X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=1510a14e6c2bfcda582e27ff8b53b97ed787b01c;hb=496a78f25054b4003f6115c7194a2a466c44197f;hp=5c8135d2fde3cb4d8c85379972549030d1563342;hpb=f69e96788c2ae3a08f56c4461d8d197a3b3a06a2;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 5c8135d..1510a14 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -103,6 +103,7 @@ import jalview.structure.StructureSelectionManager;
 import jalview.structures.models.AAStructureBindingModel;
 import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
 
 public class AlignFrame extends EmbmenuFrame implements ActionListener,
         ItemListener, KeyListener, AlignViewControllerGuiI
@@ -155,6 +156,20 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   public AlignFrame(AlignmentI al, JalviewLite applet,
           String title, boolean embedded, boolean addToDisplay)
   {
+    this(al, null, null, applet, title, embedded, addToDisplay);
+  }
+
+  public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
+          ColumnSelection columnSelection, JalviewLite applet,
+          String title, boolean embedded)
+  {
+    this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
+  }
+
+  public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
+          ColumnSelection columnSelection, JalviewLite applet,
+          String title, boolean embedded, boolean addToDisplay)
+  {
     if (applet != null)
     {
       jalviewServletURL = applet.getParameter("APPLICATION_URL");
@@ -190,6 +205,17 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       }
     }
     viewport = new AlignViewport(al, applet);
+
+    if (hiddenSeqs != null && hiddenSeqs.length > 0)
+    {
+      viewport.hideSequence(hiddenSeqs);
+      viewport.setHasHiddenRows(true);
+    }
+    if (columnSelection != null)
+    {
+      viewport.setColumnSelection(columnSelection);
+    }
+
     alignPanel = new AlignmentPanel(this, viewport);
     avc = new jalview.controller.AlignViewController(this, viewport,
             alignPanel);
@@ -197,7 +223,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     viewport.updateConsensus(alignPanel);
 
     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
-    followMouseOverFlag.setState(viewport.getFollowHighlight());
+    followMouseOverFlag.setState(viewport.isFollowHighlight());
     showGroupConsensus.setState(viewport.isShowGroupConsensus());
     showGroupConservation.setState(viewport.isShowGroupConservation());
     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
@@ -926,7 +952,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   private void mouseOverFlag_stateChanged()
   {
-    viewport.followHighlight = followMouseOverFlag.getState();
+    viewport.setFollowHighlight(followMouseOverFlag.getState());
     // TODO: could kick the scrollTo mechanism to reset view for current
     // searchresults.
   }
@@ -1312,7 +1338,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
             "label.alignment_output_command", new Object[]
             { e.getActionCommand() }), 600, 500);
-    cap.setText(new AppletFormatAdapter().formatSequences(
+
+    FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
+    viewport.setFeatureRenderer(fr);
+    viewport.setIncludeHiddenRegion(false);
+    cap.setText(new AppletFormatAdapter(viewport).formatSequences(
             e.getActionCommand(), viewport.getAlignment(),
             viewport.getShowJVSuffix()));
   }
@@ -1594,7 +1624,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     viewport.addToRedoList(command);
     command.undoCommand(null);
 
-    AlignViewport originalSource = getOriginatingSource(command);
+    AlignmentViewport originalSource = getOriginatingSource(command);
     // JBPNote Test
     if (originalSource != viewport)
     {
@@ -1626,7 +1656,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     viewport.addToHistoryList(command);
     command.doCommand(null);
 
-    AlignViewport originalSource = getOriginatingSource(command);
+    AlignmentViewport originalSource = getOriginatingSource(command);
     // JBPNote Test
     if (originalSource != viewport)
     {
@@ -1642,9 +1672,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
             .getAlignment().getSequences());
   }
 
-  AlignViewport getOriginatingSource(CommandI command)
+  AlignmentViewport getOriginatingSource(CommandI command)
   {
-    AlignViewport originalSource = null;
+    AlignmentViewport originalSource = null;
     // For sequence removal and addition, we need to fire
     // the property change event FROM the viewport where the
     // original alignment was altered
@@ -2541,7 +2571,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   }
 
-  void changeColour(ColourSchemeI cs)
+  public void changeColour(ColourSchemeI cs)
   {
     int threshold = 0;