needs: testing, proper error messages and dialogs, code cleanup, cache mechanism...

diff --git a/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java b/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java
index ba0a6df..0d1465a 100644 (file)
--- a/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java
+++ b/forester/java/src/org/forester/analysis/AncestralTaxonomyInference.java
@@ -31,6 +31,7 @@ import java.util.List;
 import java.util.SortedSet;
 import java.util.TreeSet;
 
+import org.forester.archaeopteryx.tools.AncestralTaxonomyInferenceException;
 import org.forester.io.parsers.phyloxml.PhyloXmlDataFormatException;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyNode;
@@ -146,21 +147,19 @@ public final class AncestralTaxonomyInference {
         return UniProtWsTools.getTaxonomiesFromTaxonomyCode( query, MAX_TAXONOMIES_TO_RETURN );
     }
 
-    synchronized public static SortedSet<String> inferTaxonomyFromDescendents( final Phylogeny phy ) throws IOException {
+    synchronized public static void inferTaxonomyFromDescendents( final Phylogeny phy ) throws IOException,
+            AncestralTaxonomyInferenceException {
         clearCachesIfTooLarge();
-        final SortedSet<String> not_found = new TreeSet<String>();
         for( final PhylogenyNodeIterator iter = phy.iteratorPostorder(); iter.hasNext(); ) {
             final PhylogenyNode node = iter.next();
             if ( !node.isExternal() ) {
-                inferTaxonomyFromDescendents( node, not_found );
+                inferTaxonomyFromDescendents( node );
             }
         }
-        return not_found;
     }
 
-    synchronized private static void inferTaxonomyFromDescendents( final PhylogenyNode n,
-                                                                   final SortedSet<String> not_found )
-            throws IOException {
+    synchronized private static void inferTaxonomyFromDescendents( final PhylogenyNode n ) throws IOException,
+            AncestralTaxonomyInferenceException {
         if ( n.isExternal() ) {
             throw new IllegalArgumentException( "attempt to infer taxonomy from descendants of external node" );
         }
@@ -174,18 +173,14 @@ public final class AncestralTaxonomyInference {
                             || !ForesterUtil.isEmpty( desc.getNodeData().getTaxonomy().getScientificName() )
                             || !ForesterUtil.isEmpty( desc.getNodeData().getTaxonomy().getTaxonomyCode() ) || !ForesterUtil
                             .isEmpty( desc.getNodeData().getTaxonomy().getCommonName() ) ) ) {
-             
                 final UniProtTaxonomy up_tax = obtainUniProtTaxonomy( desc.getNodeData().getTaxonomy(), null, null );
                 String[] lineage = null;
                 if ( up_tax != null ) {
-                    //lineage = obtainLineagePlusOwnScientificName( up_tax );
                     lineage = up_tax.getLineageAsArray();
                 }
                 if ( ( lineage == null ) || ( lineage.length < 1 ) ) {
-                    //TODO remove me
-                    System.out.println( "node " + desc.getNodeData().getTaxonomy().toString() + " has no lineage!" );
-                    not_found.add( desc.getNodeData().getTaxonomy().asText().toString() );
-                    return;
+                    throw new AncestralTaxonomyInferenceException( "a taxonomic lineage for node \""
+                            + desc.getNodeData().getTaxonomy().toString() + "\" could not be found" );
                 }
                 if ( lineage.length < shortest_lin_length ) {
                     shortest_lin_length = lineage.length;
@@ -193,7 +188,6 @@ public final class AncestralTaxonomyInference {
                 lineages.add( lineage );
             }
             else {
-                String msg = "Node(s) with no or inappropriate taxonomic information found";
                 String node = "";
                 if ( !ForesterUtil.isEmpty( desc.getName() ) ) {
                     node = "\"" + desc.getName() + "\"";
@@ -201,22 +195,22 @@ public final class AncestralTaxonomyInference {
                 else {
                     node = "[" + desc.getId() + "]";
                 }
-                msg = "Node " + node + " has no or inappropriate taxonomic information";
-             //   final List<PhylogenyNode> e = desc.getAllExternalDescendants();
+                //   final List<PhylogenyNode> e = desc.getAllExternalDescendants();
                 //TODO remove me!
-//                System.out.println();
-//                int x = 0;
-//                for( final PhylogenyNode object : e ) {
-//                    System.out.println( x + ":" );
-//                    System.out.println( object.getName() + "  " );
-//                    x++;
-//                }
-//                System.out.println();
+                //                System.out.println();
+                //                int x = 0;
+                //                for( final PhylogenyNode object : e ) {
+                //                    System.out.println( x + ":" );
+                //                    System.out.println( object.getName() + "  " );
+                //                    x++;
+                //                }
+                //                System.out.println();
                 //
-                throw new IllegalArgumentException( msg );
+                throw new AncestralTaxonomyInferenceException( "node " + node
+                        + " has no or inappropriate taxonomic information" );
             }
         }
-        List<String> last_common_lineage = new ArrayList<String>();
+        final List<String> last_common_lineage = new ArrayList<String>();
         String last_common = null;
         if ( shortest_lin_length > 0 ) {
             I: for( int i = 0; i < shortest_lin_length; ++i ) {
@@ -226,24 +220,24 @@ public final class AncestralTaxonomyInference {
                         break I;
                     }
                 }
-               // last_common_lineage = lineage_0;
-                last_common_lineage.add( lineage_0 ) ;
-                last_common =lineage_0;
+                // last_common_lineage = lineage_0;
+                last_common_lineage.add( lineage_0 );
+                last_common = lineage_0;
             }
         }
-       // if ( last_common_lineage == null ) {
+        // if ( last_common_lineage == null ) {
         if ( last_common_lineage.isEmpty() ) {
-            System.out.println( "No common lineage for:" );
+            String msg = "no common lineage for:\n";
             int counter = 0;
             for( final String[] strings : lineages ) {
-                System.out.print( counter + ": " );
+                msg += counter + ": ";
                 ++counter;
                 for( final String string : strings ) {
-                    System.out.print( string + " " );
+                    msg += string + " ";
                 }
-                System.out.println();
+                msg += "\n";
             }
-            return;
+            throw new AncestralTaxonomyInferenceException( msg );
         }
         final Taxonomy tax = new Taxonomy();
         n.getNodeData().setTaxonomy( tax );
@@ -275,7 +269,6 @@ public final class AncestralTaxonomyInference {
                     }
                 }
             }
-            
         }
         for( final PhylogenyNode desc : descs ) {
             if ( !desc.isExternal() && desc.getNodeData().isHasTaxonomy()
@@ -362,13 +355,13 @@ public final class AncestralTaxonomyInference {
         if ( isHasAppropriateId( tax ) ) {
             query = tax.getIdentifier().getValue();
             qt = QUERY_TYPE.ID;
-            System.out.println( "query by id: " + query);
+            System.out.println( "query by id: " + query );
             return getTaxonomies( getIdTaxCacheMap(), query, qt );
         }
         else if ( !ForesterUtil.isEmpty( tax.getScientificName() ) ) {
             query = tax.getScientificName();
             qt = QUERY_TYPE.SN;
-            System.out.println( "query by sn: " + query);
+            System.out.println( "query by sn: " + query );
             return getTaxonomies( getSnTaxCacheMap(), query, qt );
         }
         else if ( !ForesterUtil.isEmpty( tax.getTaxonomyCode() ) ) {
@@ -383,7 +376,7 @@ public final class AncestralTaxonomyInference {
         }
     }
 
