import javax.swing.JOptionPane;
import javax.swing.text.MaskFormatter;
-import org.forester.archaeopteryx.ControlPanel.TreeDisplayType;
import org.forester.io.parsers.PhylogenyParser;
import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
import org.forester.io.parsers.nhx.NHXParser;
public final class AptxUtil {
public static enum GraphicsExportType {
- BMP( "bmp" ), GIF( "gif" ), JPG( "jpg" ), PDF( "pdf" ), PNG( "png" ), TIFF( "tif" );
+ BMP( "bmp" ),
+ GIF( "gif" ),
+ JPG( "jpg" ),
+ PDF( "pdf" ),
+ PNG( "png" ),
+ TIFF( "tif" );
private final String _suffix;
}
return false;
}
-
+
+ final static public boolean isHasAtLeast50PercentBranchLengthLargerThanZero( final Phylogeny phy ) {
+ final PhylogenyNodeIterator it = phy.iteratorPostorder();
+ int positive = 0;
+ int total = 0;
+ while ( it.hasNext() ) {
+ if ( it.next().getDistanceToParent() > 0.0 ) {
+ ++positive;
+ }
+ ++total;
+ }
+ if ( total == 0 ) {
+ return false;
+ }
+ return (((( double ) positive) / total) >= 0.5 );
+ }
+
final static public boolean isHasNoBranchLengthSmallerThanZero( final Phylogeny phy ) {
final PhylogenyNodeIterator it = phy.iteratorPostorder();
while ( it.hasNext() ) {
- final PhylogenyNode n = it.next();
+ final PhylogenyNode n = it.next();
if ( n.getDistanceToParent() < 0.0 && !n.isRoot() ) {
return false;
}
return false;
}
- final public static void launchWebBrowser( final URI uri,
- final String frame_name ) throws IOException {
-
- // This requires Java 1.6:
- // =======================
- // boolean no_desktop = false;
- // try {
- // if ( Desktop.isDesktopSupported() ) {
- // System.out.println( "desktop supported" );
- // final Desktop dt = Desktop.getDesktop();
- // dt.browse( uri );
- // }
- // else {
- // no_desktop = true;
- // }
- // }
- // catch ( final Exception ex ) {
- // ex.printStackTrace();
- // no_desktop = true;
- // }
- // catch ( final Error er ) {
- // er.printStackTrace();
- // no_desktop = true;
- // }
- // if ( no_desktop ) {
- // System.out.println( "desktop not supported" );
- try {
- openUrlInWebBrowser( uri.toString() );
- }
- catch ( final Exception e ) {
- throw new IOException( e );
- }
- // }
-
+ final public static void launchWebBrowser( final URI uri, final String frame_name ) throws IOException {
+ // This requires Java 1.6:
+ // =======================
+ // boolean no_desktop = false;
+ // try {
+ // if ( Desktop.isDesktopSupported() ) {
+ // System.out.println( "desktop supported" );
+ // final Desktop dt = Desktop.getDesktop();
+ // dt.browse( uri );
+ // }
+ // else {
+ // no_desktop = true;
+ // }
+ // }
+ // catch ( final Exception ex ) {
+ // ex.printStackTrace();
+ // no_desktop = true;
+ // }
+ // catch ( final Error er ) {
+ // er.printStackTrace();
+ // no_desktop = true;
+ // }
+ // if ( no_desktop ) {
+ // System.out.println( "desktop not supported" );
+ try {
+ openUrlInWebBrowser( uri.toString() );
+ }
+ catch ( final Exception e ) {
+ throw new IOException( e );
+ }
+ // }
}
public static Set<Taxonomy> obtainAllDistinctTaxonomies( final PhylogenyNode node ) {
final boolean internal_numbers_are_confidences,
final TAXONOMY_EXTRACTION taxonomy_extraction,
final boolean midpoint_reroot )
- throws FileNotFoundException, IOException {
+ throws FileNotFoundException, IOException {
final PhylogenyParser parser;
boolean nhx_or_nexus = false;
if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {
