Merge branch 'releases/Release_2_11_3_Branch'

[jalview.git] / src / jalview / renderer / AnnotationRenderer.java

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index ea54393..b5dac0d 100644 (file)
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -95,7 +95,7 @@ public class AnnotationRenderer
 
   private boolean av_ignoreGapsConsensus;
 
-  private boolean vectorRendition = false;
+  private boolean renderingVectors = false;
 
   private boolean glyphLineDrawn = false;
 
@@ -175,7 +175,6 @@ public class AnnotationRenderer
           int x, int y, int iconOffset, int startRes, int column,
           boolean validRes, boolean validEnd)
   {
-    g.setColor(STEM_COLOUR);
     int sCol = (lastSSX / charWidth)
             + hiddenColumns.visibleToAbsoluteColumn(startRes);
     int x1 = lastSSX;
@@ -185,11 +184,19 @@ public class AnnotationRenderer
             : row_annotations[column - 1].secondaryStructure;
 
     boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
-            || dc != row_annotations[sCol - 1].secondaryStructure;
+            || dc != row_annotations[sCol - 1].secondaryStructure
+            || !validEnd;
     boolean diffdownstream = !validRes || !validEnd
             || row_annotations[column] == null
             || dc != row_annotations[column].secondaryStructure;
 
+    if (diffupstream || diffdownstream)
+    {
+      // draw glyphline under arrow
+      drawGlyphLine(g, lastSSX, x, y, iconOffset);
+    }
+    g.setColor(STEM_COLOUR);
+
     if (column > 0 && Rna.isClosingParenthesis(dc))
     {
       if (diffupstream)
@@ -202,7 +209,8 @@ 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;
       }
@@ -220,9 +228,10 @@ public class AnnotationRenderer
          * if annotation ending with an opeing base pair half of the stem, 
          * display a forward arrow
          */
-        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;
       }
@@ -232,7 +241,8 @@ public class AnnotationRenderer
       }
     }
     // draw arrow body
-    fillRect(g, x1, y + 4 + iconOffset, x2 - x1, 7);
+    unsetAntialias(g);
+    fillRect(g, x1, y + 4 + iconOffset, x2 - x1, 6);
   }
 
   void drawNotCanonicalAnnot(Graphics g, Color nonCanColor,
@@ -251,7 +261,8 @@ public class AnnotationRenderer
             : row_annotations[column - 1].displayCharacter;
 
     boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
-            || !dc.equals(row_annotations[sCol - 1].displayCharacter);
+            || !dc.equals(row_annotations[sCol - 1].displayCharacter)
+            || !validEnd;
     boolean diffdownstream = !validRes || !validEnd
             || row_annotations[column] == null
             || !dc.equals(row_annotations[column].displayCharacter);
@@ -304,7 +315,7 @@ public class AnnotationRenderer
     }
     // draw arrow body
     unsetAntialias(g);
-    fillRect(g, x1 - 1, y + 4 + iconOffset, x2 - x1 + 1, 6);
+    fillRect(g, x1, y + 4 + iconOffset, x2 - x1, 6);
   }
 
   // public void updateFromAnnotationPanel(FontMetrics annotFM, AlignViewportI
@@ -469,7 +480,7 @@ public class AnnotationRenderer
   {
     if (g instanceof EpsGraphics2D || g instanceof SVGGraphics2D)
     {
-      this.setVectorRendition(true);
+      this.setVectorRendering(true);
     }
     Graphics2D g2d = (Graphics2D) g;
 
@@ -622,6 +633,9 @@ public class AnnotationRenderer
         // first pass sets up state for drawing continuation from left-hand
         // column
         // of startRes
+
+        // flag used for vector rendition
+        this.glyphLineDrawn = false;
         x = (startRes == 0) ? 0 : -1;
         while (x < endRes - startRes)
         {
@@ -908,7 +922,7 @@ public class AnnotationRenderer
                   // temp = x;
                   break;
                 default:
-                  if (isVectorRendition())
+                  if (isVectorRendering())
                   {
                     // draw single full width glyphline
                     drawGlyphLine(g, lastSSX, endRes - x, y, iconOffset);
@@ -1049,7 +1063,7 @@ public class AnnotationRenderer
                     x, y, iconOffset, startRes, column, validRes, validEnd);
             break;
           default:
-            if (isVectorRendition())
+            if (isVectorRendering())
             {
               // draw single full width glyphline
               drawGlyphLine(g, lastSSX, endRes - x, y, iconOffset);
@@ -1204,13 +1218,7 @@ public class AnnotationRenderer
     }
     unsetAntialias(g);
     g.setColor(GLYPHLINE_COLOR);
-    g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth) - lastSSX - 1,
-            2);
-    if (!isVectorRendition())
-    {
-      g.drawRect(lastSSX, y + 6 + iconOffset, (x * charWidth) - lastSSX - 1,
-              2);
-    }
+    g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth) - lastSSX, 2);
   }
 
