From a96205d346a06161a2afdc001ff0eae5fb5f60ea Mon Sep 17 00:00:00 2001
From: kjvdheide <kjvanderheide@dundee.ac.uk>
Date: Tue, 19 Dec 2017 14:34:24 +0000
Subject: [PATCH] JAL-281 created Nexus and PhyloXML parser classes

---
 src/jalview/ext/forester/io/NexusParser.java    |  105 +++++++++++++++++++++++
 src/jalview/ext/forester/io/PhyloXMLParser.java |  100 +++++++++++++++++++++
 src/jalview/ext/forester/io/TreeParser.java     |   10 ---
 3 files changed, 205 insertions(+), 10 deletions(-)
 create mode 100644 src/jalview/ext/forester/io/NexusParser.java
 create mode 100644 src/jalview/ext/forester/io/PhyloXMLParser.java
 delete mode 100644 src/jalview/ext/forester/io/TreeParser.java

diff --git a/src/jalview/ext/forester/io/NexusParser.java b/src/jalview/ext/forester/io/NexusParser.java
new file mode 100644
index 0000000..d48b033
--- /dev/null
+++ b/src/jalview/ext/forester/io/NexusParser.java
@@ -0,0 +1,105 @@
+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 NexusParser implements TreeParserI, AlignmentFileReaderI
+{
+
+
+  public NexusParser()
+  {
+
+  }
+
+  @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;
+  }
+
+  @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;
+  }
+}
diff --git a/src/jalview/ext/forester/io/PhyloXMLParser.java b/src/jalview/ext/forester/io/PhyloXMLParser.java
new file mode 100644
index 0000000..8194d21
--- /dev/null
+++ b/src/jalview/ext/forester/io/PhyloXMLParser.java
@@ -0,0 +1,100 @@
+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;
+  }
+
+}
diff --git a/src/jalview/ext/forester/io/TreeParser.java b/src/jalview/ext/forester/io/TreeParser.java
deleted file mode 100644
index 29131c5..0000000
--- a/src/jalview/ext/forester/io/TreeParser.java
+++ /dev/null
@@ -1,10 +0,0 @@
-package jalview.ext.forester.io;
-
-public class TreeParser // implements ExternalTreeParserI<MainFrame>
-{
-
-  public TreeParser()
-  {
-
-  }
-}
-- 
1.7.10.2