JAL-1807 explicit imports (jalview.appletgui)

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

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 0225dc7..1fd4231 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -37,6 +37,7 @@ import jalview.commands.RemoveGapColCommand;
 import jalview.commands.RemoveGapsCommand;
 import jalview.commands.SlideSequencesCommand;
 import jalview.commands.TrimRegionCommand;
+import jalview.controller.AlignViewController;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
@@ -46,9 +47,11 @@ import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.io.AlignmentProperties;
 import jalview.io.AnnotationFile;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.FeaturesFile;
+import jalview.io.NewickFile;
 import jalview.io.TCoffeeScoreFile;
 import jalview.schemes.Blosum62ColourScheme;
 import jalview.schemes.BuriedColourScheme;
@@ -68,6 +71,7 @@ import jalview.schemes.TurnColourScheme;
 import jalview.schemes.ZappoColourScheme;
 import jalview.structure.StructureSelectionManager;
 import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.Comparison;
 import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
@@ -219,7 +223,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }
 
     alignPanel = new AlignmentPanel(this, viewport);
-    avc = new jalview.controller.AlignViewController(this, viewport,
+    avc = new AlignViewController(this, viewport,
             alignPanel);
     viewport.updateConservation(alignPanel);
     viewport.updateConsensus(alignPanel);
@@ -366,7 +370,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     boolean featuresFile = false;
     try
     {
-      featuresFile = new jalview.io.FeaturesFile(file, type)
+      featuresFile = new FeaturesFile(file, type)
               .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
                       .getFeatureRenderer().getFeatureColours(), featureLinks,
                       true, viewport.applet.getDefaultParameter(
@@ -1171,13 +1175,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }
     else if (source == alProperties)
     {
-      StringBuffer contents = new jalview.io.AlignmentProperties(
+      StringBuffer contents = new AlignmentProperties(
               viewport.getAlignment()).formatAsString();
       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
       cap.setText(contents.toString());
       Frame frame = new Frame();
       frame.add(cap);
-      jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+      JalviewLite.addFrame(frame, MessageManager.formatMessage(
               "label.alignment_properties", new String[]
               { getTitle() }), 400, 250);
     }
@@ -1330,7 +1334,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
     Frame frame = new Frame();
     frame.add(cap);
-    jalview.bin.JalviewLite.addFrame(frame,
+    JalviewLite.addFrame(frame,
             MessageManager.getString("label.input_cut_paste"), 500, 500);
   }
 
@@ -1339,7 +1343,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
     Frame frame = new Frame();
     frame.add(cap);
-    jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+    JalviewLite.addFrame(frame, MessageManager.formatMessage(
             "label.alignment_output_command", new Object[]
             { e.getActionCommand() }), 600, 500);
 
@@ -1357,7 +1361,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     cap.setAnnotationImport();
     Frame frame = new Frame();
     frame.add(cap);
-    jalview.bin.JalviewLite.addFrame(frame,
+    JalviewLite.addFrame(frame,
             MessageManager.getString("action.paste_annotations"), 400, 300);
 
   }
@@ -1372,7 +1376,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
       Frame frame = new Frame();
       frame.add(cap);
-      jalview.bin.JalviewLite.addFrame(frame,
+      JalviewLite.addFrame(frame,
               MessageManager.getString("label.annotations"), 600, 500);
       cap.setText(annotation);
     }
@@ -1422,7 +1426,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       }
       Frame frame = new Frame();
       frame.add(cap);
-      jalview.bin.JalviewLite.addFrame(frame,
+      JalviewLite.addFrame(frame,
               MessageManager.getString("label.features"), 600, 500);
       cap.setText(features);
     }
@@ -1918,7 +1922,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
       {
         ch = seq.getCharAt(j);
-        if (!jalview.util.Comparison.isGap((ch)))
+        if (!Comparison.isGap((ch)))
         {
           endRes++;
         }
@@ -1998,7 +2002,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
           }
         }
 
