X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FIdCanvas.java;h=8f13ecadab066787fb37047fe50752344a8a5922;hb=d7e95f458ebcbbdcc13f8b07357542ab2d7e4547;hp=22652354d09f9aacbdb7da4aee9129bd09a824b9;hpb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;p=jalview.git

diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index 2265235..8f13eca 100755
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -21,6 +21,8 @@
 package jalview.gui;
 
 import jalview.datamodel.SequenceI;
+import jalview.viewmodel.ViewportListenerI;
+import jalview.viewmodel.ViewportRanges;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
@@ -30,6 +32,7 @@ import java.awt.Graphics;
 import java.awt.Graphics2D;
 import java.awt.RenderingHints;
 import java.awt.image.BufferedImage;
+import java.beans.PropertyChangeEvent;
 import java.util.List;
 
 import javax.swing.JPanel;
@@ -40,7 +43,7 @@ import javax.swing.JPanel;
  * @author $author$
  * @version $Revision$
  */
-public class IdCanvas extends JPanel
+public class IdCanvas extends JPanel implements ViewportListenerI
 {
   protected AlignViewport av;
 
@@ -79,7 +82,8 @@ public class IdCanvas extends JPanel
     setLayout(new BorderLayout());
     this.av = av;
     PaintRefresher.Register(this, av.getSequenceSetId());
-  }
+    av.getRanges().addPropertyChangeListener(this);
+    }
 
   /**
    * DOCUMENT ME!
@@ -151,40 +155,45 @@ public class IdCanvas extends JPanel
    */
   public void fastPaint(int vertical)
   {
-    if (gg == null)
+    /*
+     * for now, not attempting fast paint of wrapped ids...
+     */
+    if (gg == null || av.getWrapAlignment())
     {
       repaint();
 
       return;
     }
 
+    ViewportRanges ranges = av.getRanges();
+
     gg.copyArea(0, 0, getWidth(), imgHeight, 0,
             -vertical * av.getCharHeight());
 
-    int ss = av.startSeq;
-    int es = av.endSeq;
+    int ss = ranges.getStartSeq();
+    int es = ranges.getEndSeq();
     int transY = 0;
 
     if (vertical > 0) // scroll down
     {
       ss = es - vertical;
 
-      if (ss < av.startSeq)
+      if (ss < ranges.getStartSeq())
       { // ie scrolling too fast, more than a page at a time
-        ss = av.startSeq;
+        ss = ranges.getStartSeq();
       }
       else
       {
-        transY = imgHeight - (vertical * av.getCharHeight());
+        transY = imgHeight - ((vertical + 1) * av.getCharHeight());
       }
     }
-    else if (vertical < 0)
+    else if (vertical < 0) // scroll up
     {
       es = ss - vertical;
 
-      if (es > av.endSeq)
+      if (es > ranges.getEndSeq())
       {
-        es = av.endSeq;
+        es = ranges.getEndSeq();
       }
     }
 
@@ -195,7 +204,11 @@ public class IdCanvas extends JPanel
     gg.translate(0, -transY);
 
     fastPaint = true;
-    repaint();
+
+    // Call repaint on alignment panel so that repaints from other alignment
+    // panel components can be aggregated. Otherwise performance of the overview
+    // window and others may be adversely affected.
+    av.getAlignPanel().repaint();
   }
 
   /**
@@ -204,43 +217,46 @@ public class IdCanvas extends JPanel
    * @param g
    *          DOCUMENT ME!
    */
+  @Override
   public void paintComponent(Graphics g)
   {
+    super.paintComponent(g);
+
     g.setColor(Color.white);
     g.fillRect(0, 0, getWidth(), getHeight());
-
+    
     if (fastPaint)
     {
       fastPaint = false;
       g.drawImage(image, 0, 0, this);
-
+    
       return;
     }
-
+    
     int oldHeight = imgHeight;
-
+    
     imgHeight = getHeight();
     imgHeight -= (imgHeight % av.getCharHeight());
-
+    
     if (imgHeight < 1)
     {
       return;
     }
-
+    
     if (oldHeight != imgHeight || image.getWidth(this) != getWidth())
     {
-      image = new BufferedImage(getWidth(), imgHeight,
-              BufferedImage.TYPE_INT_RGB);
+    	image = new BufferedImage(getWidth(), imgHeight,
+                BufferedImage.TYPE_INT_RGB);
     }
-
+    
     gg = (Graphics2D) image.getGraphics();
-
+    
     // Fill in the background
     gg.setColor(Color.white);
     gg.fillRect(0, 0, getWidth(), imgHeight);
-
-    drawIds(av.getStartSeq(), av.endSeq);
-
+    
+    drawIds(av.getRanges().getStartSeq(), av.getRanges().getEndSeq());
+    
     g.drawImage(image, 0, 0, this);
   }
 
