fileFormat enum wip changes

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

diff --git a/src/jalview/io/PhylipFile.java b/src/jalview/io/PhylipFile.java
index 2c8beae..e8fe7e9 100644 (file)
--- a/src/jalview/io/PhylipFile.java
+++ b/src/jalview/io/PhylipFile.java
@@ -240,15 +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
@@ -260,7 +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
@@ -311,7 +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