import java.util.Set;
import java.util.SortedSet;
import java.util.TreeSet;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
import javax.imageio.IIOImage;
import javax.imageio.ImageIO;
import javax.swing.JOptionPane;
import javax.swing.text.MaskFormatter;
-import org.forester.analysis.AncestralTaxonomyInference;
+import org.forester.analysis.TaxonomyDataManager;
import org.forester.io.parsers.PhylogenyParser;
import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
import org.forester.io.parsers.tol.TolParser;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.data.Accession;
import org.forester.phylogeny.data.BranchColor;
import org.forester.phylogeny.data.Distribution;
import org.forester.phylogeny.data.Sequence;
import org.forester.phylogeny.factories.PhylogenyFactory;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
import org.forester.phylogeny.iterators.PreorderTreeIterator;
+import org.forester.util.AsciiHistogram;
import org.forester.util.DescriptiveStatistics;
import org.forester.util.ForesterUtil;
-import org.forester.ws.uniprot.UniProtTaxonomy;
+import org.forester.ws.seqdb.UniProtTaxonomy;
public final class AptxUtil {
+ private final static Pattern seq_identifier_pattern_1 = Pattern
+ .compile( "^([A-Za-z]{2,5})[|=:]([0-9A-Za-z_\\.]{5,40})\\s*$" );
+ private final static Pattern seq_identifier_pattern_2 = Pattern
+ .compile( "^([A-Za-z]{2,5})[|=:]([0-9A-Za-z_\\.]{5,40})[|,; ].*$" );
private final static String[] AVAILABLE_FONT_FAMILIES_SORTED = GraphicsEnvironment.getLocalGraphicsEnvironment()
.getAvailableFontFamilyNames();
static {
Arrays.sort( AVAILABLE_FONT_FAMILIES_SORTED );
}
- public static void ensurePresenceOfTaxonomy( final PhylogenyNode node ) {
- if ( !node.getNodeData().isHasTaxonomy() ) {
- node.getNodeData().setTaxonomy( new Taxonomy() );
- }
- }
-
- public static void ensurePresenceOfSequence( final PhylogenyNode node ) {
- if ( !node.getNodeData().isHasSequence() ) {
- node.getNodeData().setSequence( new Sequence() );
- }
- }
-
- final public static void ensurePresenceOfDistribution( final PhylogenyNode node ) {
- if ( !node.getNodeData().isHasDistribution() ) {
- node.getNodeData().setDistribution( new Distribution( "" ) );
- }
- }
-
- final public static void ensurePresenceOfDate( final PhylogenyNode node ) {
- if ( !node.getNodeData().isHasDate() ) {
- node.getNodeData().setDate( new org.forester.phylogeny.data.Date() );
- }
- }
-
- final static public boolean isHasAtLeastOneBranchWithSupportValues( final Phylogeny phy ) {
- final PhylogenyNodeIterator it = phy.iteratorPostorder();
- while ( it.hasNext() ) {
- if ( it.next().getBranchData().isHasConfidences() ) {
- return true;
- }
- }
- return false;
- }
-
- public static void writePhylogenyToGraphicsFile( final File intree,
- final File outfile,
- final int width,
- final int height,
- final GraphicsExportType type,
- final Configuration config ) throws IOException {
- final PhylogenyParser parser = ParserUtils.createParserDependingOnFileType( intree, true );
- Phylogeny[] phys = null;
- phys = PhylogenyMethods.readPhylogenies( parser, intree );
- final MainFrameApplication mf = MainFrameApplication.createInstance( phys, config );
- AptxUtil.writePhylogenyToGraphicsFileNonInteractive( outfile, width, height, mf.getMainPanel()
- .getCurrentTreePanel(), mf.getMainPanel().getControlPanel(), type, mf.getOptions() );
- mf.end();
- }
-
- /**
- * Returns true if at least one branch has a length larger than zero.
