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=038f96513541acac0157a46b18660bb0eba721a0;hpb=ff79eee1cd2e65925ada2e6fd484010122c74d22;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/Constants.java b/forester/java/src/org/forester/archaeopteryx/Constants.java index 038f965..b9c91cd 100644 --- a/forester/java/src/org/forester/archaeopteryx/Constants.java +++ b/forester/java/src/org/forester/archaeopteryx/Constants.java @@ -37,13 +37,13 @@ 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 = "0.989 beta"; - final static String PRG_DATE = "140514"; + 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 = { "Arial", "Helvetica", "Verdana", "Tahoma", "Dialog", "Lucida Sans", "SansSerif", "Sans-serif", "Sans" }; @@ -59,7 +59,7 @@ 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 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 ); @@ -76,10 +76,11 @@ public final class Constants { 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_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 = 3; @@ -104,10 +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="; + 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; }