// $Id: // 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: phylosoft @ gmail . com // WWW: https://sites.google.com/site/cmzmasek/home/software/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 AptxConstants { final static boolean __ALLOW_PHYLOGENETIC_INFERENCE = true; public final static String PRG_NAME = "Archaeopteryx"; final static String VERSION = "0.9921 beta"; final static String PRG_DATE = "170712"; final static String DEFAULT_CONFIGURATION_FILE_NAME = "_aptx_configuration_file"; final static String[] DEFAULT_FONT_CHOICES = { "Arial Unicode MS", "Dialog", "SansSerif", "Sans", "Arial", "Helvetica" }; final static boolean VERBOSE_DEFAULT = false; final static int DOMAIN_STRUCTURE_DEFAULT_WIDTH = 100; final static String AUTHOR_EMAIL = "phyloxml@gmail.com"; final static int DOMAIN_STRUCTURE_E_VALUE_THR_DEFAULT_EXP = -3; final static float BUTTON_ZOOM_IN_FACTOR = 1.25f; final static float BUTTON_ZOOM_OUT_FACTOR = 1 / AptxConstants.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 / AptxConstants.BUTTON_ZOOM_IN_X_CORRECTION_FACTOR; final static float WHEEL_ZOOM_IN_FACTOR = 1.08f; final static float WHEEL_ZOOM_OUT_FACTOR = 1 / AptxConstants.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 / AptxConstants.WHEEL_ZOOM_IN_X_CORRECTION_FACTOR; static final boolean SPECIAL_CUSTOM = false; //TODO remove me static final double EXT_NODE_INFO_LENGTH_MAX_RATIO = 0.95; static final Dimension NODE_PANEL_SPLIT_MINIMUM_SIZE = new Dimension( 100, 50 ); static final Dimension NODE_PANEL_SIZE = new Dimension( 500, 540 ); 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_URL_OF_SPECIES_TREE_TO_LOAD = "url_of_species_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; final static float PDF_LINE_WIDTH_DEFAULT = 0.5f; final static String APTX_WEB_SITE = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx"; final static String APTX_JS_WEB_SITE = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx-js"; final static String APTX_MAILING_LIST = "https://groups.google.com/forum/?fromgroups#!forum/archaeopteryx"; final static String APTX_DOC_SITE = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/documentation"; 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 = 3; final static short NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT = 2; public static final boolean NH_PARSING_IGNORE_QUOTES_DEFAULT = false; static final CLADOGRAM_TYPE CLADOGRAM_TYPE_DEFAULT = CLADOGRAM_TYPE.LINED_UP; 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 String NCBI_ALL_DATABASE_SEARCH = "http://www.ncbi.nlm.nih.gov/gquery/?term="; public final static Color DOMAIN_BASE_COLOR_FOR_PDF = new Color( 100, 100, 100 ); public final static Color DOMAIN_LABEL_COLOR_FOR_PDF = new Color( 0, 0, 0 ); final static short DEFAULT_NODE_SHAPE_SIZE_DEFAULT = 7; static final int MAX_LENGTH_FOR_COLLAPSED_NAME = 8; }