// 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;
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() {
}
}
- private MainFrameApplet getMainFrameApplet() {
- return _mainframe_applet;
+ /**
+ * This method returns the current external node data which
+ * has been selected by the user by clicking the "Return ..."
+ * menu item. This method is expected to be called from Javascript or
+ * something like it.
+ *
+ * @return current external node data as String
+ */
+ public String getCurrentExternalNodesDataBuffer() {
+ return getMainFrameApplet().getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString();
}
- private String getMessage1() {
- return _message_1;
+ public int getCurrentExternalNodesDataBufferChangeCounter() {
+ return getMainFrameApplet().getCurrentTreePanel().getCurrentExternalNodesDataBufferChangeCounter();
}
- private String getMessage2() {
- return _message_2;
+ public int getCurrentExternalNodesDataBufferLength() {
+ return getMainFrameApplet().getCurrentTreePanel().getCurrentExternalNodesDataBufferAsString().length();
+ }
+
+ public String getSpeciesTreeUrlStr() {
+ return _species_tree_url_str;
}
- public String getUrlString() {
- return _url_string;
+ 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( AptxConstants.APPLET_PARAM_NAME_FOR_URL_OF_TREE_TO_LOAD ) );
+ setSpeciesTreeUrlStr( getParameter( AptxConstants.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 );
setMessage2( "[Your Java version: " + s + "]" );
repaint();
}
- final String config_filename = getParameter( Constants.APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL );
+ final String config_filename = getParameter( AptxConstants.APPLET_PARAM_NAME_FOR_CONFIG_FILE_URL );
AptxUtil.printAppletMessage( NAME, "URL for configuration file is: " + config_filename );
final Configuration configuration = new Configuration( config_filename, true, true, true );
try {
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.isValidatePhyloXmlAgainstSchema() );
+ _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(), configuration
+ .isMidpointReroot() );
+ if ( phys == null ) {
+ ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + tree_url + "] are null" );
+ }
+ else if ( phys.length < 1 ) {
+ ForesterUtil.printErrorMessage( NAME, "phylogenies from [" + tree_url + "] are empty" );
+ }
+ else {
+ AptxUtil.printAppletMessage( NAME, "loaded " + phys.length + " phylogenies from: " + tree_url );
+ }
+ 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();
getMainFrameApplet().requestFocusInWindow();
getMainFrameApplet().requestFocus();
/* GUILHEM_BEG */
- final String default_relation = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE );
+ final String default_relation = getParameter( AptxConstants.APPLET_PARAM_NAME_FOR_DEFAULT_SEQUENCE_RELATION_TYPE );
if ( default_relation != null ) {
getMainFrameApplet().getMainPanel().getControlPanel().getSequenceRelationTypeBox()
.setSelectedItem( default_relation );
}
- final String default_sequence = getParameter( Constants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
+ final String default_sequence = getParameter( AptxConstants.APPLET_PARAM_NAME_FOR_DEFAULT_QUERY_SEQUENCE );
if ( default_sequence != null ) {
getMainFrameApplet().getMainPanel().getControlPanel().getSequenceRelationBox()
.setSelectedItem( default_sequence );
- /* GUILHEM_END */
}
+ /* GUILHEM_END */
}
/**
* Prints message when initialization is finished. Called automatically.
- *
+ *
* @param g
* Graphics
*/
g.drawString( getMessage1(), 10, 40 );
}
+ @Override
+ public void start() {
+ getMainFrameApplet().getMainPanel().validate();
+ getMainFrameApplet().requestFocus();
+ getMainFrameApplet().requestFocusInWindow();
+ getMainFrameApplet().requestFocus();
+ AptxUtil.printAppletMessage( NAME, "started" );
+ }
+
+ private MainFrameApplet getMainFrameApplet() {
+ return _mainframe_applet;
+ }
+
+ private String getMessage1() {
+ return _message_1;
+ }
+
+ private String getMessage2() {
+ return _message_2;
+ }
+
private void setMessage1( final String message_1 ) {
_message_1 = message_1;
}
_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;
}
- @Override
- public void start() {
- getMainFrameApplet().getMainPanel().validate();
- getMainFrameApplet().requestFocus();
- getMainFrameApplet().requestFocusInWindow();
- getMainFrameApplet().requestFocus();
- AptxUtil.printAppletMessage( NAME, "started" );
+ private void setTreeUrlStr( final String url_string ) {
+ _tree_url_str = url_string;
}
}
git://source.jalview.org / jalview.git / blobdiff