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

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

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 5ad212e..062dbf8 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -25,6 +25,7 @@ import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.analysis.TreeBuilder;
 import jalview.analysis.scoremodels.PIDModel;
 import jalview.analysis.scoremodels.ScoreModels;
+import jalview.api.AlignFrameI;
 import jalview.api.AlignViewControllerGuiI;
 import jalview.api.AlignViewControllerI;
 import jalview.api.AlignViewportI;
@@ -118,7 +119,8 @@ import java.util.Vector;
 
 import org.jmol.viewer.Viewer;
 
-public class AlignFrame extends EmbmenuFrame implements ActionListener,
+public class AlignFrame extends EmbmenuFrame implements AlignFrameI,
+        ActionListener,
         ItemListener, KeyListener, AlignViewControllerGuiI
 {
   public AlignViewControllerI avc;
@@ -416,7 +418,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         viewport.featureSettings.refreshTable();
       }
       alignPanel.paintAlignment(true, true);
-      statusBar.setText(MessageManager
+      setStatus(MessageManager
               .getString("label.successfully_added_features_alignment"));
     }
     return featuresFile;
@@ -574,7 +576,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
     case KeyEvent.VK_F2:
       viewport.cursorMode = !viewport.cursorMode;
-      statusBar.setText(MessageManager
+      setStatus(MessageManager
               .formatMessage("label.keyboard_editing_mode", new String[]
               { (viewport.cursorMode ? "on" : "off") }));
       if (viewport.cursorMode)
@@ -880,7 +882,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }
     else if (source == autoCalculate)
     {
-      viewport.autoCalculateConsensus = autoCalculate.getState();
+      viewport.setAutoCalculateConsensusAndConservation(autoCalculate.getState());
     }
     else if (source == sortByTree)
     {
@@ -1447,14 +1449,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       features = formatter.printJalviewFormat(
               viewport.getAlignment().getSequencesArray(),
-              getDisplayedFeatureCols(), null, getDisplayedFeatureGroups(),
-              true);
+              alignPanel.getFeatureRenderer(), true);
     }
     else
     {
       features = formatter.printGffFormat(viewport.getAlignment()
-              .getSequencesArray(), getDisplayedFeatureCols(),
-              getDisplayedFeatureGroups(), true);
+              .getSequencesArray(), alignPanel.getFeatureRenderer(), true);
     }
 
     if (displayTextbox)
@@ -2073,7 +2073,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
             seqs, 0, viewport.getAlignment().getWidth(),
             viewport.getAlignment()));
 
-    viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight());
+    viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight() - 1); // BH
+                                                                             // 2019.04.18
     viewport.getAlignment().getWidth();
     viewport.firePropertyChange("alignment", null,
             viewport.getAlignment().getSequences());
@@ -2349,7 +2350,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
                 column, al);
       }
 
-      statusBar.setText(MessageManager
+      setStatus(MessageManager
               .formatMessage("label.removed_columns", new String[]
               { Integer.valueOf(trimRegion.getSize()).toString() }));
       addHistoryItem(trimRegion);
@@ -2393,7 +2394,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
     addHistoryItem(removeGapCols);
 
-    statusBar.setText(MessageManager
+    setStatus(MessageManager
             .formatMessage("label.removed_empty_columns", new String[]
             { Integer.valueOf(removeGapCols.getSize()).toString() }));
 
@@ -3815,7 +3816,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
      */
     statusBar.setBackground(Color.white);
     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
-    statusBar.setText(MessageManager.getString("label.status_bar"));
+    setStatus(MessageManager.getString("label.status_bar"));
     this.add(statusBar, BorderLayout.SOUTH);
   }
 
@@ -4183,7 +4184,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }
     else
     {
-      new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
+      new mc_view.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
     }
 
   }