JAL-1807 explicit imports (jalview.bin)

[jalview.git] / src / jalview / bin / JalviewLite.java

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 3d1e275..5d1f0b0 100644 (file)
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -20,6 +20,7 @@
  */
 package jalview.bin;
 
+import jalview.analysis.SequenceIdMatcher;
 import jalview.api.StructureSelectionManagerProvider;
 import jalview.appletgui.AlignFrame;
 import jalview.appletgui.AlignViewport;
@@ -44,6 +45,11 @@ import jalview.io.NewickFile;
 import jalview.javascript.JSFunctionExec;
 import jalview.javascript.JalviewLiteJsApi;
 import jalview.javascript.JsCallBack;
+import jalview.javascript.JsSelectionSender;
+import jalview.javascript.MouseOverListener;
+import jalview.javascript.MouseOverStructureListener;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.UserColourScheme;
 import jalview.structure.SelectionListener;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
@@ -178,7 +184,7 @@ public class JalviewLite extends Applet implements
           final String position, final String alignedPosition)
   {
     // TODO: could try to highlight in all alignments if alf==null
-    jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
+    SequenceIdMatcher matcher = new SequenceIdMatcher(
             alf.viewport.getAlignment().getSequencesArray());
     final SequenceI sq = matcher.findIdMatch(sequenceId);
     if (sq != null)
@@ -284,7 +290,7 @@ public class JalviewLite extends Applet implements
     final SequenceGroup sel = new SequenceGroup();
     final ColumnSelection csel = new ColumnSelection();
     AlignmentI al = alf.viewport.getAlignment();
-    jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
+    SequenceIdMatcher matcher = new SequenceIdMatcher(
             alf.viewport.getAlignment().getSequencesArray());
     int start = 0, end = al.getWidth(), alw = al.getWidth();
     boolean seqsfound = true;
@@ -598,7 +604,7 @@ public class JalviewLite extends Applet implements
     SequenceI[] sqs = null;
     if (ids != null && ids.length > 0)
     {
-      jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
+      SequenceIdMatcher matcher = new SequenceIdMatcher(
               alf.viewport.getAlignment().getSequencesArray());
       int s = 0;
       sqs = new SequenceI[ids.length];
@@ -847,7 +853,7 @@ public class JalviewLite extends Applet implements
    */
   public AlignFrame loadAlignment(String text, String title)
   {
-    Alignment al = null;
+    AlignmentI al = null;
 
     String format = new IdentifyFile().Identify(text,
             AppletFormatAdapter.PASTE);
@@ -876,7 +882,7 @@ public class JalviewLite extends Applet implements
     setMouseoverListener(currentAlignFrame, listener);
   }
 
-  private Vector<jalview.javascript.JSFunctionExec> javascriptListeners = new Vector<jalview.javascript.JSFunctionExec>();
+  private Vector<JSFunctionExec> javascriptListeners = new Vector<JSFunctionExec>();
 
   /*
    * (non-Javadoc)
@@ -897,7 +903,7 @@ public class JalviewLite extends Applet implements
         return;
       }
     }
-    jalview.javascript.MouseOverListener mol = new jalview.javascript.MouseOverListener(
+    MouseOverListener mol = new MouseOverListener(
             this, af, listener);
     javascriptListeners.addElement(mol);
     StructureSelectionManager.getStructureSelectionManager(this)
@@ -941,8 +947,7 @@ public class JalviewLite extends Applet implements
         return;
       }
     }
-    jalview.javascript.JsSelectionSender mol = new jalview.javascript.JsSelectionSender(
-            this, af, listener);
+    JsSelectionSender mol = new JsSelectionSender(this, af, listener);
     javascriptListeners.addElement(mol);
     StructureSelectionManager.getStructureSelectionManager(this)
             .addSelectionListener(mol);
@@ -974,7 +979,7 @@ public class JalviewLite extends Applet implements
         return;
       }
     }
-    jalview.javascript.MouseOverStructureListener mol = new jalview.javascript.MouseOverStructureListener(
+    MouseOverStructureListener mol = new MouseOverStructureListener(
             this, listener, separatorListToArray(modelSet));
     javascriptListeners.addElement(mol);
     StructureSelectionManager.getStructureSelectionManager(this)
@@ -1071,8 +1076,7 @@ public class JalviewLite extends Applet implements
     {
       while (javascriptListeners.size() > 0)
       {
-        jalview.javascript.JSFunctionExec mol = javascriptListeners
-                .elementAt(0);
+        JSFunctionExec mol = javascriptListeners.elementAt(0);
         javascriptListeners.removeElement(mol);
         if (mol instanceof SelectionListener)
         {
@@ -1098,7 +1102,7 @@ public class JalviewLite extends Applet implements
     StructureSelectionManager.release(this);
   }
 
-  private jalview.javascript.JSFunctionExec jsFunctionExec;
+  private JSFunctionExec jsFunctionExec;
 
   /*
    * (non-Javadoc)
@@ -1996,8 +2000,8 @@ public class JalviewLite extends Applet implements
       // alignPdbStructures is true)
       Vector pdbs = new Vector();
       // create a lazy matcher if we're asked to
-      jalview.analysis.SequenceIdMatcher matcher = (applet
-              .getDefaultParameter("relaxedidmatch", false)) ? new jalview.analysis.SequenceIdMatcher(
+      SequenceIdMatcher matcher = (applet.getDefaultParameter(
+              "relaxedidmatch", false)) ? new SequenceIdMatcher(
               alignFrame.getAlignViewport().getAlignment()
                       .getSequencesArray()) : null;
 
@@ -2853,13 +2857,12 @@ public class JalviewLite extends Applet implements
     {
       return defcolour;
     }
-    Color col = jalview.schemes.ColourSchemeProperty
-            .getAWTColorFromName(colprop);
+    Color col = ColourSchemeProperty.getAWTColorFromName(colprop);
     if (col == null)
     {
       try
       {
-        col = new jalview.schemes.UserColourScheme(colprop).findColour('A');
+        col = new UserColourScheme(colprop).findColour('A');
       } catch (Exception ex)
       {
         System.err.println("Couldn't parse '" + colprop