2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
7 // Copyright (C) 2000-2001 Washington University School of Medicine
8 // and Howard Hughes Medical Institute
9 // Copyright (C) 2003-2007 Ethalinda K.S. Cannon
10 // All rights reserved
12 // This library is free software; you can redistribute it and/or
13 // modify it under the terms of the GNU Lesser General Public
14 // License as published by the Free Software Foundation; either
15 // version 2.1 of the License, or (at your option) any later version.
17 // This library is distributed in the hope that it will be useful,
18 // but WITHOUT ANY WARRANTY; without even the implied warranty of
19 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
20 // Lesser General Public License for more details.
22 // You should have received a copy of the GNU Lesser General Public
23 // License along with this library; if not, write to the Free Software
24 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
26 // Contact: phylosoft @ gmail . com
27 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
29 package org.forester.archaeopteryx;
31 import java.awt.Color;
32 import java.awt.Dimension;
34 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
35 import org.forester.util.ForesterConstants;
37 public final class AptxConstants {
39 final static boolean __ALLOW_PHYLOGENETIC_INFERENCE = true;
40 public final static String PRG_NAME = "Archaeopteryx";
41 final static String VERSION = "0.9920 beta";
42 final static String PRG_DATE = "161214";
43 final static String DEFAULT_CONFIGURATION_FILE_NAME = "_aptx_configuration_file";
44 final static String[] DEFAULT_FONT_CHOICES = {
45 "Arial Unicode MS", "Dialog", "SansSerif", "Sans", "Arial", "Helvetica" };
46 final static boolean VERBOSE_DEFAULT = false;
47 final static int DOMAIN_STRUCTURE_DEFAULT_WIDTH = 100;
48 final static String AUTHOR_EMAIL = "phyloxml@gmail.com";
49 final static int DOMAIN_STRUCTURE_E_VALUE_THR_DEFAULT_EXP = -3;
50 final static float BUTTON_ZOOM_IN_FACTOR = 1.25f;
51 final static float BUTTON_ZOOM_OUT_FACTOR = 1 / AptxConstants.BUTTON_ZOOM_IN_FACTOR;
52 final static float BUTTON_ZOOM_IN_X_CORRECTION_FACTOR = 1.2f;
53 final static float BUTTON_ZOOM_OUT_X_CORRECTION_FACTOR = 1 / AptxConstants.BUTTON_ZOOM_IN_X_CORRECTION_FACTOR;
54 final static float WHEEL_ZOOM_IN_FACTOR = 1.08f;
55 final static float WHEEL_ZOOM_OUT_FACTOR = 1 / AptxConstants.WHEEL_ZOOM_IN_FACTOR;
56 final static float WHEEL_ZOOM_IN_X_CORRECTION_FACTOR = 1.085f;
57 final static float WHEEL_ZOOM_OUT_X_CORRECTION_FACTOR = 1 / AptxConstants.WHEEL_ZOOM_IN_X_CORRECTION_FACTOR;
58 static final boolean SPECIAL_CUSTOM = false; //TODO remove me
59 static final double EXT_NODE_INFO_LENGTH_MAX_RATIO = 0.95;
60 static final Dimension NODE_PANEL_SPLIT_MINIMUM_SIZE = new Dimension( 100, 50 );
61 static final Dimension NODE_PANEL_SIZE = new Dimension( 500, 540 );
62 static final Dimension NODE_FRAME_SIZE = new Dimension( 520, 640 );
63 static final String APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD = "url_of_tree_to_load";
64 static final String APPLET_PARAM_NAME_FOR_URL_OF_SPECIES_TREE_TO_LOAD = "url_of_species_tree_to_load";
65 static final String APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL = "config_file";
66 static final String APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE = "homology_type_analysis_query_sequence";
67 static final String APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE = "homology_type_analysis_initial_relation_type";
68 static final int MAX_TREES_TO_LOAD = 100;
69 final static float PDF_LINE_WIDTH_DEFAULT = 0.5f;
70 final static String APTX_WEB_SITE = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx";
71 final static String APTX_MAILING_LIST = "https://groups.google.com/forum/?fromgroups#!forum/archaeopteryx";
72 final static String APTX_DOC_SITE = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/documentation";
73 final static String PHYLOXML_WEB_SITE = ForesterConstants.PHYLO_XML_LOCATION;
74 final static String PHYLOXML_REFERENCE_URL = "http://www.biomedcentral.com/1471-2105/10/356/";
75 final static String APTX_REFERENCE_URL = "http://www.biomedcentral.com/bmcbioinformatics/";
76 final static String APTX_REFERENCE = "Zmasek..."; //TODO
77 final static String PHYLOXML_REFERENCE = ForesterConstants.PHYLO_XML_REFERENCE;
78 final static String PHYLOXML_REFERENCE_SHORT = "Han MV and Zmasek CM (2009), BMC Bioinformatics, 10:356";
79 final static short NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT = 3;
80 final static short NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT = 2;
81 public static final boolean NH_PARSING_IGNORE_QUOTES_DEFAULT = false;
82 static final CLADOGRAM_TYPE CLADOGRAM_TYPE_DEFAULT = CLADOGRAM_TYPE.LINED_UP;
83 final static boolean VALIDATE_AGAINST_PHYLOXML_XSD_SCJEMA_DEFAULT = true;
84 final static String BACKUP_FILE_SUFFIX = ".BAK";
85 final static double MIN_NOT_COLLAPSE_DEFAULT = 50;
86 final static Color GUI_BACKGROUND_DEFAULT = new Color( 32, 32, 32 );
87 final static Color CHECKBOX_TEXT_COLOR_DEFAULT = new Color( 220,
90 final static Color CHECKBOX_AND_BUTTON_ACTIVE_COLOR_DEFAULT = new Color( 255, 0, 0 );
91 final static Color BUTTON_TEXT_COLOR_DEFAULT = new Color( 255,
94 final static Color BUTTON_BACKGROUND_COLOR_DEFAULT = new Color( 64, 64, 64 );
95 final static Color MENU_BACKGROUND_COLOR_DEFAULT = new Color( 0, 0, 0 );
96 final static Color MENU_TEXT_COLOR_DEFAULT = new Color( 255,
99 final static Color BUTTON_BORDER_COLOR_DEFAULT = new Color( 0, 0, 0 );
100 final static Color TAB_LABEL_FOREGROUND_COLOR_SELECTED = new Color( 0, 0, 0 );
101 final static String NCBI_ALL_DATABASE_SEARCH = "http://www.ncbi.nlm.nih.gov/gquery/?term=";
102 public final static Color DOMAIN_BASE_COLOR_FOR_PDF = new Color( 100,
105 public final static Color DOMAIN_LABEL_COLOR_FOR_PDF = new Color( 150,
108 final static short DEFAULT_NODE_SHAPE_SIZE_DEFAULT = 4;
109 static final int MAX_LENGTH_FOR_COLLAPSED_NAME = 8;