/*
* Copyright (c) 2009 The Jackson Laboratory
*
* This software was developed by Gary Churchill's Lab at The Jackson
* Laboratory (see http://research.jax.org/faculty/churchill).
*
* This is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This software 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 General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this software. If not, see <http://www.gnu.org/licenses/>.
*/
package org.jax.qtl;
import java.text.DecimalFormat;
/**
* @author Lei Wu
* @version 1.0
*/
// TODO Constants needs to be broken up into the packages that need the constants
// in some cases and turned into a properties bundle in other cases
@SuppressWarnings("all")
public interface Constants {
// main jframe setup stuff & labels.
static final String EMAIL_STRING = "jqtl@jax.org";
static final String EOL = System.getProperty("line.separator");
static final String TAB = "\t";
// UI settings
static final int CROSS_COMBOBOX_WIDTH = 250;
static final int STANDARD_TABLE_HEIGHT = 150;
static final int STATNDARD_TABLE_WIDTH = 250;
static final int CHECK_BOX_TABLE_CELL_WIDTH = 50;
static final int CHECK_BOX_VERTICAL_TABLE_CELL_WIDTH = 20;
static final String ERROR_TITLE = "Error";
static final String WARNING_TITLE = "Warning";
static final int TEXT_FIELD_WIDTH = 150;
static final String CHOOSE_PARMETER_TITLE = " Choose Parameters ";
// cross type
static final int BACKCROSS = 0, INTERCROSS = 1, FOURWAYCROSS = 2;
static final String[] CROSS_TYPE = new String[] {"Backcross","f2 intercross","4 way cross"};
// function option lists
static final String[] MAP_FUNCTION = {" Haldane", " Kosambi", " Carter-Falconer", " Morgan"};
static final String[] STEP_WIDTH = {" fixed", " variable"};
static final String[] RIPPLE_METHOD = {" countxo", " likelihood"};
static final String[] TRUE_FALSE = {"TRUE", "FALSE"};
// calc.genoprob, sim.geno and est.map label
static final String MAP_FUNCTION_LABEL = "Map Function";
static final String STEP_SIZE_LABEL = "Step Size(cM)";
static final String NUM_DRAWS_LABEL = "Number of Imputations";
static final String GENO_ERROR_RATE_LABEL = "Genotyping error rate";
static final String DIST_PAST_TERMINAL_LABEL = "Distance past terminal";
static final String STEP_WIDTH_TYPE_LABEL = "Step width type";
static final String M_LABEL = "Interference parameter for the chi-square model";
static final String P_LABEL = "Proportion of chiasmata from the NI mechanism, in the Stahl model";
static final String SEX_SP_LABEL = "Estimate sex specific map";
static final String ERROR_PROB_DEFAULT = "0.0001";
static final String OFF_END_DEFAULT = "0.0";
static final String ZERO = "0";
// output format
static final DecimalFormat ONE_DIGIT_FORMATTER = new DecimalFormat("0.0");
static final DecimalFormat THREE_DIGIT_FORMATTER = new DecimalFormat("0.000");
static final DecimalFormat FOUR_DIGIT_FORMATTER = new DecimalFormat("0.0000");
static final DecimalFormat FIVE_DIGIT_FORMATTER = new DecimalFormat("0.00000");
static final DecimalFormat ZERO_DIGIT_FORMATTER = new DecimalFormat("0");
// scan, ripple parameter
static final String[] USE_ALL = {" all observations"," complete observations"};
static final int MAXIT_DEFAULT = 4000;
static final String TOL_DEFAULT = "1e-4";
static final double TOL_DEFAULT_NUM = 0.0001;
static final String SELECT_PHENO_TITLE = " Select phenos ";
static final String SELECT_CHROMOSOME_TITLE = " Select Chromosomes ";
// scan summary label
static final String SCAN_MODEL_LABEL = "Phenotypic Model";
static final String SCAN_METHOD_LABEL = "Scan Method";
static final String USE_LABEL = "Use";
static final String MAXIT_LABEL = "Maximum number of iterations";
static final String TOL_LABEL = "Tolerance value for determining convergence";
static final String NUM_PERM_LABEL = "Number of Permutations";
static final String SEP_PERM_LABEL = "Separate permutations for autosomes and the X chromosome";
static final String UPPER_LABEL = "Upper";
static final String TIES_RANDOM_LABEL = "Ties.random";
static final String INCL_MARKERS_LABEL = "incl.markers";
static final String CLEAN_OUTPUT_LABEL = "clean.output";
// scan cov table header
static final String[] covTableColumnName = new String[] {"Additive","Interactive","Covariates"};
// ci plot
static final double DEFAULT_LOD_INT = 1.5;
static final double DEFAULT_BAYES_INT = 0.95;
// phenoData
static final int NOT_SEX = 0;
static final int MIX_SEX = 1;
static final int MALE_SEX = 2;
static final int FEMALE_SEX = 3;
// scantwo plot
static final int NUM_COLORS = 256;
static final String[] LOD_TYPE = new String[] {"full","add","cond-int","cond-add","int"};
static final int LOD_FULL = 0;
static final int LOD_ADD = 1;
static final int LOD_COND_INT = 2;
static final int LOD_COND_ADD = 3;
static final int LOD_INT = 4;
static final String UPPER_LOD_LABEL = "LOD scores in the upper triangle";
static final String LOWER_LOD_LABEL = "LOD scores in the lower triangle";
static final String[] COLOR_MAP_LIST = new String[] {"redblue", "cm", "gray", "heat", "terrain", "topo"};
static final String COLOR_MAP_LABEL = "Color map";
static final String ADD_COLOR_MAP_SCALE = "Add color map scale";
// RF plot
static final int MAX_RF_LOD = 12;
// organization
static final String NO_SCANONE_MESSAGE = "this cross doesn't have any scanone result";
static final String NO_SCANTWO_MESSAGE = "this cross doesn't have any scantwo result";
static final String NO_QTL_BASKET_MESSAGE = "this cross doesn't have any QTL basket";
}