@@ -256,8 +272,8 @@ public class IdCanvas extends JPanel
   {
     if (av.isSeqNameItalics())
     {
-      setIdfont(new Font(av.getFont().getName(), Font.ITALIC, av.getFont()
-              .getSize()));
+      setIdfont(new Font(av.getFont().getName(), Font.ITALIC,
+              av.getFont().getSize()));
     }
     else
     {
@@ -276,148 +292,165 @@ public class IdCanvas extends JPanel
     Color currentColor = Color.white;
     Color currentTextColor = Color.black;
 
-    final boolean doHiddenCheck = av.isDisplayReferenceSeq()
-            || av.hasHiddenRows(), hiddenRows = av.hasHiddenRows();
+    boolean hasHiddenRows = av.hasHiddenRows();
 
     if (av.getWrapAlignment())
     {
-      int maxwidth = av.getAlignment().getWidth();
-      int alheight = av.getAlignment().getHeight();
+      drawIdsWrapped(starty, hasHiddenRows);
+      return;
+    }
 
-      if (av.hasHiddenColumns())
-      {
-        maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
-      }
+    // No need to hang on to labels if we're not wrapped
+    labels = null;
+
+    // Now draw the id strings
+    int panelWidth = getWidth();
+    int xPos = 0;
 
-      int annotationHeight = 0;
+    SequenceI sequence;
+    // Now draw the id strings
+    for (int i = starty; i <= endy; i++)
+    {
+      sequence = av.getAlignment().getSequenceAt(i);
 
-      if (av.isShowAnnotation())
+      if (sequence == null)
       {
-        if (ap == null)
-        {
-          ap = new AnnotationPanel(av);
-        }
+        continue;
+      }
 
-        annotationHeight = ap.adjustPanelHeight();
-        if (labels == null)
-        {
-          labels = new AnnotationLabels(av);
-        }
+      if (hasHiddenRows || av.isDisplayReferenceSeq())
+      {
+        setHiddenFont(sequence);
       }
 
-      int hgap = av.getCharHeight();
-      if (av.getScaleAboveWrapped())
+      // Selected sequence colours
+      if ((searchResults != null) && searchResults.contains(sequence))
       {
-        hgap += av.getCharHeight();
+        currentColor = Color.black;
+        currentTextColor = Color.white;
       }
+      else if ((av.getSelectionGroup() != null) && av.getSelectionGroup()
+              .getSequences(null).contains(sequence))
+      {
+        currentColor = Color.lightGray;
+        currentTextColor = Color.black;
+      }
+      else
+      {
+        currentColor = av.getSequenceColour(sequence);
+        currentTextColor = Color.black;
+      }
+
+      gg.setColor(currentColor);
 
-      int cHeight = alheight * av.getCharHeight() + hgap + annotationHeight;
+      gg.fillRect(0, (i - starty) * av.getCharHeight(), getWidth(),
+              av.getCharHeight());
 
-      int rowSize = av.getEndRes() - av.getStartRes();
+      gg.setColor(currentTextColor);
 
-      // Draw the rest of the panels
-      for (int ypos = hgap, row = av.startRes; (ypos <= getHeight())
-              && (row < maxwidth); ypos += cHeight, row += rowSize)
+      String string = sequence.getDisplayId(av.getShowJVSuffix());
+
+      if (av.isRightAlignIds())
       {
-        for (int i = starty; i < alheight; i++)
-        {
-          SequenceI s = av.getAlignment().getSequenceAt(i);
-          if (doHiddenCheck)
-          {
-            setHiddenFont(s);
-          }
-          else
-          {
-            gg.setFont(getIdfont());
-          }
-
-          drawIdString(gg, hiddenRows, s, i, 0, ypos);
-        }
+        xPos = panelWidth - fm.stringWidth(string) - 4;
+      }
 
