import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
-import java.io.InputStream;
import java.lang.reflect.InvocationTargetException;
import java.lang.reflect.Method;
import java.net.URI;
import java.net.URL;
-import java.net.URLConnection;
+import java.security.KeyManagementException;
+import java.security.NoSuchAlgorithmException;
import java.text.ParseException;
import java.util.Arrays;
import java.util.HashSet;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.data.BranchWidth;
import org.forester.phylogeny.data.Confidence;
import org.forester.phylogeny.data.Taxonomy;
-import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
-import org.forester.phylogeny.factories.PhylogenyFactory;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
import org.forester.util.AsciiHistogram;
import org.forester.util.DescriptiveStatistics;
}
}
private final static String[] AVAILABLE_FONT_FAMILIES_SORTED = GraphicsEnvironment.getLocalGraphicsEnvironment()
- .getAvailableFontFamilyNames();
+ .getAvailableFontFamilyNames();
static {
Arrays.sort( AVAILABLE_FONT_FAMILIES_SORTED );
}
}
return false;
}
+
+ final static public boolean isHasNoBranchLengthSmallerThanZero( final Phylogeny phy ) {
+ final PhylogenyNodeIterator it = phy.iteratorPostorder();
+ while ( it.hasNext() ) {
+ final PhylogenyNode n = it.next();
+ if ( n.getDistanceToParent() < 0.0 && !n.isRoot() ) {
+ return false;
+ }
+ }
+ return true;
+ }
final static public boolean isHasAtLeastOneBranchWithSupportSD( final Phylogeny phy ) {
final PhylogenyNodeIterator it = phy.iteratorPostorder();
final boolean internal_numbers_are_confidences,
final TAXONOMY_EXTRACTION taxonomy_extraction,
final boolean midpoint_reroot )
- throws FileNotFoundException, IOException {
- final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ throws FileNotFoundException, IOException {
final PhylogenyParser parser;
boolean nhx_or_nexus = false;
if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {
}
}
AptxUtil.printAppletMessage( "Archaeopteryx", "parser is " + parser.getName() );
- final URLConnection url_connection = url.openConnection();
- url_connection.setDefaultUseCaches( false );
- final InputStream i = url_connection.getInputStream();
- final Phylogeny[] phys = factory.create( i, parser );
- i.close();
+ Phylogeny[] phys = null;
+ try {
+ phys = ForesterUtil.readPhylogeniesFromUrl( url, parser );
+ }
+ catch ( final KeyManagementException e ) {
+ throw new IOException( e.getMessage() );
+ }
+ catch ( final NoSuchAlgorithmException e ) {
+ throw new IOException( e.getMessage() );
+ }
if ( phys != null ) {
if ( nhx_or_nexus && internal_numbers_are_confidences ) {
for( final Phylogeny phy : phys ) {
}
final public static void showErrorMessage( final Component parent, final String error_msg ) {
- printAppletMessage( Constants.PRG_NAME, error_msg );
- JOptionPane.showMessageDialog( parent, error_msg, "[" + Constants.PRG_NAME + " " + Constants.VERSION
- + "] Error", JOptionPane.ERROR_MESSAGE );
+ printAppletMessage( AptxConstants.PRG_NAME, error_msg );
+ JOptionPane.showMessageDialog( parent, error_msg, "[" + AptxConstants.PRG_NAME + " " + AptxConstants.VERSION
+ + "] Error", JOptionPane.ERROR_MESSAGE );
}
public static void writePhylogenyToGraphicsFile( final File intree,
phys[ 0 ] = phy;
