JAL-161 JAL-4173 allow trees embedded as NH tags in stockholm to be loaded as trees...

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

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 3202ac9..1bea24b 100755 (executable)
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -33,6 +33,7 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.util.MessageManager;
+import jalview.util.StringUtils;
 
 /**
  * DOCUMENT ME!
@@ -378,7 +379,7 @@ public abstract class AlignFile extends FileParse
   {
     Sequence seq = null;
     id = id.trim();
-    int space = id.indexOf(" ");
+    int space = StringUtils.indexOfFirstWhitespace(id);
     if (space > -1)
     {
       seq = new Sequence(id.substring(0, space), "");
@@ -432,12 +433,24 @@ public abstract class AlignFile extends FileParse
     newickStrings.addElement(new String[] { treeName, newickString });
   }
 
-  protected int getTreeCount()
+  @Override
+  public int getTreeCount()
   {
     return newickStrings == null ? 0 : newickStrings.size();
   }
 
   @Override
+  public boolean hasTrees()
+  {
+    return getTreeCount()>0;
+  }
+  
+  @Override
+  public List<String[]> getNewickTrees()
+  {
+    return newickStrings;
+  }
+  @Override
   public void addGroups(AlignmentI al)
   {