JAL-1953 start work on storing nodes in a map per tree object instead of

[jalview.git] / src / jalview / ext / forester / io / PhyloXMLParser.java

diff --git a/src/jalview/ext/forester/io/PhyloXMLParser.java b/src/jalview/ext/forester/io/PhyloXMLParser.java
index 8194d21..e877d41 100644 (file)
--- a/src/jalview/ext/forester/io/PhyloXMLParser.java
+++ b/src/jalview/ext/forester/io/PhyloXMLParser.java
@@ -1,100 +1,86 @@
-package jalview.ext.forester.io;
-
-import jalview.api.FeatureSettingsModelI;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceI;
-import jalview.ext.treeviewer.TreeI;
-import jalview.ext.treeviewer.TreeParserI;
-import jalview.io.AlignmentFileReaderI;
-import jalview.io.DataSourceType;
-
-import java.io.IOException;
-
-public class PhyloXMLParser implements TreeParserI, AlignmentFileReaderI
-{
-
-  @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 TreeI[] parse() throws IOException
-  {
-    // TODO Auto-generated method stub
-    return null;
-  }
-
-  @Override
-  public void setSource(Object source) throws IOException
-  {
-    // TODO Auto-generated method stub
-
-  }
-
-  @Override
-  public String getName()
-  {
-    // TODO Auto-generated method stub
-    return null;
-  }
-
-}
+// package jalview.ext.forester.io;
+//
+// import jalview.api.FeatureSettingsModelI;
+// import jalview.datamodel.AlignmentI;
+// import jalview.datamodel.SequenceI;
+// import jalview.io.AlignmentFileReaderI;
+// import jalview.io.DataSourceType;
+//
+// import org.forester.io.parsers.PhylogenyParser;
+// import org.forester.io.parsers.phyloxml.PhyloXmlParser;
+//
+// public class PhyloXMLParser extends ForesterParser
+// implements AlignmentFileReaderI
+// {
+// PhyloXmlParser phxmlParser = PhyloXmlParser
+// .createPhyloXmlParserXsdValidating();
+//
+// public PhyloXMLParser(PhylogenyParser foresterParser)
+// {
+// super(foresterParser);
+// }
+//
+// @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;
+// }
+//
+// }
\ No newline at end of file