JAL-984 merged to spikes-mungo

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 0f801eb..3f5aa94 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -1344,7 +1344,7 @@ label.filters = Filters
 label.join_conditions = Join conditions with
 label.score = Score
 label.colour_by_label = Colour by label
-label.variable_colour = Variable colour
+label.variable_colour = Variable colour...
 label.select_colour = Select colour
 option.enable_disable_autosearch = When ticked, search is performed automatically
 option.autosearch = Autosearch

diff --git a/resources/lang/Messages_es.properties b/resources/lang/Messages_es.properties
index d035e73..e42d6b8 100644 (file)
--- a/resources/lang/Messages_es.properties
+++ b/resources/lang/Messages_es.properties
@@ -1345,7 +1345,7 @@ label.filters = Filtros
 label.join_conditions = Combinar condiciones con
 label.score = Puntuación
 label.colour_by_label = Colorear por texto
-label.variable_colour = Color variable
+label.variable_colour = Color variable...
 label.select_colour = Seleccionar color
 option.enable_disable_autosearch = Marcar para buscar automáticamente
 option.autosearch = Auto búsqueda

diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java
index d8f65a5..c049326 100755 (executable)
--- a/src/jalview/appletgui/AnnotationLabels.java
+++ b/src/jalview/appletgui/AnnotationLabels.java
@@ -31,6 +31,7 @@ import jalview.util.ParseHtmlBodyAndLinks;
 import java.awt.Checkbox;
 import java.awt.CheckboxMenuItem;
 import java.awt.Color;
+import java.awt.Cursor;
 import java.awt.Dimension;
 import java.awt.FlowLayout;
 import java.awt.FontMetrics;
@@ -269,6 +270,8 @@ public class AnnotationLabels extends Panel
   public void mouseMoved(MouseEvent evt)
   {
     resizePanel = evt.getY() < 10 && evt.getX() < 14;
+    setCursor(Cursor.getPredefinedCursor(
+            resizePanel ? Cursor.S_RESIZE_CURSOR : Cursor.DEFAULT_CURSOR));
     int row = getSelectedRow(evt.getY() + scrollOffset);
 
     if (row > -1)
@@ -406,6 +409,7 @@ public class AnnotationLabels extends Panel
     resizePanel = false;
     dragEvent = null;
     dragCancelled = false;
+    setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
     repaint();
     ap.annotationPanel.repaint();
   }
@@ -418,6 +422,8 @@ public class AnnotationLabels extends Panel
       resizePanel = true;
       repaint();
     }
+    setCursor(Cursor.getPredefinedCursor(
+            resizePanel ? Cursor.S_RESIZE_CURSOR : Cursor.DEFAULT_CURSOR));
   }
 
   @Override
@@ -905,10 +911,10 @@ public class AnnotationLabels extends Panel
     g.translate(0, +scrollOffset);
     if (resizePanel)
     {
-      g.setColor(Color.red);
-      g.setPaintMode();
-      g.drawLine(2, 8, 5, 2);
-      g.drawLine(5, 2, 8, 8);
+      // g.setColor(Color.red);
+      // g.setPaintMode();
+      // g.drawLine(2, 8, 5, 2);
+      // g.drawLine(5, 2, 8, 8);
     }
     else if (!dragCancelled && dragEvent != null && aa != null)
     {

diff --git a/src/jalview/appletgui/IdwidthAdjuster.java b/src/jalview/appletgui/IdwidthAdjuster.java
index 75e3243..e9722fe 100755 (executable)
--- a/src/jalview/appletgui/IdwidthAdjuster.java
+++ b/src/jalview/appletgui/IdwidthAdjuster.java
@@ -20,7 +20,7 @@
  */
 package jalview.appletgui;
 
-import java.awt.Color;
+import java.awt.Cursor;
 import java.awt.Dimension;
 import java.awt.Graphics;
 import java.awt.Image;
@@ -54,11 +54,13 @@ public class IdwidthAdjuster extends Panel
     addMouseMotionListener(this);
   }
 
+  @Override
   public void mousePressed(MouseEvent evt)
   {
     oldX = evt.getX();
   }
 
+  @Override
   public void mouseReleased(MouseEvent evt)
   {
     active = false;
@@ -85,18 +87,24 @@ public class IdwidthAdjuster extends Panel
     // }
   }
 
+  @Override
   public void mouseEntered(MouseEvent evt)
   {
     active = true;
+    setCursor(Cursor.getPredefinedCursor(Cursor.W_RESIZE_CURSOR));
+
     repaint();
   }
 
+  @Override
   public void mouseExited(MouseEvent evt)
   {
     active = false;
+    setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
     repaint();
   }
 
