// 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;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
+import java.io.UnsupportedEncodingException;
import java.lang.reflect.InvocationTargetException;
import java.lang.reflect.Method;
import java.net.URI;
import java.net.URL;
+import java.net.URLEncoder;
import java.text.ParseException;
+import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
+import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Locale;
import java.util.Map;
+import java.util.Map.Entry;
import java.util.Set;
+import java.util.SortedMap;
import java.util.SortedSet;
+import java.util.TreeMap;
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.nexus.NexusPhylogeniesParser;
+import org.forester.io.parsers.nhx.NHXParser;
+import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
import org.forester.io.parsers.tol.TolParser;
import org.forester.io.parsers.util.ParserUtils;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
+import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.data.Accession;
+import org.forester.phylogeny.data.Annotation;
import org.forester.phylogeny.data.BranchColor;
-import org.forester.phylogeny.data.Distribution;
-import org.forester.phylogeny.data.Sequence;
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.phylogeny.iterators.PreorderTreeIterator;
+import org.forester.util.AsciiHistogram;
import org.forester.util.DescriptiveStatistics;
+import org.forester.util.ForesterConstants;
import org.forester.util.ForesterUtil;
-import org.forester.ws.uniprot.UniProtTaxonomy;
+import org.forester.util.SequenceIdParser;
+import org.forester.ws.seqdb.UniProtTaxonomy;
public final class AptxUtil {
private final static String[] AVAILABLE_FONT_FAMILIES_SORTED = GraphicsEnvironment.getLocalGraphicsEnvironment()
.getAvailableFontFamilyNames();
+ private final static Pattern seq_identifier_pattern_1 = Pattern
+ .compile( "^([A-Za-z]{2,5})[|=:]([0-9A-Za-z_\\.]{5,40})\\s*$" );
+ private final static Pattern seq_identifier_pattern_2 = Pattern
+ .compile( "^([A-Za-z]{2,5})[|=:]([0-9A-Za-z_\\.]{5,40})[|,; ].*$" );
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 MaskFormatter createMaskFormatter( final String s ) {
+ MaskFormatter formatter = null;
+ try {
+ formatter = new MaskFormatter( s );
}
+ catch ( final ParseException e ) {
+ throw new IllegalArgumentException( e );
+ }
+ return formatter;
}
- public static void ensurePresenceOfSequence( final PhylogenyNode node ) {
- if ( !node.getNodeData().isHasSequence() ) {
- node.getNodeData().setSequence( new Sequence() );
+ public final static String createUriForSeqWeb( final PhylogenyNode node,
+ final Configuration conf,
+ final TreePanel tp ) {
+ String uri_str = null;
+ final String upkb = ForesterUtil.extractUniProtKbProteinSeqIdentifier( node );
+ if ( !ForesterUtil.isEmpty( upkb ) ) {
+ try {
+ uri_str = ForesterUtil.UNIPROT_KB + URLEncoder.encode( upkb, ForesterConstants.UTF8 );
+ }
+ catch ( final UnsupportedEncodingException e ) {
+ showErrorMessage( tp, e.toString() );
+ e.printStackTrace();
+ }
+ }
+ if ( ForesterUtil.isEmpty( uri_str ) ) {
+ final String v = ForesterUtil.extractGenbankAccessor( node );
+ if ( !ForesterUtil.isEmpty( v ) ) {
+ try {
+ if ( SequenceIdParser.isProtein( v ) ) {
+ uri_str = ForesterUtil.NCBI_PROTEIN + URLEncoder.encode( v, ForesterConstants.UTF8 );
+ }
+ else {
+ uri_str = ForesterUtil.NCBI_NUCCORE + URLEncoder.encode( v, ForesterConstants.UTF8 );
+ }
+ }
+ catch ( final UnsupportedEncodingException e ) {
+ showErrorMessage( tp, e.toString() );
+ e.printStackTrace();
+ }
+ }
+ }
+ if ( ForesterUtil.isEmpty( uri_str ) ) {
+ final String v = ForesterUtil.extractRefSeqAccessorAccessor( node );
+ if ( !ForesterUtil.isEmpty( v ) ) {
+ try {
+ if ( SequenceIdParser.isProtein( v ) ) {
+ uri_str = ForesterUtil.NCBI_PROTEIN + URLEncoder.encode( v, ForesterConstants.UTF8 );
+ }
+ else {
+ uri_str = ForesterUtil.NCBI_NUCCORE + URLEncoder.encode( v, ForesterConstants.UTF8 );
+ }
+ }
+ catch ( final UnsupportedEncodingException e ) {
