From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 10 Jul 2015 05:15:19 +0000 (+0100)
Subject: JAL-1807 explicit imports (jalview.javascript)
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=8146bb79670cfec703d7a7e04f1ae2e0318bd938;p=jalview.git

JAL-1807 explicit imports (jalview.javascript)
---

diff --git a/src/jalview/javascript/JalviewLiteJsApi.java b/src/jalview/javascript/JalviewLiteJsApi.java
index 51f6741..77908fd 100644
--- a/src/jalview/javascript/JalviewLiteJsApi.java
+++ b/src/jalview/javascript/JalviewLiteJsApi.java
@@ -250,7 +250,7 @@ public interface JalviewLiteJsApi
 
   /**
    * get alignment as format (format names FASTA, BLC, CLUSTAL, MSF, PILEUP,
-   * PFAM - see jalview.io.AppletFormatAdapter for full list)
+   * PFAM - see AppletFormatAdapter for full list)
    * 
    * @param format
    * @return
diff --git a/src/jalview/javascript/JsCallBack.java b/src/jalview/javascript/JsCallBack.java
index 76d6e8d..7c05be8 100644
--- a/src/jalview/javascript/JsCallBack.java
+++ b/src/jalview/javascript/JsCallBack.java
@@ -20,9 +20,11 @@
  */
 package jalview.javascript;
 
+import jalview.appletgui.AlignFrame;
+
 public interface JsCallBack
 {
-  public jalview.appletgui.AlignFrame getAlignFrame();
+  public AlignFrame getAlignFrame();
 
   public String getListenerFunction();
 
diff --git a/src/jalview/javascript/JsSelectionSender.java b/src/jalview/javascript/JsSelectionSender.java
index e4a0916..a028f61 100644
--- a/src/jalview/javascript/JsSelectionSender.java
+++ b/src/jalview/javascript/JsSelectionSender.java
@@ -21,13 +21,15 @@
 package jalview.javascript;
 
 import jalview.appletgui.AlignFrame;
+import jalview.appletgui.AlignViewport;
 import jalview.bin.JalviewLite;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.SequenceGroup;
+import jalview.structure.SelectionListener;
 import jalview.structure.SelectionSource;
 
 public class JsSelectionSender extends JSFunctionExec implements
-        jalview.structure.SelectionListener, JsCallBack
+        SelectionListener, JsCallBack
 {
 
   AlignFrame _af;
@@ -54,11 +56,11 @@ public class JsSelectionSender extends JSFunctionExec implements
       AlignFrame src = _af;
       if (source != null)
       {
-        if (source instanceof jalview.appletgui.AlignViewport
-                && ((jalview.appletgui.AlignViewport) source).applet.currentAlignFrame.viewport == source)
+        if (source instanceof AlignViewport
+                && ((AlignViewport) source).applet.currentAlignFrame.viewport == source)
         {
           // should be valid if it just generated an event!
-          src = ((jalview.appletgui.AlignViewport) source).applet.currentAlignFrame;
+          src = ((AlignViewport) source).applet.currentAlignFrame;
 
         }
       }
@@ -95,7 +97,7 @@ public class JsSelectionSender extends JSFunctionExec implements
         for (int i = 0; i < cols.length; i++)
         {
           cols[i] = ""
-                  + (1 + ((Integer) colsel.getSelected().elementAt(i))
+                  + (1 + colsel.getSelected().elementAt(i)
                           .intValue());
         }
       }
diff --git a/src/jalview/javascript/MouseOverListener.java b/src/jalview/javascript/MouseOverListener.java
index 9d0279b..8fd48d6 100644
--- a/src/jalview/javascript/MouseOverListener.java
+++ b/src/jalview/javascript/MouseOverListener.java
@@ -21,6 +21,7 @@
 package jalview.javascript;
 
 import jalview.appletgui.AlignFrame;
+import jalview.appletgui.AlignViewport;
 import jalview.bin.JalviewLite;
 import jalview.datamodel.SequenceI;
 import jalview.structure.VamsasListener;
@@ -53,11 +54,11 @@ public class MouseOverListener extends JSFunctionExec implements
       {
         if (source != null)
         {
-          if (source instanceof jalview.appletgui.AlignViewport
-                  && ((jalview.appletgui.AlignViewport) source).applet.currentAlignFrame.viewport == source)
+          if (source instanceof AlignViewport
+                  && ((AlignViewport) source).applet.currentAlignFrame.viewport == source)
           {
             // should be valid if it just generated an event!
-            src = ((jalview.appletgui.AlignViewport) source).applet.currentAlignFrame;
+            src = ((AlignViewport) source).applet.currentAlignFrame;
 
