X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FAptxUtil.java;h=8ceb398a2e08ffaf1bde034aeb7a025662f6ad2b;hb=5c4e24e304f57058fa1c3a3f1256a573b37d89f6;hp=c2dfc549b38b10317a3cae453db66a875bf4f554;hpb=37cb4c1bc15ea30a6f64953d5e23e09694083f06;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java index c2dfc54..8ceb398 100644 --- a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java +++ b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java @@ -36,19 +36,26 @@ import java.io.ByteArrayOutputStream; 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; @@ -72,8 +79,10 @@ 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.Taxonomy; import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory; @@ -82,17 +91,19 @@ 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.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*$" ); private final static Pattern seq_identifier_pattern_2 = Pattern .compile( "^([A-Za-z]{2,5})[|=:]([0-9A-Za-z_\\.]{5,40})[|,; ].*$" ); - private final static String[] AVAILABLE_FONT_FAMILIES_SORTED = GraphicsEnvironment.getLocalGraphicsEnvironment() - .getAvailableFontFamilyNames(); static { Arrays.sort( AVAILABLE_FONT_FAMILIES_SORTED ); } @@ -108,6 +119,69 @@ public final class AptxUtil { return formatter; } + 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 static public boolean isHasAtLeastNodeWithEvent( final Phylogeny phy ) { final PhylogenyNodeIterator it = phy.iteratorPostorder(); while ( it.hasNext() ) { @@ -185,6 +259,36 @@ public final class AptxUtil { } } + public static Set obtainAllDistinctTaxonomies( final PhylogenyNode node ) { + final List descs = node.getAllExternalDescendants(); + final Set tax_set = new HashSet(); + 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 obtainDistinctTaxonomies( final PhylogenyNode node ) { + final List descs = node.getAllExternalDescendants(); + final Set tax_set = new HashSet(); + 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 ); @@ -245,6 +349,10 @@ public final class AptxUtil { && !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() ) ) { @@ -300,7 +408,7 @@ public final class AptxUtil { 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, @@ -435,25 +543,41 @@ public final class AptxUtil { 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; } @@ -474,7 +598,7 @@ public final class AptxUtil { for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) { final PhylogenyNode n = it.next(); if ( !n.isExternal() && !n.isCollapse() && ( n.getNumberOfDescendants() > 1 ) ) { - final Set taxs = PhylogenyMethods.obtainDistinctTaxonomies( n ); + final Set taxs = obtainDistinctTaxonomies( n ); if ( ( taxs != null ) && ( taxs.size() == 1 ) ) { AptxUtil.collapseSubtree( n, true ); if ( !n.getNodeData().isHasTaxonomy() ) { @@ -626,6 +750,49 @@ public final class AptxUtil { return colorizations; } + final static String createAnnotationString( final SortedSet annotations ) { + final SortedMap> m = new TreeMap>(); + 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() ); + } + m.get( ref_source ).add( an ); + } + final StringBuilder sb = new StringBuilder(); + for( final Entry> e : m.entrySet() ) { + final String ref_source = e.getKey(); + final List 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 sb.toString(); + } + final static String createBasicInformation( final Phylogeny phy ) { final StringBuilder desc = new StringBuilder(); if ( ( phy != null ) && !phy.isEmpty() ) { @@ -636,7 +803,22 @@ public final class AptxUtil { } 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: " ); @@ -645,16 +827,19 @@ public final class AptxUtil { 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: " ); @@ -663,11 +848,14 @@ public final class AptxUtil { desc.append( "Maximum distance to root: " ); desc.append( ForesterUtil.round( PhylogenyMethods.calculateMaxDistanceToRoot( phy ), 6 ) ); desc.append( "\n" ); - final Set taxs = PhylogenyMethods.obtainDistinctTaxonomies( phy.getRoot() ); + final Set 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 bs = PhylogenyMethods.calculatBranchLengthStatistics( phy ); if ( bs.getN() > 3 ) { @@ -678,9 +866,8 @@ public final class AptxUtil { 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" ); @@ -699,9 +886,8 @@ public final class AptxUtil { 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" ); @@ -736,11 +922,10 @@ public final class AptxUtil { 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() ) ); @@ -804,28 +989,6 @@ public final class AptxUtil { 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 ) ) ) { @@ -838,17 +1001,6 @@ public final class AptxUtil { 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 ) { @@ -900,6 +1052,20 @@ public final class AptxUtil { } } + 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 ); } @@ -908,8 +1074,9 @@ public final class AptxUtil { 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; @@ -938,6 +1105,12 @@ public final class AptxUtil { 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; } @@ -965,20 +1138,6 @@ public final class AptxUtil { System.exit( -1 ); } - 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 unexpectedException( final Exception e ) { System.err.println(); e.printStackTrace( System.err ); @@ -1006,7 +1165,7 @@ public final class AptxUtil { 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(); } @@ -1071,7 +1230,7 @@ public final class AptxUtil { 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(); } @@ -1187,7 +1346,7 @@ public final class AptxUtil { 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 } ); @@ -1234,7 +1393,7 @@ public final class AptxUtil { // 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;