- *
- *
- * @param phy
- */
- final static public boolean isHasAtLeastOneBranchLengthLargerThanZero( final Phylogeny phy ) {
- final PhylogenyNodeIterator it = phy.iteratorPostorder();
- while ( it.hasNext() ) {
- if ( it.next().getDistanceToParent() > 0.0 ) {
- return true;
- }
- }
- return false;
- }
-
- final static public boolean isHasAtLeastNodeWithEvent( final Phylogeny phy ) {
- final PhylogenyNodeIterator it = phy.iteratorPostorder();
- while ( it.hasNext() ) {
- if ( it.next().getNodeData().isHasEvent() ) {
- return true;
- }
- }
- return false;
- }
-
- public static MaskFormatter createMaskFormatter( final String s ) {
- MaskFormatter formatter = null;
- try {
- formatter = new MaskFormatter( s );
- }
- catch ( final ParseException e ) {
- throw new IllegalArgumentException( e );
- }
- return formatter;
- }
-
final static void addPhylogeniesToTabs( final Phylogeny[] phys,
final String default_name,
final String full_path,
}
}
+ private static void colorizeSubtree( final PhylogenyNode node, final BranchColor c ) {
+ node.getBranchData().setBranchColor( c );
+ final List<PhylogenyNode> descs = PhylogenyMethods.getAllDescendants( node );
+ for( final PhylogenyNode desc : descs ) {
+ desc.getBranchData().setBranchColor( c );
+ }
+ }
+
final static void colorPhylogenyAccordingToConfidenceValues( final Phylogeny tree, final TreePanel tree_panel ) {
double max_conf = 0.0;
for( final PhylogenyNodeIterator it = tree.iteratorPreorder(); it.hasNext(); ) {
}
}
+ final static void colorPhylogenyAccordingToExternalTaxonomy( final Phylogeny tree, final TreePanel tree_panel ) {
+ for( final PhylogenyNodeIterator it = tree.iteratorPreorder(); it.hasNext(); ) {
+ it.next().getBranchData().setBranchColor( null );
+ }
+ for( final PhylogenyNodeIterator it = tree.iteratorPreorder(); it.hasNext(); ) {
+ final PhylogenyNode n = it.next();
+ if ( !n.getBranchData().isHasBranchColor() ) {
+ final Taxonomy tax = PhylogenyMethods.getExternalDescendantsTaxonomy( n );
+ if ( tax != null ) {
+ n.getBranchData().setBranchColor( new BranchColor( tree_panel.calculateTaxonomyBasedColor( tax ) ) );
+ final List<PhylogenyNode> descs = PhylogenyMethods.getAllDescendants( n );
+ for( final PhylogenyNode desc : descs ) {
+ desc.getBranchData()
+ .setBranchColor( new BranchColor( tree_panel.calculateTaxonomyBasedColor( tax ) ) );
+ }
+ }
+ }
+ }
+ }
+
final static int colorPhylogenyAccordingToRanks( final Phylogeny tree, final String rank, final TreePanel tree_panel ) {
final Map<String, Color> true_lineage_to_color_map = new HashMap<String, Color>();
int colorizations = 0;
if ( n.getNodeData().isHasTaxonomy()
&& ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() )
|| !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getCommonName() ) || !ForesterUtil
- .isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
+ .isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getRank() )
&& n.getNodeData().getTaxonomy().getRank().equalsIgnoreCase( rank ) ) {
final BranchColor c = new BranchColor( tree_panel.calculateTaxonomyBasedColor( n.getNodeData()
else {
UniProtTaxonomy up = null;
try {
- up = AncestralTaxonomyInference.obtainUniProtTaxonomy( temp_tax, null, null );
+ up = TaxonomyDataManager.obtainUniProtTaxonomy( temp_tax, null, null );
}
catch ( final Exception e ) {
e.printStackTrace();
return colorizations;
}
- private static void colorizeSubtree( final PhylogenyNode node, final BranchColor c ) {
- node.getBranchData().setBranchColor( c );
- final List<PhylogenyNode> descs = PhylogenyMethods.getAllDescendants( node );
- for( final PhylogenyNode desc : descs ) {
