X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FConstants.java;h=923c109bbceadcd3774a0168db1ac5a850e82e21;hb=70da437f494b483dac92a488bd3500e5add2e34e;hp=b604b463bae1ae490530b1ba9333d1898d40557b;hpb=2881a1837f3a38e7ea46fda39964f77b5b0b0e71;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/Constants.java b/forester/java/src/org/forester/archaeopteryx/Constants.java index b604b46..923c109 100644 --- a/forester/java/src/org/forester/archaeopteryx/Constants.java +++ b/forester/java/src/org/forester/archaeopteryx/Constants.java @@ -42,15 +42,15 @@ public final class Constants { 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 = "0.9802"; - final static String PRG_DATE = "130211"; + final static String VERSION = "0.988 SR"; + final static String PRG_DATE = "140416"; 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 int DOMAIN_STRUCTURE_DEFAULT_WIDTH = 100; final static String AUTHOR_EMAIL = "phyloxml@gmail.com"; - final static int DOMAIN_STRUCTURE_E_VALUE_THR_DEFAULT_EXP = 0; + 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; @@ -65,6 +65,7 @@ public final class Constants { 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"; @@ -81,8 +82,8 @@ public final class Constants { 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; @@ -108,5 +109,5 @@ public final class Constants { 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; + final static short DEFAULT_NODE_SHAPE_SIZE_DEFAULT = 4; }