+  @Override
   public void mouseDragged(MouseEvent evt)
   {
     active = true;
@@ -112,25 +120,28 @@ public class IdwidthAdjuster extends Panel
     }
   }
 
+  @Override
   public void mouseMoved(MouseEvent evt)
   {
   }
 
+  @Override
   public void mouseClicked(MouseEvent evt)
   {
   }
 
+  @Override
   public void paint(Graphics g)
   {
-    g.setColor(Color.white);
-    g.fillRect(0, 0, getSize().width, getSize().height);
-    if (active)
-    {
-      if (image != null)
-      {
-        g.drawImage(image, getSize().width - 20, 2, this);
-      }
-    }
+    // g.setColor(Color.white);
+    // g.fillRect(0, 0, getSize().width, getSize().height);
+    // if (active)
+    // {
+    // if (image != null)
+    // {
+    // g.drawImage(image, getSize().width - 20, 2, this);
+    // }
+    // }
   }
 
 }

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index de69907..4e181b3 100755 (executable)
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.analysis.AlignSeq;
 import jalview.analysis.AlignmentUtils;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
@@ -29,9 +30,12 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.io.FileFormat;
 import jalview.io.FormatAdapter;
+import jalview.util.Comparison;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 
 import java.awt.Color;
+import java.awt.Cursor;
 import java.awt.Dimension;
 import java.awt.Font;
 import java.awt.FontMetrics;
@@ -62,63 +66,71 @@ import javax.swing.SwingUtilities;
 import javax.swing.ToolTipManager;
 
 /**
- * DOCUMENT ME!
- * 
- * @author $author$
- * @version $Revision$
+ * The panel that holds the labels for alignment annotations, providing
+ * tooltips, context menus, drag to reorder rows, and drag to adjust panel
+ * height
  */
 public class AnnotationLabels extends JPanel
         implements MouseListener, MouseMotionListener, ActionListener
 {
+  // width in pixels within which height adjuster arrows are shown and active
+  private static final int HEIGHT_ADJUSTER_WIDTH = 50;
+
   private static final Pattern LEFT_ANGLE_BRACKET_PATTERN = Pattern
           .compile("<");
 
-  String TOGGLE_LABELSCALE = MessageManager
+  private static final Font font = new Font("Arial", Font.PLAIN, 11);
+
+  private static final String TOGGLE_LABELSCALE = MessageManager
           .getString("label.scale_label_to_column");
 
-  String ADDNEW = MessageManager.getString("label.add_new_row");
+  private static final String ADDNEW = MessageManager
+          .getString("label.add_new_row");
 
-  String EDITNAME = MessageManager
+  private static final String EDITNAME = MessageManager
           .getString("label.edit_label_description");
 
-  String HIDE = MessageManager.getString("label.hide_row");
+  private static final String HIDE = MessageManager
+          .getString("label.hide_row");
 
-  String DELETE = MessageManager.getString("label.delete_row");
+  private static final String DELETE = MessageManager
+          .getString("label.delete_row");
 
-  String SHOWALL = MessageManager.getString("label.show_all_hidden_rows");
+  private static final String SHOWALL = MessageManager
+          .getString("label.show_all_hidden_rows");
 
-  String OUTPUT_TEXT = MessageManager.getString("label.export_annotation");
+  private static final String OUTPUT_TEXT = MessageManager
+          .getString("label.export_annotation");
 
-  String COPYCONS_SEQ = MessageManager
+  private static final String COPYCONS_SEQ = MessageManager
           .getString("label.copy_consensus_sequence");
 
-  boolean resizePanel = false;
+  private static Image adjusterImage;
 
-  Image image;
+  private static int adjusterImageHeight;
 
-  AlignmentPanel ap;
+  private final boolean debugRedraw = false;
 
-  AlignViewport av;
+  private AlignmentPanel ap;
 
-  boolean resizing = false;
+  AlignViewport av;
 
-  MouseEvent dragEvent;
+  private MouseEvent dragEvent;
 
-  int oldY;
+  private int oldY;
 
-  int selectedRow;
+  private int selectedRow;
 
   private int scrollOffset = 0;
 
-  Font font = new Font("Arial", Font.PLAIN, 11);
-
   private boolean hasHiddenRows;
 
+  private boolean resizePanel = false;
+
   /**
-   * Creates a new AnnotationLabels object.
+   * Creates a new AnnotationLabels object
    * 
    * @param ap
-   *          DOCUMENT ME!
    */
   public AnnotationLabels(AlignmentPanel ap)
   {
@@ -126,12 +138,32 @@ public class AnnotationLabels extends JPanel
     av = ap.av;
     ToolTipManager.sharedInstance().registerComponent(this);
 
