package org.forester.archaeopteryx;
+import java.awt.Color;
import java.awt.Component;
import java.awt.Graphics2D;
import java.awt.GraphicsEnvironment;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.data.Confidence;
import org.forester.phylogeny.data.Taxonomy;
import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
import org.forester.phylogeny.factories.PhylogenyFactory;
public final class AptxUtil {
+ public static enum GraphicsExportType {
+ BMP( "bmp" ), GIF( "gif" ), JPG( "jpg" ), PDF( "pdf" ), PNG( "png" ), TIFF( "tif" );
+
+ private final String _suffix;
+
+ private GraphicsExportType( final String suffix ) {
+ _suffix = suffix;
+ }
+
+ @Override
+ public String toString() {
+ return _suffix;
+ }
+ }
private final static String[] AVAILABLE_FONT_FAMILIES_SORTED = GraphicsEnvironment.getLocalGraphicsEnvironment()
.getAvailableFontFamilyNames();
static {
Arrays.sort( AVAILABLE_FONT_FAMILIES_SORTED );
}
+ final public static Color calculateColorFromString( final String str, final boolean is_taxonomy ) {
+ final String my_str = str.toUpperCase();
+ char first = my_str.charAt( 0 );
+ char second = ' ';
+ char third = ' ';
+ if ( my_str.length() > 1 ) {
+ if ( is_taxonomy ) {
+ second = my_str.charAt( 1 );
+ }
+ else {
+ second = my_str.charAt( my_str.length() - 1 );
+ }
+ if ( is_taxonomy ) {
+ if ( my_str.length() > 2 ) {
+ if ( my_str.indexOf( " " ) > 0 ) {
+ third = my_str.charAt( my_str.indexOf( " " ) + 1 );
+ }
+ else {
+ third = my_str.charAt( 2 );
+ }
+ }
+ }
+ else if ( my_str.length() > 2 ) {
+ third = my_str.charAt( ( my_str.length() - 1 ) / 2 );
+ }
+ }
+ first = normalizeCharForRGB( first );
+ second = normalizeCharForRGB( second );
+ third = normalizeCharForRGB( third );
+ if ( ( first > 235 ) && ( second > 235 ) && ( third > 235 ) ) {
+ first = 0;
+ }
+ else if ( ( first < 60 ) && ( second < 60 ) && ( third < 60 ) ) {
+ second = 255;
+ }
+ return new Color( first, second, third );
+ }
+
public static MaskFormatter createMaskFormatter( final String s ) {
MaskFormatter formatter = null;
try {
/**
* Returns true if at least one branch has a length larger than zero.
- *
- *
+ *
+ *
* @param phy
*/
final static public boolean isHasAtLeastOneBranchLengthLargerThanZero( final Phylogeny phy ) {
return false;
}
+ final static public boolean isHasAtLeastOneBranchWithSupportSD( final Phylogeny phy ) {
+ final PhylogenyNodeIterator it = phy.iteratorPostorder();
+ while ( it.hasNext() ) {
+ final PhylogenyNode n = it.next();
+ if ( n.getBranchData().isHasConfidences() ) {
+ final List<Confidence> c = n.getBranchData().getConfidences();
+ for( final Confidence confidence : c ) {
+ if ( confidence.getStandardDeviation() > 0 ) {
+ return true;
+ }
+ }
+ }
+ }
+ return false;
+ }
+
final static public boolean isHasAtLeastOneBranchWithSupportValues( final Phylogeny phy ) {
final PhylogenyNodeIterator it = phy.iteratorPostorder();
while ( it.hasNext() ) {
return false;
}
+ final static public boolean isHasAtLeastOneNodeWithScientificName( final Phylogeny phy ) {
+ final PhylogenyNodeIterator it = phy.iteratorPostorder();
+ while ( it.hasNext() ) {
+ final PhylogenyNode n = it.next();
+ if ( n.getNodeData().isHasTaxonomy()
+ && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ final static public boolean isHasAtLeastOneNodeWithSequenceAnnotation( final Phylogeny phy ) {
+ final PhylogenyNodeIterator it = phy.iteratorPostorder();
+ while ( it.hasNext() ) {
+ final PhylogenyNode n = it.next();
+ if ( n.getNodeData().isHasSequence()
+ && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getAnnotations() ) ) {
+ return true;
+ }
+ }
+ return false;
+ }
+
final public static void launchWebBrowser( final URI uri,
final boolean is_applet,
final JApplet applet,
System.out.println( "[" + name + "] > " + message );
}
+ final public static Phylogeny[] readPhylogeniesFromUrl( final URL url,
+ final boolean phyloxml_validate_against_xsd,
+ final boolean replace_underscores,
+ final boolean internal_numbers_are_confidences,
+ final TAXONOMY_EXTRACTION taxonomy_extraction,
+ final boolean midpoint_reroot )
+ throws FileNotFoundException, IOException {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final PhylogenyParser parser;
+ boolean nhx_or_nexus = false;
+ if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {
+ parser = new TolParser();
+ }
+ else {
+ parser = ParserUtils.createParserDependingOnUrlContents( url, phyloxml_validate_against_xsd );
+ if ( parser instanceof NHXParser ) {
+ nhx_or_nexus = true;
+ final NHXParser nhx = ( NHXParser ) parser;
+ nhx.setReplaceUnderscores( replace_underscores );
+ nhx.setIgnoreQuotes( false );
+ nhx.setTaxonomyExtraction( taxonomy_extraction );
+ }
+ else if ( parser instanceof NexusPhylogeniesParser ) {
+ nhx_or_nexus = true;
+ final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) parser;
+ nex.setReplaceUnderscores( replace_underscores );
+ nex.setIgnoreQuotes( false );
+ }
+ }
+ 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();
+ if ( phys != null ) {
+ if ( nhx_or_nexus && internal_numbers_are_confidences ) {
+ for( final Phylogeny phy : phys ) {
+ PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" );
+ }
+ }
+ if ( midpoint_reroot ) {
+ for( final Phylogeny phy : phys ) {
+ PhylogenyMethods.midpointRoot( phy );
+ PhylogenyMethods.orderAppearance( phy.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
+ }
+ }
+ }
+ return 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
final ControlPanel ac,
final GraphicsExportType type,
final Options options ) throws IOException {
- tree_panel.calcParametersForPainting( width, height, true );
+ tree_panel.calcParametersForPainting( width, height );
tree_panel.resetPreferredSize();
tree_panel.repaint();
final RenderingHints rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING,
g2d.dispose();
}
+ final private static char normalizeCharForRGB( char c ) {
+ c -= 65;
+ c *= 10.2;
+ c = c > 255 ? 255 : c;
+ c = c < 0 ? 0 : c;
+ return c;
+ }
+
+ 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" ) ) {
+ Runtime.getRuntime().exec( "rundll32 url.dll,FileProtocolHandler " + url );
+ }
+ else if ( ForesterUtil.isMac() ) {
+ final Class<?> file_mgr = Class.forName( "com.apple.eio.FileManager" );
+ final Method open_url = file_mgr.getDeclaredMethod( "openURL", new Class[] { String.class } );
+ open_url.invoke( null, new Object[] { url } );
+ }
+ else {
+ final String[] browsers = { "firefox", "opera", "konqueror", "mozilla", "netscape", "epiphany" };
+ String browser = null;
+ for( int i = 0; ( i < browsers.length ) && ( browser == null ); ++i ) {
+ if ( runtime.exec( new String[] { "which", browsers[ i ] } ).waitFor() == 0 ) {
+ browser = browsers[ i ];
+ }
+ }
+ if ( browser == null ) {
+ throw new IOException( "could not find a web browser to open [" + url + "] in" );
+ }
+ else {
+ runtime.exec( new String[] { browser, url } );
+ }
+ }
+ }
+
final static void addPhylogeniesToTabs( final Phylogeny[] phys,
final String default_name,
final String full_path,
/**
* Exits with -1.
