JAL-4375 Fixed the following when trackpad side-scrolling in wrap format: line-graph...

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 845004b..c563c79 100644 (file)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -2251,12 +2251,9 @@ public class SeqPanel extends JPanel
          * stop trying to scroll right when limit is reached (saves
          * expensive calls to Alignment.getWidth())
          */
-        while (size-- > 0 && !ap.isScrolledFullyRight())
+        if (!ap.isScrolledFullyRight())
         {
-          if (!av.getRanges().scrollRight(true))
-          {
-            break;
-          }
+          av.getRanges().scrollRight(true, size);
         }
       }
       else
@@ -2280,13 +2277,7 @@ public class SeqPanel extends JPanel
         /*
          * scroll left
          */
-        while (size-- > 0)
-        {
-          if (!av.getRanges().scrollRight(false))
-          {
-            break;
-          }
-        }
+        av.getRanges().scrollRight(false, size);
       }
       else
       {

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index b5dac0d..3b5d656 100644 (file)
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -32,7 +32,9 @@ import java.awt.Stroke;
 import java.awt.geom.AffineTransform;
 import java.awt.image.ImageObserver;
 import java.util.BitSet;
+import java.util.HashMap;
 import java.util.Hashtable;
+import java.util.Map;
 
 import org.jfree.graphics2d.svg.SVGGraphics2D;
 import org.jibble.epsgraphics.EpsGraphics2D;
@@ -823,7 +825,7 @@ public class AnnotationRenderer
             if (!validRes || (ss != lastSS))
             {
 
-              if (x > -1)
+              if (x > 0)
               {
 
                 // int nb_annot = x - temp;
@@ -1348,11 +1350,6 @@ public class AnnotationRenderer
 
     eRes = Math.min(eRes, aa_annotations.length);
 
-    if (sRes == 0)
-    {
-      x++;
-    }
-
     int y1 = y, y2 = y;
     float range = max - min;
 
@@ -1363,15 +1360,20 @@ public class AnnotationRenderer
     }
 
     g.setColor(Color.gray);
-    drawLine(g, squareStroke, x * charWidth - charWidth, y2,
-            (eRes - sRes) * charWidth, y2);
+    drawLine(g, squareStroke, x * charWidth, y2, (eRes - sRes) * charWidth,
+            y2);
+
+    if (sRes == 0)
+    {
+      x++;
+    }
 
     eRes = Math.min(eRes, aa_annotations.length);
 
     int column;
     int aaMax = aa_annotations.length - 1;
 
-    while (x < eRes - sRes)
+    while (x <= eRes - sRes)
     {
       column = sRes + x;
       if (hasHiddenColumns)
@@ -1399,32 +1401,55 @@ public class AnnotationRenderer
         g.setColor(aa_annotations[column].colour);
       }
 
-      if (aa_annotations[column - 1] == null
-              && aa_annotations.length > column + 1
-              && aa_annotations[column + 1] == null)
+      boolean previousValueExists = column > 0
+              && aa_annotations[column - 1] != null;
+      float previousValue = previousValueExists
+              ? aa_annotations[column - 1].value
+              : 0;
+      float thisValue = aa_annotations[column].value;
+      boolean nextValueExists = aa_annotations.length > column + 1
+              && aa_annotations[column + 1] != null;
+      float nextValue = nextValueExists ? aa_annotations[column + 1].value
+              : 0;
+
+      // check for standalone value
+      if (!previousValueExists && !nextValueExists)
       {
-        // standalone value
-        y1 = y - (int) (((aa_annotations[column].value - min) / range)
-                * graphHeight);
-        drawLine(g, x * charWidth + charWidth / 4, y1,
-                x * charWidth + 3 * charWidth / 4, y1);
+        y2 = y - yValueToPixelHeight(thisValue, min, range, graphHeight);
+        drawLine(g, x * charWidth + charWidth / 4, y2,
+                x * charWidth + 3 * charWidth / 4, y2);
         x++;
         continue;
       }
 
-      if (aa_annotations[column - 1] == null)
+      if (!previousValueExists)
       {
         x++;
         continue;
       }
 
-      y1 = y - (int) (((aa_annotations[column - 1].value - min) / range)
-              * graphHeight);
-      y2 = y - (int) (((aa_annotations[column].value - min) / range)
-              * graphHeight);
+      y1 = y - yValueToPixelHeight(previousValue, min, range, graphHeight);
+      y2 = y - yValueToPixelHeight(thisValue, min, range, graphHeight);
+
+      if (x == 0)
+      {
+        // only draw an initial half-line
+        drawLine(g, x * charWidth, y1 + (y2 - y1) / 2,
+                x * charWidth + charWidth / 2, y2);
+
+      }
+      else if (x == eRes - sRes)
+      {
+        // this is one past the end to draw -- only draw a half line
+        drawLine(g, (x - 1) * charWidth + charWidth / 2, y1,
+                x * charWidth - 1, y1 + (y2 - y1) / 2);
 