-        if (labels != null && av.isShowAnnotation())
-        {
-          gg.translate(0, ypos + (alheight * av.getCharHeight()));
-          labels.drawComponent(gg, getWidth());
-          gg.translate(0, -ypos - (alheight * av.getCharHeight()));
-        }
+      gg.drawString(string, xPos,
+              (((i - starty) * av.getCharHeight()) + av.getCharHeight())
+                      - (av.getCharHeight() / 5));
+
+      if (hasHiddenRows)
+      {
+        drawMarker(i, starty, 0);
       }
     }
-    else
-    {
-      // No need to hang on to labels if we're not wrapped
-      labels = null;
+  }
 
-      // Now draw the id strings
-      int panelWidth = getWidth();
-      int xPos = 0;
+  /**
+   * Draws sequence ids in wrapped mode
+   * 
+   * @param starty
+   * @param hasHiddenRows
+   */
+  protected void drawIdsWrapped(int starty, boolean hasHiddenRows)
+  {
+    int maxwidth = av.getAlignment().getWidth();
+    int alheight = av.getAlignment().getHeight();
 
-      SequenceI sequence;
-      // Now draw the id strings
-      for (int i = starty; i < endy; i++)
-      {
-        sequence = av.getAlignment().getSequenceAt(i);
+    if (av.hasHiddenColumns())
+    {
+      maxwidth = av.getAlignment().getHiddenColumns()
+              .findColumnPosition(maxwidth) - 1;
+    }
 
-        if (sequence == null)
-        {
-          continue;
-        }
+    int annotationHeight = 0;
 
-        if (doHiddenCheck)
-        {
-          setHiddenFont(sequence);
-        }
+    if (av.isShowAnnotation())
+    {
+      if (ap == null)
+      {
+        ap = new AnnotationPanel(av);
+      }
 
-        // Selected sequence colours
-        if ((searchResults != null) && searchResults.contains(sequence))
-        {
-          currentColor = Color.black;
-          currentTextColor = Color.white;
-        }
-        else if ((av.getSelectionGroup() != null)
-                && av.getSelectionGroup().getSequences(null)
-                        .contains(sequence))
-        {
-          currentColor = Color.lightGray;
-          currentTextColor = Color.black;
-        }
-        else
-        {
-          currentColor = av.getSequenceColour(sequence);
-          currentTextColor = Color.black;
-        }
+      annotationHeight = ap.adjustPanelHeight();
+      if (labels == null)
+      {
+        labels = new AnnotationLabels(av);
+      }
+    }
 
-        gg.setColor(currentColor);
+    int hgap = av.getCharHeight();
+    if (av.getScaleAboveWrapped())
+    {
+      hgap += av.getCharHeight();
+    }
 
-        gg.fillRect(0, (i - starty) * av.getCharHeight(), getWidth(),
-                av.getCharHeight());
+    int cHeight = alheight * av.getCharHeight() + hgap + annotationHeight;
 
-        gg.setColor(currentTextColor);
+    ViewportRanges ranges = av.getRanges();
 
-        String string = sequence.getDisplayId(av.getShowJVSuffix());
+    int rowSize = ranges.getViewportWidth();
 
-        if (av.isRightAlignIds())
+    /*
+     * draw repeating sequence ids until out of sequence data or
+     * out of visible space, whichever comes first
+     */
+    int ypos = hgap;
+    int row = ranges.getStartRes();
+    while ((ypos <= getHeight()) && (row < maxwidth))
+    {
+      for (int i = starty; i < alheight; i++)
+      {
+        SequenceI s = av.getAlignment().getSequenceAt(i);
+        if (hasHiddenRows || av.isDisplayReferenceSeq())
         {
-          xPos = panelWidth - fm.stringWidth(string) - 4;
+          setHiddenFont(s);
         }
-
-        gg.drawString(string, xPos,
-                (((i - starty) * av.getCharHeight()) + av.getCharHeight())
-                        - (av.getCharHeight() / 5));
-
-        if (hiddenRows)
+        else
         {
-          drawMarker(i, starty, 0);
+          gg.setFont(getIdfont());
         }
 