+ showErrorMessage( tp, e.toString() );
+ e.printStackTrace();
+ }
+ }
+ }
+ if ( ForesterUtil.isEmpty( uri_str ) ) {
+ final String v = ForesterUtil.extractGInumber( node );
+ if ( !ForesterUtil.isEmpty( v ) ) {
+ try {
+ uri_str = ForesterUtil.NCBI_GI + URLEncoder.encode( v, ForesterConstants.UTF8 );
+ }
+ catch ( final UnsupportedEncodingException e ) {
+ showErrorMessage( tp, e.toString() );
+ e.printStackTrace();
+ }
+ }
}
+ return uri_str;
}
- final public static void ensurePresenceOfDistribution( final PhylogenyNode node ) {
- if ( !node.getNodeData().isHasDistribution() ) {
- node.getNodeData().setDistribution( new Distribution( "" ) );
+ 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;
}
- final public static void ensurePresenceOfDate( final PhylogenyNode node ) {
- if ( !node.getNodeData().isHasDate() ) {
- node.getNodeData().setDate( new org.forester.phylogeny.data.Date() );
+ /**
+ * 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 ) {
return false;
}
+ 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 );
+ }
+ else {
+ // 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 List<PhylogenyNode> descs = node.getAllExternalDescendants();
+ final Set<Taxonomy> tax_set = new HashSet<Taxonomy>();
+ for( final PhylogenyNode n : descs ) {
+ if ( n.getNodeData().isHasTaxonomy() && !n.getNodeData().getTaxonomy().isEmpty() ) {
+ tax_set.add( n.getNodeData().getTaxonomy() );
+ }
+ }
+ return tax_set;
+ }
+
+ /**
+ * Returns the set of distinct taxonomies of
+ * all external nodes of node.
+ * If at least one the external nodes has no taxonomy,
+ * null is returned.
+ *
+ */
+ public static Set<Taxonomy> obtainDistinctTaxonomies( final PhylogenyNode node ) {
+ final List<PhylogenyNode> descs = node.getAllExternalDescendants();
+ final Set<Taxonomy> tax_set = new HashSet<Taxonomy>();
+ for( final PhylogenyNode n : descs ) {
+ if ( !n.getNodeData().isHasTaxonomy() || n.getNodeData().getTaxonomy().isEmpty() ) {
+ return null;
+ }
+ tax_set.add( n.getNodeData().getTaxonomy() );
+ }
+ return tax_set;
+ }
+
+ 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 );
+ }
+
+ public final static void printWarningMessage( final String name, final String message ) {
+ System.out.println( "[" + name + "] > " + message );
+ }
+
+ 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.isShowTaxonomyCommonNames() && node.getNodeData().isHasTaxonomy()
+ && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) {
+ showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getTaxonomy().getCommonName(), 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 );
+ }
+
public static void writePhylogenyToGraphicsFile( final File intree,
final File outfile,
final int width,
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;
- }
+ public final static void writePhylogenyToGraphicsFileNonInteractive( final File outfile,
+ final int width,
+ final int height,
+ final TreePanel tree_panel,
+ final ControlPanel ac,
+ final GraphicsExportType type,
+ final Options options ) throws IOException {
+ tree_panel.calcParametersForPainting( width, height, 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 );
}
- 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;
- }
+ else {
+ rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_OFF );
+ rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
}
- return false;
- }
-
- public static MaskFormatter createMaskFormatter( final String s ) {
- MaskFormatter formatter = null;
- try {
- formatter = new MaskFormatter( s );
+ final Phylogeny phylogeny = tree_panel.getPhylogeny();
+ if ( ( phylogeny == null ) || phylogeny.isEmpty() ) {
+ return;
}
- catch ( final ParseException e ) {
- throw new IllegalArgumentException( e );
+ if ( outfile.isDirectory() ) {
+ throw new IOException( "\"" + outfile + "\" is a directory" );
}
- return formatter;
+ final BufferedImage buffered_img = new BufferedImage( width, height, BufferedImage.TYPE_INT_RGB );
+ final Graphics2D g2d = buffered_img.createGraphics();
