java.lang.String PRECURSOR_SCALING
public static final java.lang.String MIN_PEPTIDE_SIZE
public static final java.lang.String MAX_PEPTIDE_SIZE
public static final java.lang.String CHARGE_ESTIMATION
Constructor Detail |
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public IdentificationParametersReader()
Method Detail |
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public static java.util.Properties loadProperties(java.io.File aFile) throws java.io.FileNotFoundException, java.io.IOException
aFile
- a searchGUI properties file
java.io.FileNotFoundException
- exception thrown if the file is not found
java.io.IOException
- exception thrown whenever a problem occurs while
reading the filepublic static java.util.ArrayList<java.lang.String> parseModificationLine(java.lang.String aLine)
aLine
- String with the modification line from the properties file.
public static SearchParameters getSearchParameters(java.util.Properties aProps, java.io.File userModsFile) throws org.xmlpull.v1.XmlPullParserException, java.io.FileNotFoundException, java.io.IOException
aProps
- the identification propertiesuserModsFile
- if there are user modifications, provide the user
modification file (usermods.xml)
org.xmlpull.v1.XmlPullParserException
java.io.FileNotFoundException
java.io.IOException
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