/*
* EuroCarbDB, a framework for carbohydrate bioinformatics
*
* Copyright (c) 2006-2009, Eurocarb project, or third-party contributors as
* indicated by the @author tags or express copyright attribution
* statements applied by the authors.
*
* This copyrighted material is made available to anyone wishing to use, modify,
* copy, or redistribute it subject to the terms and conditions of the GNU
* Lesser General Public License, as published by the Free Software Foundation.
* A copy of this license accompanies this distribution in the file LICENSE.txt.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
* or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
* for more details.
*
* Last commit: $Rev: 1210 $ by $Author: glycoslave $ on $Date:: 2009-06-12 #$
*/
/**
@author Alessio Ceroni (a.ceroni@imperial.ac.uk)
*/
package org.eurocarbdb.application.glycoworkbench.plugin;
import org.eurocarbdb.application.glycoworkbench.*;
import org.eurocarbdb.application.glycanbuilder.*;
import java.util.*;
public class PeakFinderOptions {
public String DERIVATIZATION = "Und";
public String REDUCING_END = "freeEnd";
public String OTHER_REDEND_NAME = "XXX";
public double OTHER_REDEND_MASS = 0.;
public String OR1_NAME = "Or1";
public String OR2_NAME = "Or2";
public String OR3_NAME = "Or3";
public double OR1_MASS = 0.;
public double OR2_MASS = 0.;
public double OR3_MASS = 0.;
public int MIN_PEN=0, MAX_PEN=0;
public int MIN_HEX=0, MAX_HEX=8;
public int MIN_HEP=0, MAX_HEP=0;
public int MIN_HEXN=0, MAX_HEXN=0;
public int MIN_HEXNAC=0, MAX_HEXNAC=7;
public int MIN_DPEN=0, MAX_DPEN=0;
public int MIN_DHEX=0, MAX_DHEX=2;
public int MIN_DDHEX=0, MAX_DDHEX=0;
public int MIN_MEHEX=0, MAX_MEHEX=0;
public int MIN_OR1=0, MAX_OR1=0;
public int MIN_OR2=0, MAX_OR2=0;
public int MIN_OR3=0, MAX_OR3=0;
public int MIN_HEXA=0, MAX_HEXA=0;
public int MIN_DHEXA=0, MAX_DHEXA=0;
public int MIN_NEU5GC=0, MAX_NEU5GC=0;
public int MIN_NEU5AC=0, MAX_NEU5AC=2;
public int MIN_NEU5GCLAC=0, MAX_NEU5GCLAC=0;
public int MIN_NEU5ACLAC=0, MAX_NEU5ACLAC=0;
public int MIN_KDO=0, MAX_KDO=0;
public int MIN_KDN=0, MAX_KDN=0;
public int MIN_MUR=0, MAX_MUR=0;
public int MIN_S=0, MAX_S=0;
public int MIN_P=0, MAX_P=0;
public int MIN_AC=0, MAX_AC=0;
public int MIN_PYR=0, MAX_PYR=0;
public int MIN_PC=0, MAX_PC=0;
// serialization
public void store(Configuration config) {
config.put("PeakfinderOptions","derivatization",DERIVATIZATION);
config.put("PeakfinderOptions","reducing_end",REDUCING_END);
config.put("PeakfinderOptions","other_redend_name",OTHER_REDEND_NAME);
config.put("PeakfinderOptions","other_redend_mass",OTHER_REDEND_MASS);
config.put("PeakfinderOptions","min_pen",MIN_PEN);
config.put("PeakfinderOptions","max_pen",MAX_PEN);
config.put("PeakfinderOptions","min_hex",MIN_HEX);
config.put("PeakfinderOptions","max_hex",MAX_HEX);
config.put("PeakfinderOptions","min_hep",MIN_HEP);
config.put("PeakfinderOptions","max_hep",MAX_HEP);
config.put("PeakfinderOptions","min_hexn",MIN_HEXN);
config.put("PeakfinderOptions","max_hexn",MAX_HEXN);
config.put("PeakfinderOptions","min_hexnac",MIN_HEXNAC);
config.put("PeakfinderOptions","max_hexnac",MAX_HEXNAC);
