work on: add ability to perform GSDI in applets

[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 8ccd028..89a0cda 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
+++ b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
@@ -75,6 +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;
@@ -150,6 +151,18 @@ public final class AptxUtil {
                 }
             }
         }
+        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;
     }
 
@@ -1015,8 +1028,9 @@ 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;
@@ -1045,6 +1059,12 @@ 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;
     }