// 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.Arrays;
import java.util.HashMap;
+import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Locale;
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.BranchColor;
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.util.SequenceIdParser;
import org.forester.ws.seqdb.UniProtTaxonomy;
public final class AptxUtil {
Arrays.sort( AVAILABLE_FONT_FAMILIES_SORTED );
}
+ 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;
+ }
+
public static MaskFormatter createMaskFormatter( final String s ) {
MaskFormatter formatter = null;
try {
}
}
+ 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 );
final ControlPanel ac,
final GraphicsExportType type,
final Options options ) throws IOException {
- tree_panel.setParametersForPainting( width, height, true );
+ tree_panel.calcParametersForPainting( width, height, true );
tree_panel.resetPreferredSize();
tree_panel.repaint();
final RenderingHints rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING,
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() ) {
}
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" );
- final Set<Taxonomy> taxs = PhylogenyMethods.obtainDistinctTaxonomies( phy.getRoot() );
+ final Set<Taxonomy> taxs = obtainAllDistinctTaxonomies( phy.getRoot() );
if ( taxs != null ) {
desc.append( "Distinct external taxonomies: " );
desc.append( taxs.size() );
desc.append( "\n" );
desc.append( " Median: " + ForesterUtil.round( bs.median(), 6 ) );
desc.append( "\n" );
- desc.append( " Mean: " + ForesterUtil.round( bs.arithmeticMean(), 6 ) );
- desc.append( "\n" );
- desc.append( " SD: " + ForesterUtil.round( bs.sampleStandardDeviation(), 6 ) );
+ desc.append( " Mean: " + ForesterUtil.round( bs.arithmeticMean(), 6 ) + " (stdev: "
+ + ForesterUtil.round( bs.sampleStandardDeviation(), 6 ) + ")" );
desc.append( "\n" );
desc.append( " Minimum: " + ForesterUtil.round( bs.getMin(), 6 ) );
desc.append( "\n" );
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( " 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( " 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( " (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() ) );
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 static void lookAtSomeTreePropertiesForAptxControlSettings( final Phylogeny t,
final ControlPanel atv_control,
final Configuration configuration ) {
}
}
+ 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 );
+ }
+
final static void printAppletMessage( final String applet_name, final String message ) {
System.out.println( "[" + applet_name + "] > " + message );
}
final boolean phyloxml_validate_against_xsd,
final boolean replace_underscores,
final boolean internal_numbers_are_confidences,
- final TAXONOMY_EXTRACTION taxonomy_extraction )
- throws FileNotFoundException, IOException {
+ 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;
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 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 writePhylogenyToGraphicsByteArrayOutputStream( final ByteArrayOutputStream baos,
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 ( 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 ( os.toLowerCase().startsWith( "win" ) ) {
Runtime.getRuntime().exec( "rundll32 url.dll,FileProtocolHandler " + url );
}
- else if ( isMac() ) {
+ 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 } );
git://source.jalview.org / jalview.git / blobdiff