JAL-1807 explicit imports (jalview.appletgui)

[jalview.git] / src / jalview / appletgui / APopupMenu.java

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index f16da84..1d59202 100644 (file)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -24,6 +24,7 @@ import jalview.analysis.AAFrequency;
 import jalview.analysis.AlignmentAnnotationUtils;
 import jalview.analysis.AlignmentUtils;
 import jalview.analysis.Conservation;
+import jalview.bin.JalviewLite;
 import jalview.commands.ChangeCaseCommand;
 import jalview.commands.EditCommand;
 import jalview.commands.EditCommand.Action;
@@ -48,6 +49,7 @@ import jalview.schemes.StrandColourScheme;
 import jalview.schemes.TaylorColourScheme;
 import jalview.schemes.TurnColourScheme;
 import jalview.schemes.ZappoColourScheme;
+import jalview.util.DBRefUtils;
 import jalview.util.MessageManager;
 import jalview.util.UrlLink;
 
@@ -216,10 +218,10 @@ public class APopupMenu extends java.awt.PopupMenu implements
       e.printStackTrace();
     }
 
-    for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
+    for (int i = 0; i < AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
     {
       MenuItem item = new MenuItem(
-              jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
+AppletFormatAdapter.WRITEABLE_FORMATS[i]);
 
       item.addActionListener(this);
       outputmenu.add(item);
@@ -274,7 +276,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
         {
 
           // collect matching db-refs
-          DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
+          DBRefEntry[] dbr = DBRefUtils.selectRefs(
                   seq.getDBRef(), new String[]
                   { target });
           // collect id string too
@@ -348,16 +350,15 @@ public class APopupMenu extends java.awt.PopupMenu implements
          * 
          * String url_suff = link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
          * // collect matching db-refs DBRefEntry[] dbr =
-         * jalview.util.DBRefUtils.selectRefs(seq.getDBRef(), new
-         * String[]{target}); // collect id string too String id =
-         * seq.getName(); if (id.indexOf("|") > -1) { id =
-         * id.substring(id.lastIndexOf("|") + 1); } if (dbr!=null) { for (int
-         * r=0;r<dbr.length; r++) { if (dbr[r].getAccessionId().equals(id)) { //
-         * suppress duplicate link creation for the bare sequence ID string with
-         * this link id = null; } addshowLink(linkMenu,
-         * dbr[r].getSource()+"|"+dbr[r].getAccessionId(), target,
-         * url_pref+dbr[r].getAccessionId()+url_suff); } } if (id!=null) { //
-         * create Bare ID link for this RUL addshowLink(linkMenu, target,
+         * DBRefUtils.selectRefs(seq.getDBRef(), new String[]{target}); //
+         * collect id string too String id = seq.getName(); if (id.indexOf("|")
+         * > -1) { id = id.substring(id.lastIndexOf("|") + 1); } if (dbr!=null)
+         * { for (int r=0;r<dbr.length; r++) { if
+         * (dbr[r].getAccessionId().equals(id)) { // suppress duplicate link
+         * creation for the bare sequence ID string with this link id = null; }
+         * addshowLink(linkMenu, dbr[r].getSource()+"|"+dbr[r].getAccessionId(),
+         * target, url_pref+dbr[r].getAccessionId()+url_suff); } } if (id!=null)
+         * { // create Bare ID link for this RUL addshowLink(linkMenu, target,
          * url_pref + id + url_suff); } } else { addshowLink(linkMenu, target,
          * link.substring(link.lastIndexOf("|")+1)); }
          */
@@ -824,14 +825,14 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
     Frame frame = new Frame();
     frame.add(cap);
-    jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+    JalviewLite.addFrame(frame, MessageManager.formatMessage(
             "label.selection_output_command", new Object[]
             { e.getActionCommand() }), 600, 500);
     // JBPNote: getSelectionAsNewSequence behaviour has changed - this method
     // now returns a full copy of sequence data
     // TODO consider using getSequenceSelection instead here
 
-    cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(
+    cap.setText(new AppletFormatAdapter().formatSequences(
             e.getActionCommand(), ap.av.getShowJVSuffix(), ap, true));
 
   }
@@ -871,7 +872,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
     }
     Frame frame = new Frame();
     frame.add(cap);
-    jalview.bin.JalviewLite.addFrame(frame, "Sequence Details for "
+    JalviewLite.addFrame(frame, "Sequence Details for "
             + (sequences.length == 1 ? sequences[0].getDisplayId(true)
                     : "Selection"), 600, 500);
     cap.setText(MessageManager.formatMessage("label.html_content",
@@ -902,7 +903,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
       if (ap.av.applet.jmolAvailable)
       {
-        new jalview.appletgui.AppletJmol(entry, new SequenceI[]
+        new AppletJmol(entry, new SequenceI[]
         { seq }, null, ap, AppletFormatAdapter.URL);
       }
       else
@@ -919,7 +920,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
       cap.setPDBImport(seq);
       Frame frame = new Frame();
       frame.add(cap);
-      jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+      JalviewLite.addFrame(frame, MessageManager.formatMessage(
               "label.paste_pdb_file_for_sequence", new Object[]
               { seq.getName() }), 400, 300);
     }