JAL-1933 consensus calculation doesn’t depend on occupancy row being materialised

[jalview.git] / src / jalview / io / NewickFile.java

diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java
index 92456d5..765ea95 100755 (executable)
--- a/src/jalview/io/NewickFile.java
+++ b/src/jalview/io/NewickFile.java
@@ -26,12 +26,15 @@
 // TODO: Extended SequenceNodeI to hold parsed NHX strings
 package jalview.io;
 
-import java.io.*;
-import java.util.StringTokenizer;
-
-import jalview.datamodel.*;
+import jalview.datamodel.SequenceNode;
 import jalview.util.MessageManager;
 
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.StringTokenizer;
+
 /**
  * Parse a new hanpshire style tree Caveats: NHX files are NOT supported and the
  * tree distances and topology are unreliable when they are parsed. TODO: on
@@ -107,7 +110,7 @@ public class NewickFile extends FileParse
    */
   public NewickFile(String inStr) throws IOException
   {
-    super(inStr, "Paste");
+    super(inStr, DataSourceType.PASTE);
   }
 
   /**
@@ -115,15 +118,16 @@ public class NewickFile extends FileParse
    * 
    * @param inFile
    *          DOCUMENT ME!
-   * @param type
+   * @param protocol
    *          DOCUMENT ME!
    * 
    * @throws IOException
    *           DOCUMENT ME!
    */
-  public NewickFile(String inFile, String type) throws IOException
+  public NewickFile(String inFile, DataSourceType protocol)
+          throws IOException
   {
-    super(inFile, type);
+    super(inFile, protocol);
   }
 
   public NewickFile(FileParse source) throws IOException
@@ -612,11 +616,14 @@ public class NewickFile extends FileParse
 
     if (Error != null)
     {
-      throw (new IOException(MessageManager.formatMessage("exception.newfile", new String[]{Error.toString()})));
+      throw (new IOException(MessageManager.formatMessage(
+              "exception.newfile", new String[] { Error.toString() })));
     }
     if (root == null)
     {
-        throw (new IOException(MessageManager.formatMessage("exception.newfile", new String[]{MessageManager.getString("label.no_tree_read_in")})));
+      throw (new IOException(MessageManager.formatMessage(
+              "exception.newfile", new String[] { MessageManager
+                      .getString("label.no_tree_read_in") })));
     }
     // THe next line is failing for topali trees - not sure why yet. if
     // (root.right()!=null && root.isDummy())
@@ -960,7 +967,7 @@ public class NewickFile extends FileParse
       treefile.close();
       System.out.println("Read file :\n");
 
-      NewickFile trf = new NewickFile(args[0], "File");
+      NewickFile trf = new NewickFile(args[0], DataSourceType.FILE);
       trf.parse();
       System.out.println("Original file :\n");