JAL-1807 explicit imports (jalview.io.*)

[jalview.git] / src / jalview / io / packed / ParsePackedSet.java

diff --git a/src/jalview/io/packed/ParsePackedSet.java b/src/jalview/io/packed/ParsePackedSet.java
index 3130b9e..fda4faa 100644 (file)
--- a/src/jalview/io/packed/ParsePackedSet.java
+++ b/src/jalview/io/packed/ParsePackedSet.java
@@ -1,28 +1,33 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * Copyright (C) 2014 The Jalview Authors
+ * 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.
+ * 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/>.
+ * 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.io.packed;
 
 import jalview.datamodel.AlignmentI;
+import jalview.io.AnnotationFile;
 import jalview.io.AppletFormatAdapter;
+import jalview.io.FeaturesFile;
 import jalview.io.FileParse;
 import jalview.io.FormatAdapter;
 import jalview.io.IdentifyFile;
+import jalview.io.NewickFile;
 import jalview.io.packed.DataProvider.JvDataType;
 
 import java.io.BufferedReader;
@@ -121,8 +126,9 @@ public class ParsePackedSet
           {
             br = new BufferedReader(src.getReader());
           }
-          if (new jalview.io.AnnotationFile().parseAnnotationFrom(
-                  context.getLastAlignment(), br))
+          // TODO: add columnSelection to context
+          if (new AnnotationFile().parseAnnotationFrom(
+                  context.getLastAlignment(), null, br))
           {
             context.updateSetModified(true);
           }
@@ -158,7 +164,7 @@ public class ParsePackedSet
         }
         try
         {
-          jalview.io.FeaturesFile ff = new jalview.io.FeaturesFile(src);
+          FeaturesFile ff = new FeaturesFile(src);
           context.updateSetModified(ff.parse(context.getLastAlignment(),
                   context.featureColours, false, context.relaxedIdMatching));
         } catch (Exception e)
@@ -171,7 +177,7 @@ public class ParsePackedSet
       {
         try
         {
-          jalview.io.NewickFile nf = new jalview.io.NewickFile(src);
+          NewickFile nf = new NewickFile(src);
           if (!nf.isValid())
           {
             nf.close();