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revert to default turning off of anti-alias on apple macintosh.
[jalview.git] / forester / java / src / org / forester / archaeopteryx / AptxUtil.java
diff --git a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
index 823e18f..b874665 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
+++ b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
@@ -75,10 +75,10 @@ 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.BranchColor;
-import org.forester.phylogeny.data.Sequence;
 import org.forester.phylogeny.data.Taxonomy;
 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
 import org.forester.phylogeny.factories.PhylogenyFactory;
@@ -107,22 +107,10 @@ public final class AptxUtil {
                                                    final Configuration conf,
                                                    final TreePanel tp ) {
         String uri_str = null;
-        if ( node.getNodeData().isHasSequence() && ( node.getNodeData().getSequence().getAccession() != null )
-                && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getSource() )
-                && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().getValue() )
-                && conf.isHasWebLink( node.getNodeData().getSequence().getAccession().getSource().toLowerCase() ) ) {
-            final Sequence seq = node.getNodeData().getSequence();
-            final String source = seq.getAccession().getSource().toLowerCase();
-            String url;
-            if ( source.toLowerCase().equals( "ncbi" ) ) {
-                url = Constants.NCBI_ALL_DATABASE_SEARCH;
-            }
-            else {
-                final WebLink weblink = conf.getWebLink( source );
-                url = weblink.getUrl().toString();
-            }
+        final String upkb = ForesterUtil.extractUniProtKbProteinSeqIdentifier( node );
+        if ( !ForesterUtil.isEmpty( upkb ) ) {
             try {
-                uri_str = url + URLEncoder.encode( seq.getAccession().getValue(), ForesterConstants.UTF8 );
+                uri_str = ForesterUtil.UNIPROT_KB + URLEncoder.encode( upkb, ForesterConstants.UTF8 );
             }
             catch ( final UnsupportedEncodingException e ) {
                 showErrorMessage( tp, e.toString() );
@@ -130,10 +118,15 @@ public final class AptxUtil {
             }
         }
         if ( ForesterUtil.isEmpty( uri_str ) ) {
-            final String upkb = ForesterUtil.extractUniProtKbProteinSeqIdentifier( node );
-            if ( !ForesterUtil.isEmpty( upkb ) ) {
+            final String v = ForesterUtil.extractGenbankAccessor( node );
+            if ( !ForesterUtil.isEmpty( v ) ) {
                 try {
-                    uri_str = ForesterUtil.UNIPROT_KB + URLEncoder.encode( upkb, ForesterConstants.UTF8 );
+                    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() );
@@ -142,7 +135,7 @@ public final class AptxUtil {
             }
         }
         if ( ForesterUtil.isEmpty( uri_str ) ) {
-            final String v = ForesterUtil.extractGenbankAccessor( node );
+            final String v = ForesterUtil.extractRefSeqAccessorAccessor( node );
             if ( !ForesterUtil.isEmpty( v ) ) {
                 try {
                     if ( SequenceIdParser.isProtein( v ) ) {
@@ -159,15 +152,10 @@ public final class AptxUtil {
             }
         }
         if ( ForesterUtil.isEmpty( uri_str ) ) {
-            final String v = ForesterUtil.extractRefSeqAccessorAccessor( node );
+            final String v = ForesterUtil.extractGInumber( 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 );
-                    }
+                    uri_str = ForesterUtil.NCBI_GI + URLEncoder.encode( v, ForesterConstants.UTF8 );
                 }
                 catch ( final UnsupportedEncodingException e ) {
                     showErrorMessage( tp, e.toString() );
@@ -807,9 +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" );
@@ -828,9 +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" );
@@ -865,11 +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() ) );
@@ -933,17 +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 ) ) ) {
@@ -956,17 +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 ) {
@@ -1040,8 +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;
@@ -1070,6 +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;
     }
 
@@ -1305,7 +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 } );