           }
           // TODO: ensure that if '_af' is specified along with a handler
diff --git a/src/jalview/javascript/MouseOverStructureListener.java b/src/jalview/javascript/MouseOverStructureListener.java
index 4b1c9ce..dfe5c4f 100644
--- a/src/jalview/javascript/MouseOverStructureListener.java
+++ b/src/jalview/javascript/MouseOverStructureListener.java
@@ -20,13 +20,11 @@
  */
 package jalview.javascript;
 
-import java.util.ArrayList;
-import java.util.List;
-
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
 import jalview.api.SequenceRenderer;
 import jalview.appletgui.AlignFrame;
+import jalview.appletgui.AlignmentPanel;
 import jalview.bin.JalviewLite;
 import jalview.datamodel.SequenceI;
 import jalview.ext.jmol.JmolCommands;
@@ -36,6 +34,9 @@ import jalview.structure.StructureMapping;
 import jalview.structure.StructureMappingcommandSet;
 import jalview.structure.StructureSelectionManager;
 
+import java.util.ArrayList;
+import java.util.List;
+
 /**
  * Propagate events involving PDB structures associated with sequences to a
  * javascript function. Generally, the javascript handler is called with a
@@ -177,7 +178,7 @@ public class MouseOverStructureListener extends JSFunctionExec implements
     // {
     // ssm.reportMapping();
     // }
-    if (source instanceof jalview.api.AlignmentViewPanel)
+    if (source instanceof AlignmentViewPanel)
     {
       SequenceI[][] sequence = new SequenceI[modelSet.length][];
       for (int m = 0; m < modelSet.length; m++)
@@ -202,15 +203,15 @@ public class MouseOverStructureListener extends JSFunctionExec implements
         // }
       }
 
-      SequenceRenderer sr = ((jalview.appletgui.AlignmentPanel) source)
+      SequenceRenderer sr = ((AlignmentPanel) source)
               .getSequenceRenderer();
-      FeatureRenderer fr = ((jalview.appletgui.AlignmentPanel) source).av
+      FeatureRenderer fr = ((AlignmentPanel) source).av
               .isShowSequenceFeatures() ? new jalview.appletgui.FeatureRenderer(
-              ((jalview.appletgui.AlignmentPanel) source).av) : null;
+              ((AlignmentPanel) source).av) : null;
       if (fr != null)
       {
         ((jalview.appletgui.FeatureRenderer) fr)
-                .transferSettings(((jalview.appletgui.AlignmentPanel) source)
+                .transferSettings(((AlignmentPanel) source)
                         .getFeatureRenderer());
       }
       ;
@@ -227,7 +228,7 @@ public class MouseOverStructureListener extends JSFunctionExec implements
         return;
       }
       int sz = 0;
-      for (jalview.structure.StructureMappingcommandSet ccset : colcommands)
+      for (StructureMappingcommandSet ccset : colcommands)
       {
         sz += ccset.commands.length;
         ccomands.add(ccset.commands);
@@ -244,7 +245,7 @@ public class MouseOverStructureListener extends JSFunctionExec implements
       }
       if (jvlite.isJsMessageSetChanged(
               mclass = "colourstruct",
-              mhandle = ((jalview.appletgui.AlignmentPanel) source).av
+              mhandle = ((AlignmentPanel) source).av
                       .getViewId(), ccomandset))
       {
         jvlite.setJsMessageSet(mclass, mhandle, ccomandset);
@@ -252,7 +253,7 @@ public class MouseOverStructureListener extends JSFunctionExec implements
         String st[] = new String[]
         {
             "colourstruct",
-            "" + ((jalview.appletgui.AlignmentPanel) source).av.getViewId(),
+            "" + ((AlignmentPanel) source).av.getViewId(),
             "" + ccomandset.length,
             jvlite.arrayToSeparatorList(pdbfn.toArray(new String[pdbfn
                     .size()])) };