JAL-1807 explicit imports (jalview.gui)

[jalview.git] / src / jalview / gui / Jalview2XML_V1.java

diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java
index cb572cd..51db9df 100755 (executable)
--- a/src/jalview/gui/Jalview2XML_V1.java
+++ b/src/jalview/gui/Jalview2XML_V1.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.analysis.Conservation;
 import jalview.binding.Annotation;
 import jalview.binding.AnnotationElement;
 import jalview.binding.Features;
@@ -34,10 +35,12 @@ import jalview.binding.Setting;
 import jalview.binding.Tree;
 import jalview.binding.UserColours;
 import jalview.binding.Viewport;
+import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.PDBEntry;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.schemes.ResidueProperties;
+import jalview.schemes.UserColourScheme;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
 import jalview.util.jarInputStreamProvider;
@@ -73,8 +76,7 @@ public class Jalview2XML_V1
     this.raiseGUI = raiseGUI;
   };
 
-  jalview.schemes.UserColourScheme GetUserColourScheme(
-          JalviewModelSequence jms, String id)
+  UserColourScheme GetUserColourScheme(JalviewModelSequence jms, String id)
   {
     UserColours[] uc = jms.getUserColours();
     UserColours colours = null;
@@ -98,7 +100,7 @@ public class Jalview2XML_V1
               .getUserColourScheme().getColour(i).getRGB(), 16));
     }
 
-    return new jalview.schemes.UserColourScheme(newColours);
+    return new UserColourScheme(newColours);
   }
 
   /**
@@ -110,7 +112,7 @@ public class Jalview2XML_V1
   public AlignFrame LoadJalviewAlign(final jarInputStreamProvider jprovider)
   {
     final String file = jprovider.getFilename();
-    jalview.gui.AlignFrame af = null;
+    AlignFrame af = null;
 
     try
     {
@@ -281,17 +283,17 @@ public class Jalview2XML_V1
                   ae[aa].getValue());
         }
 
-        jalview.datamodel.AlignmentAnnotation jaa = null;
+        AlignmentAnnotation jaa = null;
 
         if (an[i].getGraph())
         {
-          jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
+          jaa = new AlignmentAnnotation(an[i].getLabel(),
                   an[i].getDescription(), anot, 0, 0,
-                  jalview.datamodel.AlignmentAnnotation.BAR_GRAPH);
+                  AlignmentAnnotation.BAR_GRAPH);
         }
         else
         {
-          jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
+          jaa = new AlignmentAnnotation(an[i].getLabel(),
                   an[i].getDescription(), anot);
         }
 
@@ -361,7 +363,7 @@ public class Jalview2XML_V1
 
         if (groups[i].getConsThreshold() != 0)
         {
-          jalview.analysis.Conservation c = new jalview.analysis.Conservation(
+          Conservation c = new Conservation(
                   "All", ResidueProperties.propHash, 3,
                   sg.getSequences(null), 0, sg.getWidth() - 1);
           c.calculate();