JAL-4250 Conservative setting of ANTIALIAS and readjustment of glyphs to avoid scroll...

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index 5aea2cf..9a0081f 100644 (file)
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -234,7 +234,6 @@ public class AnnotationRenderer
   {
     // Console.info(nonCanColor);
 
-    g.setColor(nonCanColor);
     int sCol = (lastSSX / charWidth)
             + hiddenColumns.visibleToAbsoluteColumn(startRes);
     int x1 = lastSSX;
@@ -252,6 +251,13 @@ public class AnnotationRenderer
     // "+diffupstream+"
     // down:"+diffdownstream);
     // If a closing base pair half of the stem, display a backward arrow
+    if (diffupstream || diffdownstream)
+    {
+      // draw glyphline under arrow
+      this.drawGlyphLine(g, row_annotations, lastSSX, x, y, iconOffset,
+              startRes, column, validRes, validEnd);
+    }
+    g.setColor(nonCanColor);
     if (column > 0 && Rna.isClosingParenthesis(dc))
     {
 
@@ -261,7 +267,8 @@ public class AnnotationRenderer
       {
         fillPolygon(g, new int[] { lastSSX + 5, lastSSX + 5, lastSSX },
                 new int[]
-                { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset },
+                { y + iconOffset + 1, y + 13 + iconOffset,
+                    y + 7 + iconOffset },
                 3);
         x1 += 5;
       }
@@ -276,9 +283,10 @@ public class AnnotationRenderer
       // display a forward arrow
       if (diffdownstream)
       {
-        fillPolygon(g, new int[] { x2 - 5, x2 - 5, x2 },
+        fillPolygon(g, new int[] { x2 - 6, x2 - 6, x2 - 1 },
                 new int[]
-                { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset },
+                { y + iconOffset + 1, y + 13 + iconOffset,
+                    y + 7 + iconOffset },
                 3);
         x2 -= 5;
       }
@@ -288,7 +296,8 @@ public class AnnotationRenderer
       }
     }
     // draw arrow body
-    fillRect(g, x1, y + 4 + iconOffset, x2 - x1, 7);
+    unsetAntialias(g);
+    fillRect(g, x1 - 1, y + 4 + iconOffset, x2 - x1 + 1, 6);
   }
 
   // public void updateFromAnnotationPanel(FontMetrics annotFM, AlignViewportI
@@ -452,6 +461,7 @@ public class AnnotationRenderer
           int endRes)
   {
     Graphics2D g2d = (Graphics2D) g;
+    /*
     if (Cache.getDefault("ANTI_ALIAS", true))
     {
       g2d.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
@@ -459,6 +469,7 @@ public class AnnotationRenderer
       g2d.setRenderingHint(RenderingHints.KEY_STROKE_CONTROL,
               RenderingHints.VALUE_STROKE_PURE);
     }
+    */
 
     long stime = System.currentTimeMillis();
     boolean usedFaded = false;
@@ -639,6 +650,7 @@ public class AnnotationRenderer
                   : null;
           if (x > -1)
           {
+            unsetAntialias(g);
             if (activeRow == i)
             {
               g.setColor(Color.red);
@@ -714,6 +726,7 @@ public class AnnotationRenderer
                 g2d.transform(
                         AffineTransform.getScaleInstance(fmScaling, 1.0));
               }
+              setAntialias(g);
               if (column == 0 || row.graph > 0)
               {
                 g2d.drawString(displayChar, 0, 0);
@@ -892,9 +905,12 @@ public class AnnotationRenderer
                   // temp = x;
                   break;
                 default:
+                  unsetAntialias(g);
                   g.setColor(GLYPHLINE_COLOR);
                   g.fillRect(lastSSX, y + 6 + iconOffset,
                           (x * charWidth) - lastSSX, 2);
+                  g.drawRect(lastSSX, y + 6 + iconOffset,
+                          (x * charWidth) - lastSSX - 1, 2);
                   // temp = x;
                   break;
                 }
@@ -1166,9 +1182,11 @@ public class AnnotationRenderer
           int y, int iconOffset, int startRes, int column, boolean validRes,
           boolean validEnd)
   {
+    unsetAntialias(g);
     g.setColor(GLYPHLINE_COLOR);
-    unsetAntiAlias(g);
     g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth) - lastSSX, 2);
+    g.drawRect(lastSSX, y + 6 + iconOffset, (x * charWidth) - lastSSX - 1,
+            2);
   }
 