+        drawIdString(gg, hasHiddenRows, s, i, 0, ypos);
+      }
+
+      if (labels != null && av.isShowAnnotation())
+      {
+        gg.translate(0, ypos + (alheight * av.getCharHeight()));
+        labels.drawComponent(gg, getWidth());
+        gg.translate(0, -ypos - (alheight * av.getCharHeight()));
       }
 
+      ypos += cHeight;
+      row += rowSize;
     }
   }
 
   void drawMarker(int i, int starty, int yoffset)
   {
 
-    SequenceI[] hseqs = av.getAlignment().getHiddenSequences().hiddenSequences;
+    SequenceI[] hseqs = av.getAlignment()
+            .getHiddenSequences().hiddenSequences;
     // Use this method here instead of calling hiddenSeq adjust
     // 3 times.
     int hSize = hseqs.length;
@@ -452,34 +485,38 @@ public class IdCanvas extends JPanel
     if (below)
     {
       gg.fillPolygon(
-              new int[] { getWidth() - av.getCharHeight(),
+              new int[]
+              { getWidth() - av.getCharHeight(),
                   getWidth() - av.getCharHeight(), getWidth() },
-              new int[] {
-                  (i - starty) * av.getCharHeight() + yoffset,
+              new int[]
+              { (i - starty) * av.getCharHeight() + yoffset,
                   (i - starty) * av.getCharHeight() + yoffset
                           + av.getCharHeight() / 4,
-                  (i - starty) * av.getCharHeight() + yoffset }, 3);
+                  (i - starty) * av.getCharHeight() + yoffset },
+              3);
     }
     if (above)
     {
       gg.fillPolygon(
-              new int[] { getWidth() - av.getCharHeight(),
+              new int[]
+              { getWidth() - av.getCharHeight(),
                   getWidth() - av.getCharHeight(), getWidth() },
-              new int[] {
-                  (i - starty + 1) * av.getCharHeight() + yoffset,
+              new int[]
+              { (i - starty + 1) * av.getCharHeight() + yoffset,
                   (i - starty + 1) * av.getCharHeight() + yoffset
                           - av.getCharHeight() / 4,
-                  (i - starty + 1) * av.getCharHeight() + yoffset }, 3);
+                  (i - starty + 1) * av.getCharHeight() + yoffset },
+              3);
 
     }
   }
 
   void setHiddenFont(SequenceI seq)
   {
-    Font bold = new Font(av.getFont().getName(), Font.BOLD, av.getFont()
-            .getSize());
+    Font bold = new Font(av.getFont().getName(), Font.BOLD,
+            av.getFont().getSize());
 
-    if (av.isHiddenRepSequence(seq))
+    if (av.isReferenceSeq(seq) || av.isHiddenRepSequence(seq))
     {
       gg.setFont(bold);
     }
@@ -510,4 +547,37 @@ public class IdCanvas extends JPanel
   {
     this.idfont = idfont;
   }
+
+  /**
+   * Respond to viewport range changes (e.g. alignment panel was scrolled). Both
+   * scrolling and resizing change viewport ranges. Scrolling changes both start
+   * and end points, but resize only changes end values. Here we only want to
+   * fastpaint on a scroll, with resize using a normal paint, so scroll events
+   * are identified as changes to the horizontal or vertical start value.
+   * <p>
+   * In unwrapped mode, only responds to a vertical scroll, as horizontal scroll
+   * leaves sequence ids unchanged. In wrapped mode, only vertical scroll is
+   * provided, but it generates a change of "startres" which does require an
+   * update here.
+   */
+  @Override
+  public void propertyChange(PropertyChangeEvent evt)
+  {
+    String propertyName = evt.getPropertyName();
+    if (propertyName.equals(ViewportRanges.STARTSEQ)
+            || (av.getWrapAlignment()
+                    && propertyName.equals(ViewportRanges.STARTRES)))
+    {
+      fastPaint((int) evt.getNewValue() - (int) evt.getOldValue());
+    }
+    else if (propertyName.equals(ViewportRanges.STARTRESANDSEQ))
+    {
+      fastPaint(((int[]) evt.getNewValue())[1]
+              - ((int[]) evt.getOldValue())[1]);
+    }
+    else if (propertyName.equals(ViewportRanges.MOVE_VIEWPORT))
+    {
+      repaint();
+    }
+  }
 }