Merge remote-tracking branch 'origin/releases/Release_2_10_2b1_Branch'

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

diff --git a/src/jalview/io/PhylipFile.java b/src/jalview/io/PhylipFile.java
index e8fe7e9..2a961a2 100644 (file)
--- 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;
@@ -313,9 +314,8 @@ 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);
         }
       }