-    synchronized private static UniProtTaxonomy obtainUniProtTaxonomyFromSn( final String sn) throws IOException {
+    synchronized private static UniProtTaxonomy obtainUniProtTaxonomyFromSn( final String sn ) throws IOException {
         UniProtTaxonomy up_tax = null;
         if ( getSnTaxCacheMap().containsKey( sn ) ) {
             up_tax = getSnTaxCacheMap().get( sn ).copy();
@@ -402,56 +395,54 @@ public final class AncestralTaxonomyInference {
                 if ( !ForesterUtil.isEmpty( up_tax.getId() ) ) {
                     getIdTaxCacheMap().put( up_tax.getId(), up_tax );
                 }
-                
             }
         }
         return up_tax;
     }
-    
-    synchronized private static UniProtTaxonomy obtainUniProtTaxonomyFromCommonLineage( List<String> lineage ) throws IOException {
-        UniProtTaxonomy up_tax = null;
-      // -- if ( getSnTaxCacheMap().containsKey( sn ) ) {
-      // --     up_tax = getSnTaxCacheMap().get( sn ).copy();
-      // -- }
-      //  else {
-            final List<UniProtTaxonomy> up_taxonomies = getTaxonomiesFromScientificName( lineage.get(lineage.size() -1 ) );
-            //-- if ( ( up_taxonomies != null ) && ( up_taxonomies.size() == 1 ) ) {
-           
-            if ( ( up_taxonomies != null ) && ( up_taxonomies.size() > 0 ) ) {
-                for( UniProtTaxonomy up_taxonomy : up_taxonomies ) {
-                    boolean match = true;
 
