// $Id: Constants.java,v 1.109 2010/10/06 04:24:25 cmzmasek Exp $
// FORESTER -- software libraries and applications
// for evolutionary biology research and applications.
//
// Copyright (C) 2008-2009 Christian M. Zmasek
// Copyright (C) 2008-2009 Burnham Institute for Medical Research
// Copyright (C) 2000-2001 Washington University School of Medicine
// and Howard Hughes Medical Institute
// Copyright (C) 2003-2007 Ethalinda K.S. Cannon
// All rights reserved
//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// version 2.1 of the License, or (at your option) any later version.
//
// This library 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.
//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: cmzmasek@yahoo.com
// WWW: www.phylosoft.org/forester
package org.forester.archaeopteryx;
import java.awt.Color;
import java.awt.Dimension;
import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
import org.forester.util.ForesterConstants;
public final class Constants {
final static boolean __ALLOW_PHYLOGENETIC_INFERENCE = true;
final static boolean __RELEASE = false; // TODO remove me
final static boolean __SNAPSHOT_RELEASE = false; // TODO remove me
final static String PRG_NAME = "Archaeopteryx";
final static String VERSION = "0.959 beta X";
final static String PRG_DATE = "2010.10.XX";
final static String DEFAULT_CONFIGURATION_FILE_NAME = "_aptx_configuration_file";
final static String[] DEFAULT_FONT_CHOICES = { "Verdana", "Tahoma",
"Arial", "Helvetica", "Dialog", "Lucida Sans", "SansSerif", "Sans-serif", "Sans" };
final static boolean VERBOSE_DEFAULT = false;
final static int DOMAIN_STRUCTURE_DEFAULT_WIDTH = 200;
final static String AUTHOR_EMAIL = "cmzmasek@yahoo.com";
final static int DOMAIN_STRUCTURE_E_VALUE_THR_DEFAULT_EXP = 0;
final static float BUTTON_ZOOM_IN_FACTOR = 1.25f;
final static float BUTTON_ZOOM_OUT_FACTOR = 1 / Constants.BUTTON_ZOOM_IN_FACTOR;
final static float BUTTON_ZOOM_IN_X_CORRECTION_FACTOR = 1.2f;
final static float BUTTON_ZOOM_OUT_X_CORRECTION_FACTOR = 1 / Constants.BUTTON_ZOOM_IN_X_CORRECTION_FACTOR;
final static float WHEEL_ZOOM_IN_FACTOR = 1.08f;
final static float WHEEL_ZOOM_OUT_FACTOR = 1 / Constants.WHEEL_ZOOM_IN_FACTOR;
final static float WHEEL_ZOOM_IN_X_CORRECTION_FACTOR = 1.085f;
final static float WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR = 1 / Constants.WHEEL_ZOOM_IN_X_CORRECTION_FACTOR;
static final boolean SPECIAL_CUSTOM = false; //TODO remove me
static final int EXT_NODE_INFO_LENGTH_MAX = 300;
static final Dimension NODE_PANEL_SPLIT_MINIMUM_SIZE = new Dimension( 100, 50 );
static final Dimension NODE_PANEL_SIZE = new Dimension( 500, 600 );
static final Dimension NODE_FRAME_SIZE = new Dimension( 520, 640 );
static final String APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD = "url_of_tree_to_load";
static final String APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL = "config_file";
static final String APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE = "homology_type_analysis_query_sequence";
static final String APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE = "homology_type_analysis_initial_relation_type";
static final int MAX_TREES_TO_LOAD = 100;
static final int US_LETTER_SIZE_X = 612;
static final int US_LETTER_SIZE_Y = 792;
static final int A4_SIZE_X = 595;
static final int A4_SIZE_Y = 845;
final static float PDF_LINE_WIDTH_DEFAULT = 0.5f;
final static String APTX_WEB_SITE = "http://www.phylosoft.org/archaeopteryx/";
final static String PHYLOXML_WEB_SITE = ForesterConstants.PHYLO_XML_LOCATION;
final static String PHYLOXML_REFERENCE_URL = "http://www.biomedcentral.com/1471-2105/10/356/";
final static String APTX_REFERENCE_URL = "http://www.biomedcentral.com/bmcbioinformatics/";
final static String APTX_REFERENCE = "Zmasek..."; //TODO
final static String PHYLOXML_REFERENCE = ForesterConstants.PHYLO_XML_REFERENCE;
final static String PHYLOXML_REFERENCE_SHORT = "Han MV and Zmasek CM (2009), BMC Bioinformatics, 10:356";
final static short NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT = 2;
final static short NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT = 1;
public static final boolean NH_PARSING_IGNORE_QUOTES_DEFAULT = false;
static final CLADOGRAM_TYPE CLADOGRAM_TYPE_DEFAULT = CLADOGRAM_TYPE.EXT_NODE_SUM_DEP;
final static boolean VALIDATE_AGAINST_PHYLOXML_XSD_SCJEMA_DEFAULT = true;
final static String BACKUP_FILE_SUFFIX = ".BAK";
final static double MIN_NOT_COLLAPSE_DEFAULT = 50;
final static Color GUI_BACKGROUND_DEFAULT = new Color( 32, 32, 32 );
final static Color CHECKBOX_TEXT_COLOR_DEFAULT = new Color( 220,
220,
220 );
final static Color CHECKBOX_AND_BUTTON_ACTIVE_COLOR_DEFAULT = new Color( 255, 0, 0 );
final static Color BUTTON_TEXT_COLOR_DEFAULT = new Color( 255,
255,
255 );
final static Color BUTTON_BACKGROUND_COLOR_DEFAULT = new Color( 64, 64, 64 );
final static Color MENU_BACKGROUND_COLOR_DEFAULT = new Color( 0, 0, 0 );
final static Color MENU_TEXT_COLOR_DEFAULT = new Color( 255,
255,
255 );
final static Color BUTTON_BORDER_COLOR_DEFAULT = new Color( 0, 0, 0 );
final static Color TAB_LABEL_FOREGROUND_COLOR_SELECTED = new Color( 0, 0, 0 );
final static Color DOMAIN_STRUCTURE_BASE_COLOR_DEFAULT = new Color( 32, 32, 32 );
final static Color DOMAIN_STRUCTURE_FONT_COLOR_DEFAULT = new Color( 144,
144,
144 );
final static String NCBI_ALL_DATABASE_SEARCH = "http://www.ncbi.nlm.nih.gov/gquery/?term=";
}