X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FConstants.java;h=b9c91cd8354fd17b277c9a6bbb96ea3846642e40;hb=362bd0a813f302f28631d9c9447dd8aa9ee0ceda;hp=8832d0ba481c5db441822765c32ef86ab66b7b58;hpb=9dd14be21a9f6b122df48932df53b33730d398cc;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/Constants.java b/forester/java/src/org/forester/archaeopteryx/Constants.java index 8832d0b..b9c91cd 100644 --- a/forester/java/src/org/forester/archaeopteryx/Constants.java +++ b/forester/java/src/org/forester/archaeopteryx/Constants.java @@ -24,7 +24,7 @@ // 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; @@ -37,20 +37,20 @@ import org.forester.util.ForesterConstants; public final class Constants { 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 __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 = "0.971 9M"; - final static String PRG_DATE = "2012.03.29"; + 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; @@ -59,12 +59,13 @@ public final class Constants { 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"; @@ -74,15 +75,16 @@ public final class Constants { 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; @@ -103,10 +105,12 @@ public final class Constants { 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; }