public class ArchaeopteryxA extends JApplet {
- private static final long serialVersionUID = 2314899014580484146L;
- private final static Color background_color = new Color( 0, 0, 0 );
- private final static Color font_color = new Color( 0, 255, 0 );
- private final static Color ex_background_color = new Color( 0, 0, 0 );
- private final static Color ex_font_color = new Color( 255, 0, 0 );
- private final static Font font = new Font( Configuration.getDefaultFontFamilyName(), Font.BOLD, 9 );
+ private static final long serialVersionUID = 2314899014580484146L;
+ private final static Color background_color = new Color( 0, 0, 0 );
+ private final static Color font_color = new Color( 0, 255, 0 );
+ private final static Color ex_background_color = new Color( 0, 0, 0 );
+ private final static Color ex_font_color = new Color( 255, 0, 0 );
+ private final static Font font = new Font( Configuration.getDefaultFontFamilyName(), Font.BOLD, 9 );
private MainFrameApplet _mainframe_applet;
- private String _url_string = "";
- private String _message_1 = "";
- private String _message_2 = "";
- public final static String NAME = "ArchaeopteryxA";
+ private String _tree_url_str = "";
+ private String _species_tree_url_str = "";
+ private String _message_1 = "";
+ private String _message_2 = "";
+ public final static String NAME = "ArchaeopteryxA";
@Override
public void destroy() {
return getMainFrameApplet().getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();
}
- public String getUrlString() {
- return _url_string;
+ public String getSpeciesTreeUrlStr() {
+ return _species_tree_url_str;
+ }
+
+ public String getTreeUrlStr() {
+ return _tree_url_str;
}
@Override
public void init() {
boolean has_exception = false;
setName( NAME );
- setUrlString( getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD ) );
- AptxUtil.printAppletMessage( NAME, "URL of phylogenies to load: \"" + getUrlString() + "\"" );
+ setTreeUrlStr( getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD ) );
+ setSpeciesTreeUrlStr( getParameter( Constants.APPLET_PARAM_NAME_FOR_URL_OF_SPECIES_TREE_TO_LOAD ) );
+ if ( !ForesterUtil.isEmpty( getTreeUrlStr() ) ) {
+ AptxUtil.printAppletMessage( NAME, "URL of tree(s) to load: " + getTreeUrlStr() );
+ }
+ else {
+ ForesterUtil.printErrorMessage( NAME, "no URL for tree(s) to load!" );
+ setBackground( ex_background_color );
+ setForeground( ex_font_color );
+ has_exception = true;
+ setMessage1( "no URL for tree(s) to load" );
+ repaint();
+ }
+ if ( !ForesterUtil.isEmpty( getSpeciesTreeUrlStr() ) ) {
+ AptxUtil.printAppletMessage( NAME, "URL of species tree to load: " + getSpeciesTreeUrlStr() );
+ }
setBackground( background_color );
setForeground( font_color );
setFont( font );
UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
}
setVisible( false );
- _mainframe_applet = new MainFrameApplet( this, configuration );
- URL url = null;
- url = new URL( getUrlString() );
- final Phylogeny[] phys = AptxUtil.readPhylogeniesFromUrl( url, configuration
+ _mainframe_applet = new MainFrameApplet( this, configuration, getSpeciesTreeUrlStr() );
+ final URL tree_url = new URL( getTreeUrlStr() );
+ final Phylogeny[] phys = AptxUtil.readPhylogeniesFromUrl( tree_url, configuration
.isValidatePhyloXmlAgainstSchema(), configuration.isReplaceUnderscoresInNhParsing(), configuration
- .isInternalNumberAreConfidenceForNhParsing(), configuration.getTaxonomyExtraction() );
+ .isInternalNumberAreConfidenceForNhParsing(), configuration.getTaxonomyExtraction(), configuration
+ .isMidpointReroot() );
+ AptxUtil.printAppletMessage( ArchaeopteryxA.NAME, "loaded " + phys.length + " phylogenies from: "
+ + tree_url );
AptxUtil.addPhylogeniesToTabs( phys,
- new File( url.getFile() ).getName(),
- getUrlString(),
+ new File( tree_url.getFile() ).getName(),
+ getTreeUrlStr(),
getMainFrameApplet().getConfiguration(),
getMainFrameApplet().getMainPanel() );
getMainFrameApplet().getMainPanel().getControlPanel().showWholeAll();
if ( default_sequence != null ) {
getMainFrameApplet().getMainPanel().getControlPanel().getSequenceRelationBox()
.setSelectedItem( default_sequence );
- /* GUILHEM_END */
}
+ /* GUILHEM_END */
}
/**
_message_2 = message_2;
}
- private void setUrlString( final String url_string ) {
- _url_string = url_string;
+ private void setSpeciesTreeUrlStr( final String url_string ) {
+ _species_tree_url_str = url_string;
+ }
+
+ private void setTreeUrlStr( final String url_string ) {
+ _tree_url_str = url_string;
}
}