final MainFrameApplication mf = MainFrameApplication.createInstance( phys, config );
AptxUtil.writePhylogenyToGraphicsFileNonInteractive( outfile, width, height, mf.getMainPanel()
- .getCurrentTreePanel(), mf.getMainPanel().getControlPanel(), type, mf.getOptions() );
+ .getCurrentTreePanel(), mf.getMainPanel().getControlPanel(), type, mf.getOptions() );
mf.end();
}
}
final private static void openUrlInWebBrowser( final String url ) throws IOException, ClassNotFoundException,
- SecurityException, NoSuchMethodException, IllegalArgumentException, IllegalAccessException,
- InvocationTargetException, InterruptedException {
+ SecurityException, NoSuchMethodException, IllegalArgumentException, IllegalAccessException,
+ InvocationTargetException, InterruptedException {
final String os = System.getProperty( "os.name" );
final Runtime runtime = Runtime.getRuntime();
if ( os.toLowerCase().startsWith( "win" ) ) {
final String full_path,
final Configuration configuration,
final MainPanel main_panel ) {
- if ( phys.length > Constants.MAX_TREES_TO_LOAD ) {
+ if ( phys.length > AptxConstants.MAX_TREES_TO_LOAD ) {
JOptionPane.showMessageDialog( main_panel, "Attempt to load " + phys.length
- + " phylogenies,\ngoing to load only the first " + Constants.MAX_TREES_TO_LOAD, Constants.PRG_NAME
- + " more than " + Constants.MAX_TREES_TO_LOAD + " phylogenies", JOptionPane.WARNING_MESSAGE );
+ + " phylogenies,\ngoing to load only the first " + AptxConstants.MAX_TREES_TO_LOAD, AptxConstants.PRG_NAME
+ + " more than " + AptxConstants.MAX_TREES_TO_LOAD + " phylogenies", JOptionPane.WARNING_MESSAGE );
}
int i = 1;
for( final Phylogeny phy : phys ) {
if ( !phy.isEmpty() ) {
- if ( i <= Constants.MAX_TREES_TO_LOAD ) {
+ if ( i <= AptxConstants.MAX_TREES_TO_LOAD ) {
String my_name = "";
String my_name_for_file = "";
if ( phys.length > 1 ) {
System.out.println( t.toString() );
}
desc.append( "\n" );
- final DescriptiveStatistics bs = PhylogenyMethods.calculatBranchLengthStatistics( phy );
+ final DescriptiveStatistics bs = PhylogenyMethods.calculateBranchLengthStatistics( phy );
if ( bs.getN() > 3 ) {
desc.append( "\n" );
desc.append( "Branch-length statistics: " );
desc.append( histo.toStringBuffer( 12, '#', 40, 7, " " ) );
}
}
- final DescriptiveStatistics ds = PhylogenyMethods.calculatNumberOfDescendantsPerNodeStatistics( phy );
+ final DescriptiveStatistics ds = PhylogenyMethods.calculateNumberOfDescendantsPerNodeStatistics( phy );
if ( ds.getN() > 2 ) {
desc.append( "\n" );
desc.append( "Descendants per node statistics: " );
}
List<DescriptiveStatistics> css = null;
try {
- css = PhylogenyMethods.calculatConfidenceStatistics( phy );
+ css = PhylogenyMethods.calculateConfidenceStatistics( phy );
}
catch ( final IllegalArgumentException e ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, e.getMessage() );
+ ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, e.getMessage() );
}
if ( ( css != null ) && ( css.size() > 0 ) ) {
desc.append( "\n" );
*/
final static void dieWithSystemError( final String message ) {
System.out.println();
- System.out.println( Constants.PRG_NAME + " encountered the following system error: " + message );
+ System.out.println( AptxConstants.PRG_NAME + " encountered the following system error: " + message );
System.out.println( "Please contact the authors." );
- System.out.println( Constants.PRG_NAME + " needs to close." );
