JAL-3541 ensure deletion of cloverReportDir

[jalview.git] / src / jalview / ext / rbvi / chimera / AtomSpecModel.java

diff --git a/src/jalview/ext/rbvi/chimera/AtomSpecModel.java b/src/jalview/ext/rbvi/chimera/AtomSpecModel.java
index f3c9c1e..39d6704 100644 (file)
--- a/src/jalview/ext/rbvi/chimera/AtomSpecModel.java
+++ b/src/jalview/ext/rbvi/chimera/AtomSpecModel.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ext.rbvi.chimera;
 
 import jalview.util.IntRangeComparator;
@@ -26,7 +46,7 @@ import java.util.TreeMap;
  * </ul>
  * 
  * <pre>
- * @see http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/frameatom_spec.html
+ * &#64;see http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/frameatom_spec.html
  * </pre>
  */
 public class AtomSpecModel
@@ -100,7 +120,7 @@ public class AtomSpecModel
 
       for (String chain : modelData.keySet())
       {
-        chain = chain.trim();
+        chain = " ".equals(chain) ? chain : chain.trim();
 
         List<int[]> rangeList = modelData.get(chain);
 
@@ -172,9 +192,10 @@ public class AtomSpecModel
     {
       sb.append(start).append("-").append(end);
     }
-    if (chain.length() > 0)
-    {
-      sb.append(".").append(chain);
+
+    sb.append(".");
+    if (!" ".equals(chain)) {
+      sb.append(chain);
     }
   }
 }