+ g2d.setRenderingHints( rendering_hints );
+ tree_panel.paintPhylogeny( g2d, false, true, width, height, 0, 0 );
+ if ( type == GraphicsExportType.TIFF ) {
+ writeToTiff( outfile, buffered_img );
+ }
+ else {
+ ImageIO.write( buffered_img, type.toString(), outfile );
+ }
+ g2d.dispose();
}
final static void addPhylogeniesToTabs( final Phylogeny[] phys,
lookAtSomeTreePropertiesForAptxControlSettings( phy, main_panel.getControlPanel(), configuration );
}
- final static Color calculateColorFromString( final String str ) {
- final String species_uc = str.toUpperCase();
- char first = species_uc.charAt( 0 );
+ final 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 ( species_uc.length() > 1 ) {
- second = species_uc.charAt( 1 );
- if ( species_uc.length() > 2 ) {
- if ( species_uc.indexOf( " " ) > 0 ) {
- third = species_uc.charAt( species_uc.indexOf( " " ) + 1 );
- }
- else {
- third = species_uc.charAt( 2 );
+ 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 = ( char ) ( Math.abs( str.hashCode() / 16909320 ) );
+ System.out.println( str.hashCode() );
+ }
}
first = AptxUtil.normalizeCharForRGB( first );
second = AptxUtil.normalizeCharForRGB( second );
- third = AptxUtil.normalizeCharForRGB( third );
+ if ( is_taxonomy ) {
+ third = AptxUtil.normalizeCharForRGB( third );
+ }
+ else {
+ third = third > 255 ? 255 : third;
+ }
if ( ( first > 235 ) && ( second > 235 ) && ( third > 235 ) ) {
first = 0;
}
return iter.hasNext();
}
- final public static void collapseSpeciesSpecificSubtrees( final Phylogeny phy ) {
+ final static void collapseSpeciesSpecificSubtrees( final Phylogeny phy ) {
boolean inferred = false;
for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {
final PhylogenyNode n = it.next();
if ( !n.isExternal() && !n.isCollapse() && ( n.getNumberOfDescendants() > 1 ) ) {
- final Set<Taxonomy> taxs = PhylogenyMethods.obtainDistinctTaxonomies( n );
+ final Set<Taxonomy> taxs = obtainDistinctTaxonomies( n );
if ( ( taxs != null ) && ( taxs.size() == 1 ) ) {
AptxUtil.collapseSubtree( n, true );
if ( !n.getNodeData().isHasTaxonomy() ) {
}
}
+ 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;
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() );
+ final static String createAnnotationString( final SortedSet<Annotation> annotations ) {
+ final SortedMap<String, List<Annotation>> m = new TreeMap<String, List<Annotation>>();
+ for( final Annotation an : annotations ) {
+ final String ref_source = ForesterUtil.isEmpty( an.getRefSource() ) ? "?" : an.getRefSource();
+ if ( !m.containsKey( ref_source ) ) {
+ m.put( ref_source, new ArrayList<Annotation>() );
}
- }
- 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;
+ m.get( ref_source ).add( an );
+ }
+ final StringBuilder sb = new StringBuilder();
+ for( final Entry<String, List<Annotation>> e : m.entrySet() ) {
+ final String ref_source = e.getKey();
+ final List<Annotation> ans = e.getValue();
+ if ( m.size() > 1 ) {
+ sb.append( "[" );
+ }
+ if ( !ref_source.equals( "?" ) ) {
+ sb.append( ref_source );
+ sb.append( ": " );
+ }
+ for( int i = 0; i < ans.size(); ++i ) {
+ final Annotation an = ans.get( i );
+ if ( !ForesterUtil.isEmpty( an.getRefValue() ) ) {
+ sb.append( an.getRefValue() );
+ sb.append( " " );
+ }
+ if ( !ForesterUtil.isEmpty( an.getDesc() ) ) {
+ sb.append( an.getDesc() );
+ }
+ if ( sb.charAt( sb.length() - 1 ) == ' ' ) {
+ sb.deleteCharAt( sb.length() - 1 );
+ }
+ if ( i < ans.size() - 1 ) {
+ sb.append( ", " );
+ }
+ }
+ if ( m.size() > 1 ) {
+ sb.append( "] " );
}
}
- return str_array;
+ return sb.toString();
}
- 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() ) ) {
}
if ( phy.getIdentifier() != null ) {
desc.append( "Id: " );
- desc.append( phy.getIdentifier() );
+ desc.append( phy.getIdentifier().toString() );
+ desc.append( "\n" );
+ }
+ if ( !ForesterUtil.isEmpty( phy.getDescription() ) ) {
+ desc.append( "Description: " );
+ desc.append( phy.getDescription() );
+ desc.append( "\n" );
+ }
+ if ( !ForesterUtil.isEmpty( phy.getDistanceUnit() ) ) {