-                    I: for( int i = 0; i < lineage.size(); ++i ) {
-                        if ( !lineage.get( i ).equalsIgnoreCase( up_taxonomy.getLineage().get( i ) )  ) { 
-                            match = false;
-                            break I;
-                        }
-                    }
-                    if ( match ) {
-                        if ( up_tax != null ) {
-                            throw new IOException( "not unique!");
-                        }
-                        up_tax = up_taxonomy;
+    synchronized private static UniProtTaxonomy obtainUniProtTaxonomyFromCommonLineage( final List<String> lineage )
+            throws AncestralTaxonomyInferenceException, IOException {
+        UniProtTaxonomy up_tax = null;
+        // -- if ( getSnTaxCacheMap().containsKey( sn ) ) {
+        // --     up_tax = getSnTaxCacheMap().get( sn ).copy();
+        // -- }
+        //  else {
+        final List<UniProtTaxonomy> up_taxonomies = getTaxonomiesFromScientificName( lineage.get( lineage.size() - 1 ) );
+        //-- if ( ( up_taxonomies != null ) && ( up_taxonomies.size() == 1 ) ) {
+        if ( ( up_taxonomies != null ) && ( up_taxonomies.size() > 0 ) ) {
+            for( final UniProtTaxonomy up_taxonomy : up_taxonomies ) {
+                boolean match = true;
+                I: for( int i = 0; i < lineage.size(); ++i ) {
+                    if ( !lineage.get( i ).equalsIgnoreCase( up_taxonomy.getLineage().get( i ) ) ) {
+                        match = false;
+                        break I;
                     }
                 }
-
-                if ( up_tax == null ) {
-                    throw new IOException( "not found!");
-                }
-                //-- up_tax = up_taxonomies.get( 0 );
-               //-- getSnTaxCacheMap().put( sn, up_tax );
-                if ( !ForesterUtil.isEmpty( up_tax.getCode() ) ) {
-                    getCodeTaxCacheMap().put( up_tax.getCode(), up_tax );
-                }
-                if ( !ForesterUtil.isEmpty( up_tax.getCommonName() ) ) {
-                    getCnTaxCacheMap().put( up_tax.getCommonName(), up_tax );
-                }
-                if ( !ForesterUtil.isEmpty( up_tax.getId() ) ) {
-                    getIdTaxCacheMap().put( up_tax.getId(), up_tax );
+                if ( match ) {
+                    if ( up_tax != null ) {
+                        throw new AncestralTaxonomyInferenceException( "lineage \""
+                                + ForesterUtil.stringListToString( lineage, " > " ) + "\" is not unique" );
+                    }
+                    up_tax = up_taxonomy;
                 }
-                
             }
-      //  }
+            if ( up_tax == null ) {
+                throw new AncestralTaxonomyInferenceException( "lineage \""
+                        + ForesterUtil.stringListToString( lineage, " > " ) + "\" not found" );
+            }
+            //-- up_tax = up_taxonomies.get( 0 );
+            //-- getSnTaxCacheMap().put( sn, up_tax );
+            if ( !ForesterUtil.isEmpty( up_tax.getCode() ) ) {
+                getCodeTaxCacheMap().put( up_tax.getCode(), up_tax );
+            }
+            if ( !ForesterUtil.isEmpty( up_tax.getCommonName() ) ) {
+                getCnTaxCacheMap().put( up_tax.getCommonName(), up_tax );
+            }
+            if ( !ForesterUtil.isEmpty( up_tax.getId() ) ) {
+                getIdTaxCacheMap().put( up_tax.getId(), up_tax );
+            }
+        }
+        //  }
         return up_tax;
     }
 
@@ -494,7 +485,6 @@ public final class AncestralTaxonomyInference {
                 }
             }
         }
-        
     }
 
