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

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

public class IdentificationParametersReader
extends Object

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

Author:
Marc

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 parameters file
static ArrayList<String> parseModificationLine(String aLine, PTMFactory ptmFactory)
          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

DATABASE_FILE

public static final String DATABASE_FILE
Reference for the database file

See Also:
Constant Field Values

ENZYME

public static final String ENZYME
Reference for the enzyme

See Also:
Constant Field Values

MODIFICATION_SEPARATOR

public static final String MODIFICATION_SEPARATOR
Reference for the separation of modifications

See Also:
Constant Field Values

MODIFICATION_USE_SEPARATOR

public static final String MODIFICATION_USE_SEPARATOR
Reference for the separation of modification and its frequency

See Also:
Constant Field Values

FIXED_MODIFICATIONS

public static final String FIXED_MODIFICATIONS
Reference for the fixed modifications

See Also:
Constant Field Values

VARIABLE_MODIFICATIONS

public static final String VARIABLE_MODIFICATIONS
Reference for the variable modifications

See Also:
Constant Field Values

MISSED_CLEAVAGES

public static final String MISSED_CLEAVAGES
Reference for the missed cleavages

See Also:
Constant Field Values

PRECURSOR_MASS_TOLERANCE

public static final String PRECURSOR_MASS_TOLERANCE
Reference for the precursor mass tolerance

See Also:
Constant Field Values

PRECURSOR_MASS_ACCURACY_UNIT

public static final String PRECURSOR_MASS_ACCURACY_UNIT
Reference for the precursor mass tolerance unit

See Also:
Constant Field Values

FRAGMENT_ION_MASS_ACCURACY

public static final String FRAGMENT_ION_MASS_ACCURACY
Reference for the fragment ion mass tolerance

See Also:
Constant Field Values

PRECURSOR_CHARGE_LOWER_BOUND

public static final String PRECURSOR_CHARGE_LOWER_BOUND
Reference for the lower precursor charge

See Also:
Constant Field Values

PRECURSOR_CHARGE_UPPER_BOUND

public static final String PRECURSOR_CHARGE_UPPER_BOUND
Reference for the upper precursor charge

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Constant Field Values

FRAGMENT_ION_TYPE_1

public static final String FRAGMENT_ION_TYPE_1
Reference for the type of fragment ion 1

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Constant Field Values

FRAGMENT_ION_TYPE_2

public static final String FRAGMENT_ION_TYPE_2
Reference for the type of fragment ion 2

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Constant Field Values

EVALUE_CUTOFF

public static final String EVALUE_CUTOFF
Reference for the e-value cutoff

See Also:
Constant Field Values

MAXIMUM_HITLIST_LENGTH

public static final String MAXIMUM_HITLIST_LENGTH
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
Reference for the precursor charge to start considering multiply charged fragments

See Also:
Constant Field Values

PRECURSOR_ELIMINATION

public static final String PRECURSOR_ELIMINATION
Reference for the precursor elimination option

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Constant Field Values

PRECURSOR_SCALING

public static final String PRECURSOR_SCALING
Reference for the precursor scaling option

See Also:
Constant Field Values

MIN_PEPTIDE_SIZE

public static final String MIN_PEPTIDE_SIZE
Reference for the minimal peptide size

See Also:
Constant Field Values

MAX_PEPTIDE_SIZE

public static final String MAX_PEPTIDE_SIZE
Reference for the maximal peptide size

See Also:
Constant Field Values

CHARGE_ESTIMATION

public static final String CHARGE_ESTIMATION
Reference for the charge estimation

See Also:
Constant Field Values
Constructor Detail

IdentificationParametersReader

public IdentificationParametersReader()
Method Detail

loadProperties

public static Properties loadProperties(File aFile)
                                 throws FileNotFoundException,
                                        IOException
Loads the search properties from a SearchGUI parameters file

Parameters:
aFile - a searchGUI parameter 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,
                                                      PTMFactory ptmFactory)
                                               throws Exception
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.
Throws:
Exception


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