+ desc.append( "Distance Unit: " );
+ desc.append( phy.getDistanceUnit() );
+ desc.append( "\n" );
+ }
+ if ( !ForesterUtil.isEmpty( phy.getType() ) ) {
+ desc.append( "Type: " );
+ desc.append( phy.getType() );
desc.append( "\n" );
}
desc.append( "Rooted: " );
desc.append( "Rerootable: " );
desc.append( phy.isRerootable() );
desc.append( "\n" );
- desc.append( "Node sum: " );
+ desc.append( "Nodes: " );
desc.append( phy.getNodeCount() );
desc.append( "\n" );
- desc.append( "External node sum: " );
+ desc.append( "External nodes: " );
desc.append( phy.getNumberOfExternalNodes() );
desc.append( "\n" );
- desc.append( "Internal node sum: " );
+ desc.append( "Internal nodes: " );
desc.append( phy.getNodeCount() - phy.getNumberOfExternalNodes() );
desc.append( "\n" );
- desc.append( "Branche sum: " );
+ desc.append( "Internal nodes with polytomies: " );
+ desc.append( PhylogenyMethods.countNumberOfPolytomies( phy ) );
+ desc.append( "\n" );
+ desc.append( "Branches: " );
desc.append( phy.getNumberOfBranches() );
desc.append( "\n" );
desc.append( "Depth: " );
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 = obtainAllDistinctTaxonomies( phy.getRoot() );
+ if ( taxs != null ) {
+ desc.append( "Distinct external taxonomies: " );
+ desc.append( taxs.size() );
+ }
+ for( final Taxonomy t : taxs ) {
+ System.out.println( t.toString() );
+ }
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( " Branches with support: " + cs.getN() );
+ desc.append( " Median: " + ForesterUtil.round( bs.median(), 6 ) );
desc.append( "\n" );
- desc.append( " Median: " + ForesterUtil.round( cs.median(), 6 ) );
+ desc.append( " Mean: " + ForesterUtil.round( bs.arithmeticMean(), 6 ) + " (stdev: "
+ + 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( " Median: " + ForesterUtil.round( ds.median(), 2 ) );
desc.append( "\n" );
- desc.append( " Maximum: " + ForesterUtil.roundToInt( cs.getMax() ) );
+ desc.append( " Mean: " + ForesterUtil.round( ds.arithmeticMean(), 2 ) + " (stdev: "
+ + 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 ) );
+ if ( cs.getN() > 2 ) {
+ desc.append( " (stdev: " + 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();
System.exit( -1 );
}
- final static String[] getAvailableFontFamiliesSorted() {
- return AVAILABLE_FONT_FAMILIES_SORTED;
+ final 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 inferCommonPartOfScientificNames( final Phylogeny tree ) {
- boolean inferred = false;
- for( final PhylogenyNodeIterator it = tree.iteratorPostorder(); it.hasNext(); ) {
+ 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() && !n.isExternal() ) {
- final String sn = PhylogenyMethods.inferCommonPartOfScientificNameOfDescendants( n );
- if ( !ForesterUtil.isEmpty( sn ) ) {
- n.getNodeData().setTaxonomy( new Taxonomy() );
- n.getNodeData().getTaxonomy().setScientificName( sn );
- inferred = true;
- }
+ if ( n.getNodeData().isHasTaxonomy() && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getRank() ) ) {
+ ranks.add( n.getNodeData().getTaxonomy().getRank() );
}
}
- if ( inferred ) {
- tree.setRerootable( false );
- }
+ return ForesterUtil.stringSetToArray( ranks );
+ }
+
+ final static String[] getAvailableFontFamiliesSorted() {
+ return AVAILABLE_FONT_FAMILIES_SORTED;
}
final static boolean isHasAssignedEvent( final PhylogenyNode node ) {
return true;
}
- final static boolean isJava15() {
- try {
- final String s = ForesterUtil.JAVA_VERSION;
- return s.startsWith( "1.5" );
- }
- catch ( final Exception e ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "minor error: " + e );
- return false;
- }
- }
-
- final static boolean isMac() {
- try {
- final String s = ForesterUtil.OS_NAME.toLowerCase();
- return s.startsWith( "mac" );
- }
- catch ( final Exception e ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "minor error: " + e );
- return false;
- }
- }
-
final static boolean isUsOrCanada() {
try {
if ( ( Locale.getDefault().equals( Locale.CANADA ) ) || ( Locale.getDefault().equals( Locale.US ) ) ) {
return false;
}
