X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPhylipFile.java;h=e8fe7e94b9a371b5cdb0b4778246585211a065b9;hb=7d67fb613ec026dc9a265e351e7fab542e3f1d61;hp=ce65eea1486deb4d83e5f4924c1866896583859e;hpb=77abb3fac2965a8966410cd77cd749c7c1dc6453;p=jalview.git

diff --git a/src/jalview/io/PhylipFile.java b/src/jalview/io/PhylipFile.java
index ce65eea..e8fe7e9 100644
--- a/src/jalview/io/PhylipFile.java
+++ b/src/jalview/io/PhylipFile.java
@@ -1,9 +1,25 @@
-/**
- *
+/*
+ * 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.
+ *  
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.io;
 
-import jalview.datamodel.Alignment;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 
@@ -43,9 +59,6 @@ import java.io.IOException;
 public class PhylipFile extends AlignFile
 {
 
-  // Define file extension and description to save repeating it elsewhere
-  public static final String FILE_EXT = "phy";
-
   public static final String FILE_DESC = "PHYLIP";
 
   /**
@@ -69,13 +82,14 @@ public class PhylipFile extends AlignFile
 
   /**
    * @param inFile
-   * @param type
+   * @param sourceType
    * @throws IOException
    * @see {@link AlignFile#AlignFile(FileParse)}
    */
-  public PhylipFile(String inFile, String type) throws IOException
+  public PhylipFile(String inFile, DataSourceType sourceType)
+          throws IOException
   {
-    super(inFile, type);
+    super(inFile, sourceType);
   }
 
   /**
@@ -171,13 +185,6 @@ public class PhylipFile extends AlignFile
         seqs.add(sequenceElements[i]);
       }
 
-      // create an alignment based on the sequences
-      Alignment a = new Alignment(sequenceElements);
-      // add annotations - although comments say addAnnotations
-      // is used by AppletFormatAdapter, it doesn't say other
-      // classes should/can not use it
-      addAnnotations(a);
-
     } catch (IOException e)
     {
       System.err.println("Exception parsing PHYLIP file " + e);
@@ -209,8 +216,8 @@ public class PhylipFile extends AlignFile
    */
   private String validateName(String name) throws IOException
   {
-    char[] invalidCharacters = new char[]
-    { '(', ')', '[', ']', ':', ';', ',' };
+    char[] invalidCharacters = new char[] { '(', ')', '[', ']', ':', ';',
+        ',' };
     for (char c : invalidCharacters)
     {
       if (name.indexOf(c) > -1)
@@ -233,15 +240,15 @@ public class PhylipFile extends AlignFile
    * @see {@link AlignFile#print()}
    */
   @Override
-  public String print()
+  public String print(SequenceI[] sqs, boolean jvsuffix)
   {
 
-    StringBuffer sb = new StringBuffer(Integer.toString(seqs.size()));
+    StringBuffer sb = new StringBuffer(Integer.toString(sqs.length));
     sb.append(" ");
     // if there are no sequences, then define the number of characters as 0
     sb.append(
-            (seqs.size() > 0) ? Integer
-                    .toString(seqs.get(0).getSequence().length) : "0")
+            (sqs.length > 0) ? Integer.toString(sqs[0].getSequence().length)
+                    : "0")
             .append(newline);
 
     // Due to how IO is handled, there doesn't appear to be a way to store
@@ -253,7 +260,7 @@ public class PhylipFile extends AlignFile
     int numInterleavedColumns = 60;
 
     int sequenceLength = 0;
-    for (SequenceI s : seqs)
+    for (SequenceI s : sqs)
     {
 
       // ensure name is only 10 characters
@@ -304,7 +311,7 @@ public class PhylipFile extends AlignFile
         // add blank line to separate this matrix from previous
         sb.append(newline);
         int start = i * numInterleavedColumns;
-        for (SequenceI s : seqs)
+        for (SequenceI s : sqs)
         {
           sb.append(
                   s.getSequence(start, Math.min(start
@@ -317,4 +324,4 @@ public class PhylipFile extends AlignFile
 
     return sb.toString();
   }
-}
\ No newline at end of file
+}