final public static void showErrorMessage( final Component parent, final String error_msg ) {
printAppletMessage( AptxConstants.PRG_NAME, error_msg );
- JOptionPane.showMessageDialog( parent, error_msg, "[" + AptxConstants.PRG_NAME + " " + AptxConstants.VERSION
- + "] Error", JOptionPane.ERROR_MESSAGE );
+ JOptionPane.showMessageDialog( parent,
+ error_msg,
+ "[" + AptxConstants.PRG_NAME + " " + AptxConstants.VERSION + "] Error",
+ JOptionPane.ERROR_MESSAGE );
}
public static void writePhylogenyToGraphicsFile( final File intree,
final int width,
final int height,
final GraphicsExportType type,
- final Configuration config ) throws IOException {
+ final Configuration config )
+ throws IOException {
final PhylogenyParser parser = ParserUtils.createParserDependingOnFileType( intree, true );
Phylogeny[] phys = null;
phys = PhylogenyMethods.readPhylogenies( parser, intree );
final int width,
final int height,
final GraphicsExportType type,
- final Configuration config ) throws IOException {
+ final Configuration config )
+ throws IOException {
final Phylogeny[] phys = new Phylogeny[ 1 ];
phys[ 0 ] = phy;
final MainFrameApplication mf = MainFrameApplication.createInstance( phys, config );
- AptxUtil.writePhylogenyToGraphicsFileNonInteractive( outfile, width, height, mf.getMainPanel()
- .getCurrentTreePanel(), mf.getMainPanel().getControlPanel(), type, mf.getOptions() );
+ AptxUtil.writePhylogenyToGraphicsFileNonInteractive( outfile,
+ width,
+ height,
+ mf.getMainPanel().getCurrentTreePanel(),
+ mf.getMainPanel().getControlPanel(),
+ type,
+ mf.getOptions() );
mf.end();
}
final TreePanel tree_panel,
final ControlPanel ac,
final GraphicsExportType type,
- final Options options ) throws IOException {
+ final Options options )
+ throws IOException {
tree_panel.calcParametersForPainting( width, height );
tree_panel.resetPreferredSize();
tree_panel.repaint();
return c;
}
- final private static void openUrlInWebBrowser( final String url ) throws IOException, ClassNotFoundException,
- SecurityException, NoSuchMethodException, IllegalArgumentException, IllegalAccessException,
- InvocationTargetException, InterruptedException {
+ final private static void openUrlInWebBrowser( final String url )
+ throws IOException, ClassNotFoundException, SecurityException, NoSuchMethodException,
+ IllegalArgumentException, IllegalAccessException, InvocationTargetException, InterruptedException {
final String os = System.getProperty( "os.name" );
final Runtime runtime = Runtime.getRuntime();
if ( os.toLowerCase().startsWith( "win" ) ) {
final Configuration configuration,
final MainPanel main_panel ) {
if ( phys.length > AptxConstants.MAX_TREES_TO_LOAD ) {
- JOptionPane.showMessageDialog( main_panel, "Attempt to load " + phys.length
- + " 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 );
+ JOptionPane.showMessageDialog( main_panel,
+ "Attempt to load " + phys.length
+ + " 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 ) {
}
return str_array;
}
-
- final static String[] getAllPossibleRanks(final Map<String, Integer> present_ranks) {
+
+ final static String[] getAllPossibleRanks( final Map<String, Integer> present_ranks ) {
final String[] str_array = new String[ TaxonomyUtil.TAXONOMY_RANKS_LIST.size() - 2 ];
int i = 0;
for( final String e : TaxonomyUtil.TAXONOMY_RANKS_LIST ) {