- final static boolean isWindows() {
- try {
- final String s = ForesterUtil.OS_NAME.toLowerCase();
- return s.indexOf( "win" ) > -1;
- }
- catch ( final Exception e ) {
- ForesterUtil.printWarningMessage( Constants.PRG_NAME, "minor error: " + e );
- return false;
- }
- }
-
- 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 );
- }
- else {
- // 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 static void lookAtSomeTreePropertiesForAptxControlSettings( final Phylogeny t,
final ControlPanel atv_control,
final Configuration configuration ) {
}
}
- 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 ( 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 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 );
}
}
- final static void printAppletMessage( final String applet_name, final String message ) {
- System.out.println( "[" + applet_name + "] > " + message );
+ final static void outOfMemoryError( final OutOfMemoryError e ) {
+ System.err.println();
+ System.err.println( "Java memory allocation might be too small, try \"-Xmx2048m\" java command line option" );
+ System.err.println();
+ e.printStackTrace();
+ System.err.println();
+ 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 );
+ System.exit( -1 );
}
- public final static void printWarningMessage( final String name, final String message ) {
- System.out.println( "[" + name + "] > " + message );
+ final static void printAppletMessage( final String applet_name, final String message ) {
+ System.out.println( "[" + applet_name + "] > " + message );
}
- final static Phylogeny[] readPhylogeniesFromUrl( final URL url, final boolean phyloxml_validate_against_xsd )
- throws FileNotFoundException, IOException {
+ final 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();
- PhylogenyParser parser = null;
+ 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 );
+ }
}
- return factory.create( url.openStream(), parser );
+ final Phylogeny[] phys = factory.create( url.openStream(), parser );
+ 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 ) {
}
}
- 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 );
- }
-
- final static void unexpectedError( final Error err ) {
- err.printStackTrace();
+ final static void unexpectedError( final Error e ) {
+ System.err.println();
+ e.printStackTrace( System.err );
+ System.err.println();
final StringBuffer sb = new StringBuffer();
- for( final StackTraceElement s : err.getStackTrace() ) {
+ for( final StackTraceElement s : e.getStackTrace() ) {
sb.append( s + "\n" );
}
JOptionPane
.showMessageDialog( null,
"An unexpected (possibly severe) error has occured - terminating. \nPlease contact: "
- + Constants.AUTHOR_EMAIL + " \nError: " + err + "\n" + sb,
+ + Constants.AUTHOR_EMAIL + " \nError: " + e.getLocalizedMessage() + "\n"
+ + sb,
"Unexpected Severe Error [" + Constants.PRG_NAME + " " + Constants.VERSION + "]",
JOptionPane.ERROR_MESSAGE );
System.exit( -1 );
}
- final static void unexpectedException( final Exception ex ) {
- ex.printStackTrace();
+ final static void unexpectedException( final Exception e ) {
+ System.err.println();
+ e.printStackTrace( System.err );
+ System.err.println();
final StringBuffer sb = new StringBuffer();
- for( final StackTraceElement s : ex.getStackTrace() ) {
+ for( final StackTraceElement s : e.getStackTrace() ) {
sb.append( s + "\n" );
}
- JOptionPane.showMessageDialog( null, "An unexpected exception has occured. \nPlease contact: "
- + Constants.AUTHOR_EMAIL + " \nException: " + ex + "\n" + sb, "Unexpected Exception ["
- + Constants.PRG_NAME + Constants.VERSION + "]", JOptionPane.ERROR_MESSAGE );
+ JOptionPane.showMessageDialog( null,
+ "An unexpected exception has occured. \nPlease contact: "
+ + Constants.AUTHOR_EMAIL + " \nException: " + e.getLocalizedMessage()
+ + "\n" + sb,
+ "Unexpected Exception [" + Constants.PRG_NAME + Constants.VERSION + "]",
+ JOptionPane.ERROR_MESSAGE );
}
- final static String writePhylogenyToGraphicsFile( final String file_name,
- int width,
- int height,
- final TreePanel tree_panel,