+    if (adjusterImage == null)
+    {
+      loadAdjusterImage();
+    }
+
+    addMouseListener(this);
+    addMouseMotionListener(this);
+    addMouseWheelListener(ap.getAnnotationPanel());
+  }
+
+  public AnnotationLabels(AlignViewport av)
+  {
+    this.av = av;
+  }
+
+  /**
+   * Loads the gif for the panel height adjustment
+   */
+  protected void loadAdjusterImage()
+  {
     java.net.URL url = getClass().getResource("/images/idwidth.gif");
     Image temp = null;
 
     if (url != null)
     {
-      temp = java.awt.Toolkit.getDefaultToolkit().createImage(url);
+      temp = Toolkit.getDefaultToolkit().createImage(url);
     }
 
     try
@@ -148,16 +180,8 @@ public class AnnotationLabels extends JPanel
     Graphics2D g = (Graphics2D) bi.getGraphics();
     g.rotate(Math.toRadians(90));
     g.drawImage(temp, 0, -bi.getWidth(this), this);
-    image = bi;
-
-    addMouseListener(this);
-    addMouseMotionListener(this);
-    addMouseWheelListener(ap.getAnnotationPanel());
-  }
-
-  public AnnotationLabels(AlignViewport av)
-  {
-    this.av = av;
+    adjusterImage = bi;
+    adjusterImageHeight = bi.getHeight();
   }
 
   /**
@@ -605,10 +629,9 @@ public class AnnotationLabels extends JPanel
   }
 
   /**
-   * DOCUMENT ME!
+   * Reorders annotation rows after a drag of a label
    * 
    * @param evt
-   *          DOCUMENT ME!
    */
   @Override
   public void mouseReleased(MouseEvent evt)
@@ -623,6 +646,9 @@ public class AnnotationLabels extends JPanel
     getSelectedRow(evt.getY() - getScrollOffset());
     int end = selectedRow;
 
+    /*
+     * if dragging to resize instead, start == end
+     */
     if (start != end)
     {
       // Swap these annotations
@@ -646,31 +672,13 @@ public class AnnotationLabels extends JPanel
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param evt
-   *          DOCUMENT ME!
-   */
-  @Override
-  public void mouseEntered(MouseEvent evt)
-  {
-    if (evt.getY() < 10)
-    {
-      resizePanel = true;
-      repaint();
-    }
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param evt
-   *          DOCUMENT ME!
+   * Removes the height adjuster image on leaving the panel, unless currently
+   * dragging it
    */
   @Override
   public void mouseExited(MouseEvent evt)
   {
-    if (dragEvent == null)
+    if (resizePanel && dragEvent == null)
     {
       resizePanel = false;
       repaint();
@@ -678,10 +686,11 @@ public class AnnotationLabels extends JPanel
   }
 
   /**
-   * DOCUMENT ME!
+   * A mouse drag may be either an adjustment of the panel height (if flag
+   * resizePanel is set on), or a reordering of the annotation rows. The former
+   * is dealt with by this method, the latter in mouseReleased.
    * 
    * @param evt
-   *          DOCUMENT ME!
    */
   @Override
   public void mouseDragged(MouseEvent evt)
@@ -715,15 +724,14 @@ public class AnnotationLabels extends JPanel
   }
 
   /**
-   * DOCUMENT ME!
+   * Updates the tooltip as the mouse moves over the labels
    * 
    * @param evt
-   *          DOCUMENT ME!
    */
   @Override
   public void mouseMoved(MouseEvent evt)
   {
-    resizePanel = evt.getY() < 10;
+    showOrHideAdjuster(evt);
 
     getSelectedRow(evt.getY() - getScrollOffset());
 
