X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=4ead210a6f4b778975db4bf191e190ae0579b62c;hb=5159fba45b219bdf320e78091db53486e782bb39;hp=db531a0dfca83ff30dbf455bc40eb31d7cfd7084;hpb=14208707a204bf8f7f2f714eebfdfd937094b943;p=jalview.git

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index db531a0..4ead210 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -21,10 +21,12 @@
 package jalview.gui;
 
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SequenceI;
+import jalview.gui.JalviewColourChooser.ColourChooserListener;
 import jalview.renderer.AnnotationRenderer;
 import jalview.renderer.AwtRenderPanelI;
 import jalview.schemes.ResidueProperties;
@@ -58,7 +60,6 @@ import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
 
-import javax.swing.JColorChooser;
 import javax.swing.JMenuItem;
 import javax.swing.JPanel;
 import javax.swing.JPopupMenu;
@@ -76,6 +77,11 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         MouseListener, MouseWheelListener, MouseMotionListener,
         ActionListener, AdjustmentListener, Scrollable, ViewportListenerI
 {
+  enum DragMode
+  {
+    Select, Resize, Undefined
+  };
+
   String HELIX = MessageManager.getString("label.helix");
 
   String SHEET = MessageManager.getString("label.sheet");
@@ -108,7 +114,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
   public volatile BufferedImage fadedImage;
 
-  Graphics2D gg;
+  // private Graphics2D gg;
 
   public FontMetrics fm;
 
@@ -119,11 +125,11 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   // Used For mouse Dragging and resizing graphs
   int graphStretch = -1;
 
-  int graphStretchY = -1;
+  int mouseDragLastX = -1;
 
-  int min; // used by mouseDragged to see if user
+  int mouseDragLastY = -1;
 
-  int max; // used by mouseDragged to see if user
+  DragMode dragMode = DragMode.Undefined;
 
   boolean mouseDragging = false;
 
@@ -309,7 +315,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     else if (action.equals(LABEL))
     {
       String exMesg = collectAnnotVals(anot, LABEL);
-      String label = JvOptionPane.showInputDialog(this,
+      String label = JvOptionPane.showInputDialog(
               MessageManager.getString("label.enter_label"), exMesg);
 
       if (label == null)
@@ -341,24 +347,29 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     }
     else if (action.equals(COLOUR))
     {
-      Color col = JColorChooser.showDialog(this,
-              MessageManager.getString("label.select_foreground_colour"),
-              Color.black);
-
-      for (int index : av.getColumnSelection().getSelected())
+      final Annotation[] fAnot = anot;
+      String title = MessageManager
+              .getString("label.select_foreground_colour");
+      ColourChooserListener listener = new ColourChooserListener()
       {
-        if (!av.getAlignment().getHiddenColumns().isVisible(index))
+        @Override
+        public void colourSelected(Color c)
         {
-          continue;
-        }
-
-        if (anot[index] == null)
-        {
-          anot[index] = new Annotation("", "", ' ', 0);
-        }
-
-        anot[index].colour = col;
-      }
+          HiddenColumns hiddenColumns = av.getAlignment().getHiddenColumns();
+          for (int index : av.getColumnSelection().getSelected())
+          {
+            if (hiddenColumns.isVisible(index))
+            {
+              if (fAnot[index] == null)
+              {
+                fAnot[index] = new Annotation("", "", ' ', 0);
+              }
+              fAnot[index].colour = c;
+            }
+        }};
+      };
+      JalviewColourChooser.showColourChooser(this,
+              title, Color.black, listener);
     }
     else
     // HELIX, SHEET or STEM
@@ -499,10 +510,11 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   }
 
   /**
-   * DOCUMENT ME!
+   * Action on right mouse pressed on Mac is to show a pop-up menu for the
+   * annotation. Action on left mouse pressed is to find which annotation is
+   * pressed and mark the start of a column selection or graph resize operation.
    * 
    * @param evt
-   *          DOCUMENT ME!
    */
   @Override
   public void mousePressed(MouseEvent evt)
@@ -513,7 +525,13 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     {
       return;
     }
+    mouseDragLastX = evt.getX();
+    mouseDragLastY = evt.getY();
 
