X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FClustalFile.java;h=3594afa1b7b4324f33a2f8a78ca34e9a49ef755a;hb=60d2bc892983abad01d082cbff73466f093879f2;hp=98c500abae471d5c117feb49a2137605da977213;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git

diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java
index 98c500a..3594afa 100755
--- a/src/jalview/io/ClustalFile.java
+++ b/src/jalview/io/ClustalFile.java
@@ -60,14 +60,16 @@ public class ClustalFile extends AlignFile {
 		  headers.addElement(id);
 		}
 
-		tempseq.append(str.nextToken());
+                if(str.hasMoreTokens())
+                  tempseq.append(str.nextToken());
 	      }
 	    }
 	  }
 	}
       }
     } catch (IOException e) {
-      System.out.println("Exception parsing clustal file " + e);
+      System.err.println("Exception parsing clustal file " + e);
+      e.printStackTrace();
     }
 
     if (flag) {
@@ -111,7 +113,7 @@ public class ClustalFile extends AlignFile {
           seqs.addElement(newSeq);
 
         } else {
-          System.out.println("Can't find sequence for " + headers.elementAt(i));
+          System.err.println("Clustal File Reader: Can't find sequence for " + headers.elementAt(i));
         }
       }
     }
@@ -122,6 +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;
@@ -155,18 +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();
   }