-      drawLine(g, (x - 1) * charWidth + charWidth / 2, y1,
-              x * charWidth + charWidth / 2, y2);
+      }
+      else
+      {
+        drawLine(g, (x - 1) * charWidth + charWidth / 2, y1,
+                x * charWidth + charWidth / 2, y2);
+      }
       x++;
     }
 
@@ -1432,16 +1457,50 @@ public class AnnotationRenderer
     {
       g.setColor(_aa.threshold.colour);
       Graphics2D g2 = (Graphics2D) g;
-      Stroke s = new BasicStroke(1, BasicStroke.CAP_SQUARE,
-              BasicStroke.JOIN_ROUND, 3f, new float[]
-              { 5f, 3f }, 0f);
-
       y2 = (int) (y - ((_aa.threshold.value - min) / range) * graphHeight);
-      drawLine(g, s, 0, y2, (eRes - sRes) * charWidth, y2);
+      drawLine(g, dashedLine(charWidth), 0, y2, (eRes - sRes) * charWidth,
+              y2);
     }
     g2d.setStroke(prevStroke);
   }
 
+  private static double log2 = Math.log(2);
+
+  // Cached dashed line Strokes
+  private static Map<Integer, Stroke> dashedLineLookup = new HashMap<>();
+
+  /**
+   * Returns a dashed line stroke as close to 6-4 pixels as fits within the
+   * charWidth. This allows translations of multiples of charWidth without
+   * disrupting the dashed line. The exact values are 0.6-0.4 proportions of
+   * charWidth for charWidth under 16. For charWidth 16 or over, the number of
+   * dashes doubles as charWidth doubles.
+   * 
+   * @param charWidth
+   * @return Stroke with appropriate dashed line fitting exactly within the
+   *         charWidth
+   */
+  private static Stroke dashedLine(int charWidth)
+  {
+    if (!dashedLineLookup.containsKey(charWidth))
+    {
+      int power2 = charWidth >= 16 ? (int) (Math.log(charWidth) / log2) : 2;
+      float width = ((float) charWidth) / ((float) Math.pow(2, power2 - 2));
+      float segment1 = width * 0.6f;
+      float segment2 = width - segment1;
+      dashedLineLookup.put(charWidth, new BasicStroke(1,
+              BasicStroke.CAP_BUTT, BasicStroke.JOIN_ROUND, 3f, new float[]
+              { segment1, segment2 }, 0f));
+    }
+    return dashedLineLookup.get(charWidth);
+  }
+
+  private static int yValueToPixelHeight(float value, float min,
+          float range, int graphHeight)
+  {
+    return (int) (((value - min) / range) * graphHeight);
+  }
+
   @SuppressWarnings("unused")
   void drawBarGraph(Graphics g, AlignmentAnnotation _aa,
           Annotation[] aa_annotations, int sRes, int eRes, float min,
@@ -1606,12 +1665,6 @@ public class AnnotationRenderer
             }
             g.setColor(colour == Color.white ? Color.lightGray : colour);
 
-            // Debug - render boxes around characters
-            // g.setColor(Color.red);
-            // g.drawRect(x*av.charWidth, (int)ht, av.charWidth,
-            // (int)(scl));
-            // g.setColor(profcolour.findColour(dc[0]).darker());
-
             double sx = 1f * charWidth / fm.charsWidth(dc, 0, dc.length);
             double sy = newHeight / asc;
             double newAsc = asc * sy;

diff --git a/src/jalview/viewmodel/ViewportRanges.java b/src/jalview/viewmodel/ViewportRanges.java
index 04db165..f842736 100644 (file)
--- a/src/jalview/viewmodel/ViewportRanges.java
+++ b/src/jalview/viewmodel/ViewportRanges.java
@@ -523,23 +523,28 @@ public class ViewportRanges extends ViewportProperties
    */
   public boolean scrollRight(boolean right)
   {
+    return scrollRight(right, 1);
+  }
+
+  public boolean scrollRight(boolean right, int jump)
+  {
     if (!right)
     {
-      if (startRes < 1)
+      if (startRes < jump)
       {
         return false;
       }
 
-      setStartRes(startRes - 1);
+      setStartRes(startRes - jump);
     }
     else
     {
-      if (endRes >= getVisibleAlignmentWidth() - 1)
+      if (endRes >= getVisibleAlignmentWidth() - jump)
       {
         return false;
       }
 
-      setStartRes(startRes + 1);
+      setStartRes(startRes + jump);
     }
 
     return true;