+ System.out.println( AptxConstants.PRG_NAME + " needs to close." );
System.out.println();
System.exit( -1 );
}
}
return false;
}
-
+ final static void lookAtRealBranchLengthsForAptxControlSettings( final Phylogeny t,
+ final ControlPanel cp ) {
+ if ( ( t != null ) && !t.isEmpty() ) {
+ final boolean has_bl = AptxUtil.isHasAtLeastOneBranchLengthLargerThanZero( t );
+
+ if ( !has_bl ) {
+ cp.setDrawPhylogram( false );
+ cp.setDrawPhylogramEnabled( false );
+ }
+ else {
+ final boolean has_all_bl = AptxUtil.isHasNoBranchLengthSmallerThanZero( t );
+ cp.setDrawPhylogram( has_all_bl );
+ if ( cp.getDisplayAsPhylogramCb() != null ) {
+ cp.setDrawPhylogramEnabled( true );
+ }
+ }
+ }
+ }
final static void lookAtSomeTreePropertiesForAptxControlSettings( final Phylogeny t,
final ControlPanel atv_control,
final Configuration configuration ) {
if ( ( t != null ) && !t.isEmpty() ) {
- if ( !AptxUtil.isHasAtLeastOneBranchLengthLargerThanZero( t ) ) {
+ final boolean has_bl = AptxUtil.isHasAtLeastOneBranchLengthLargerThanZero( t );
+ if ( !has_bl ) {
atv_control.setDrawPhylogram( false );
atv_control.setDrawPhylogramEnabled( false );
}
+ if ( t.getFirstExternalNode().getBranchData().getBranchColor() != null
+ && atv_control.getUseVisualStylesCb() != null ) {
+ atv_control.getUseVisualStylesCb().setSelected( true );
+ }
+ if ( t.getFirstExternalNode().getBranchData().getBranchWidth() != null
+ && t.getFirstExternalNode().getBranchData().getBranchWidth().getValue()
+ != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE
+ && atv_control.getUseBranchWidthsCb() != null ) {
+ atv_control.getUseBranchWidthsCb().setSelected( true );
+ }
+
+
if ( configuration.doGuessCheckOption( Configuration.display_as_phylogram ) ) {
if ( atv_control.getDisplayAsPhylogramCb() != null ) {
- if ( AptxUtil.isHasAtLeastOneBranchLengthLargerThanZero( t ) ) {
- atv_control.setDrawPhylogram( true );
+ if ( has_bl ) {
+ final boolean has_all_bl = AptxUtil.isHasNoBranchLengthSmallerThanZero( t );
+
+ atv_control.setDrawPhylogram( has_all_bl );
atv_control.setDrawPhylogramEnabled( true );
}
else {
final static void openWebsite( final String url, final boolean is_applet, final JApplet applet ) throws IOException {
try {
- AptxUtil.launchWebBrowser( new URI( url ), is_applet, applet, Constants.PRG_NAME );
+ AptxUtil.launchWebBrowser( new URI( url ), is_applet, applet, AptxConstants.PRG_NAME );
}
catch ( final Exception e ) {
throw new IOException( e );
JOptionPane.showMessageDialog( null,
"Java memory allocation might be too small, try \"-Xmx2048m\" java command line option"
+ "\n\nError: " + e.getLocalizedMessage(),
- "Out of Memory Error [" + Constants.PRG_NAME + " " + Constants.VERSION + "]",
- JOptionPane.ERROR_MESSAGE );
+ "Out of Memory Error [" + AptxConstants.PRG_NAME + " " + AptxConstants.VERSION + "]",
+ JOptionPane.ERROR_MESSAGE );
System.exit( -1 );
}
sb.append( s + "\n" );
}
JOptionPane
- .showMessageDialog( null,
- "An unexpected (possibly severe) error has occured - terminating. \nPlease contact: "
- + Constants.AUTHOR_EMAIL + " \nError: " + e.getLocalizedMessage() + "\n"
- + sb,
- "Unexpected Severe Error [" + Constants.PRG_NAME + " " + Constants.VERSION + "]",
+ .showMessageDialog( null,
+ "An unexpected (possibly severe) error has occured - terminating. \nPlease contact: "
