forester/java/src/org/forester/archaeopteryx/AptxConstants.java

   1 // $Id:
   2 // FORESTER -- software libraries and applications
   3 // for evolutionary biology research and applications.
   4 //
   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
  11 //
  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.
  16 //
  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.
  21 //
  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
  25 //
  26 // Contact: phylosoft @ gmail . com
  27 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
  28
  29 package org.forester.archaeopteryx;
  30
  31 import java.awt.Color;
  32 import java.awt.Dimension;
  33
  34 import org.forester.archaeopteryx.Options.CLADOGRAM_TYPE;
  35 import org.forester.util.ForesterConstants;
  36
  37 public final class AptxConstants {
  38
  39     final static boolean        __ALLOW_PHYLOGENETIC_INFERENCE                                = true;
  40     public final static String  PRG_NAME                                                      = "Archaeopteryx";
  41     final static String         VERSION                                                       = "0.9921 beta";
  42     final static String         PRG_DATE                                                      = "170712";
  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_JS_WEB_SITE                                              = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx-js";
  72     final static String         APTX_MAILING_LIST                                             = "https://groups.google.com/forum/?fromgroups#!forum/archaeopteryx";
  73     final static String         APTX_DOC_SITE                                                 = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/documentation";
  74     final static String         PHYLOXML_WEB_SITE                                             = ForesterConstants.PHYLO_XML_LOCATION;
  75     final static String         PHYLOXML_REFERENCE_URL                                        = "http://www.biomedcentral.com/1471-2105/10/356/";
  76     final static String         APTX_REFERENCE_URL                                            = "http://www.biomedcentral.com/bmcbioinformatics/";
  77     final static String         APTX_REFERENCE                                                = "Zmasek...";                                                                       //TODO
  78     final static String         PHYLOXML_REFERENCE                                            = ForesterConstants.PHYLO_XML_REFERENCE;
  79     final static String         PHYLOXML_REFERENCE_SHORT                                      = "Han MV and Zmasek CM (2009), BMC Bioinformatics, 10:356";
  80     final static short          NUMBER_OF_DIGITS_AFTER_COMMA_FOR_BRANCH_LENGTH_VALUES_DEFAULT = 3;
  81     final static short          NUMBER_OF_DIGITS_AFTER_COMMA_FOR_CONFIDENCE_VALUES_DEFAULT    = 2;
  82     public static final boolean NH_PARSING_IGNORE_QUOTES_DEFAULT                              = false;
  83     static final CLADOGRAM_TYPE CLADOGRAM_TYPE_DEFAULT                                        = CLADOGRAM_TYPE.LINED_UP;
  84     final static boolean        VALIDATE_AGAINST_PHYLOXML_XSD_SCJEMA_DEFAULT                  = true;
  85     final static String         BACKUP_FILE_SUFFIX                                            = ".BAK";
  86     final static double         MIN_NOT_COLLAPSE_DEFAULT                                      = 50;
  87     final static Color          GUI_BACKGROUND_DEFAULT                                        = new Color( 32, 32, 32 );
  88     final static Color          CHECKBOX_TEXT_COLOR_DEFAULT                                   = new Color( 220,
  89                                                                                                            220,
  90                                                                                                            220 );
  91     final static Color          CHECKBOX_AND_BUTTON_ACTIVE_COLOR_DEFAULT                      = new Color( 255, 0, 0 );
  92     final static Color          BUTTON_TEXT_COLOR_DEFAULT                                     = new Color( 255,
  93                                                                                                            255,
  94                                                                                                            255 );
  95     final static Color          BUTTON_BACKGROUND_COLOR_DEFAULT                               = new Color( 64, 64, 64 );
  96     final static Color          MENU_BACKGROUND_COLOR_DEFAULT                                 = new Color( 0, 0, 0 );
  97     final static Color          MENU_TEXT_COLOR_DEFAULT                                       = new Color( 255,
  98                                                                                                            255,
  99                                                                                                            255 );
 100     final static Color          BUTTON_BORDER_COLOR_DEFAULT                                   = new Color( 0, 0, 0 );
 101     final static Color          TAB_LABEL_FOREGROUND_COLOR_SELECTED                           = new Color( 0, 0, 0 );
 102     final static String         NCBI_ALL_DATABASE_SEARCH                                      = "http://www.ncbi.nlm.nih.gov/gquery/?term=";
 103     public final static Color   DOMAIN_BASE_COLOR_FOR_PDF                                     = new Color( 100,
 104                                                                                                            100,
 105                                                                                                            100 );
 106     public final static Color   DOMAIN_LABEL_COLOR_FOR_PDF                                    = new Color( 0,
 107                                                                                                            0,
 108                                                                                                            0 );
 109     final static short          DEFAULT_NODE_SHAPE_SIZE_DEFAULT                               = 7;
 110     static final int            MAX_LENGTH_FOR_COLLAPSED_NAME = 8;
 111 }