+    /*
+     * add visible annotation heights until we reach the y
+     * position, to find which annotation it is in
+     */
     int height = 0;
     activeRow = -1;
 
@@ -533,11 +551,11 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         }
         else if (aa[i].graph > 0)
         {
-          // Stretch Graph
+          /*
+           * we have clicked on a resizable graph annotation
+           */
           graphStretch = i;
-          graphStretchY = y;
         }
-
         break;
       }
     }
@@ -603,17 +621,20 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   }
 
   /**
-   * DOCUMENT ME!
+   * Action on mouse up is to clear mouse drag data and call mouseReleased on
+   * ScalePanel, to deal with defining the selection group (if any) defined by
+   * the mouse drag
    * 
    * @param evt
-   *          DOCUMENT ME!
    */
   @Override
   public void mouseReleased(MouseEvent evt)
   {
     graphStretch = -1;
-    graphStretchY = -1;
+    mouseDragLastX = -1;
+    mouseDragLastY = -1;
     mouseDragging = false;
+    dragMode = DragMode.Undefined;
     ap.getScalePanel().mouseReleased(evt);
 
     /*
@@ -636,14 +657,15 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   @Override
   public void mouseEntered(MouseEvent evt)
   {
+    this.mouseDragging = false;
     ap.getScalePanel().mouseEntered(evt);
   }
 
   /**
-   * DOCUMENT ME!
+   * On leaving the panel, calls ScalePanel.mouseExited to deal with scrolling
+   * with column selection on a mouse drag
    * 
    * @param evt
-   *          DOCUMENT ME!
    */
   @Override
   public void mouseExited(MouseEvent evt)
@@ -660,24 +682,73 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   @Override
   public void mouseDragged(MouseEvent evt)
   {
-    if (graphStretch > -1)
+    /*
+     * todo: if dragMode is Undefined:
+     * - set to Select if dx > dy
+     * - set to Resize if dy > dx
+     * - do nothing if dx == dy
+     */
+    final int x = evt.getX();
+    final int y = evt.getY();
+    if (dragMode == DragMode.Undefined)
     {
-      av.getAlignment()
-              .getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY
-                      - evt.getY();
-      if (av.getAlignment()
-              .getAlignmentAnnotation()[graphStretch].graphHeight < 0)
+      int dx = Math.abs(x - mouseDragLastX);
+      int dy = Math.abs(y - mouseDragLastY);
+      if (graphStretch == -1 || dx > dy)
       {
-        av.getAlignment()
-                .getAlignmentAnnotation()[graphStretch].graphHeight = 0;
+        /*
+         * mostly horizontal drag, or not a graph annotation
+         */
+        dragMode = DragMode.Select;
+      }
+      else if (dy > dx)
+      {
+        /*
+         * mostly vertical drag
+         */
+        dragMode = DragMode.Resize;
       }
-      graphStretchY = evt.getY();
-      adjustPanelHeight();
-      ap.paintAlignment(false, false);
     }
-    else
+
+    if (dragMode == DragMode.Undefined)
     {
-      ap.getScalePanel().mouseDragged(evt);
+      /*
+       * drag is diagonal - defer deciding whether to
+       * treat as up/down or left/right
+       */
+      return;
+    }
+
+    try
+    {
+      if (dragMode == DragMode.Resize)
+      {
+        /*
+         * resize graph annotation if mouse was dragged up or down
+         */
+        int deltaY = mouseDragLastY - evt.getY();
+        if (deltaY != 0)
+        {
+          AlignmentAnnotation graphAnnotation = av.getAlignment()
+                  .getAlignmentAnnotation()[graphStretch];
+          int newHeight = Math.max(0, graphAnnotation.graphHeight + deltaY);
+          graphAnnotation.graphHeight = newHeight;
+          adjustPanelHeight();
+          ap.paintAlignment(false, false);
+        }
+      }
+      else
+      {
+        /*
+         * for mouse drag left or right, delegate to 
+         * ScalePanel to adjust the column selection
+         */
+        ap.getScalePanel().mouseDragged(evt);
+      }
+    } finally
+    {
+      mouseDragLastX = x;
+      mouseDragLastY = y;
     }
   }
 
@@ -690,30 +761,10 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   @Override
   public void mouseMoved(MouseEvent evt)
   {
+    int yPos = evt.getY();
     AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
 
