X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPhylipFile.java;h=12e87a6b7e9775bfd0da211fd212c9965d370733;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=e8fe7e94b9a371b5cdb0b4778246585211a065b9;hpb=4a5137b64f7ec23db2a09290bfcd392984a52150;p=jalview.git

diff --git a/src/jalview/io/PhylipFile.java b/src/jalview/io/PhylipFile.java
index e8fe7e9..12e87a6 100644
--- a/src/jalview/io/PhylipFile.java
+++ b/src/jalview/io/PhylipFile.java
@@ -27,9 +27,9 @@ import java.io.IOException;
 
 /**
  * <p>
- * Parser and exporter for PHYLIP file format, as defined <a
- * href="http://evolution.genetics.washington.edu/phylip/doc/main.html">in the
- * documentation</a>. The parser imports PHYLIP files in both sequential and
+ * Parser and exporter for PHYLIP file format, as defined
+ * <a href="http://evolution.genetics.washington.edu/phylip/doc/main.html">in
+ * the documentation</a>. The parser imports PHYLIP files in both sequential and
  * interleaved format, and (currently) exports in interleaved format (using 60
  * characters per matrix for the sequence).
  * <p>
@@ -38,7 +38,8 @@ import java.io.IOException;
  * The following assumptions have been made for input
  * <ul>
  * <li>Sequences are expressed as letters, not real numbers with decimal points
- * separated by blanks (which is a valid option according to the specification)</li>
+ * separated by blanks (which is a valid option according to the
+ * specification)</li>
  * </ul>
  *
  * The following assumptions have been made for output
@@ -112,8 +113,8 @@ public class PhylipFile extends AlignFile
                 "First line must contain the number of specifies and number of characters");
       }
 
-      int numberSpecies = Integer.parseInt(lineElements[0]), numberCharacters = Integer
-              .parseInt(lineElements[1]);
+      int numberSpecies = Integer.parseInt(lineElements[0]),
+              numberCharacters = Integer.parseInt(lineElements[1]);
 
       if (numberSpecies <= 0)
       {
@@ -144,8 +145,8 @@ public class PhylipFile extends AlignFile
         }
         else
         {
-          sequenceElements[i] = parseId(validateName(potentialName
-                  .substring(0, tabIndex)));
+          sequenceElements[i] = parseId(
+                  validateName(potentialName.substring(0, tabIndex)));
           sequences[i] = new StringBuffer(
                   removeWhitespace(line.substring(tabIndex)));
         }
@@ -222,8 +223,8 @@ public class PhylipFile extends AlignFile
     {
       if (name.indexOf(c) > -1)
       {
-        throw new IOException("Species name contains illegal character "
-                + c);
+        throw new IOException(
+                "Species name contains illegal character " + c);
       }
     }
     return name;
@@ -246,9 +247,7 @@ public class PhylipFile extends AlignFile
     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(
-            (sqs.length > 0) ? Integer.toString(sqs[0].getSequence().length)
-                    : "0")
+    sb.append((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
@@ -279,13 +278,13 @@ 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,
@@ -313,9 +312,8 @@ public class PhylipFile extends AlignFile
         int start = i * numInterleavedColumns;
         for (SequenceI s : sqs)
         {
-          sb.append(
-                  s.getSequence(start, Math.min(start
-                          + numInterleavedColumns, sequenceLength)))
+          sb.append(s.getSequence(start,
+                  Math.min(start + numInterleavedColumns, sequenceLength)))
                   .append(newline);
         }
       }