X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=01be3b5343881266c7849ed4294fbb32023920d0;hb=be8b1d254f658181eec3c29dc696114e3ffdd4df;hp=5d8540ca6d9cca52188a6fda71a2af9b08226307;hpb=9c3f777f8d20fef0fcf80a01874a5d24728ca229;p=jalview.git

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 5d8540c..01be3b5 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -20,21 +20,6 @@
  */
 package jalview.gui;
 
-import jalview.datamodel.AlignmentAnnotation;
-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.FeatureColour;
-import jalview.schemes.ResidueProperties;
-import jalview.util.Comparison;
-import jalview.util.MessageManager;
-import jalview.viewmodel.ViewportListenerI;
-import jalview.viewmodel.ViewportRanges;
-
 import java.awt.AlphaComposite;
 import java.awt.Color;
 import java.awt.Dimension;
@@ -59,14 +44,28 @@ import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
 
-import javax.swing.JColorChooser;
-import javax.swing.JDialog;
 import javax.swing.JMenuItem;
 import javax.swing.JPanel;
 import javax.swing.JPopupMenu;
 import javax.swing.Scrollable;
 import javax.swing.ToolTipManager;
 
+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;
+import jalview.util.Comparison;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.viewmodel.ViewportListenerI;
+import jalview.viewmodel.ViewportRanges;
+
 /**
  * AnnotationPanel displays visible portion of annotation rows below unwrapped
  * alignment
@@ -115,7 +114,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
   public volatile BufferedImage fadedImage;
 
-  Graphics2D gg;
+  // private Graphics2D gg;
 
   public FontMetrics fm;
 
@@ -214,7 +213,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   @Override
   public Dimension getPreferredScrollableViewportSize()
   {
-    return getPreferredSize();
+    Dimension ps = getPreferredSize();
+    return new Dimension(ps.width, adjustForAlignFrame(false, ps.height));
   }
 
   @Override
@@ -315,7 +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)
@@ -657,14 +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)
@@ -760,30 +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)
     {
@@ -793,6 +774,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
     int column = (evt.getX() / av.getCharWidth())
             + av.getRanges().getStartRes();
+    column = Math.min(column, av.getRanges().getEndRes());
 
     if (av.hasHiddenColumns())
     {
@@ -804,76 +786,109 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     if (row > -1 && ann.annotations != null
             && column < ann.annotations.length)
     {
-      buildToolTip(ann, column, aa);
-      setStatusMessage(column, ann);
+      String toolTip = buildToolTip(ann, column, aa);
+      setToolTipText(toolTip == null ? null
+              : JvSwingUtils.wrapTooltip(true, toolTip));
+      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, not
+   * wrapped in &lt;html&gt; tags (apply if wanted). Answers null if there is no
+   * tooltip to show.
    * 
    * @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);
-      tip.append("<html>");
+      boolean first = true;
       for (int i = 0; i < anns.length; i++)
       {
         if (anns[i].graphGroup == ann.graphGroup
                 && anns[i].annotations[column] != null)
         {
+          if (!first)
+          {
+            tip.append("<br>");
+          }
+          first = false;
           tip.append(anns[i].label);
           String description = anns[i].annotations[column].description;
           if (description != null && description.length() > 0)
           {
             tip.append(" ").append(description);
           }
-          tip.append("<br>");
         }
       }
-      if (tip.length() != 6)
-      {
-        tip.setLength(tip.length() - 4);
-        this.setToolTipText(tip.toString() + "</html>");
-      }
+      tooltip = first ? null : tip.toString();
     }
-    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));
-      }
-      else
-      {
-        this.setToolTipText(null); // no tooltip if null or empty description
-      }
-    }
-    else
-    {
-      // clear the tooltip.
-      this.setToolTipText(null);
+      tooltip = ann.annotations[column].description;
     }
+
+    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
@@ -882,7 +897,7 @@ 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)
@@ -898,7 +913,7 @@ 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"))
@@ -908,7 +923,7 @@ 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));
@@ -929,7 +944,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       }
     }
 
