From a6dca333c60641ceb0b54ccb2bd0f5ab457c7f88 Mon Sep 17 00:00:00 2001
From: kjvdheide <kjvanderheide@dundee.ac.uk>
Date: Tue, 9 Jan 2018 10:53:43 +0000
Subject: [PATCH] JAL-2805 parser is now File based (instead of FileParse) and
 source is now properly set

---
 src/jalview/ext/forester/io/ForesterParser.java |   99 ++++-------------------
 1 file changed, 15 insertions(+), 84 deletions(-)

diff --git a/src/jalview/ext/forester/io/ForesterParser.java b/src/jalview/ext/forester/io/ForesterParser.java
index 6e86d7b..a6d7831 100644
--- a/src/jalview/ext/forester/io/ForesterParser.java
+++ b/src/jalview/ext/forester/io/ForesterParser.java
@@ -1,48 +1,49 @@
 package jalview.ext.forester.io;
 
-import jalview.api.FeatureSettingsModelI;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceI;
 import jalview.ext.archaeopteryx.Tree;
 import jalview.ext.treeviewer.TreeI;
 import jalview.ext.treeviewer.TreeParserI;
-import jalview.io.AlignFile;
-import jalview.io.DataSourceType;
-import jalview.io.FileParse;
 
+import java.io.File;
 import java.io.IOException;
 
 import org.forester.io.parsers.PhylogenyParser;
 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
 import org.forester.io.parsers.phyloxml.PhyloXmlParser;
+import org.forester.io.parsers.util.PhylogenyParserException;
 import org.forester.phylogeny.Phylogeny;
 
-public class ForesterParser extends AlignFile
+public class ForesterParser
         implements TreeParserI
 {
   private final PhylogenyParser parser;
 
   private TreeI[] parsedTrees;
 
-  protected ForesterParser(PhylogenyParser foresterParser, FileParse source)
+  protected ForesterParser(PhylogenyParser foresterParser, File file)
+          throws PhylogenyParserException, IOException
   {
     parser = foresterParser;
+    parser.setSource(file);
   }
 
-  public static ForesterParser createNexusParser(FileParse source)
+  public static ForesterParser createNexusParser(File file)
+          throws PhylogenyParserException, IOException
   {
-    return new ForesterParser(new NexusPhylogeniesParser(), source);
+    return new ForesterParser(new NexusPhylogeniesParser(), file);
   }
 
-  public static ForesterParser createPhyloXmlParser(FileParse source)
+  public static ForesterParser createPhyloXmlParser(File file)
+          throws PhylogenyParserException, IOException
   {
     // support non-xsd validating?
     return new ForesterParser(
-            PhyloXmlParser.createPhyloXmlParserXsdValidating(), source);
+            PhyloXmlParser.createPhyloXmlParserXsdValidating(), file);
   }
 
+  // ParserBasedPhylogenyFactory.getInstance().create(foresterParser, source)
   @Override
-  public void parse() throws IOException
+  public TreeI[] parse() throws IOException
   {
     Phylogeny[] foresterTrees = parser.parse();
     parsedTrees = new TreeI[foresterTrees.length];
@@ -51,6 +52,7 @@ public class ForesterParser extends AlignFile
     {
       parsedTrees[i] = new Tree(foresterTrees[i]);
     }
+    return parsedTrees;
 
   }
 
@@ -67,77 +69,6 @@ public class ForesterParser extends AlignFile
     return parser.getName();
   }
 
-  @Override
-  public SequenceI[] getSeqsAsArray()
-  {
-    // TODO Auto-generated method stub
-    return null;
-  }
-
-  @Override
-  public void addAnnotations(AlignmentI al)
-  {
-    // TODO Auto-generated method stub
-
-  }
-
-  @Override
-  public void addGroups(AlignmentI al)
-  {
-    // TODO Auto-generated method stub
-
-  }
-
-  @Override
-  public void setSeqs(SequenceI[] sequencesArray)
-  {
-    // TODO Auto-generated method stub
-
-  }
-
-  @Override
-  public boolean hasWarningMessage()
-  {
-    // TODO Auto-generated method stub
-    return false;
-  }
-
-  @Override
-  public String getWarningMessage()
-  {
-    // TODO Auto-generated method stub
-    return null;
-  }
-
-  @Override
-  public String getInFile()
-  {
-    // TODO Auto-generated method stub
-    return null;
-  }
-
-  @Override
-  public DataSourceType getDataSourceType()
-  {
-    // TODO Auto-generated method stub
-    return null;
-  }
-
-  @Override
-  public FeatureSettingsModelI getFeatureColourScheme()
-  {
-    // TODO Auto-generated method stub
-    return null;
-  }
-
-
-
-  @Override
-  public String print(SequenceI[] seqs, boolean jvsuffix)
-  {
-    // TODO Auto-generated method stub
-    return null;
-  }
 
   @Override
   public TreeI[] getParsedTrees()
-- 
1.7.10.2