From 8dbeca869699c196f4239fb1f8909d5a4c23ee86 Mon Sep 17 00:00:00 2001
From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Mon, 11 Jan 2016 11:16:03 +0000
Subject: [PATCH] JAL-1991 bug fix for some flat-file printers to check for
 exact modulus in order to avoid outputing an extra
 redundant header line with empty sequences

---
 src/jalview/io/ClustalFile.java |    5 ++++-
 src/jalview/io/FastaFile.java   |    7 +++++--
 src/jalview/io/MSFfile.java     |    9 +++------
 src/jalview/io/PIRFile.java     |    5 ++++-
 src/jalview/io/PileUpfile.java  |    9 +++------
 5 files changed, 19 insertions(+), 16 deletions(-)

diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java
index a9295a3..f7a45de 100755
--- a/src/jalview/io/ClustalFile.java
+++ b/src/jalview/io/ClustalFile.java
@@ -47,11 +47,13 @@ public class ClustalFile extends AlignFile
     super(source);
   }
 
+  @Override
   public void initData()
   {
     super.initData();
   }
 
+  @Override
   public void parse() throws IOException
   {
     int i = 0;
@@ -193,6 +195,7 @@ public class ClustalFile extends AlignFile
     }
   }
 
+  @Override
   public String print()
   {
     return print(getSeqsAsArray());
@@ -233,7 +236,7 @@ public class ClustalFile extends AlignFile
     maxid++;
 
     int len = 60;
-    int nochunks = (max / len) + 1;
+    int nochunks = (max / len) + (max % len > 0 ? 1 : 0);
 
     for (i = 0; i < nochunks; i++)
     {
diff --git a/src/jalview/io/FastaFile.java b/src/jalview/io/FastaFile.java
index b867ba4..4c2265c 100755
--- a/src/jalview/io/FastaFile.java
+++ b/src/jalview/io/FastaFile.java
@@ -77,6 +77,7 @@ public class FastaFile extends AlignFile
    * @throws IOException
    *           DOCUMENT ME!
    */
+  @Override
   public void parse() throws IOException
   {
     StringBuffer sb = new StringBuffer();
@@ -173,7 +174,7 @@ public class FastaFile extends AlignFile
     addProperties(al);
     for (int i = 0; i < annotations.size(); i++)
     {
-      AlignmentAnnotation aa = (AlignmentAnnotation) annotations
+      AlignmentAnnotation aa = annotations
               .elementAt(i);
       aa.setPadGaps(true, al.getGapCharacter());
       al.addAnnotation(aa);
@@ -209,7 +210,8 @@ public class FastaFile extends AlignFile
 
       out.append(newline);
 
-      int nochunks = (s[i].getLength() / len) + 1;
+      int nochunks = (s[i].getLength() / len)
+              + (s[i].getLength() % len > 0 ? 1 : 0);
 
       for (int j = 0; j < nochunks; j++)
       {
@@ -238,6 +240,7 @@ public class FastaFile extends AlignFile
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public String print()
   {
     return print(getSeqsAsArray());
diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java
index 3de5b30..f62ad81 100755
--- a/src/jalview/io/MSFfile.java
+++ b/src/jalview/io/MSFfile.java
@@ -69,6 +69,7 @@ public class MSFfile extends AlignFile
   /**
    * DOCUMENT ME!
    */
+  @Override
   public void parse() throws IOException
   {
     int i = 0;
@@ -343,12 +344,7 @@ public class MSFfile extends AlignFile
     out.append(newline);
     int len = 50;
 
-    int nochunks = (max / len) + 1;
-
-    if ((max % len) == 0)
-    {
-      nochunks--;
-    }
+    int nochunks = (max / len) + (max % len > 0 ? 1 : 0);
 
     for (i = 0; i < nochunks; i++)
     {
@@ -410,6 +406,7 @@ public class MSFfile extends AlignFile
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public String print()
   {
     return print(getSeqsAsArray());
diff --git a/src/jalview/io/PIRFile.java b/src/jalview/io/PIRFile.java
index cd3c7a0..5f5c23c 100755
--- a/src/jalview/io/PIRFile.java
+++ b/src/jalview/io/PIRFile.java
@@ -46,6 +46,7 @@ public class PIRFile extends AlignFile
     super(source);
   }
 
+  @Override
   public void parse() throws IOException
   {
     StringBuffer sequence;
@@ -100,6 +101,7 @@ public class PIRFile extends AlignFile
     }
   }
 
+  @Override
   public String print()
   {
     return print(getSeqsAsArray());
@@ -174,7 +176,8 @@ public class PIRFile extends AlignFile
           }
         }
       }
-      int nochunks = (seq.length() / len) + 1;
+      int nochunks = (seq.length() / len)
+              + (seq.length() % len > 0 ? 1 : 0);
 
       for (int j = 0; j < nochunks; j++)
       {
diff --git a/src/jalview/io/PileUpfile.java b/src/jalview/io/PileUpfile.java
index 9570552..79c6531 100755
--- a/src/jalview/io/PileUpfile.java
+++ b/src/jalview/io/PileUpfile.java
@@ -76,11 +76,13 @@ public class PileUpfile extends MSFfile
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public String print()
   {
     return print(getSeqsAsArray());
   }
 
+  @Override
   public String print(SequenceI[] s)
   {
     StringBuffer out = new StringBuffer("PileUp");
@@ -141,12 +143,7 @@ public class PileUpfile extends MSFfile
 
     int len = 50;
 
-    int nochunks = (max / len) + 1;
-
-    if ((max % len) == 0)
-    {
-      nochunks--;
-    }
+    int nochunks = (max / len) + (max % len > 0 ? 1 : 0);
 
     for (i = 0; i < nochunks; i++)
     {
-- 
1.7.10.2