-    if (aa == null)
-    {
-      this.setToolTipText(null);
-      return;
-    }
-
-    int row = -1;
-    int height = 0;
-
-    for (int i = 0; i < aa.length; i++)
-    {
-      if (aa[i].visible)
-      {
-        height += aa[i].height;
-      }
-
-      if (evt.getY() < height)
-      {
-        row = i;
-        break;
-      }
-    }
+    int row = getRowIndex(yPos, aa);
 
     if (row == -1)
     {
@@ -735,26 +786,63 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     if (row > -1 && ann.annotations != null
             && column < ann.annotations.length)
     {
-      buildToolTip(ann, column, aa);
-      setStatusMessage(column, ann);
+      setToolTipText(buildToolTip(ann, column, aa));
+      String msg = getStatusMessage(av.getAlignment(), column, ann);
+      ap.alignFrame.setStatus(msg);
     }
     else
     {
       this.setToolTipText(null);
-      ap.alignFrame.statusBar.setText(" ");
+      ap.alignFrame.setStatus(" ");
     }
   }
 
   /**
-   * Builds a tooltip for the annotation at the current mouse position.
+   * Answers the index in the annotations array of the visible annotation at the
+   * given y position. This is done by adding the heights of visible annotations
+   * until the y position has been exceeded. Answers -1 if no annotations are
+   * visible, or the y position is below all annotations.
+   * 
+   * @param yPos
+   * @param aa
+   * @return
+   */
+  static int getRowIndex(int yPos, AlignmentAnnotation[] aa)
+  {
+    if (aa == null)
+    {
+      return -1;
+    }
+    int row = -1;
+    int height = 0;
+
+    for (int i = 0; i < aa.length; i++)
+    {
+      if (aa[i].visible)
+      {
+        height += aa[i].height;
+      }
+
+      if (height > yPos)
+      {
+        row = i;
+        break;
+      }
+    }
+    return row;
+  }
+
+  /**
+   * Answers a tooltip for the annotation at the current mouse position
    * 
    * @param ann
    * @param column
    * @param anns
    */
-  void buildToolTip(AlignmentAnnotation ann, int column,
+  static String buildToolTip(AlignmentAnnotation ann, int column,
           AlignmentAnnotation[] anns)
   {
+    String tooltip = null;
     if (ann.graphGroup > -1)
     {
       StringBuilder tip = new StringBuilder(32);
@@ -776,35 +864,39 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       if (tip.length() != 6)
       {
         tip.setLength(tip.length() - 4);
-        this.setToolTipText(tip.toString() + "</html>");
+        tooltip = tip.toString() + "</html>";
       }
     }
-    else if (ann.annotations[column] != null)
+    else if (column < ann.annotations.length
+            && ann.annotations[column] != null)
     {
       String description = ann.annotations[column].description;
       if (description != null && description.length() > 0)
       {
-        this.setToolTipText(JvSwingUtils.wrapTooltip(true, description));
+        tooltip = JvSwingUtils.wrapTooltip(true, description);
       }
       else
       {
-        this.setToolTipText(null); // no tooltip if null or empty description
+        tooltip = null; // no tooltip if null or empty description
       }
     }
     else
     {
       // clear the tooltip.
-      this.setToolTipText(null);
+      tooltip = null;
     }
+    return tooltip;
   }
 
   /**
-   * Constructs and displays the status bar message
+   * Constructs and returns the status bar message
    * 
+   * @param al
    * @param column
    * @param ann
    */
-  void setStatusMessage(int column, AlignmentAnnotation ann)
+  static String getStatusMessage(AlignmentI al, int column,
+          AlignmentAnnotation ann)
   {
     /*
      * show alignment column and annotation description if any
@@ -813,7 +905,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     text.append(MessageManager.getString("label.column")).append(" ")
             .append(column + 1);
 
