From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 27 May 2005 15:40:31 +0000 (+0000)
Subject: ignores blank lines read in and write out
X-Git-Tag: Release_2_0~141
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=52a2a91b4d96ca34476e39dc5444051613bb0190;p=jalview.git

ignores blank lines read in and write out
---

diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java
index 4138a88..3594afa 100755
--- a/src/jalview/io/ClustalFile.java
+++ b/src/jalview/io/ClustalFile.java
@@ -60,7 +60,8 @@ public class ClustalFile extends AlignFile {
 		  headers.addElement(id);
 		}
 
-		tempseq.append(str.nextToken());
+                if(str.hasMoreTokens())
+                  tempseq.append(str.nextToken());
 	      }
 	    }
 	  }
@@ -123,6 +124,7 @@ public class ClustalFile extends AlignFile {
     return print(getSeqsAsArray());
   }
   public static String print(SequenceI[] s) {
+
     StringBuffer out = new StringBuffer("CLUSTAL\n\n");
 
     int max = 0;
@@ -156,18 +158,20 @@ public class ClustalFile extends AlignFile {
         int start = i*len;
         int end = start + len;
 
-        if (end < s[j].getSequence().length() && start < s[j].getSequence().length() ) {
-          out.append(s[j].getSequence().substring(start,end) + "\n");
-        } else {
-          if (start < s[j].getSequence().length()) {
-            out.append(s[j].getSequence().substring(start) + "\n");
-          }
+        if (end < s[j].getSequence().length() && start < s[j].getSequence().length() )
+          out.append(s[j].getSequence().substring(start,end));
+        else
+        {
+          if (start < s[j].getSequence().length())
+            out.append(s[j].getSequence().substring(start));
         }
+        out.append("\n");
         j++;
       }
       out.append("\n");
 
     }
+
     return out.toString();
   }