Merge branch 'feature/JAL-3551Pymol' into develop

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

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 8740f51..0fd0945 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -95,6 +95,7 @@ import java.awt.Menu;
 import java.awt.MenuBar;
 import java.awt.MenuItem;
 import java.awt.Panel;
+import java.awt.Rectangle;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.FocusEvent;
@@ -106,6 +107,7 @@ import java.awt.event.KeyListener;
 import java.awt.event.WindowAdapter;
 import java.awt.event.WindowEvent;
 import java.io.IOException;
+import java.io.UnsupportedEncodingException;
 import java.net.URL;
 import java.net.URLEncoder;
 import java.util.Arrays;
@@ -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)
@@ -1202,7 +1204,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }
     else if (source == featureSettings)
     {
-      new FeatureSettings(alignPanel);
+      showFeatureSettingsUI();
     }
     else if (source == alProperties)
     {
@@ -1447,14 +1449,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       features = formatter.printJalviewFormat(
               viewport.getAlignment().getSequencesArray(),
-              getDisplayedFeatureCols(), null, getDisplayedFeatureGroups(),
-              true);
+              alignPanel.getFeatureRenderer(), true, false);
     }
     else
     {
       features = formatter.printGffFormat(viewport.getAlignment()
-              .getSequencesArray(), getDisplayedFeatureCols(),
-              getDisplayedFeatureGroups(), true);
+              .getSequencesArray(), alignPanel.getFeatureRenderer(), true,
+              false);
     }
 
     if (displayTextbox)
@@ -1571,7 +1572,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     try
     {
       new URL(url);
-      url = URLEncoder.encode(url);
+      url = URLEncoder.encode(url, "UTF-8");
     }
     /*
      * When we finally deprecate 1.1 compatibility, we can start to use
@@ -1584,6 +1585,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       url = viewport.applet.getCodeBase() + url;
     }
+    catch (UnsupportedEncodingException ex)
+    {
+      System.err.println(
+              "WARNING = IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "
+                      + url);
+      ex.printStackTrace();
+    }
     return url;
   }
 
@@ -2073,7 +2081,8 @@ 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 +2358,7 @@ 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 +2402,7 @@ 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 +3824,7 @@ 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);
   }
 
@@ -3955,7 +3964,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
    * without an additional javascript library to exchange messages between the
    * distinct applets. See http://issues.jalview.org/browse/JAL-621
    * 
-   * @param viewer
+   * @param jmolViewer
    *          JmolViewer instance
    * @param sequenceIds
    *          - sequence Ids to search for associations
@@ -4331,4 +4340,24 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     return alignPanel.av.featureSettings;
   }
 
+  @Override
+  public FeatureSettingsControllerI showFeatureSettingsUI()
+  {
+    return new FeatureSettings(alignPanel);
+  }
+
+  private Rectangle fs_bounds = null;
+
+  @Override
+  public void setFeatureSettingsGeometry(Rectangle bounds)
+  {
+    fs_bounds = bounds;
+  }
+
+  @Override
+  public Rectangle getFeatureSettingsGeometry()
+  {
+    return fs_bounds;
+  }
+
 }