JAL-3253-applet adds NOMENUBAR, NOSTATUS, NOCALCULATION, SHOWOVERVIEW

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index b56f269..d87f0f0 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -28,10 +28,12 @@ import jalview.analysis.GeneticCodeI;
 import jalview.analysis.ParseProperties;
 import jalview.analysis.SequenceIdMatcher;
 import jalview.api.AlignExportSettingsI;
+import jalview.api.AlignFrameI;
 import jalview.api.AlignViewControllerGuiI;
 import jalview.api.AlignViewControllerI;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
+//from JalviewLite imports import jalview.api.FeatureRenderer;
 import jalview.api.FeatureSettingsControllerI;
 import jalview.api.SplitContainerI;
 import jalview.api.ViewStyleI;
@@ -162,7 +164,8 @@ import ext.vamsas.ServiceHandle;
  * @version $Revision$
  */
 @SuppressWarnings("serial")
-public class AlignFrame extends GAlignFrame implements DropTargetListener,
+public class AlignFrame extends GAlignFrame
+        implements AlignFrameI, DropTargetListener,
         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 {
 
@@ -350,6 +353,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if (!Jalview.isHeadlessMode())
     {
       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
+      statusPanel.setVisible(Jalview.getInstance().getShowStatus());
+      alignFrameMenuBar.setVisible(Jalview.getInstance().getAllowMenuBar());
     }
 
     avc = new jalview.controller.AlignViewController(this, viewport,
@@ -790,9 +795,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
         ap.av.getAlignment().padGaps();
       }
-      ap.av.updateConservation(ap);
-      ap.av.updateConsensus(ap);
-      ap.av.updateStrucConsensus(ap);
+      if (Jalview.getInstance().getStartCalculations())
+      {
+        ap.av.updateConservation(ap);
+        ap.av.updateConsensus(ap);
+        ap.av.updateStrucConsensus(ap);
+      }
     }
   }
 
@@ -923,10 +931,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     /*
      * Show/hide annotations only enabled if annotation panel is shown
      */
-    showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
-    hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
-    showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
-    hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
+    syncAnnotationMenuItems();
+
     viewBoxesMenuItem.setSelected(av.getShowBoxes());
     viewTextMenuItem.setSelected(av.getShowText());
     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
@@ -944,7 +950,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
-    autoCalculate.setSelected(av.autoCalculateConsensus);
+    autoCalculate.setSelected(av.getAutoCalculateConsensusAndConservation());
     sortByTree.setSelected(av.sortByTree);
     listenToViewSelections.setSelected(av.followSelection);
 
@@ -3294,13 +3300,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     final boolean setVisible = annotationPanelMenuItem.isSelected();
     viewport.setShowAnnotation(setVisible);
-    this.showAllSeqAnnotations.setEnabled(setVisible);
-    this.hideAllSeqAnnotations.setEnabled(setVisible);
-    this.showAllAlAnnotations.setEnabled(setVisible);
-    this.hideAllAlAnnotations.setEnabled(setVisible);
+    syncAnnotationMenuItems();
     alignPanel.updateLayout();
   }
 
+  private void syncAnnotationMenuItems()
+  {
+    final boolean setVisible = annotationPanelMenuItem.isSelected();
+    showAllSeqAnnotations.setEnabled(setVisible);
+    hideAllSeqAnnotations.setEnabled(setVisible);
+    showAllAlAnnotations.setEnabled(setVisible);
+    hideAllAlAnnotations.setEnabled(setVisible);
+  }
+
+
   @Override
   public void alignmentProperties()
   {
@@ -3366,7 +3379,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     Desktop.addInternalFrame(frame, MessageManager
             .formatMessage("label.overview_params", new Object[]
             { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
-            true, true);
+            true, true, "overview");
     frame.pack();
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
     frame.addInternalFrameListener(
@@ -3646,8 +3659,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void autoCalculate_actionPerformed(ActionEvent e)
   {
-    viewport.autoCalculateConsensus = autoCalculate.isSelected();
-    if (viewport.autoCalculateConsensus)
+    viewport.setAutoCalculateConsensusAndConservation(autoCalculate.isSelected());
+    if (viewport.getAutoCalculateConsensusAndConservation())
     {
       viewport.firePropertyChange("alignment", null,
               viewport.getAlignment().getSequences());
@@ -5787,6 +5800,67 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   }
 
+  /**
+   * BH 2019 from JalviewLite
+   * 
+   * get sequence feature groups that are hidden or shown
+   * 
+   * @param visible
+   *          true is visible
+   * @return list
+   */
+  public String[] getFeatureGroupsOfState(boolean visible)
+  {
+    jalview.api.FeatureRenderer fr = null;
+    if (alignPanel != null
+            && (fr = alignPanel
+                    .getFeatureRenderer()) != null)
+    {
+      List<String> gps = fr.getGroups(visible);
+      String[] _gps = gps.toArray(new String[gps.size()]);
+      return _gps;
+    }
+    return null;
+  }
+
+  public void scrollTo(int row, int column)
+  {
+    alignPanel.getSeqPanel().scrollTo(row, column);
+  }
+
+  public void scrollToRow(int row)
+  {
+    alignPanel.getSeqPanel().scrollToRow(row);
+  }
+
+  public void scrollToColumn(int column)
+  {
+    alignPanel.getSeqPanel().scrollToColumn(column);
+  }
+
+  /**
+   * 
+   * @return list of feature groups on the view
+   */
+  public String[] getFeatureGroups()
+  {
+    jalview.api.FeatureRenderer fr = null;
+    if (alignPanel != null
+            && (fr = alignPanel.getFeatureRenderer()) != null)
+    {
+      List<String> gps = fr.getFeatureGroups();
+      String[] _gps = gps.toArray(new String[gps.size()]);
+      return _gps;
+    }
+    return null;
+  }
+
+  public void select(SequenceGroup sel, ColumnSelection csel,
+          HiddenColumns hidden)
+  {
+    alignPanel.getSeqPanel().selection(sel, csel, hidden, null);
+  }
+
 }
 
 class PrintThread extends Thread