JAL-1858 handle hidden columns when computing region to redraw

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

diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java
index 166984f..d618809 100755 (executable)
--- a/src/jalview/io/ClustalFile.java
+++ b/src/jalview/io/ClustalFile.java
@@ -197,13 +197,7 @@ public class ClustalFile extends AlignFile
   }
 
   @Override
-  public String print()
-  {
-    return print(getSeqsAsArray());
-    // TODO: locaRNA style aln output
-  }
-
-  public String print(SequenceI[] s)
+  public String print(SequenceI[] s, boolean jvsuffix)
   {
     StringBuffer out = new StringBuffer("CLUSTAL" + newline + newline);
 
@@ -214,12 +208,9 @@ public class ClustalFile extends AlignFile
 
     while ((i < s.length) && (s[i] != null))
     {
-      String tmp = printId(s[i]);
+      String tmp = printId(s[i], jvsuffix);
 
-      if (s[i].getSequence().length > max)
-      {
-        max = s[i].getSequence().length;
-      }
+      max = Math.max(max, s[i].getLength());
 
       if (tmp.length() > maxid)
       {
@@ -245,19 +236,20 @@ public class ClustalFile extends AlignFile
 
       while ((j < s.length) && (s[j] != null))
       {
-        out.append(new Format("%-" + maxid + "s").form(printId(s[j]) + " "));
+        out.append(new Format("%-" + maxid + "s").form(printId(s[j],
+                jvsuffix) + " "));
 
         int start = i * len;
         int end = start + len;
 
-        if ((end < s[j].getSequence().length)
-                && (start < s[j].getSequence().length))
+        int length = s[j].getLength();
+        if ((end < length) && (start < length))
         {
           out.append(s[j].getSequenceAsString(start, end));
         }
         else
         {
-          if (start < s[j].getSequence().length)
+          if (start < length)
           {
             out.append(s[j].getSequenceAsString().substring(start));
           }