- desc.getBranchData().setBranchColor( c );
- }
- }
-
- final static String[] getAllRanks( final Phylogeny tree ) {
- final SortedSet<String> ranks = new TreeSet<String>();
- for( final PhylogenyNodeIterator it = tree.iteratorPreorder(); it.hasNext(); ) {
- final PhylogenyNode n = it.next();
- if ( n.getNodeData().isHasTaxonomy() && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getRank() ) ) {
- ranks.add( n.getNodeData().getTaxonomy().getRank() );
- }
- }
- return ForesterUtil.stringSetToArray( ranks );
- }
-
- public static String[] getAllPossibleRanks() {
- final String[] str_array = new String[ PhyloXmlUtil.TAXONOMY_RANKS_LIST.size() - 2 ];
- int i = 0;
- for( final String e : PhyloXmlUtil.TAXONOMY_RANKS_LIST ) {
- if ( !e.equals( PhyloXmlUtil.UNKNOWN ) && !e.equals( PhyloXmlUtil.OTHER ) ) {
- str_array[ i++ ] = e;
- }
- }
- return str_array;
- }
-
- final static void colorPhylogenyAccordingToExternalTaxonomy( final Phylogeny tree, final TreePanel tree_panel ) {
- for( final PhylogenyNodeIterator it = tree.iteratorPreorder(); it.hasNext(); ) {
- it.next().getBranchData().setBranchColor( null );
- }
- for( final PhylogenyNodeIterator it = tree.iteratorPreorder(); it.hasNext(); ) {
- final PhylogenyNode n = it.next();
- if ( !n.getBranchData().isHasBranchColor() ) {
- final Taxonomy tax = PhylogenyMethods.getExternalDescendantsTaxonomy( n );
- if ( tax != null ) {
- n.getBranchData().setBranchColor( new BranchColor( tree_panel.calculateTaxonomyBasedColor( tax ) ) );
- final List<PhylogenyNode> descs = PhylogenyMethods.getAllDescendants( n );
- for( final PhylogenyNode desc : descs ) {
- desc.getBranchData()
- .setBranchColor( new BranchColor( tree_panel.calculateTaxonomyBasedColor( tax ) ) );
- }
- }
- }
- }
- }
-
- final static String crateBasicInformation( final Phylogeny phy ) {
+ final static String createBasicInformation( final Phylogeny phy ) {
final StringBuilder desc = new StringBuilder();
if ( ( phy != null ) && !phy.isEmpty() ) {
if ( !ForesterUtil.isEmpty( phy.getName() ) ) {
desc.append( "Maximum distance to root: " );
desc.append( ForesterUtil.round( PhylogenyMethods.calculateMaxDistanceToRoot( phy ), 6 ) );
desc.append( "\n" );
- desc.append( "Descendants per node statistics: " );
- final DescriptiveStatistics ds = PhylogenyMethods.calculatNumberOfDescendantsPerNodeStatistics( phy );
- desc.append( "\n" );
- desc.append( " Median: " + ForesterUtil.round( ds.median(), 2 ) );
- desc.append( "\n" );
- desc.append( " Mean: " + ForesterUtil.round( ds.arithmeticMean(), 2 ) );
- desc.append( "\n" );
- desc.append( " SD: " + ForesterUtil.round( ds.sampleStandardDeviation(), 2 ) );
- desc.append( "\n" );
- desc.append( " Minimum: " + ForesterUtil.roundToInt( ds.getMin() ) );
- desc.append( "\n" );
- desc.append( " Maximum: " + ForesterUtil.roundToInt( ds.getMax() ) );
+ final Set<Taxonomy> taxs = PhylogenyMethods.obtainDistinctTaxonomies( phy.getRoot() );
+ if ( taxs != null ) {
+ desc.append( "Distinct external taxonomies: " );
+ desc.append( taxs.size() );
+ }
desc.append( "\n" );
- final DescriptiveStatistics cs = PhylogenyMethods.calculatConfidenceStatistics( phy );
- if ( cs.getN() > 1 ) {
- desc.append( "Support statistics: " );
+ final DescriptiveStatistics bs = PhylogenyMethods.calculatBranchLengthStatistics( phy );
+ if ( bs.getN() > 3 ) {
+ desc.append( "\n" );
+ desc.append( "Branch-length statistics: " );
+ desc.append( "\n" );
+ desc.append( " Number of branches with non-negative branch-lengths: " + bs.getN() );
+ desc.append( "\n" );
+ desc.append( " Median: " + ForesterUtil.round( bs.median(), 6 ) );
desc.append( "\n" );
