X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FAptxUtil.java;h=e35596765ffbf79ac368e1f9fd7846f21eded4d1;hb=7ad84913635263ddc191fcbebd8a9bd46a9ac7e3;hp=cc0c3657e08a05a73d652eb9df6849c5aa32b779;hpb=3be5f9e46469980f068a9f8170e1d20849b5eaf8;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
index cc0c365..e355967 100644
--- a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
+++ b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
@@ -62,7 +62,7 @@ import javax.swing.JApplet;
 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.phyloxml.PhyloXmlUtil;
 import org.forester.io.parsers.tol.TolParser;
@@ -79,9 +79,10 @@ 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.ForesterUtil;
-import org.forester.ws.uniprot.UniProtTaxonomy;
+import org.forester.ws.seqdb.UniProtTaxonomy;
 
 public final class AptxUtil {
 
@@ -463,7 +464,7 @@ public final class AptxUtil {
                         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();
@@ -536,7 +537,7 @@ public final class AptxUtil {
         }
     }
 
-    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() ) ) {
@@ -573,42 +574,88 @@ public final class AptxUtil {
             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 = PhylogenyMethods.obtainDistinctTaxonomies( phy.getRoot() );
+            if ( taxs != null ) {
+                desc.append( "Distinct external taxonomies: " );
+                desc.append( taxs.size() );
+            }
             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() > 2 ) {
                 desc.append( "\n" );
-                desc.append( "    Branches with support: " + cs.getN() );
+                desc.append( "Branch-length statistics: " );
                 desc.append( "\n" );
-                desc.append( "    Median: " + ForesterUtil.round( cs.median(), 6 ) );
+                desc.append( "    Number of branches with non-negative branch-lengths: " + bs.getN() );
                 desc.append( "\n" );
-                desc.append( "    Mean: " + ForesterUtil.round( cs.arithmeticMean(), 6 ) );
+                desc.append( "    Median: " + ForesterUtil.round( bs.median(), 6 ) );
                 desc.append( "\n" );
-                if ( cs.getN() > 2 ) {
-                    desc.append( "    SD: " + ForesterUtil.round( cs.sampleStandardDeviation(), 6 ) );
-                    desc.append( "\n" );
-                }
-                desc.append( "    Minimum: " + ForesterUtil.roundToInt( cs.getMin() ) );
+                desc.append( "    Mean: " + ForesterUtil.round( bs.arithmeticMean(), 6 ) );
+                desc.append( "\n" );
+                desc.append( "    SD: " + ForesterUtil.round( bs.sampleStandardDeviation(), 6 ) );
+                desc.append( "\n" );
+                desc.append( "    Minimum: " + ForesterUtil.round( bs.getMin(), 6 ) );
+                desc.append( "\n" );
+                desc.append( "    Maximum: " + ForesterUtil.round( bs.getMax(), 6 ) );
                 desc.append( "\n" );
-                desc.append( "    Maximum: " + ForesterUtil.roundToInt( cs.getMax() ) );
                 desc.append( "\n" );
+                final AsciiHistogram histo = new AsciiHistogram( bs );
+                desc.append( histo.toStringBuffer( 12, '#', 40, 7, "    " ) );
             }
-            final Set<Taxonomy> taxs = PhylogenyMethods.obtainDistinctTaxonomies( phy.getRoot() );
-            if ( taxs != null ) {
-                desc.append( "Distinct external taxonomies: " );
-                desc.append( taxs.size() );
+            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( "    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() ) );
+                desc.append( "\n" );
+            }
+            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 ) );
+                        desc.append( "\n" );
+                        if ( cs.getN() > 2 ) {
+                            desc.append( "    SD: " + 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();