com.compomics.util.experiment.io.identifications
Class IdentificationParametersReader

java.lang.Object
  extended by com.compomics.util.experiment.io.identifications.IdentificationParametersReader

Deprecated. use the SearchParameters class instead

public class IdentificationParametersReader
extends Object

The identification parameters reader returns the parameters used for identification from a searchGUI parameters file

Author:
Marc Vaudel

Field Summary
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
IdentificationParametersReader()
          Deprecated.  
 
Method Summary
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
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

DATABASE_FILE

public static final String DATABASE_FILE
Deprecated. use the SearchParameters class instead Reference for the database file
See Also:
Constant Field Values

ENZYME

public static final String ENZYME
Deprecated. use the SearchParameters class instead Reference for the enzyme
See Also:
Constant Field Values

MODIFICATION_SEPARATOR

public static final String MODIFICATION_SEPARATOR
Deprecated. use the SearchParameters class instead
Reference for the separation of modifications

See Also:
Constant Field Values

MODIFICATION_USE_SEPARATOR

public static final String MODIFICATION_USE_SEPARATOR
Deprecated. use the SearchParameters class instead
Reference for the separation of modification and its frequency

See Also:
Constant Field Values

FIXED_MODIFICATIONS

public static final String FIXED_MODIFICATIONS
Deprecated. use the SearchParameters class instead
Reference for the fixed modifications

See Also:
Constant Field Values

VARIABLE_MODIFICATIONS

public static final String VARIABLE_MODIFICATIONS
Deprecated. use the SearchParameters class instead
Reference for the variable modifications

See Also:
Constant Field Values

MISSED_CLEAVAGES

public static final String MISSED_CLEAVAGES
Deprecated. use the SearchParameters class instead
Reference for the missed cleavages

See Also:
Constant Field Values

PRECURSOR_MASS_TOLERANCE

public static final String PRECURSOR_MASS_TOLERANCE
Deprecated. use the SearchParameters class instead
Reference for the precursor mass tolerance

See Also:
Constant Field Values

PRECURSOR_MASS_ACCURACY_UNIT

public static final String PRECURSOR_MASS_ACCURACY_UNIT
Deprecated. use the SearchParameters class instead
Reference for the precursor mass tolerance unit

See Also:
Constant Field Values

FRAGMENT_ION_MASS_ACCURACY

public static final String FRAGMENT_ION_MASS_ACCURACY
Deprecated. use the SearchParameters class instead
Reference for the fragment ion mass tolerance

See Also:
Constant Field Values

PRECURSOR_CHARGE_LOWER_BOUND

public static final String PRECURSOR_CHARGE_LOWER_BOUND
Deprecated. use the SearchParameters class instead
Reference for the lower precursor charge

See Also:
Constant Field Values

PRECURSOR_CHARGE_UPPER_BOUND

public static final String PRECURSOR_CHARGE_UPPER_BOUND
Deprecated. use the SearchParameters class instead
Reference for the upper precursor charge

See Also:
Constant Field Values

FRAGMENT_ION_TYPE_1

public static final String FRAGMENT_ION_TYPE_1
Deprecated. use the SearchParameters class instead
Reference for the type of fragment ion 1

See Also:
Constant Field Values

FRAGMENT_ION_TYPE_2

public static final String FRAGMENT_ION_TYPE_2
Deprecated. use the SearchParameters class instead
Reference for the type of fragment ion 2

See Also:
Constant Field Values

EVALUE_CUTOFF

public static final String EVALUE_CUTOFF
Deprecated. use the SearchParameters class instead
Reference for the e-value cutoff

See Also:
Constant Field Values

MAXIMUM_HITLIST_LENGTH

public static final String MAXIMUM_HITLIST_LENGTH
Deprecated. use the SearchParameters class instead
Reference for the maximum length of the hitlist

See Also:
Constant Field Values

PRECURSOR_CHARGE_TO_CONSIDER_MULTIPLY_CHARGED_FRAGMENTS

public static final String PRECURSOR_CHARGE_TO_CONSIDER_MULTIPLY_CHARGED_FRAGMENTS
Deprecated. use the SearchParameters class instead
Reference for the precursor charge to start considering multiply charged fragments

See Also:
Constant Field Values

PRECURSOR_ELIMINATION

public static final String PRECURSOR_ELIMINATION
Deprecated. use the SearchParameters class instead
Reference for the precursor elimination option

See Also:
Constant Field Values

PRECURSOR_SCALING

public static final String PRECURSOR_SCALING
Deprecated. use the SearchParameters class instead
Reference for the precursor scaling option

See Also:
Constant Field Values

MIN_PEPTIDE_SIZE

public static final String MIN_PEPTIDE_SIZE
Deprecated. use the SearchParameters class instead
Reference for the minimal peptide size

See Also:
Constant Field Values

MAX_PEPTIDE_SIZE

public static final String MAX_PEPTIDE_SIZE
Deprecated. use the SearchParameters class instead
Reference for the maximal peptide size

See Also:
Constant Field Values

CHARGE_ESTIMATION

public static final String CHARGE_ESTIMATION
Deprecated. use the SearchParameters class instead
Reference for the charge estimation

See Also:
Constant Field Values
Constructor Detail

IdentificationParametersReader

public IdentificationParametersReader()
Deprecated. 
Method Detail

loadProperties

public static Properties loadProperties(File aFile)
                                 throws FileNotFoundException,
                                        IOException
Deprecated. use the SearchParameters class instead

Loads the search properties from a SearchGUI properties file.

Parameters:
aFile - a searchGUI properties file
Returns:
the corresponding properties, indexed by the static fields
Throws:
FileNotFoundException - exception thrown if the file is not found
IOException - exception thrown whenever a problem occurs while reading the file

parseModificationLine

public static ArrayList<String> parseModificationLine(String aLine)
Deprecated. use the SearchParameters class instead

This method parses a modification line from a properties file.

Parameters:
aLine - String with the modification line from the properties file.
Returns:
ArrayList with the parsed PTM indexes.

getSearchParameters

public static SearchParameters getSearchParameters(Properties aProps,
                                                   File userModsFile)
                                            throws org.xmlpull.v1.XmlPullParserException,
                                                   FileNotFoundException,
                                                   IOException
Deprecated. 
Conversion methods which converts an old school set of identification properties into a SearchParameters instance. The enzymes must be loaded in the Enzyme factory. The PTMs in the PTM factory.

Parameters:
aProps - the identification properties
userModsFile - if there are user modifications, provide the user modification file (usermods.xml)
Returns:
the corresponding SearchParameters object
Throws:
org.xmlpull.v1.XmlPullParserException
FileNotFoundException
IOException


Copyright © 2013. All Rights Reserved.