From a01b86ddf621af845f71d04441870c4b52220c52 Mon Sep 17 00:00:00 2001
From: kjvdheide <kjvanderheide@dundee.ac.uk>
Date: Fri, 5 Jan 2018 04:00:58 +0000
Subject: [PATCH] JAL-281 ForesterParser now extends from AlignFile

---
 src/jalview/ext/forester/io/ForesterParser.java |   41 ++++++++++++++++-------
 src/jalview/ext/treeviewer/TreeParserI.java     |    4 ++-
 2 files changed, 32 insertions(+), 13 deletions(-)

diff --git a/src/jalview/ext/forester/io/ForesterParser.java b/src/jalview/ext/forester/io/ForesterParser.java
index 851b12b..6e86d7b 100644
--- a/src/jalview/ext/forester/io/ForesterParser.java
+++ b/src/jalview/ext/forester/io/ForesterParser.java
@@ -6,7 +6,7 @@ import jalview.datamodel.SequenceI;
 import jalview.ext.archaeopteryx.Tree;
 import jalview.ext.treeviewer.TreeI;
 import jalview.ext.treeviewer.TreeParserI;
-import jalview.io.AlignmentFileReaderI;
+import jalview.io.AlignFile;
 import jalview.io.DataSourceType;
 import jalview.io.FileParse;
 
@@ -17,26 +17,40 @@ import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
 import org.forester.phylogeny.Phylogeny;
 
-public class ForesterParser implements TreeParserI, AlignmentFileReaderI
+public class ForesterParser extends AlignFile
+        implements TreeParserI
 {
   private final PhylogenyParser parser;
 
+  private TreeI[] parsedTrees;
+
   protected ForesterParser(PhylogenyParser foresterParser, FileParse source)
   {
     parser = foresterParser;
   }
 
+  public static ForesterParser createNexusParser(FileParse source)
+  {
+    return new ForesterParser(new NexusPhylogeniesParser(), source);
+  }
+
+  public static ForesterParser createPhyloXmlParser(FileParse source)
+  {
+    // support non-xsd validating?
+    return new ForesterParser(
+            PhyloXmlParser.createPhyloXmlParserXsdValidating(), source);
+  }
+
   @Override
-  public TreeI[] parse() throws IOException
+  public void parse() throws IOException
   {
     Phylogeny[] foresterTrees = parser.parse();
-    TreeI[] jalviewTrees = new TreeI[foresterTrees.length];
+    parsedTrees = new TreeI[foresterTrees.length];
 
     for (int i = 0; i < foresterTrees.length; i++)
     {
-      jalviewTrees[i] = new Tree(foresterTrees[i]);
+      parsedTrees[i] = new Tree(foresterTrees[i]);
     }
-    return jalviewTrees;
 
   }
 
@@ -116,15 +130,18 @@ public class ForesterParser implements TreeParserI, AlignmentFileReaderI
     return null;
   }
 
-  public static ForesterParser createNexusParser(FileParse source)
+
+
+  @Override
+  public String print(SequenceI[] seqs, boolean jvsuffix)
   {
-    return new ForesterParser(new NexusPhylogeniesParser(), source);
+    // TODO Auto-generated method stub
+    return null;
   }
 
-  public static ForesterParser createPhyloXmlParser(FileParse source)
+  @Override
+  public TreeI[] getParsedTrees()
   {
-    // support non-xsd validating?
-    return new ForesterParser(
-            PhyloXmlParser.createPhyloXmlParserXsdValidating(), source);
+    return parsedTrees;
   }
 }
\ No newline at end of file
diff --git a/src/jalview/ext/treeviewer/TreeParserI.java b/src/jalview/ext/treeviewer/TreeParserI.java
index 00c8334..52b4f2c 100644
--- a/src/jalview/ext/treeviewer/TreeParserI.java
+++ b/src/jalview/ext/treeviewer/TreeParserI.java
@@ -4,10 +4,12 @@ import java.io.IOException;
 
 public interface TreeParserI
  {
-  public TreeI[] parse() throws IOException;
+  public void parse() throws IOException;
 
   public void setSource(Object source) throws IOException;
 
   public String getName();
 
+  public TreeI[] getParsedTrees();
+
  }
-- 
1.7.10.2