if ( !e.equals( TaxonomyUtil.UNKNOWN ) && !e.equals( TaxonomyUtil.OTHER ) ) {
if ( present_ranks != null && present_ranks.containsKey( e ) ) {
- str_array[ i++ ] = e + " (" + present_ranks.get(e) + ")";
+ str_array[ i++ ] = e + " (" + present_ranks.get( e ) + ")";
}
else {
str_array[ i++ ] = e;
}
return false;
}
- final static void lookAtRealBranchLengthsForAptxControlSettings( final Phylogeny t,
- final ControlPanel cp ) {
+
+ 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.setTreeDisplayType( TreeDisplayType.CLADOGRAM );
+ cp.setTreeDisplayType( Options.PHYLOGENY_DISPLAY_TYPE.CLADOGRAM );
cp.setDrawPhylogramEnabled( false );
}
else {
final boolean has_all_bl = AptxUtil.isHasNoBranchLengthSmallerThanZero( t );
- if (has_all_bl) {
- cp.setTreeDisplayType( TreeDisplayType.UNALIGNED_PHYLOGRAM );
+ if ( has_all_bl ) {
+ cp.setTreeDisplayType( Options.PHYLOGENY_DISPLAY_TYPE.UNALIGNED_PHYLOGRAM );
}
-
if ( cp.getDisplayAsUnalignedPhylogramRb() != null ) {
cp.setDrawPhylogramEnabled( true );
}
}
}
}
- final static void lookAtSomeTreePropertiesForAptxControlSettings( final Phylogeny t,
- final ControlPanel atv_control,
+
+ public final static void lookAtSomeTreePropertiesForAptxControlSettings( final Phylogeny t,
+ final ControlPanel cp,
final Configuration configuration ) {
if ( ( t != null ) && !t.isEmpty() ) {
final boolean has_bl = AptxUtil.isHasAtLeastOneBranchLengthLargerThanZero( t );
if ( !has_bl ) {
- atv_control.setTreeDisplayType( TreeDisplayType.CLADOGRAM );
- atv_control.setDrawPhylogramEnabled( false );
+ cp.setTreeDisplayType( Options.PHYLOGENY_DISPLAY_TYPE.CLADOGRAM );
+ cp.setDrawPhylogramEnabled( false );
}
if ( t.getFirstExternalNode().getBranchData().getBranchColor() != null
- && atv_control.getUseVisualStylesCb() != null ) {
- atv_control.getUseVisualStylesCb().setSelected( true );
+ && cp.getUseVisualStylesCb() != null ) {
+ cp.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 );
+ && t.getFirstExternalNode().getBranchData().getBranchWidth()
+ .getValue() != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE
+ && cp.getUseBranchWidthsCb() != null ) {
+ cp.getUseBranchWidthsCb().setSelected( true );
}
-
-
if ( configuration.doGuessCheckOption( Configuration.display_as_phylogram ) ) {
- if ( atv_control.getDisplayAsAlignedPhylogramRb() != null ) {
+ if ( cp.getDisplayAsAlignedPhylogramRb() != null ) {
if ( has_bl ) {
- final boolean has_all_bl = AptxUtil.isHasNoBranchLengthSmallerThanZero( t );
- if (has_all_bl) {
- atv_control.setTreeDisplayType( TreeDisplayType.UNALIGNED_PHYLOGRAM );
+ final boolean has_mostly_bl = AptxUtil.isHasAtLeast50PercentBranchLengthLargerThanZero( t );
+ if ( has_mostly_bl ) {
+ cp.setTreeDisplayType( Options.PHYLOGENY_DISPLAY_TYPE.UNALIGNED_PHYLOGRAM );
}
-
- atv_control.setDrawPhylogramEnabled( true );
+ cp.setDrawPhylogramEnabled( true );
}
else {
- atv_control.setTreeDisplayType( TreeDisplayType.CLADOGRAM );
+ cp.setTreeDisplayType( Options.PHYLOGENY_DISPLAY_TYPE.CLADOGRAM );
}
}
}
if ( configuration.doGuessCheckOption( Configuration.write_confidence_values ) ) {
- if ( atv_control.getWriteConfidenceCb() != null ) {
+ if ( cp.getWriteConfidenceCb() != null ) {
if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( t ) ) {
- atv_control.setCheckbox( Configuration.write_confidence_values, true );
+ cp.setCheckbox( Configuration.write_confidence_values, true );
}
else {
