X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FAptxUtil.java;h=b874665d18f1a91f131c725e8475e649dce2e28a;hb=b43f94dd9ce1416a2459997d1a1b69cf81036684;hp=2ca3b8732c77fb99accc5ad77029dc96e6616da7;hpb=0e23c7a534e22c1b4238bf59e676a7a500395bd3;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java index 2ca3b87..b874665 100644 --- a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java +++ b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java @@ -36,10 +36,12 @@ 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.Arrays; import java.util.HashMap; @@ -73,6 +75,7 @@ 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.BranchColor; @@ -83,14 +86,13 @@ 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 { - final static String UNIPROT_KB = "http://www.uniprot.org/uniprot/"; - final static Pattern UNIPROT_KB_PATTERN = Pattern - .compile( "\\b[A-Z0-9]{5,6}_[A-Z9][A-Z]{2}[A-Z0-9]{2}|RAT|PIG|PEA\\b" ); 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 @@ -101,6 +103,69 @@ 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 { @@ -730,9 +795,8 @@ 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" ); @@ -751,9 +815,8 @@ 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" ); @@ -788,11 +851,10 @@ 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() ) ); @@ -856,17 +918,6 @@ public final class AptxUtil { return true; } - 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 ) ) ) { @@ -879,17 +930,6 @@ 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 ) { @@ -963,8 +1003,9 @@ 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; @@ -993,6 +1034,12 @@ 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; } @@ -1228,7 +1275,7 @@ 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 } );