config.put("PeakfinderOptions","min_dpen",MIN_DPEN);
config.put("PeakfinderOptions","max_dpen",MAX_DPEN);
config.put("PeakfinderOptions","min_dhex",MIN_DHEX);
config.put("PeakfinderOptions","max_dhex",MAX_DHEX);
config.put("PeakfinderOptions","min_ddhex",MIN_DDHEX);
config.put("PeakfinderOptions","max_ddhex",MAX_DDHEX);
config.put("PeakfinderOptions","min_mehex",MIN_MEHEX);
config.put("PeakfinderOptions","max_mehex",MAX_MEHEX);
config.put("PeakfinderOptions","min_or1",MIN_OR1);
config.put("PeakfinderOptions","max_or1",MAX_OR1);
config.put("PeakfinderOptions","min_or2",MIN_OR2);
config.put("PeakfinderOptions","max_or2",MAX_OR2);
config.put("PeakfinderOptions","min_or3",MIN_OR3);
config.put("PeakfinderOptions","max_or3",MAX_OR3);
config.put("PeakfinderOptions","or1_mass",OR1_MASS);
config.put("PeakfinderOptions","or2_mass",OR2_MASS);
config.put("PeakfinderOptions","or3_mass",OR3_MASS);
config.put("PeakfinderOptions","min_hexa",MIN_HEXA);
config.put("PeakfinderOptions","max_hexa",MAX_HEXA);
config.put("PeakfinderOptions","min_dhexa",MIN_DHEXA);
config.put("PeakfinderOptions","max_dhexa",MAX_DHEXA);
config.put("PeakfinderOptions","min_neu5gc",MIN_NEU5GC);
config.put("PeakfinderOptions","max_neu5gc",MAX_NEU5GC);
config.put("PeakfinderOptions","min_neu5ac",MIN_NEU5AC);
config.put("PeakfinderOptions","max_neu5ac",MAX_NEU5AC);
config.put("PeakfinderOptions","min_neu5gclac",MIN_NEU5GCLAC);
config.put("PeakfinderOptions","max_neu5gclac",MAX_NEU5GCLAC);
config.put("PeakfinderOptions","min_neu5aclac",MIN_NEU5ACLAC);
config.put("PeakfinderOptions","max_neu5aclac",MAX_NEU5ACLAC);
config.put("PeakfinderOptions","min_kdp",MIN_KDO);
config.put("PeakfinderOptions","max_kdo",MAX_KDO);
config.put("PeakfinderOptions","min_kdn",MIN_KDN);
config.put("PeakfinderOptions","max_kdn",MAX_KDN);
config.put("PeakfinderOptions","min_mur",MIN_MUR);
config.put("PeakfinderOptions","max_mur",MAX_MUR);
config.put("PeakfinderOptions","min_s",MIN_S);
config.put("PeakfinderOptions","max_s",MAX_S);
config.put("PeakfinderOptions","min_p",MIN_P);
config.put("PeakfinderOptions","max_p",MAX_P);
config.put("PeakfinderOptions","min_ac",MIN_AC);
config.put("PeakfinderOptions","max_ac",MAX_AC);
config.put("PeakfinderOptions","min_pyr",MIN_PYR);
config.put("PeakfinderOptions","max_pyr",MAX_PYR);
config.put("PeakfinderOptions","min_pc",MIN_PC);
config.put("PeakfinderOptions","max_pc",MAX_PC);
}
public void retrieve(Configuration config) {
DERIVATIZATION = config.get("PeakfinderOptions","derivatization",DERIVATIZATION);
REDUCING_END = config.get("PeakfinderOptions","reducing_end",REDUCING_END);
OTHER_REDEND_NAME = config.get("PeakfinderOptions","other_redend_name",OTHER_REDEND_NAME);
OTHER_REDEND_MASS = config.get("PeakfinderOptions","other_redend_mass",OTHER_REDEND_MASS);
MIN_PEN = config.get("PeakfinderOptions","min_pen",MIN_PEN);
MAX_PEN = config.get("PeakfinderOptions","max_pen",MAX_PEN);
MIN_HEX = config.get("PeakfinderOptions","min_hex",MIN_HEX);
MAX_HEX = config.get("PeakfinderOptions","max_hex",MAX_HEX);
MIN_HEP = config.get("PeakfinderOptions","min_hep",MIN_HEP);
MAX_HEP = config.get("PeakfinderOptions","max_hep",MAX_HEP);
