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

diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java
index 98c500a..3594afa 100755 (executable)
--- a/src/jalview/io/ClustalFile.java
+++ b/src/jalview/io/ClustalFile.java
@@ -60,14 +60,16 @@ public class ClustalFile extends AlignFile {
                  headers.addElement(id);\r
                }\r
 \r
-               tempseq.append(str.nextToken());\r
+                if(str.hasMoreTokens())\r
+                  tempseq.append(str.nextToken());\r
              }\r
            }\r
          }\r
        }\r
       }\r
     } catch (IOException e) {\r
-      System.out.println("Exception parsing clustal file " + e);\r
+      System.err.println("Exception parsing clustal file " + e);\r
+      e.printStackTrace();\r
     }\r
 \r
     if (flag) {\r
@@ -111,7 +113,7 @@ public class ClustalFile extends AlignFile {
           seqs.addElement(newSeq);\r
 \r
         } else {\r
-          System.out.println("Can't find sequence for " + headers.elementAt(i));\r
+          System.err.println("Clustal File Reader: Can't find sequence for " + headers.elementAt(i));\r
         }\r
       }\r
     }\r
@@ -122,6 +124,7 @@ public class ClustalFile extends AlignFile {
     return print(getSeqsAsArray());\r
   }\r
   public static String print(SequenceI[] s) {\r
+\r
     StringBuffer out = new StringBuffer("CLUSTAL\n\n");\r
 \r
     int max = 0;\r
@@ -155,18 +158,20 @@ public class ClustalFile extends AlignFile {
         int start = i*len;\r
         int end = start + len;\r
 \r
-        if (end < s[j].getSequence().length() && start < s[j].getSequence().length() ) {\r
-          out.append(s[j].getSequence().substring(start,end) + "\n");\r
-        } else {\r
-          if (start < s[j].getSequence().length()) {\r
-            out.append(s[j].getSequence().substring(start) + "\n");\r
-          }\r
+        if (end < s[j].getSequence().length() && start < s[j].getSequence().length() )\r
+          out.append(s[j].getSequence().substring(start,end));\r
+        else\r
+        {\r
+          if (start < s[j].getSequence().length())\r
+            out.append(s[j].getSequence().substring(start));\r
         }\r
+        out.append("\n");\r
         j++;\r
       }\r
       out.append("\n");\r
 \r
     }\r
+\r
     return out.toString();\r
   }\r
 \r