Merge branch 'Jalview-JS/develop' into merge_js_develop

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

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index bad2383..063e949 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;
@@ -234,6 +236,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
             alignPanel);
     viewport.updateConservation(alignPanel);
     viewport.updateConsensus(alignPanel);
+    viewport.initInformationWorker(alignPanel);
 
     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
     followMouseOverFlag.setState(viewport.isFollowHighlight());
@@ -880,7 +883,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }
     else if (source == autoCalculate)
     {
-      viewport.autoCalculateConsensus = autoCalculate.getState();
+      viewport.setAutoCalculateConsensusAndConservation(autoCalculate.getState());
     }
     else if (source == sortByTree)
     {
@@ -1202,7 +1205,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }
     else if (source == featureSettings)
     {
-      new FeatureSettings(alignPanel);
+      showFeatureSettingsUI();
     }
     else if (source == alProperties)
     {
@@ -1322,6 +1325,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       sortGroupMenuItem_actionPerformed();
     }
+    else if (source == sortEValueMenuItem)
+    {
+      sortEValueMenuItem_actionPerformed();
+    }
+    else if (source == sortBitScoreMenuItem)
+    {
+      sortBitScoreMenuItem_actionPerformed();
+    }
     else if (source == removeRedundancyMenuItem)
     {
       removeRedundancyMenuItem_actionPerformed();
@@ -1447,12 +1458,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       features = formatter.printJalviewFormat(
               viewport.getAlignment().getSequencesArray(),
-              alignPanel.getFeatureRenderer(), true);
+              alignPanel.getFeatureRenderer(), true, false);
     }
     else
     {
       features = formatter.printGffFormat(viewport.getAlignment()
-              .getSequencesArray(), alignPanel.getFeatureRenderer(), true);
+              .getSequencesArray(), alignPanel.getFeatureRenderer(), true,
+              false);
     }
 
     if (displayTextbox)
@@ -1569,7 +1581,7 @@ 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
@@ -1582,6 +1594,13 @@ 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;
   }
 
@@ -1691,8 +1710,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
                                           // viewport.getColumnSelection().getHiddenColumns()
                                           // != null;
     updateEditMenuBar();
-    originalSource.firePropertyChange("alignment", null,
-            originalSource.getAlignment().getSequences());
+    originalSource.notifyAlignment();
   }
 
   /**
@@ -1724,8 +1742,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
                                           // != null;
 
     updateEditMenuBar();
-    originalSource.firePropertyChange("alignment", null,
-            originalSource.getAlignment().getSequences());
+    originalSource.notifyAlignment();
   }
 
   AlignmentViewport getOriginatingSource(CommandI command)
@@ -2071,10 +2088,10 @@ 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());
+    viewport.notifyAlignment();
 
   }
 
@@ -2148,8 +2165,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     viewport.setSelectionGroup(null);
     viewport.getAlignment().deleteGroup(sg);
 
-    viewport.firePropertyChange("alignment", null,
-            viewport.getAlignment().getSequences());
+    viewport.notifyAlignment();
 
     if (viewport.getAlignment().getHeight() < 1)
     {
@@ -2361,7 +2377,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         }
       }
 
-      viewport.firePropertyChange("alignment", null, al.getSequences());
+      viewport.notifyAlignment();
     }
   }
 
@@ -2405,7 +2421,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     // if (viewport.hasHiddenColumns)
     // viewport.getColumnSelection().compensateForEdits(shifts);
     ranges.setStartRes(seq.findIndex(startRes) - 1);
-    viewport.firePropertyChange("alignment", null, al.getSequences());
+    viewport.notifyAlignment();
 
   }
 
@@ -2439,7 +2455,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
     ranges.setStartRes(seq.findIndex(startRes) - 1);
 
-    viewport.firePropertyChange("alignment", null, al.getSequences());
+    viewport.notifyAlignment();
 
   }
 
@@ -2763,6 +2779,26 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   }
 
+  public void sortEValueMenuItem_actionPerformed()
+  {
+    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+    AlignmentSorter.sortByEValue(viewport.getAlignment());
+    addHistoryItem(new OrderCommand("Group Sort", oldOrder,
+            viewport.getAlignment()));
+    alignPanel.paintAlignment(true, false);
+
+  }
+
+  public void sortBitScoreMenuItem_actionPerformed()
+  {
+    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+    AlignmentSorter.sortByBitScore(viewport.getAlignment());
+    addHistoryItem(new OrderCommand("Group Sort", oldOrder,
+            viewport.getAlignment()));
+    alignPanel.paintAlignment(true, false);
+
+  }
+
   public void removeRedundancyMenuItem_actionPerformed()
   {
     new RedundancyPanel(alignPanel);
@@ -3113,6 +3149,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   MenuItem sortGroupMenuItem = new MenuItem();
 
+  MenuItem sortEValueMenuItem = new MenuItem();
+
+  MenuItem sortBitScoreMenuItem = new MenuItem();
+
   MenuItem removeRedundancyMenuItem = new MenuItem();
 
   MenuItem pairwiseAlignmentMenuItem = new MenuItem();
@@ -4329,4 +4369,24 @@ 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;
+  }
+
 }