X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPhylipFile.java;h=e1d82ee0303c7ee63640af9e87a581e61f6f8c6e;hb=e6798fd04b1d7a35836a2e84deae5a94a35b88b9;hp=656e103bf5c9927ccad4f1e2ba7cb9911c8a074f;hpb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;p=jalview.git

diff --git a/src/jalview/io/PhylipFile.java b/src/jalview/io/PhylipFile.java
index 656e103..e1d82ee 100644
--- a/src/jalview/io/PhylipFile.java
+++ b/src/jalview/io/PhylipFile.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 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.
  * 
@@ -59,9 +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";
 
   /**
@@ -85,13 +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);
   }
 
   /**
@@ -242,15 +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].getLength())
+                    : "0")
             .append(newline);
 
     // Due to how IO is handled, there doesn't appear to be a way to store
@@ -262,7 +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
@@ -281,13 +279,13 @@ public class PhylipFile extends AlignFile
       // sequential has the entire sequence following the name
       if (sequential)
       {
-        sb.append(s.getSequence());
+        sb.append(s.getSequenceAsString());
       }
       else
       {
         // Jalview ensures all sequences are of same length so no need
         // to keep track of min/max length
-        sequenceLength = s.getSequence().length;
+        sequenceLength = s.getLength();
         // interleaved breaks the sequence into chunks for
         // interleavedColumns characters
         sb.append(s.getSequence(0,
@@ -313,7 +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