JAL-2344 FileFormats singleton for formats, FileFormatI simplified

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

diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java
index 15e901a..765ea95 100755 (executable)
--- a/src/jalview/io/NewickFile.java
+++ b/src/jalview/io/NewickFile.java
@@ -1,19 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 // NewickFile.java
@@ -24,10 +26,14 @@
 // TODO: Extended SequenceNodeI to hold parsed NHX strings
 package jalview.io;
 
-import java.io.*;
-import java.util.StringTokenizer;
+import jalview.datamodel.SequenceNode;
+import jalview.util.MessageManager;
 
-import jalview.datamodel.*;
+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
@@ -104,7 +110,7 @@ public class NewickFile extends FileParse
    */
   public NewickFile(String inStr) throws IOException
   {
-    super(inStr, "Paste");
+    super(inStr, DataSourceType.PASTE);
   }
 
   /**
@@ -112,15 +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
@@ -293,7 +300,7 @@ public class NewickFile extends FileParse
 
     int nextcp = 0;
     int ncp = cp;
-    boolean parsednodename=false;
+    boolean parsednodename = false;
     while (majorsyms.searchFrom(nf, cp) && (Error == null))
     {
       int fcp = majorsyms.matchedFrom();
@@ -359,12 +366,13 @@ public class NewickFile extends FileParse
           nodename = new String(qnodename.stringMatched().substring(1,
                   nl - 1));
           // unpack any escaped colons
-          com.stevesoft.pat.Regex xpandquotes = com.stevesoft.pat.Regex.perlCode("s/''/'/");
+          com.stevesoft.pat.Regex xpandquotes = com.stevesoft.pat.Regex
+                  .perlCode("s/''/'/");
           String widernodename = xpandquotes.replaceAll(nodename);
-          nodename=widernodename;
+          nodename = widernodename;
           // jump to after end of quoted nodename
           nextcp = fcp + nl + 1;
-          parsednodename=true;
+          parsednodename = true;
         }
         else
         {
@@ -433,7 +441,8 @@ public class NewickFile extends FileParse
         com.stevesoft.pat.Regex ndist = new com.stevesoft.pat.Regex(
                 ":([-0-9Ee.+]+)");
 
-        if (!parsednodename && uqnodename.search(fstring)
+        if (!parsednodename
+                && uqnodename.search(fstring)
                 && ((uqnodename.matchedFrom(1) == 0) || (fstring
                         .charAt(uqnodename.matchedFrom(1) - 1) != ':'))) // JBPNote
         // HACK!
@@ -592,7 +601,7 @@ public class NewickFile extends FileParse
         distance = DefDistance;
         bootstrap = DefBootstrap;
         commentString2 = null;
-        parsednodename=false;
+        parsednodename = false;
       }
       if (nextcp == 0)
       {
@@ -607,11 +616,14 @@ public class NewickFile extends FileParse
 
     if (Error != null)
     {
-      throw (new IOException("NewickFile: " + Error + "\n"));
+      throw (new IOException(MessageManager.formatMessage(
+              "exception.newfile", new String[] { Error.toString() })));
     }
     if (root == null)
     {
-      throw (new IOException("NewickFile: No Tree read in\n"));
+      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())
@@ -955,7 +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");