-    if (ann.annotations[column] != null)
+    if (column < ann.annotations.length && ann.annotations[column] != null)
     {
       String description = ann.annotations[column].description;
       if (description != null && description.trim().length() > 0)
@@ -829,7 +921,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     SequenceI seqref = ann.sequenceRef;
     if (seqref != null)
     {
-      int seqIndex = av.getAlignment().findIndex(seqref);
+      int seqIndex = al.findIndex(seqref);
       if (seqIndex != -1)
       {
         text.append(", ").append(MessageManager.getString("label.sequence"))
@@ -839,7 +931,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         {
           text.append(" ");
           String name;
-          if (av.getAlignment().isNucleotide())
+          if (al.isNucleotide())
           {
             name = ResidueProperties.nucleotideName
                     .get(String.valueOf(residue));
@@ -860,7 +952,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       }
     }
 
-    ap.alignFrame.statusBar.setText(text.toString());
+    return text.toString();
   }
 
   /**
@@ -902,6 +994,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   }
 
   private volatile boolean imageFresh = false;
+  private Rectangle visibleRect = new Rectangle(), clipBounds = new Rectangle();
 
   /**
    * DOCUMENT ME!
@@ -912,17 +1005,27 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   @Override
   public void paintComponent(Graphics g)
   {
-    super.paintComponent(g);
-
+	  
+	  // BH: note that this method is generally recommended to 
+	  // call super.paintComponent(g). Otherwise, the children of this
+	  // component will not be rendered. That is not needed here 
+	  // because AnnotationPanel does not have any children. It is
+	  // just a JPanel contained in a JViewPort. 
+
+    computeVisibleRect(visibleRect);
+    
     g.setColor(Color.white);
-    g.fillRect(0, 0, getWidth(), getHeight());
+    g.fillRect(0, 0, visibleRect.width, visibleRect.height);
 
     if (image != null)
     {
-      if (fastPaint || (getVisibleRect().width != g.getClipBounds().width)
-              || (getVisibleRect().height != g.getClipBounds().height))
+    	// BH 2018 optimizing generation of new Rectangle().
+      if (fastPaint || (visibleRect.width != (clipBounds = g.getClipBounds(clipBounds)).width)
+            || (visibleRect.height != clipBounds.height))
       {
-        g.drawImage(image, 0, 0, this);
+
+    	  
+    	  g.drawImage(image, 0, 0, this);
         fastPaint = false;
         return;
       }
@@ -933,6 +1036,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     {
       return;
     }
+    Graphics2D gg;
     if (image == null || imgWidth != image.getWidth(this)
             || image.getHeight(this) != getHeight())
     {
@@ -968,10 +1072,14 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       gg.setColor(Color.white);
       gg.fillRect(0, 0, imgWidth, image.getHeight());
       imageFresh = true;
+    } else {
+        gg = (Graphics2D) image.getGraphics();
+
     }
     
     drawComponent(gg, av.getRanges().getStartRes(),
             av.getRanges().getEndRes() + 1);
+    gg.dispose();
     imageFresh = false;
     g.drawImage(image, 0, 0, this);
   }
@@ -989,7 +1097,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
    */
   public void fastPaint(int horizontal)
   {
-    if ((horizontal == 0) || gg == null
+    if ((horizontal == 0) || image == null
             || av.getAlignment().getAlignmentAnnotation() == null
             || av.getAlignment().getAlignmentAnnotation().length < 1
             || av.isCalcInProgress())
@@ -1002,6 +1110,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     int er = av.getRanges().getEndRes() + 1;
     int transX = 0;
 
+    Graphics2D gg = (Graphics2D) image.getGraphics();
+
     gg.copyArea(0, 0, imgWidth, getHeight(),
             -horizontal * av.getCharWidth(), 0);
 
@@ -1021,6 +1131,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
     gg.translate(-transX, 0);
 
+    gg.dispose();
+    
     fastPaint = true;
 
     // Call repaint on alignment panel so that repaints from other alignment
@@ -1164,7 +1276,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     ap = null;
     image = null;
     fadedImage = null;
-    gg = null;
+//    gg = null;
     _mwl = null;
 
     /*
@@ -1218,7 +1330,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
      * hscroll, status bar, insets. 
      */
     int stuff = (ap.getViewName() != null ? 30 : 0)
-            + (Platform.isAMac() ? 120 : 140);
+            + (Platform.isAMacAndNotJS() ? 120 : 140);
     int availableHeight = ap.alignFrame.getHeight() - stuff;
     int rowHeight = av.getCharHeight();