@@ -799,6 +807,26 @@ public class AnnotationLabels extends JPanel
     }
   }
 
+  /**
+   * Shows the height adjuster image if the mouse moves into the top left
+   * region, or hides it if the mouse leaves the regio
+   * 
+   * @param evt
+   */
+  protected void showOrHideAdjuster(MouseEvent evt)
+  {
+    boolean was = resizePanel;
+    resizePanel = evt.getY() < adjusterImageHeight && evt.getX() < HEIGHT_ADJUSTER_WIDTH;
+
+    if (resizePanel != was)
+    {
+      setCursor(Cursor.getPredefinedCursor(
+              resizePanel ? Cursor.S_RESIZE_CURSOR
+                      : Cursor.DEFAULT_CURSOR));
+      repaint();
+    }
+  }
+
   @Override
   public void mouseClicked(MouseEvent evt)
   {
@@ -818,11 +846,9 @@ public class AnnotationLabels extends JPanel
             // process modifiers
             SequenceGroup sg = ap.av.getSelectionGroup();
             if (sg == null || sg == aa[selectedRow].groupRef
-                    || !(jalview.util.Platform.isControlDown(evt)
-                            || evt.isShiftDown()))
+                    || !(Platform.isControlDown(evt) || evt.isShiftDown()))
             {
-              if (jalview.util.Platform.isControlDown(evt)
-                      || evt.isShiftDown())
+              if (Platform.isControlDown(evt) || evt.isShiftDown())
               {
                 // clone a new selection group from the associated group
                 ap.av.setSelectionGroup(
@@ -881,8 +907,7 @@ public class AnnotationLabels extends JPanel
               // we make a copy rather than edit the current selection if no
               // modifiers pressed
               // see Enhancement JAL-1557
-              if (!(jalview.util.Platform.isControlDown(evt)
-                      || evt.isShiftDown()))
+              if (!(Platform.isControlDown(evt) || evt.isShiftDown()))
               {
                 sg = new SequenceGroup(sg);
                 sg.clear();
@@ -890,7 +915,7 @@ public class AnnotationLabels extends JPanel
               }
               else
               {
-                if (jalview.util.Platform.isControlDown(evt))
+                if (Platform.isControlDown(evt))
                 {
                   sg.addOrRemove(aa[selectedRow].sequenceRef, true);
                 }
@@ -935,8 +960,8 @@ public class AnnotationLabels extends JPanel
     if (dseqs[0] == null)
     {
       dseqs[0] = new Sequence(sq);
-      dseqs[0].setSequence(jalview.analysis.AlignSeq.extractGaps(
-              jalview.util.Comparison.GapChars, sq.getSequenceAsString()));
+      dseqs[0].setSequence(AlignSeq.extractGaps(Comparison.GapChars,
+              sq.getSequenceAsString()));
 
       sq.setDatasetSequence(dseqs[0]);
     }
@@ -1018,8 +1043,6 @@ public class AnnotationLabels extends JPanel
     drawComponent(g, false, width);
   }
 
-  private final boolean debugRedraw = false;
-
   /**
    * Draw the full set of annotation Labels for the alignment at the given
    * cursor
@@ -1204,7 +1227,7 @@ public class AnnotationLabels extends JPanel
 
     if (resizePanel)
     {
-      g.drawImage(image, 2, 0 - getScrollOffset(), this);
+      // g.drawImage(adjusterImage, 2, 0 - getScrollOffset(), this);
     }
     else if (dragEvent != null && aa != null)
     {
@@ -1225,4 +1248,9 @@ public class AnnotationLabels extends JPanel
   {
     return scrollOffset;
   }
+
+  @Override
+  public void mouseEntered(MouseEvent e)
+  {
+  }
 }

diff --git a/src/jalview/gui/IdwidthAdjuster.java b/src/jalview/gui/IdwidthAdjuster.java
index 8400543..99792c6 100755 (executable)
--- a/src/jalview/gui/IdwidthAdjuster.java
+++ b/src/jalview/gui/IdwidthAdjuster.java
@@ -23,6 +23,7 @@ package jalview.gui;
 import jalview.api.AlignViewportI;
 
 import java.awt.Color;
+import java.awt.Cursor;
 import java.awt.Graphics;
 import java.awt.Image;
 import java.awt.event.MouseEvent;
@@ -198,7 +199,12 @@ public class IdwidthAdjuster extends JPanel
     {
       if (image != null)
       {
-        g.drawImage(image, getWidth() - 20, 2, this);
+        // g.drawImage(image, getWidth() - 20, 2, this);
+        setCursor(Cursor.getPredefinedCursor(Cursor.W_RESIZE_CURSOR));
+      }
+      else
+      {
+        setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
       }
     }
   }

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 97d051b..0cf7ef4 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -550,24 +550,27 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       {
         desc = String.format("%s %d-%d", sf.getType(), start, end);
       }
+      String tooltip = desc;
       String description = sf.getDescription();
       if (description != null)
       {
         description = StringUtils.stripHtmlTags(description);
-        if (description.length() <= 6)
+        if (description.length() > 12)
         {
-          desc = desc + " " + description;
+          desc = desc + " " + description.substring(0, 12) + "..";
         }
         else
         {
-          desc = desc + " " + description.substring(0, 6) + "..";
+          desc = desc + " " + description;
         }
+        tooltip = tooltip + " " + description;
       }
       if (sf.getFeatureGroup() != null)
       {
-        desc = desc + " (" + sf.getFeatureGroup() + ")";
+        tooltip = tooltip + (" (" + sf.getFeatureGroup() + ")");
       }
       JMenuItem item = new JMenuItem(desc);
+      item.setToolTipText(tooltip);
       item.addActionListener(new ActionListener()
       {
         @Override