+ + AptxConstants.AUTHOR_EMAIL + " \nError: " + e.getLocalizedMessage() + "\n"
+ + sb,
+ "Unexpected Severe Error [" + AptxConstants.PRG_NAME + " " + AptxConstants.VERSION + "]",
JOptionPane.ERROR_MESSAGE );
System.exit( -1 );
}
}
JOptionPane.showMessageDialog( null,
"An unexpected exception has occured. \nPlease contact: "
- + Constants.AUTHOR_EMAIL + " \nException: " + e.getLocalizedMessage()
+ + AptxConstants.AUTHOR_EMAIL + " \nException: " + e.getLocalizedMessage()
+ "\n" + sb,
- "Unexpected Exception [" + Constants.PRG_NAME + Constants.VERSION + "]",
- JOptionPane.ERROR_MESSAGE );
+ "Unexpected Exception [" + AptxConstants.PRG_NAME + AptxConstants.VERSION + "]",
+ JOptionPane.ERROR_MESSAGE );
}
final static String writePhylogenyToGraphicsByteArrayOutputStream( final ByteArrayOutputStream baos,
final ControlPanel ac,
final GraphicsExportType type,
final Options options ) throws IOException {
- if ( !options.isGraphicsExportUsingActualSize() ) {
- if ( options.isGraphicsExportVisibleOnly() ) {
- throw new IllegalArgumentException( "cannot export visible rectangle only without exporting in actual size" );
- }
- tree_panel.calcParametersForPainting( options.getPrintSizeX(), options.getPrintSizeY() );
- tree_panel.resetPreferredSize();
- tree_panel.repaint();
- }
+
final RenderingHints rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING,
RenderingHints.VALUE_RENDER_QUALITY );
rendering_hints.put( RenderingHints.KEY_COLOR_RENDERING, RenderingHints.VALUE_COLOR_RENDER_QUALITY );
return "";
}
Rectangle visible = null;
- if ( !options.isGraphicsExportUsingActualSize() ) {
- width = options.getPrintSizeX();
- height = options.getPrintSizeY();
- }
- else if ( options.isGraphicsExportVisibleOnly() ) {
+// if ( !options.isGraphicsExportUsingActualSize() ) {
+// width = options.getPrintSizeX();
+// height = options.getPrintSizeY();
+// }
+ /* else*/ if ( options.isGraphicsExportVisibleOnly() ) {
visible = tree_panel.getVisibleRect();
width = visible.width;
height = visible.height;
final ControlPanel ac,
final GraphicsExportType type,
final Options options ) throws IOException {
- if ( !options.isGraphicsExportUsingActualSize() ) {
- if ( options.isGraphicsExportVisibleOnly() ) {
- throw new IllegalArgumentException( "cannot export visible rectangle only without exporting in actual size" );
- }
- tree_panel.calcParametersForPainting( options.getPrintSizeX(), options.getPrintSizeY() );
- tree_panel.resetPreferredSize();
- tree_panel.repaint();
- }
+
final RenderingHints rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING,
RenderingHints.VALUE_RENDER_QUALITY );
rendering_hints.put( RenderingHints.KEY_COLOR_RENDERING, RenderingHints.VALUE_COLOR_RENDER_QUALITY );
throw new IOException( "\"" + file_name + "\" is a directory" );
}
Rectangle visible = null;
- if ( !options.isGraphicsExportUsingActualSize() ) {
- width = options.getPrintSizeX();
- height = options.getPrintSizeY();
- }
- else if ( options.isGraphicsExportVisibleOnly() ) {
+// if ( !options.isGraphicsExportUsingActualSize() ) {
+// width = options.getPrintSizeX();
+// height = options.getPrintSizeY();
+// }
+ /*else*/ if ( options.isGraphicsExportVisibleOnly() ) {
visible = tree_panel.getVisibleRect();
width = visible.width;
height = visible.height;
git://source.jalview.org / jalview.git / blobdiff