in progress..

[jalview.git] / forester / java / src / org / forester / phylogeny / Phylogeny.java

diff --git a/forester/java/src/org/forester/phylogeny/Phylogeny.java b/forester/java/src/org/forester/phylogeny/Phylogeny.java
index 379a933..0416f41 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/Phylogeny.java
+++ b/forester/java/src/org/forester/phylogeny/Phylogeny.java
@@ -37,6 +37,8 @@ import java.util.List;
 import java.util.Map;
 import java.util.NoSuchElementException;
 import java.util.Vector;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 
 import org.forester.io.parsers.nhx.NHXParser;
 import org.forester.io.writers.PhylogenyWriter;
@@ -56,6 +58,7 @@ import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
 import org.forester.phylogeny.iterators.PostorderTreeIterator;
 import org.forester.phylogeny.iterators.PreorderTreeIterator;
 import org.forester.util.FailedConditionCheckException;
+import org.forester.util.ForesterUtil;
 
 public class Phylogeny {
 
@@ -448,6 +451,23 @@ public class Phylogeny {
         return nodes;
     }
 
+    public List<PhylogenyNode> getNodes( final Pattern p ) {
+        if ( isEmpty() ) {
+            return null;
+        }
+        final List<PhylogenyNode> nodes = new ArrayList<>();
+        for( final PhylogenyNodeIterator iter = iteratorPreorder(); iter.hasNext(); ) {
+            final PhylogenyNode n = iter.next();
+            if ( n.getName() != null ) {
+                final Matcher m = p.matcher( n.getName() );
+                if ( m.find() ) {
+                    nodes.add( n );
+                }
+            }
+        }
+        return nodes;
+    }
+
     public List<PhylogenyNode> getNodesViaSequenceName( final String seq_name ) {
         if ( isEmpty() ) {
             return null;