X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FAptxConstants.java;h=775f5e6dfad392fe0dfee3037beb204232166838;hb=f6b29c53c14e1ef16e4cd614c7f9465e0073309e;hp=3a608f4a017ea2e7b7c11fc35bdfb99af1cd74d3;hpb=b0fd64a5d558885627ba7a7295d9ef612fe76cd0;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/AptxConstants.java b/forester/java/src/org/forester/archaeopteryx/AptxConstants.java index 3a608f4..775f5e6 100644 --- a/forester/java/src/org/forester/archaeopteryx/AptxConstants.java +++ b/forester/java/src/org/forester/archaeopteryx/AptxConstants.java @@ -37,15 +37,12 @@ import org.forester.util.ForesterConstants; public final class AptxConstants { 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 String PRG_NAME = "Archaeopteryx"; - final static String VERSION = "0.9909 experimental"; - final static String PRG_DATE = "160622"; + final static String VERSION = "0.9918 beta"; + final static String PRG_DATE = "161019"; final static String DEFAULT_CONFIGURATION_FILE_NAME = "_aptx_configuration_file"; final static String[] DEFAULT_FONT_CHOICES = { - "SansSerif", "Sans-serif", "Sans", "Dialog", "Lucida Sans", "Tahoma", "Helvetica", "Arial", "Verdana" }; + "Arial Unicode MS", "Dialog", "SansSerif", "Sans", "Arial", "Helvetica" }; final static boolean VERBOSE_DEFAULT = false; final static int DOMAIN_STRUCTURE_DEFAULT_WIDTH = 100; final static String AUTHOR_EMAIL = "phyloxml@gmail.com"; @@ -61,7 +58,7 @@ public final class AptxConstants { 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_PANEL_SIZE = new Dimension( 500, 540 ); 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"; @@ -69,12 +66,9 @@ public final class AptxConstants { 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 MAX_TREES_TO_LOAD = 100; - static final int US_LETTER_SIZE_X = 612; - static final int US_LETTER_SIZE_Y = 792; - 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 = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx"; + final static String APTX_MAILING_LIST = "https://groups.google.com/forum/?fromgroups#!forum/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/"; @@ -85,7 +79,7 @@ public final class AptxConstants { 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; + static final CLADOGRAM_TYPE CLADOGRAM_TYPE_DEFAULT = CLADOGRAM_TYPE.LINED_UP; final static boolean VALIDATE_AGAINST_PHYLOXML_XSD_SCJEMA_DEFAULT = true; final static String BACKUP_FILE_SUFFIX = ".BAK"; final static double MIN_NOT_COLLAPSE_DEFAULT = 50; @@ -112,4 +106,5 @@ public final class AptxConstants { 150, 150 ); final static short DEFAULT_NODE_SHAPE_SIZE_DEFAULT = 4; + static final int MAX_LENGTH_FOR_COLLAPSED_NAME = 8; }