From c810eb34827563f43c265fd88981c952f3803a99 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 8 Oct 2015 10:51:42 +0100
Subject: [PATCH] JAL-1499 consistent use of FileFormatException

---
 src/jalview/io/MegaFile.java |   37 ++++++++++++++++++++++---------------
 1 file changed, 22 insertions(+), 15 deletions(-)

diff --git a/src/jalview/io/MegaFile.java b/src/jalview/io/MegaFile.java
index 97d7775..fcb7a93 100644
--- a/src/jalview/io/MegaFile.java
+++ b/src/jalview/io/MegaFile.java
@@ -659,9 +659,9 @@ public class MegaFile extends AlignFile
    * Comments in MEGA are within [ ] brackets, and may be nested.
    * 
    * @return
-   * @throws IOException
+   * @throws FileFormatException
    */
-  protected String nextNonCommentLine() throws IOException
+  protected String nextNonCommentLine() throws FileFormatException
   {
     return nextNonCommentLine(0);
   }
@@ -675,12 +675,19 @@ public class MegaFile extends AlignFile
    * @param depth
    *          current depth of nesting of comments while parsing
    * @return
-   * @throws IOException
+   * @throws FileFormatException
    */
-  protected String nextNonCommentLine(final int depth) throws IOException
+  protected String nextNonCommentLine(final int depth)
+          throws FileFormatException
   {
     String data = null;
-    data = nextLine();
+    try
+    {
+      data = nextLine();
+    } catch (IOException e)
+    {
+      throw new FileFormatException(e.getMessage());
+    }
     if (data == null)
     {
       if (depth > 0)
@@ -817,10 +824,10 @@ public class MegaFile extends AlignFile
    * 
    * @param dataLine
    * @return
-   * @throws IOException
+   * @throws FileFormatException
    */
   protected String parseDataLine(String dataLine)
-          throws IOException
+          throws FileFormatException
   {
     String seqId = getSequenceId(dataLine);
     if (seqId == null)
@@ -853,7 +860,7 @@ public class MegaFile extends AlignFile
    * a new one if we haven't seen it before.
    * 
    * @param dataLine
-   * @throws IOException
+   * @throws FileFormatException
    */
   protected void parseNoninterleavedDataLine(String dataLine)
           throws FileFormatException
@@ -1021,9 +1028,9 @@ public class MegaFile extends AlignFile
    * Save as alignment properties in case useful.
    * 
    * @return the next non-blank line following the header lines.
-   * @throws IOException
+   * @throws FileFormatException
    */
-  protected String parseHeaderLines() throws IOException
+  protected String parseHeaderLines() throws FileFormatException
   {
     String inputLine = null;
     while ((inputLine = nextNonCommentLine()) != null)
@@ -1075,9 +1082,9 @@ public class MegaFile extends AlignFile
    * semicolon.
    * 
    * @param inputLine
-   * @throws IOException
+   * @throws FileFormatException
    */
-  protected void parseFormat(String inputLine) throws IOException
+  protected void parseFormat(String inputLine) throws FileFormatException
   {
     while (inputLine != null)
     {
@@ -1292,10 +1299,10 @@ public class MegaFile extends AlignFile
    * Reads lines until terminated by semicolon, appending each to the
    * Description property value.
    * 
-   * @throws IOException
+   * @throws FileFormatException
    */
   protected void parseDescription(String firstDescriptionLine)
-          throws IOException
+          throws FileFormatException
   {
     StringBuilder desc = new StringBuilder(256);
     desc.append(getValue(firstDescriptionLine));
@@ -1588,7 +1595,7 @@ public class MegaFile extends AlignFile
    * 
    * @param isIt
    * @param dataLine
-   * @throws IOException
+   * @throws FileFormatException
    */
   protected void assertInterleaved(boolean isIt, String dataLine)
           throws FileFormatException
-- 
1.7.10.2