- *
- *
+ *
+ *
* @param message
* to message to be printed
*/
System.out.println( "[" + applet_name + "] > " + message );
}
- final public static Phylogeny[] readPhylogeniesFromUrl( final URL url,
- final boolean phyloxml_validate_against_xsd,
- final boolean replace_underscores,
- final boolean internal_numbers_are_confidences,
- final TAXONOMY_EXTRACTION taxonomy_extraction,
- final boolean midpoint_reroot )
- throws FileNotFoundException, IOException {
- final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
- final PhylogenyParser parser;
- boolean nhx_or_nexus = false;
- if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {
- parser = new TolParser();
- }
- else {
- parser = ParserUtils.createParserDependingOnUrlContents( url, phyloxml_validate_against_xsd );
- if ( parser instanceof NHXParser ) {
- nhx_or_nexus = true;
- final NHXParser nhx = ( NHXParser ) parser;
- nhx.setReplaceUnderscores( replace_underscores );
- nhx.setIgnoreQuotes( false );
- nhx.setTaxonomyExtraction( taxonomy_extraction );
- }
- else if ( parser instanceof NexusPhylogeniesParser ) {
- nhx_or_nexus = true;
- final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) parser;
- nex.setReplaceUnderscores( replace_underscores );
- nex.setIgnoreQuotes( false );
- }
- }
- 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();
- if ( phys != null ) {
- if ( nhx_or_nexus && internal_numbers_are_confidences ) {
- for( final Phylogeny phy : phys ) {
- PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" );
- }
- }
- if ( midpoint_reroot ) {
- for( final Phylogeny phy : phys ) {
- PhylogenyMethods.midpointRoot( phy );
- PhylogenyMethods.orderAppearance( phy.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
- }
- }
- }
- return phys;
- }
-
final static void removeBranchColors( final Phylogeny phy ) {
for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {
it.next().getBranchData().setBranchColor( null );
if ( options.isGraphicsExportVisibleOnly() ) {
throw new IllegalArgumentException( "cannot export visible rectangle only without exporting in actual size" );
}
- tree_panel.calcParametersForPainting( options.getPrintSizeX(), options.getPrintSizeY(), true );
+ tree_panel.calcParametersForPainting( options.getPrintSizeX(), options.getPrintSizeY() );
tree_panel.resetPreferredSize();
tree_panel.repaint();
}
if ( options.isGraphicsExportVisibleOnly() ) {
throw new IllegalArgumentException( "cannot export visible rectangle only without exporting in actual size" );
}
- tree_panel.calcParametersForPainting( options.getPrintSizeX(), options.getPrintSizeY(), true );
+ tree_panel.calcParametersForPainting( options.getPrintSizeX(), options.getPrintSizeY() );
tree_panel.resetPreferredSize();
tree_panel.repaint();
}
final IIOImage iio_image = new IIOImage( image, null, null );
writer.write( null, iio_image, image_write_param );
}
-
- 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" ) ) {
- Runtime.getRuntime().exec( "rundll32 url.dll,FileProtocolHandler " + url );
- }
- else if ( ForesterUtil.isMac() ) {
- final Class<?> file_mgr = Class.forName( "com.apple.eio.FileManager" );
- final Method open_url = file_mgr.getDeclaredMethod( "openURL", new Class[] { String.class } );
- open_url.invoke( null, new Object[] { url } );
- }
- else {
- final String[] browsers = { "firefox", "opera", "konqueror", "mozilla", "netscape", "epiphany" };
- String browser = null;
- for( int i = 0; ( i < browsers.length ) && ( browser == null ); ++i ) {
- if ( runtime.exec( new String[] { "which", browsers[ i ] } ).waitFor() == 0 ) {
- browser = browsers[ i ];
- }
- }
- if ( browser == null ) {
- throw new IOException( "could not find a web browser to open [" + url + "] in" );
- }
- else {
- runtime.exec( new String[] { browser, url } );
- }
- }
- }
-
- // See: http://www.xml.nig.ac.jp/tutorial/rest/index.html#2.2
- // static void openDDBJRest() throws IOException {
- // //set URL
- // URL url = new URL( "http://xml.nig.ac.jp/rest/Invoke" );
- // //set parameter
- // String query = "service=GetEntry&method=getDDBJEntry&accession=AB000100";
- // //make connection
- // URLConnection urlc = url.openConnection();
- // //use post mode
- // urlc.setDoOutput( true );
- // urlc.setAllowUserInteraction( false );
- // //send query
- // PrintStream ps = new PrintStream( urlc.getOutputStream() );
- // ps.print( query );
- // ps.close();
- // //get result
- // BufferedReader br = new BufferedReader( new InputStreamReader(
- // urlc.getInputStream() ) );
- // String l = null;
- // while ( ( l = br.readLine() ) != null ) {
- // System.out.println( l );
- // }
- // br.close();
- // }
- public static enum GraphicsExportType {
- BMP( "bmp" ), GIF( "gif" ), JPG( "jpg" ), PDF( "pdf" ), PNG( "png" ), TIFF( "tif" );
-
- private final String _suffix;
-
- private GraphicsExportType( final String suffix ) {
- _suffix = suffix;
- }
-
- @Override
- public String toString() {
- return _suffix;
- }
- }
}
git://source.jalview.org / jalview.git / blobdiff