- atv_control.setCheckbox( Configuration.write_confidence_values, false );
+ cp.setCheckbox( Configuration.write_confidence_values, false );
}
}
}
if ( configuration.doGuessCheckOption( Configuration.write_events ) ) {
- if ( atv_control.getShowEventsCb() != null ) {
+ if ( cp.getShowEventsCb() != null ) {
if ( AptxUtil.isHasAtLeastNodeWithEvent( t ) ) {
- atv_control.setCheckbox( Configuration.write_events, true );
+ cp.setCheckbox( Configuration.write_events, true );
}
else {
- atv_control.setCheckbox( Configuration.write_events, false );
+ cp.setCheckbox( Configuration.write_events, false );
}
}
}
final static void openWebsite( final String url ) throws IOException {
try {
- AptxUtil.launchWebBrowser( new URI( url ), AptxConstants.PRG_NAME );
+ AptxUtil.launchWebBrowser( new URI( url ), 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 [" + AptxConstants.PRG_NAME + " " + AptxConstants.VERSION + "]",
- JOptionPane.ERROR_MESSAGE );
+ "Out of Memory Error [" + AptxConstants.PRG_NAME + " " + AptxConstants.VERSION
+ + "]",
+ JOptionPane.ERROR_MESSAGE );
System.exit( -1 );
}
for( final StackTraceElement s : e.getStackTrace() ) {
sb.append( s + "\n" );
}
- JOptionPane
- .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 );
+ JOptionPane.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 );
}
"An unexpected exception has occured. \nPlease contact: "
+ AptxConstants.AUTHOR_EMAIL + " \nException: " + e.getLocalizedMessage()
+ "\n" + sb,
- "Unexpected Exception [" + AptxConstants.PRG_NAME + AptxConstants.VERSION + "]",
- JOptionPane.ERROR_MESSAGE );
+ "Unexpected Exception [" + AptxConstants.PRG_NAME + AptxConstants.VERSION + "]",
+ JOptionPane.ERROR_MESSAGE );
}
final static String writePhylogenyToGraphicsByteArrayOutputStream( final ByteArrayOutputStream baos,
final TreePanel tree_panel,
final ControlPanel ac,
final GraphicsExportType type,
- final Options options ) throws IOException {
-
+ final Options options )
+ throws IOException {
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 TreePanel tree_panel,
final ControlPanel ac,
final GraphicsExportType type,
- final Options options ) throws IOException {
-
+ final Options options )
+ throws IOException {
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();
-// }
+ // if ( !options.isGraphicsExportUsingActualSize() ) {
+ // width = options.getPrintSizeX();
+ // height = options.getPrintSizeY();
+ // }
/*else*/ if ( options.isGraphicsExportVisibleOnly() ) {
visible = tree_panel.getVisibleRect();
width = visible.width;
writer.write( null, iio_image, image_write_param );
}
- final static Map<String, Integer> getRankCounts(final Phylogeny tree) {
+ final static Map<String, Integer> getRankCounts( final Phylogeny tree ) {
final Map<String, Integer> present_ranks = new HashMap<String, Integer>();
-
if ( ( tree != null ) && !tree.isEmpty() ) {
for( final PhylogenyNodeIterator it = tree.iteratorPostorder(); it.hasNext(); ) {
final PhylogenyNode n = it.next();
if ( !n.isExternal() && n.getNodeData().isHasTaxonomy()
&& !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getRank() ) && !n.isRoot() ) {
final String rank = n.getNodeData().getTaxonomy().getRank().toLowerCase();
- if (present_ranks.containsKey( rank ) ) {
+ if ( present_ranks.containsKey( rank ) ) {
present_ranks.put( rank, present_ranks.get( rank ) + 1 );
}
else {
git://source.jalview.org / jalview.git / blobdiff