// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
package org.forester.archaeopteryx;
public final class Constants {
- final static boolean __ALLOW_PHYLOGENETIC_INFERENCE = false;
- public final static boolean __RELEASE = true; // TODO remove me
- public final static boolean __SNAPSHOT_RELEASE = true; // TODO remove me
- public final static boolean __SYNTH_LF = false; // TODO remove me
+ final static boolean __ALLOW_PHYLOGENETIC_INFERENCE = true;
+ public final static boolean __RELEASE = false; // TODO remove me
+ public final static boolean __SNAPSHOT_RELEASE = false; // TODO remove me
+ public final static boolean __SYNTH_LF = false; // TODO remove me
public final static boolean ALLOW_DDBJ_BLAST = false;
public final static String PRG_NAME = "Archaeopteryx";
- final static String VERSION = "0.970 9M";
- final static String PRG_DATE = "2012.03.28";
+ final static String VERSION = "0.9899 beta";
+ final static String PRG_DATE = "140925";
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 String[] DEFAULT_FONT_CHOICES = { "Arial", "Helvetica",
+ "Verdana", "Tahoma", "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 = "phylosoft@gmail.com";
- final static int DOMAIN_STRUCTURE_E_VALUE_THR_DEFAULT_EXP = 0;
+ 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 / Constants.BUTTON_ZOOM_IN_FACTOR;
final static float BUTTON_ZOOM_IN_X_CORRECTION_FACTOR = 1.2f;
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 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, 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_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 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 APTX_WEB_SITE = "https://sites.google.com/site/cmzmasek/home/software/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 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;
+ 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.EXT_NODE_SUM_DEP;
final static boolean VALIDATE_AGAINST_PHYLOXML_XSD_SCJEMA_DEFAULT = true;
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=";
- final static short DEFAULT_NODE_SHAPE_SIZE_DEFAULT = 6;
+ 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( 150,
+ 150,
+ 150 );
+ final static short DEFAULT_NODE_SHAPE_SIZE_DEFAULT = 4;
}
git://source.jalview.org / jalview.git / blobdiff