-        jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
+        JalviewLite.addFrame(af, newtitle, frameWidth,
                 frameHeight);
       }
       else
@@ -2550,7 +2554,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     OverviewPanel overview = new OverviewPanel(alignPanel);
     frame.add(overview);
     // +50 must allow for applet frame window
-    jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+    JalviewLite.addFrame(frame, MessageManager.formatMessage(
             "label.overview_params", new String[]
             { this.getTitle() }), overview.getPreferredSize().width,
             overview.getPreferredSize().height + 50);
@@ -2603,8 +2607,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       alignPanel.getOverviewPanel().updateOverviewImage();
     }
 
-    jalview.structure.StructureSelectionManager
-            .getStructureSelectionManager(viewport.applet)
+    StructureSelectionManager.getStructureSelectionManager(viewport.applet)
             .sequenceColoursChanged(alignPanel);
 
     alignPanel.paintAlignment(true);
@@ -2707,7 +2710,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       Frame frame = new Frame();
       frame.add(new PairwiseAlignPanel(alignPanel));
-      jalview.bin.JalviewLite.addFrame(frame,
+      JalviewLite.addFrame(frame,
               MessageManager.getString("action.pairwise_alignment"), 600,
               500);
     }
@@ -2799,7 +2802,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
       addTreeMenuItem(tp, title);
 
-      jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
+      JalviewLite.addFrame(tp, title, 600, 500);
     }
   }
 
@@ -2810,15 +2813,15 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     cap.setTreeImport();
     Frame frame = new Frame();
     frame.add(cap);
-    jalview.bin.JalviewLite.addFrame(frame,
+    JalviewLite.addFrame(frame,
             MessageManager.getString("label.paste_newick_file"), 400, 300);
   }
 
-  public void loadTree(jalview.io.NewickFile tree, String treeFile)
+  public void loadTree(NewickFile tree, String treeFile)
   {
     TreePanel tp = new TreePanel(alignPanel, treeFile,
             MessageManager.getString("label.load_tree_from_file"), tree);
-    jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
+    JalviewLite.addFrame(tp, treeFile, 600, 500);
     addTreeMenuItem(tp, treeFile);
   }
 
@@ -2968,7 +2971,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     Frame frame = new Frame();
     frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
             .getBuildDate()));
-    jalview.bin.JalviewLite.addFrame(frame,
+    JalviewLite.addFrame(frame,
             MessageManager.getString("label.jalview"), 580, 220);
 
   }
@@ -3198,11 +3201,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     inputText.addActionListener(this);
     Menu outputTextboxMenu = new Menu(
             MessageManager.getString("label.out_to_textbox"));
-    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]);
+      MenuItem item = new MenuItem(AppletFormatAdapter.WRITEABLE_FORMATS[i]);
 
       item.addActionListener(new java.awt.event.ActionListener()
       {
@@ -3806,7 +3808,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       add(statusBar, BorderLayout.SOUTH);
       add(alignPanel, BorderLayout.CENTER);
       // and register with the applet so it can pass external API calls to us
-      jalview.bin.JalviewLite.addFrame(this, this.getTitle(),
+      JalviewLite.addFrame(this, this.getTitle(),
               frameWidth,
               frameHeight);
     }
@@ -4064,12 +4066,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       // can only do alignments with Jmol
       // find the last jmol window assigned to this alignment
-      jalview.appletgui.AppletJmol ajm = null, tajm;
+      AppletJmol ajm = null, tajm;
       Vector jmols = applet
-              .getAppletWindow(jalview.appletgui.AppletJmol.class);
+.getAppletWindow(AppletJmol.class);
       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
       {
-        tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
+        tajm = (AppletJmol) jmols.elementAt(i);
         if (tajm.ap.alignFrame == this)
         {
           ajm = tajm;
@@ -4088,8 +4090,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     // otherwise, create a new window
     if (applet.jmolAvailable)
     {
-      new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
-              protocol);
+      new AppletJmol(pdb, seqs, chains, alignPanel, protocol);
       applet.lastFrameX += 40;
       applet.lastFrameY += 40;
     }