- desc.append( " Branches with support: " + cs.getN() );
+ desc.append( " Mean: " + ForesterUtil.round( bs.arithmeticMean(), 6 ) );
desc.append( "\n" );
- desc.append( " Median: " + ForesterUtil.round( cs.median(), 6 ) );
+ desc.append( " SD: " + ForesterUtil.round( bs.sampleStandardDeviation(), 6 ) );
desc.append( "\n" );
- desc.append( " Mean: " + ForesterUtil.round( cs.arithmeticMean(), 6 ) );
+ desc.append( " Minimum: " + ForesterUtil.round( bs.getMin(), 6 ) );
desc.append( "\n" );
- if ( cs.getN() > 2 ) {
- desc.append( " SD: " + ForesterUtil.round( cs.sampleStandardDeviation(), 6 ) );
+ desc.append( " Maximum: " + ForesterUtil.round( bs.getMax(), 6 ) );
+ desc.append( "\n" );
+ if ( Math.abs( bs.getMax() - bs.getMin() ) > 0.0001 ) {
desc.append( "\n" );
+ final AsciiHistogram histo = new AsciiHistogram( bs );
+ desc.append( histo.toStringBuffer( 12, '#', 40, 7, " " ) );
}
- desc.append( " Minimum: " + ForesterUtil.roundToInt( cs.getMin() ) );
+ }
+ final DescriptiveStatistics ds = PhylogenyMethods.calculatNumberOfDescendantsPerNodeStatistics( phy );
+ if ( ds.getN() > 2 ) {
+ desc.append( "\n" );
+ desc.append( "Descendants per node statistics: " );
desc.append( "\n" );
- desc.append( " Maximum: " + ForesterUtil.roundToInt( cs.getMax() ) );
+ desc.append( " Median: " + ForesterUtil.round( ds.median(), 2 ) );
+ desc.append( "\n" );
+ desc.append( " Mean: " + ForesterUtil.round( ds.arithmeticMean(), 2 ) );
+ desc.append( "\n" );
+ desc.append( " SD: " + ForesterUtil.round( ds.sampleStandardDeviation(), 2 ) );
+ desc.append( "\n" );
+ desc.append( " Minimum: " + ForesterUtil.roundToInt( ds.getMin() ) );
+ desc.append( "\n" );
+ desc.append( " Maximum: " + ForesterUtil.roundToInt( ds.getMax() ) );
desc.append( "\n" );
}
- final Set<Taxonomy> taxs = PhylogenyMethods.obtainDistinctTaxonomies( phy.getRoot() );
- if ( taxs != null ) {
- desc.append( "Distinct external taxonomies: " );
- desc.append( taxs.size() );
+ List<DescriptiveStatistics> css = null;
+ try {
+ css = PhylogenyMethods.calculatConfidenceStatistics( phy );
+ }
+ catch ( final IllegalArgumentException e ) {
+ ForesterUtil.printWarningMessage( Constants.PRG_NAME, e.getMessage() );
+ }
+ if ( ( css != null ) && ( css.size() > 0 ) ) {
+ desc.append( "\n" );
+ for( int i = 0; i < css.size(); ++i ) {
+ final DescriptiveStatistics cs = css.get( i );
+ if ( ( cs != null ) && ( cs.getN() > 1 ) ) {
+ if ( css.size() > 1 ) {
+ desc.append( "Support statistics " + ( i + 1 ) + ": " );
+ }
+ else {
+ desc.append( "Support statistics: " );
+ }
+ if ( !ForesterUtil.isEmpty( cs.getDescription() ) ) {
+ desc.append( "\n" );
+ desc.append( " Type: " + cs.getDescription() );
+ }
+ desc.append( "\n" );
+ desc.append( " Branches with support: " + cs.getN() );
+ desc.append( "\n" );
+ desc.append( " Median: " + ForesterUtil.round( cs.median(), 6 ) );
+ desc.append( "\n" );
+ desc.append( " Mean: " + ForesterUtil.round( cs.arithmeticMean(), 6 ) );
+ desc.append( "\n" );
+ if ( cs.getN() > 2 ) {
+ desc.append( " SD: " + ForesterUtil.round( cs.sampleStandardDeviation(), 6 ) );
+ desc.append( "\n" );
+ }
+ desc.append( " Minimum: " + ForesterUtil.roundToInt( cs.getMin() ) );
+ desc.append( "\n" );
+ desc.append( " Maximum: " + ForesterUtil.roundToInt( cs.getMax() ) );
+ desc.append( "\n" );
+ }
+ }
}
}
return desc.toString();
}
+ public static MaskFormatter createMaskFormatter( final String s ) {
+ MaskFormatter formatter = null;
+ try {
+ formatter = new MaskFormatter( s );
+ }
+ catch ( final ParseException e ) {
+ throw new IllegalArgumentException( e );
+ }
+ return formatter;
+ }
+
/**
* Exits with -1.