     private enum QUERY_TYPE {

diff --git a/forester/java/src/org/forester/archaeopteryx/NodePanel.java b/forester/java/src/org/forester/archaeopteryx/NodePanel.java
index fb4ac82..4cfb7b2 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/NodePanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/NodePanel.java
@@ -209,13 +209,12 @@ class NodePanel extends JPanel implements TreeSelectionListener {
             }
         }
     }
-    
+
     private static void addLineage( final DefaultMutableTreeNode top,
-                                 final List<String> lineage,
-                                 final DefaultMutableTreeNode category ) {
-        if ( ( lineage != null ) && (  lineage.size() > 0 ) ) {
-          
-            StringBuilder sb = new StringBuilder();
+                                    final List<String> lineage,
+                                    final DefaultMutableTreeNode category ) {
+        if ( ( lineage != null ) && ( lineage.size() > 0 ) ) {
+            final StringBuilder sb = new StringBuilder();
             for( final String lin : lineage ) {
                 if ( !ForesterUtil.isEmpty( lin ) ) {
                     sb.append( lin );
@@ -223,7 +222,7 @@ class NodePanel extends JPanel implements TreeSelectionListener {
                 }
             }
             String str = null;
-            if (sb.length() > 1 ) {
+            if ( sb.length() > 1 ) {
                 str = sb.substring( 0, sb.length() - 3 );
             }
             if ( !ForesterUtil.isEmpty( str ) ) {
@@ -231,8 +230,6 @@ class NodePanel extends JPanel implements TreeSelectionListener {
             }
         }
     }
-    
-    
 
     private static void addBasics( final DefaultMutableTreeNode top,
                                    final PhylogenyNode phylogeny_node,

diff --git a/forester/java/src/org/forester/archaeopteryx/tools/AncestralTaxonomyInferenceException.java b/forester/java/src/org/forester/archaeopteryx/tools/AncestralTaxonomyInferenceException.java
new file mode 100644 (file)
index 0000000..601a719
--- /dev/null
+++ b/forester/java/src/org/forester/archaeopteryx/tools/AncestralTaxonomyInferenceException.java
@@ -0,0 +1,40 @@
+// $Id:
+// $
+// FORESTER -- software libraries and applications
+// for evolutionary biology research and applications.
+//
+// Copyright (C) 2008-2009 Christian M. Zmasek
+// Copyright (C) 2008-2009 Burnham Institute for Medical Research
+// All rights reserved
+//
+// This library is free software; you can redistribute it and/or
+// modify it under the terms of the GNU Lesser General Public
+// License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+//
+// This library is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+// Lesser General Public License for more details.
+//
+// You should have received a copy of the GNU Lesser General Public
+// License along with this library; if not, write to the Free Software
+// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+//
+// Contact: phylosoft @ gmail . com
+// WWW: www.phylosoft.org/forester
+
+package org.forester.archaeopteryx.tools;
+
+public class AncestralTaxonomyInferenceException extends Exception {
+
+    private static final long serialVersionUID = 1L;
+
+    public AncestralTaxonomyInferenceException() {
+        super();
+    }
+
+    public AncestralTaxonomyInferenceException( final String message ) {
+        super( message );
+    }
+}

diff --git a/forester/java/src/org/forester/archaeopteryx/tools/AncestralTaxonomyInferrer.java b/forester/java/src/org/forester/archaeopteryx/tools/AncestralTaxonomyInferrer.java
index fbcc0bf..09e8804 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/tools/AncestralTaxonomyInferrer.java
+++ b/forester/java/src/org/forester/archaeopteryx/tools/AncestralTaxonomyInferrer.java
@@ -26,7 +26,6 @@
 package org.forester.archaeopteryx.tools;
 
 import java.net.UnknownHostException;
-import java.util.SortedSet;
 
 import javax.swing.JOptionPane;
 