- final ControlPanel ac,
- final GraphicsExportType type,
- final Options options ) throws IOException {
+ 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.calcParametersForPainting( options.getPrintSizeX(), options.getPrintSizeY(), true );
tree_panel.resetPreferredSize();
tree_panel.repaint();
}
if ( ( phylogeny == null ) || phylogeny.isEmpty() ) {
return "";
}
- final File file = new File( file_name );
- if ( file.isDirectory() ) {
- throw new IOException( "\"" + file_name + "\" is a directory" );
- }
Rectangle visible = null;
if ( !options.isGraphicsExportUsingActualSize() ) {
width = options.getPrintSizeX();
y = visible.y;
}
tree_panel.paintPhylogeny( g2d, false, true, width, height, x, y );
- if ( type == GraphicsExportType.TIFF ) {
- writeToTiff( file, buffered_img );
- }
- else {
- ImageIO.write( buffered_img, type.toString(), file );
- }
+ ImageIO.write( buffered_img, type.toString(), baos );
g2d.dispose();
System.gc();
if ( !options.isGraphicsExportUsingActualSize() ) {
tree_panel.getMainPanel().getControlPanel().showWhole();
}
- String msg = file.toString();
+ String msg = baos.toString();
if ( ( width > 0 ) && ( height > 0 ) ) {
msg += " [size: " + width + ", " + height + "]";
}
return msg;
}
- public final static void writePhylogenyToGraphicsFileNonInteractive( final File outfile,
- final int width,
- final int height,
- final TreePanel tree_panel,
- final ControlPanel ac,
- final GraphicsExportType type,
- final Options options ) throws IOException {
- tree_panel.setParametersForPainting( width, height, 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;
- }
- if ( outfile.isDirectory() ) {
- throw new IOException( "\"" + outfile + "\" is a directory" );
- }
- final BufferedImage buffered_img = new BufferedImage( width, height, BufferedImage.TYPE_INT_RGB );
- final Graphics2D g2d = buffered_img.createGraphics();
- g2d.setRenderingHints( rendering_hints );
- tree_panel.paintPhylogeny( g2d, false, true, width, height, 0, 0 );
- if ( type == GraphicsExportType.TIFF ) {
- writeToTiff( outfile, buffered_img );
- }
- else {
- ImageIO.write( buffered_img, type.toString(), outfile );
- }
- 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 {
+ final static String writePhylogenyToGraphicsFile( final String file_name,
+ 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.calcParametersForPainting( options.getPrintSizeX(), options.getPrintSizeY(), true );
tree_panel.resetPreferredSize();
tree_panel.repaint();
}
if ( ( phylogeny == null ) || phylogeny.isEmpty() ) {
return "";
}
+ final File file = new File( file_name );
+ if ( file.isDirectory() ) {
+ throw new IOException( "\"" + file_name + "\" is a directory" );
+ }
Rectangle visible = null;
if ( !options.isGraphicsExportUsingActualSize() ) {
width = options.getPrintSizeX();
y = visible.y;
}
tree_panel.paintPhylogeny( g2d, false, true, width, height, x, y );
- ImageIO.write( buffered_img, type.toString(), baos );
+ if ( type == GraphicsExportType.TIFF ) {
+ writeToTiff( file, buffered_img );
+ }
+ else {
+ ImageIO.write( buffered_img, type.toString(), file );
+ }
g2d.dispose();
System.gc();
if ( !options.isGraphicsExportUsingActualSize() ) {
tree_panel.getMainPanel().getControlPanel().showWhole();
}
- String msg = baos.toString();
+ String msg = file.toString();
if ( ( width > 0 ) && ( height > 0 ) ) {
msg += " [size: " + width + ", " + height + "]";
}
writer.write( null, iio_image, image_write_param );
}
+ 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 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 } );
+ }
+ }
+ }
+
// See: http://www.xml.nig.ac.jp/tutorial/rest/index.html#2.2
// static void openDDBJRest() throws IOException {
// //set URL
// br.close();
// }
public static enum GraphicsExportType {
- GIF( "gif" ), JPG( "jpg" ), PDF( "pdf" ), PNG( "png" ), TIFF( "tif" ), BMP( "bmp" );
+ BMP( "bmp" ), GIF( "gif" ), JPG( "jpg" ), PDF( "pdf" ), PNG( "png" ), TIFF( "tif" );
private final String _suffix;
git://source.jalview.org / jalview.git / blobdiff