*
System.exit( -1 );
}
+ final public static void ensurePresenceOfDate( final PhylogenyNode node ) {
+ if ( !node.getNodeData().isHasDate() ) {
+ node.getNodeData().setDate( new org.forester.phylogeny.data.Date() );
+ }
+ }
+
+ final public static void ensurePresenceOfDistribution( final PhylogenyNode node ) {
+ if ( !node.getNodeData().isHasDistribution() ) {
+ node.getNodeData().setDistribution( new Distribution( "" ) );
+ }
+ }
+
+ public static void ensurePresenceOfSequence( final PhylogenyNode node ) {
+ if ( !node.getNodeData().isHasSequence() ) {
+ node.getNodeData().setSequence( new Sequence() );
+ }
+ }
+
+ public static void ensurePresenceOfTaxonomy( final PhylogenyNode node ) {
+ if ( !node.getNodeData().isHasTaxonomy() ) {
+ node.getNodeData().setTaxonomy( new Taxonomy() );
+ }
+ }
+
+ public static String[] getAllPossibleRanks() {
+ final String[] str_array = new String[ PhyloXmlUtil.TAXONOMY_RANKS_LIST.size() - 2 ];
+ int i = 0;
+ for( final String e : PhyloXmlUtil.TAXONOMY_RANKS_LIST ) {
+ if ( !e.equals( PhyloXmlUtil.UNKNOWN ) && !e.equals( PhyloXmlUtil.OTHER ) ) {
+ str_array[ i++ ] = e;
+ }
+ }
+ return str_array;
+ }
+
+ final static String[] getAllRanks( final Phylogeny tree ) {
+ final SortedSet<String> ranks = new TreeSet<String>();
+ for( final PhylogenyNodeIterator it = tree.iteratorPreorder(); it.hasNext(); ) {
+ final PhylogenyNode n = it.next();
+ if ( n.getNodeData().isHasTaxonomy() && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getRank() ) ) {
+ ranks.add( n.getNodeData().getTaxonomy().getRank() );
+ }
+ }
+ return ForesterUtil.stringSetToArray( ranks );
+ }
+
final static String[] getAvailableFontFamiliesSorted() {
return AVAILABLE_FONT_FAMILIES_SORTED;
}
return true;
}
+ final static public boolean isHasAtLeastNodeWithEvent( final Phylogeny phy ) {
+ final PhylogenyNodeIterator it = phy.iteratorPostorder();
+ while ( it.hasNext() ) {
+ if ( it.next().getNodeData().isHasEvent() ) {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ /**
+ * Returns true if at least one branch has a length larger than zero.
+ *
+ *
+ * @param phy
+ */
+ final static public boolean isHasAtLeastOneBranchLengthLargerThanZero( final Phylogeny phy ) {
+ final PhylogenyNodeIterator it = phy.iteratorPostorder();
+ while ( it.hasNext() ) {
+ if ( it.next().getDistanceToParent() > 0.0 ) {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ final static public boolean isHasAtLeastOneBranchWithSupportValues( final Phylogeny phy ) {
+ final PhylogenyNodeIterator it = phy.iteratorPostorder();
+ while ( it.hasNext() ) {
+ if ( it.next().getBranchData().isHasConfidences() ) {
+ return true;
+ }
+ }
+ return false;
+ }
+
final static boolean isJava15() {
try {
final String s = ForesterUtil.JAVA_VERSION;
}
}
- final static void launchWebBrowser( final URI uri,
- final boolean is_applet,
- final JApplet applet,
- final String frame_name ) throws IOException {
+ final public static void launchWebBrowser( final URI uri,
+ final boolean is_applet,
+ final JApplet applet,
+ final String frame_name ) throws IOException {
if ( is_applet ) {
applet.getAppletContext().showDocument( uri.toURL(), frame_name );
}
return c;
}
+ public final static Accession obtainSequenceAccessionFromName( final String sequence_name ) {
+ final String n = sequence_name.trim();
+ final Matcher matcher1 = seq_identifier_pattern_1.matcher( n );
+ String group1 = "";
+ String group2 = "";
+ if ( matcher1.matches() ) {
+ group1 = matcher1.group( 1 );
+ group2 = matcher1.group( 2 );
+ }
+ else {
+ final Matcher matcher2 = seq_identifier_pattern_2.matcher( n );
+ if ( matcher2.matches() ) {
+ group1 = matcher2.group( 1 );
+ group2 = matcher2.group( 2 );
+ }
+ }
+ if ( ForesterUtil.isEmpty( group1 ) || ForesterUtil.isEmpty( group2 ) ) {
+ return null;
+ }
+ return new Accession( group2, group1 );
+ }
+
final private static void openUrlInWebBrowser( final String url ) throws IOException, ClassNotFoundException,