-    ap.alignFrame.statusBar.setText(text.toString());
+    return text.toString();
   }
 
   /**
@@ -971,6 +986,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   }
 
   private volatile boolean imageFresh = false;
+  private Rectangle visibleRect = new Rectangle(), clipBounds = new Rectangle();
 
   /**
    * DOCUMENT ME!
@@ -981,27 +997,43 @@ 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);
 
+    ViewportRanges ranges = av.getRanges();
+    
+    
+    
     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;
       }
     }
-    imgWidth = (av.getRanges().getEndRes() - av.getRanges().getStartRes()
+    
+    imgWidth = (ranges.getEndRes() - ranges.getStartRes()
             + 1) * av.getCharWidth();
+    
     if (imgWidth < 1)
     {
+      fastPaint = false;
       return;
     }
+    Graphics2D gg;
     if (image == null || imgWidth != image.getWidth(this)
             || image.getHeight(this) != getHeight())
     {
@@ -1037,20 +1069,19 @@ 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(),
+   
+    drawComponent(gg, ranges.getStartRes(),
             av.getRanges().getEndRes() + 1);
+    gg.dispose();
     imageFresh = false;
     g.drawImage(image, 0, 0, this);
   }
 
   /**
-   * set true to enable redraw timing debug output on stderr
-   */
-  private final boolean debugRedraw = false;
-
-  /**
    * non-Thread safe repaint
    * 
    * @param horizontal
@@ -1058,7 +1089,7 @@ 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())
@@ -1070,6 +1101,13 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     int sr = av.getRanges().getStartRes();
     int er = av.getRanges().getEndRes() + 1;
     int transX = 0;
+    
+    if (er == sr + 1) {
+      fastPaint = false;
+      return;
+    }
+
+    Graphics2D gg = (Graphics2D) image.getGraphics();
 
     gg.copyArea(0, 0, imgWidth, getHeight(),
             -horizontal * av.getCharWidth(), 0);
@@ -1090,6 +1128,8 @@ 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
@@ -1233,7 +1273,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     ap = null;
     image = null;
     fadedImage = null;
-    gg = null;
+//    gg = null;
     _mwl = null;
 
     /*
@@ -1268,4 +1308,49 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       repaint();
     }
   }
+
+  /**
+   * computes the visible height of the annotation panel
+   * 
+   * @param adjustPanelHeight
+   *          - when false, just adjust existing height according to other
+   *          windows
+   * @param annotationHeight
+   * @return height to use for the ScrollerPreferredVisibleSize
+   */
+  public int adjustForAlignFrame(boolean adjustPanelHeight,
+          int annotationHeight)
+  {
+    /*
+     * Estimate available height in the AlignFrame for alignment +
+     * annotations. Deduct an estimate for title bar, menu bar, scale panel,
+     * hscroll, status bar, insets. 
+     */
+    int stuff = (ap.getViewName() != null ? 30 : 0)
+            + (Platform.isAMacAndNotJS() ? 120 : 140);
+    int availableHeight = ap.alignFrame.getHeight() - stuff;
+    int rowHeight = av.getCharHeight();
+
+    if (adjustPanelHeight)
+    {
+      int alignmentHeight = rowHeight * av.getAlignment().getHeight();
+
+      /*
+       * If not enough vertical space, maximize annotation height while keeping
+       * at least two rows of alignment visible
+       */
+      if (annotationHeight + alignmentHeight > availableHeight)
+      {
+        annotationHeight = Math.min(annotationHeight,
+                availableHeight - 2 * rowHeight);
+      }
+    }
+    else
+    {
+      // maintain same window layout whilst updating sliders
+      annotationHeight = Math.min(ap.annotationScroller.getSize().height,
+              availableHeight - 2 * rowHeight);
+    }
+    return annotationHeight;
+  }
 }