@@ -54,11 +53,10 @@ public class AncestralTaxonomyInferrer implements Runnable {
 
     private void inferTaxonomies() {
         _mf.getMainPanel().getCurrentTreePanel().setWaitCursor();
-        SortedSet<String> not_found = null;
         try {
-            not_found = AncestralTaxonomyInference.inferTaxonomyFromDescendents( _phy );
+            AncestralTaxonomyInference.inferTaxonomyFromDescendents( _phy );
         }
-        catch ( final IllegalArgumentException e ) {
+        catch ( final AncestralTaxonomyInferenceException e ) {
             _mf.getMainPanel().getCurrentTreePanel().setArrowCursor();
             JOptionPane.showMessageDialog( _mf,
                                            e.getMessage(),
@@ -88,54 +86,14 @@ public class AncestralTaxonomyInferrer implements Runnable {
         _treepanel.setTree( _phy );
         _mf.showWhole();
         _treepanel.setEdited( true );
-        if ( ( not_found != null ) && ( not_found.size() > 0 ) ) {
-            int max = not_found.size();
-            boolean more = false;
-            if ( max > 20 ) {
-                more = true;
-                max = 20;
-            }
-            final StringBuffer sb = new StringBuffer();
-            sb.append( "Not all taxonomies could be resolved.\n" );
-            sb.append( "The result is incomplete, and, possibly, misleading.\n" );
-            if ( not_found.size() == 1 ) {
-                sb.append( "The following taxonomy was not found:\n" );
-            }
-            else {
-                sb.append( "The following taxonomies were not found (total: " + not_found.size() + "):\n" );
-            }
-            int i = 0;
-            for( final String string : not_found ) {
-                if ( i > 19 ) {
-                    break;
-                }
-                sb.append( string );
-                sb.append( "\n" );
-                ++i;
-            }
-            if ( more ) {
-                sb.append( "..." );
-            }
-            try {
-                JOptionPane.showMessageDialog( _mf,
-                                               sb.toString(),
-                                               "Ancestral Taxonomy Inference Completed",
-                                               JOptionPane.WARNING_MESSAGE );
-            }
-            catch ( final Exception e ) {
-                // Not important if this fails, do nothing. 
-            }
+        try {
+            JOptionPane.showMessageDialog( _mf,
+                                           "Ancestral taxonomy inference successfully completed",
+                                           "Ancestral Taxonomy Inference Completed",
+                                           JOptionPane.INFORMATION_MESSAGE );
         }
-        else {
-            try {
-                JOptionPane.showMessageDialog( _mf,
-                                               "Ancestral taxonomy inference successfully completed",
-                                               "Ancestral Taxonomy Inference Completed",
-                                               JOptionPane.INFORMATION_MESSAGE );
-            }
-            catch ( final Exception e ) {
-                // Not important if this fails, do nothing.
-            }
+        catch ( final Exception e ) {
+            // Not important if this fails, do nothing.
         }
     }
 

diff --git a/forester/java/src/org/forester/phylogeny/data/Taxonomy.java b/forester/java/src/org/forester/phylogeny/data/Taxonomy.java
index ee78912..40115c9 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/data/Taxonomy.java
+++ b/forester/java/src/org/forester/phylogeny/data/Taxonomy.java
@@ -230,7 +230,8 @@ public class Taxonomy implements PhylogenyData, MultipleUris, Comparable<Taxonom
         return ( ( getIdentifier() == null ) && ForesterUtil.isEmpty( getTaxonomyCode() )
                 && ForesterUtil.isEmpty( getCommonName() ) && ForesterUtil.isEmpty( getScientificName() )
                 && ForesterUtil.isEmpty( getRank() ) && ForesterUtil.isEmpty( _uris )
-                && ForesterUtil.isEmpty( getAuthority() ) && ForesterUtil.isEmpty( _synonyms ) && ForesterUtil.isEmpty( _lineage ) );
+                && ForesterUtil.isEmpty( getAuthority() ) && ForesterUtil.isEmpty( _synonyms ) && ForesterUtil
+                .isEmpty( _lineage ) );
     }
 
     /**
@@ -412,7 +413,7 @@ public class Taxonomy implements PhylogenyData, MultipleUris, Comparable<Taxonom
         return 0;
     }
 
-    public void setLineage( List<String> lineage ) {
+    public void setLineage( final List<String> lineage ) {
         _lineage = lineage;
     }
 

diff --git a/forester/java/src/org/forester/util/ForesterUtil.java b/forester/java/src/org/forester/util/ForesterUtil.java
index ebbb8fe..b68d89b 100644 (file)
--- a/forester/java/src/org/forester/util/ForesterUtil.java
+++ b/forester/java/src/org/forester/util/ForesterUtil.java
@@ -1088,17 +1088,32 @@ public final class ForesterUtil {
         return str.split( regex );
     }
 
-    final public static String stringArrayToString( final String[] a ) {
-        final StringBuffer sb = new StringBuffer();
+    final public static String stringArrayToString( final String[] a, final String separator ) {
+        final StringBuilder sb = new StringBuilder();
         if ( ( a != null ) && ( a.length > 0 ) ) {
             for( int i = 0; i < a.length - 1; ++i ) {
-                sb.append( a[ i ] + ", " );
+                sb.append( a[ i ] + separator );
             }
             sb.append( a[ a.length - 1 ] );
         }
         return sb.toString();
     }
 
+    final public static String stringListToString( final List<String> l, final String separator ) {
+        final StringBuilder sb = new StringBuilder();
+        if ( ( l != null ) && ( l.size() > 0 ) ) {
+            for( int i = 0; i < l.size() - 1; ++i ) {
+                sb.append( l.get( i ) + separator );
+            }
+            sb.append( l.get( l.size() - 1 ) );
+        }
+        return sb.toString();
+    }
+
+    final public static String stringArrayToString( final String[] a ) {
+        return stringArrayToString( a, ", " );
+    }
+
     final public static String[] stringSetToArray( final Set<String> strings ) {
         final String[] str_array = new String[ strings.size() ];
         int i = 0;