MIN_HEXN = config.get("PeakfinderOptions","min_hexn",MIN_HEXN);
MAX_HEXN = config.get("PeakfinderOptions","max_hexn",MAX_HEXN);
MIN_HEXNAC = config.get("PeakfinderOptions","min_hexnac",MIN_HEXNAC);
MAX_HEXNAC = config.get("PeakfinderOptions","max_hexnac",MAX_HEXNAC);
MIN_DPEN = config.get("PeakfinderOptions","min_dpen",MIN_DPEN);
MAX_DPEN = config.get("PeakfinderOptions","max_dpen",MAX_DPEN);
MIN_DHEX = config.get("PeakfinderOptions","min_dhex",MIN_DHEX);
MAX_DHEX = config.get("PeakfinderOptions","max_dhex",MAX_DHEX);
MIN_DDHEX = config.get("PeakfinderOptions","min_ddhex",MIN_DDHEX);
MAX_DDHEX = config.get("PeakfinderOptions","max_ddhex",MAX_DDHEX);
MIN_MEHEX = config.get("PeakfinderOptions","min_mehex",MIN_MEHEX);
MAX_MEHEX = config.get("PeakfinderOptions","max_mehex",MAX_MEHEX);
MIN_OR1 = config.get("PeakfinderOptions","min_or1",MIN_OR1);
MAX_OR1 = config.get("PeakfinderOptions","max_or1",MAX_OR1);
MIN_OR2 = config.get("PeakfinderOptions","min_or2",MIN_OR2);
MAX_OR2 = config.get("PeakfinderOptions","max_or2",MAX_OR2);
MIN_OR3 = config.get("PeakfinderOptions","min_or3",MIN_OR3);
MAX_OR3 = config.get("PeakfinderOptions","max_or3",MAX_OR3);
OR1_MASS = config.get("PeakfinderOptions","or1_mass",OR1_MASS);
OR2_MASS = config.get("PeakfinderOptions","or2_mass",OR2_MASS);
OR3_MASS = config.get("PeakfinderOptions","or3_mass",OR3_MASS);
MIN_HEXA = config.get("PeakfinderOptions","min_hexa",MIN_HEXA);
MAX_HEXA = config.get("PeakfinderOptions","max_hexa",MAX_HEXA);
MIN_DHEXA = config.get("PeakfinderOptions","min_dhexa",MIN_DHEXA);
MAX_DHEXA = config.get("PeakfinderOptions","max_dhexa",MAX_DHEXA);
MIN_NEU5GC = config.get("PeakfinderOptions","min_neu5gc",MIN_NEU5GC);
MAX_NEU5GC = config.get("PeakfinderOptions","max_neu5gc",MAX_NEU5GC);
MIN_NEU5AC = config.get("PeakfinderOptions","min_neu5ac",MIN_NEU5AC);
MAX_NEU5AC = config.get("PeakfinderOptions","max_neu5ac",MAX_NEU5AC);
MIN_NEU5GCLAC = config.get("PeakfinderOptions","min_neu5gclac",MIN_NEU5GCLAC);
MAX_NEU5GCLAC = config.get("PeakfinderOptions","max_neu5gclac",MAX_NEU5GCLAC);
MIN_NEU5ACLAC = config.get("PeakfinderOptions","min_neu5aclac",MIN_NEU5ACLAC);
MAX_NEU5ACLAC = config.get("PeakfinderOptions","max_neu5aclac",MAX_NEU5ACLAC);
MIN_KDO = config.get("PeakfinderOptions","min_kdp",MIN_KDO);
MAX_KDO = config.get("PeakfinderOptions","max_kdo",MAX_KDO);
MIN_KDN = config.get("PeakfinderOptions","min_kdn",MIN_KDN);
MAX_KDN = config.get("PeakfinderOptions","max_kdn",MAX_KDN);
MIN_MUR = config.get("PeakfinderOptions","min_mur",MIN_MUR);
MAX_MUR = config.get("PeakfinderOptions","max_mur",MAX_MUR);
MIN_S = config.get("PeakfinderOptions","min_s",MIN_S);
MAX_S = config.get("PeakfinderOptions","max_s",MAX_S);
MIN_P = config.get("PeakfinderOptions","min_p",MIN_P);
MAX_P = config.get("PeakfinderOptions","max_p",MAX_P);
MIN_AC = config.get("PeakfinderOptions","min_ac",MIN_AC);
MAX_AC = config.get("PeakfinderOptions","max_ac",MAX_AC);
MIN_PYR = config.get("PeakfinderOptions","min_pyr",MIN_PYR);
MAX_PYR = config.get("PeakfinderOptions","max_pyr",MAX_PYR);
MIN_PC = config.get("PeakfinderOptions","min_pc",MIN_PC);
MAX_PC = config.get("PeakfinderOptions","max_pc",MAX_PC);
}
}