SecurityException, NoSuchMethodException, IllegalArgumentException, IllegalAccessException,
InvocationTargetException, InterruptedException {
}
}
- final static void showErrorMessage( final Component parent, final String error_msg ) {
+ 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 );
}
+ public final static void showExtDescNodeDataUserSelectedHelper( final ControlPanel cp,
+ final PhylogenyNode node,
+ final List<String> data ) {
+ final StringBuilder sb = new StringBuilder();
+ if ( cp.isShowNodeNames() && !ForesterUtil.isEmpty( node.getName() ) ) {
+ showExtDescNodeDataUserSelectedHelperHelper( node.getName(), sb );
+ }
+ if ( cp.isShowGeneNames() && node.getNodeData().isHasSequence()
+ && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) ) {
+ showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getName(), sb );
+ }
+ if ( cp.isShowGeneSymbols() && node.getNodeData().isHasSequence()
+ && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getSymbol() ) ) {
+ showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getSymbol(), sb );
+ }
+ if ( cp.isShowSequenceAcc() && node.getNodeData().isHasSequence()
+ && ( node.getNodeData().getSequence().getAccession() != null )
+ && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().toString() ) ) {
+ showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getAccession().toString(), sb );
+ }
+ if ( cp.isShowTaxonomyCode() && node.getNodeData().isHasTaxonomy()
+ && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
+ showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getTaxonomy().getTaxonomyCode(), sb );
+ }
+ if ( cp.isShowTaxonomyScientificNames() && node.getNodeData().isHasTaxonomy()
+ && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) ) {
+ showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getTaxonomy().getScientificName(), sb );
+ }
+ if ( ( cp.isShowGeneNames() || cp.isShowGeneSymbols() || cp.isShowSequenceAcc() )
+ && node.getNodeData().isHasSequence()
+ && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) {
+ showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getMolecularSequence(), sb );
+ }
+ final String s = sb.toString().trim();
+ if ( !ForesterUtil.isEmpty( s ) ) {
+ data.add( s );
+ }
+ }
+
+ public final static void showExtDescNodeDataUserSelectedHelperHelper( final String s, final StringBuilder sb ) {
+ if ( sb.length() > 0 ) {
+ sb.append( "\t" );
+ }
+ sb.append( s );
+ }
+
+ final public static void showInformationMessage( final Component parent, final String title, final String msg ) {
+ JOptionPane.showMessageDialog( parent, msg, title, JOptionPane.INFORMATION_MESSAGE );
+ }
+
final static void unexpectedError( final Error err ) {
err.printStackTrace();
final StringBuffer sb = new StringBuffer();
+ Constants.PRG_NAME + Constants.VERSION + "]", JOptionPane.ERROR_MESSAGE );
}
+ final static String writePhylogenyToGraphicsByteArrayOutputStream( final ByteArrayOutputStream baos,
+ int width,
+ int height,
+ final TreePanel tree_panel,
+ 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.setParametersForPainting( options.getPrintSizeX(), options.getPrintSizeY(), true );
+ 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 );
+ if ( options.isAntialiasPrint() ) {
+ rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON );
+ rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON );
+ }
+ else {
+ rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_OFF );
+ rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
+ }
+ final Phylogeny phylogeny = tree_panel.getPhylogeny();
+ if ( ( phylogeny == null ) || phylogeny.isEmpty() ) {
+ return "";
+ }
+ Rectangle visible = null;
+ if ( !options.isGraphicsExportUsingActualSize() ) {
+ width = options.getPrintSizeX();
+ height = options.getPrintSizeY();
+ }
+ else if ( options.isGraphicsExportVisibleOnly() ) {
+ visible = tree_panel.getVisibleRect();