   void drawSheetAnnot(Graphics g, Annotation[] row,
@@ -1176,26 +1194,29 @@ public class AnnotationRenderer
           int lastSSX, int x, int y, int iconOffset, int startRes,
           int column, boolean validRes, boolean validEnd)
   {
-    g.setColor(SHEET_COLOUR);
-
     if (!validEnd || !validRes || row == null || row[column] == null
             || row[column].secondaryStructure != 'E')
     {
+      // draw the glyphline underneath
+      drawGlyphLine(g, row, lastSSX, x, y, iconOffset, startRes, column,
+              validRes, validEnd);
+      g.setColor(SHEET_COLOUR);
       fillRect(g, lastSSX, y + 4 + iconOffset,
               (x * charWidth) - lastSSX - 4, 6);
       fillPolygon(g,
               new int[]
-              { (x * charWidth) - 4, (x * charWidth) - 4, (x * charWidth) },
+              { (x * charWidth) - 6, (x * charWidth) - 6,
+                  (x * charWidth - 1) },
               new int[]
-              { y + iconOffset, y + 14 + iconOffset, y + 7 + iconOffset },
+              { y + iconOffset + 1, y + 13 + iconOffset,
+                  y + 7 + iconOffset },
               3);
     }
     else
     {
-      fillRect(g, lastSSX, y + 4 + iconOffset,
-              (x + 1) * charWidth - lastSSX, 6);
+      g.setColor(SHEET_COLOUR);
+      fillRect(g, lastSSX, y + 4 + iconOffset, x * charWidth - lastSSX, 6);
     }
-
   }
 
   void drawHelixAnnot(Graphics g, Annotation[] row, int lastSSX, int x,
@@ -1216,7 +1237,7 @@ public class AnnotationRenderer
       int ofs = charWidth / 2;
       // Off by 1 offset when drawing rects and ovals
       // to offscreen image on the MAC
-      fillRoundRect(g, lastSSX, y + 4 + iconOffset, x2 - x1, 8, 8, 8);
+      fillRoundRect(g, lastSSX, y + 4 + iconOffset, x2 - x1 - 1, 8, 8, 8);
       if (sCol == 0 || row[sCol - 1] == null
               || row[sCol - 1].secondaryStructure != 'H')
       {
@@ -1224,8 +1245,8 @@ public class AnnotationRenderer
       else
       {
         // g.setColor(Color.orange);
-        fillRoundRect(g, lastSSX, y + 4 + iconOffset, x2 - x1 - ofs + 1, 8,
-                0, 0);
+        fillRoundRect(g, lastSSX, y + 4 + iconOffset, x2 - x1 - ofs, 8, 0,
+                0);
       }
       if (!validRes || row[column] == null
               || row[column].secondaryStructure != 'H')
@@ -1235,8 +1256,8 @@ public class AnnotationRenderer
       else
       {
         // g.setColor(Color.magenta);
-        fillRoundRect(g, lastSSX + ofs, y + 4 + iconOffset,
-                x2 - x1 - ofs + 1, 8, 0, 0);
+        fillRoundRect(g, lastSSX + ofs, y + 4 + iconOffset, x2 - x1 - ofs,
+                8, 0, 0);
 
       }
 
@@ -1253,8 +1274,8 @@ public class AnnotationRenderer
     if (!validRes || row[column] == null
             || row[column].secondaryStructure != 'H')
     {
-      fillArc(g, (x * charWidth) - charWidth, y + 4 + iconOffset, charWidth,
-              8, 270, 180);
+      fillArc(g, (x * charWidth) - charWidth - 1, y + 4 + iconOffset,
+              charWidth, 8, 270, 180);
       x2 -= charWidth / 2;
     }
 
@@ -1294,6 +1315,7 @@ public class AnnotationRenderer
       y2 = y - (int) ((0 - min / range) * graphHeight);
     }
 
+    setAntialias(g);
     g.setColor(Color.gray);
     g.drawLine(x - charWidth, y2, (eRes - sRes + 1) * charWidth, y2);
 
@@ -1774,14 +1796,15 @@ public class AnnotationRenderer
   private static void fillPolygon(Graphics g, int[] xpoints, int[] ypoints,
           int n)
   {
-    setAntiAlias(g);
+    unsetAntialias(g);
+    g.fillPolygon(xpoints, ypoints, n);
+    setAntialias(g);
     g.fillPolygon(xpoints, ypoints, n);
     g.drawPolygon(xpoints, ypoints, n);
   }
 
   private static void fillRect(Graphics g, int a, int b, int c, int d)
   {
-    setAntiAlias(g);
     g.fillRect(a, b, c, d);
     g.drawRect(a, b, c, d);
   }
@@ -1789,7 +1812,7 @@ public class AnnotationRenderer
   private static void fillRoundRect(Graphics g, int a, int b, int c, int d,
           int e, int f)
   {
-    setAntiAlias(g);
+    setAntialias(g);
     g.fillRoundRect(a, b, c, d, e, f);
     g.drawRoundRect(a, b, c, d, e, f);
   }
@@ -1797,12 +1820,12 @@ public class AnnotationRenderer
   private static void fillArc(Graphics g, int a, int b, int c, int d, int e,
           int f)
   {
-    setAntiAlias(g);
+    setAntialias(g);
     g.fillArc(a, b, c, d, e, f);
     g.drawArc(a, b, c, d, e, f);
   }
 
-  private static void setAntiAlias(Graphics g)
+  private static void setAntialias(Graphics g)
   {
     if (Cache.getDefault("ANTI_ALIAS", true))
     {
@@ -1812,7 +1835,7 @@ public class AnnotationRenderer
     }
   }
 
-  private static void unsetAntiAlias(Graphics g)
+  private static void unsetAntialias(Graphics g)
   {
     Graphics2D g2d = (Graphics2D) g;
     g2d.setRenderingHint(RenderingHints.KEY_ANTIALIASING,