JAL-4353 Preserve the user given 'linkedId' with ArgValue, to help with deciding...

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

diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java
index a37afd9..b6f36e8 100755 (executable)
--- a/src/jalview/io/ClustalFile.java
+++ b/src/jalview/io/ClustalFile.java
@@ -77,7 +77,9 @@ public class ClustalFile extends AlignFile
         {
           top = true;
         }
-        if (line.indexOf(" ") != 0)
+        boolean isConservation = line.startsWith(SPACE)
+                || line.startsWith(TAB);
+        if (!isConservation)
         {
           str = new StringTokenizer(line);
 
@@ -138,7 +140,7 @@ public class ClustalFile extends AlignFile
       }
     } catch (IOException e)
     {
-      System.err.println("Exception parsing clustal file " + e);
+      jalview.bin.Console.errPrintln("Exception parsing clustal file " + e);
       e.printStackTrace();
     }
 
@@ -166,8 +168,9 @@ public class ClustalFile extends AlignFile
         }
         else
         {
-          System.err.println("Clustal File Reader: Can't find sequence for "
-                  + headers.elementAt(i));
+          jalview.bin.Console.errPrintln(
+                  "Clustal File Reader: Can't find sequence for "
+                          + headers.elementAt(i));
         }
       }
       AlignmentAnnotation lastssa = null;