+ width = visible.width;
+ height = visible.height;
+ }
+ final BufferedImage buffered_img = new BufferedImage( width, height, BufferedImage.TYPE_INT_RGB );
+ Graphics2D g2d = buffered_img.createGraphics();
+ g2d.setRenderingHints( rendering_hints );
+ int x = 0;
+ int y = 0;
+ if ( options.isGraphicsExportVisibleOnly() ) {
+ g2d = ( Graphics2D ) g2d.create( -visible.x, -visible.y, visible.width, visible.height );
+ g2d.setClip( null );
+ x = visible.x;
+ y = visible.y;
+ }
+ tree_panel.paintPhylogeny( g2d, false, true, width, height, x, y );
+ ImageIO.write( buffered_img, type.toString(), baos );
+ g2d.dispose();
+ System.gc();
+ if ( !options.isGraphicsExportUsingActualSize() ) {
+ tree_panel.getMainPanel().getControlPanel().showWhole();
+ }
+ String msg = baos.toString();
+ if ( ( width > 0 ) && ( height > 0 ) ) {
+ msg += " [size: " + width + ", " + height + "]";
+ }
+ return msg;
+ }
+
+ public static void writePhylogenyToGraphicsFile( final File intree,
+ final File outfile,
+ final int width,
+ final int height,
+ final GraphicsExportType type,
+ final Configuration config ) throws IOException {
+ final PhylogenyParser parser = ParserUtils.createParserDependingOnFileType( intree, true );
+ Phylogeny[] phys = null;
+ phys = PhylogenyMethods.readPhylogenies( parser, intree );
+ writePhylogenyToGraphicsFile( phys[ 0 ], outfile, width, height, type, config );
+ }
+
+ public static void writePhylogenyToGraphicsFile( final Phylogeny phy,
+ final File outfile,
+ final int width,
+ final int height,
+ final GraphicsExportType type,
+ 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() );
+ mf.end();
+ }
+
final static String writePhylogenyToGraphicsFile( final String file_name,
int width,
int height,
g2d.dispose();
}
- final static String writePhylogenyToGraphicsByteArrayOutputStream( final ByteArrayOutputStream baos,
- int width,
- int height,
- final TreePanel tree_panel,
- 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.setParametersForPainting( options.getPrintSizeX(), options.getPrintSizeY(), true );
- 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 );
- if ( options.isAntialiasPrint() ) {
- rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON );
- rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON );
- }
- else {
- rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_OFF );
- rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
- }
- final Phylogeny phylogeny = tree_panel.getPhylogeny();
- if ( ( phylogeny == null ) || phylogeny.isEmpty() ) {
- return "";
- }
- Rectangle visible = null;
- if ( !options.isGraphicsExportUsingActualSize() ) {
- width = options.getPrintSizeX();
- height = options.getPrintSizeY();
- }
- else if ( options.isGraphicsExportVisibleOnly() ) {
- visible = tree_panel.getVisibleRect();
- width = visible.width;
- height = visible.height;
- }
- final BufferedImage buffered_img = new BufferedImage( width, height, BufferedImage.TYPE_INT_RGB );
- Graphics2D g2d = buffered_img.createGraphics();
- g2d.setRenderingHints( rendering_hints );
- int x = 0;
- int y = 0;
- if ( options.isGraphicsExportVisibleOnly() ) {
- g2d = ( Graphics2D ) g2d.create( -visible.x, -visible.y, visible.width, visible.height );
- g2d.setClip( null );
- x = visible.x;
- y = visible.y;
- }
- tree_panel.paintPhylogeny( g2d, false, true, width, height, x, y );
- ImageIO.write( buffered_img, type.toString(), baos );
- g2d.dispose();
- System.gc();
- if ( !options.isGraphicsExportUsingActualSize() ) {
- tree_panel.getMainPanel().getControlPanel().showWhole();
- }
- String msg = baos.toString();
- if ( ( width > 0 ) && ( height > 0 ) ) {
- msg += " [size: " + width + ", " + height + "]";
- }
- return msg;
- }
-
final static void writeToTiff( final File file, final BufferedImage image ) throws IOException {
// See: http://log.robmeek.com/2005/08/write-tiff-in-java.html
ImageWriter writer = null;
git://source.jalview.org / jalview.git / blobdiff