   void drawSheetAnnot(Graphics g, Annotation[] row,
@@ -1226,7 +1234,7 @@ public class AnnotationRenderer
 
       g.setColor(SHEET_COLOUR);
       fillRect(g, lastSSX, y + 4 + iconOffset,
-              (x * charWidth) - lastSSX - 4, isVectorRendition() ? 6 : 7);
+              (x * charWidth) - lastSSX - 4, 6);
       fillPolygon(g,
               new int[]
               { (x * charWidth) - 6, (x * charWidth) - 6,
@@ -1239,8 +1247,8 @@ public class AnnotationRenderer
     else
     {
       g.setColor(SHEET_COLOUR);
-      fillRect(g, lastSSX, y + 4 + iconOffset, x * charWidth - lastSSX,
-              isVectorRendition() ? 6 : 7);
+      fillRect(g, lastSSX, y + 4 + iconOffset, (x * charWidth) - lastSSX,
+              6);
     }
   }
 
@@ -1253,7 +1261,7 @@ public class AnnotationRenderer
     int x1 = lastSSX;
     int x2 = (x * charWidth);
 
-    if (USE_FILL_ROUND_RECT || isVectorRendition())
+    if (USE_FILL_ROUND_RECT || isVectorRendering())
     {
       // draw glyph line behind helix (visible in EPS or SVG output)
       drawGlyphLine(g, lastSSX, x, y, iconOffset);
@@ -1270,7 +1278,6 @@ public class AnnotationRenderer
       }
       else
       {
-        // g.setColor(Color.orange);
         fillRoundRect(g, lastSSX, y + 3 + iconOffset, x2 - x1 - ofs, 8, 0,
                 0);
       }
@@ -1281,7 +1288,6 @@ public class AnnotationRenderer
       }
       else
       {
-        // g.setColor(Color.magenta);
         fillRoundRect(g, lastSSX + ofs, y + 3 + iconOffset, x2 - x1 - ofs,
                 8, 0, 0);
       }
@@ -1308,8 +1314,8 @@ public class AnnotationRenderer
 
     if (rightEnd)
     {
-      fillArc(g, (x * charWidth) - charWidth - 1, y + 3 + iconOffset,
-              charWidth, 8, 270, 180);
+      fillArc(g, ((x - 1) * charWidth), y + 3 + iconOffset, charWidth, 8,
+              270, 180);
       x2 -= charWidth / 2;
     }
 
@@ -1834,14 +1840,8 @@ public class AnnotationRenderer
 
   private void fillPolygon(Graphics g, int[] xpoints, int[] ypoints, int n)
   {
-    unsetAntialias(g);
+    setAntialias(g);
     g.fillPolygon(xpoints, ypoints, n);
-    if (!isVectorRendition())
-    {
-      setAntialias(g);
-      g.fillPolygon(xpoints, ypoints, n);
-      g.drawPolygon(xpoints, ypoints, n);
-    }
   }
 
   /*
@@ -1852,13 +1852,8 @@ public class AnnotationRenderer
 
   private void fillRect(Graphics g, int a, int b, int c, int d)
   {
+    unsetAntialias(g);
     g.fillRect(a, b, c, d);
-    /*
-    if (false && !isVectorRendition() && drawRect)
-    {
-      g.drawRect(a, b, c, d);
-    }
-    */
   }
 
   private void fillRoundRect(Graphics g, int a, int b, int c, int d, int e,
@@ -1866,20 +1861,12 @@ public class AnnotationRenderer
   {
     setAntialias(g);
     g.fillRoundRect(a, b, c, d, e, f);
-    if (!isVectorRendition())
-    {
-      g.drawRoundRect(a, b, c, d, e, f);
-    }
   }
 
   private void fillArc(Graphics g, int a, int b, int c, int d, int e, int f)
   {
     setAntialias(g);
     g.fillArc(a, b, c, d, e, f);
-    if (!isVectorRendition())
-    {
-      g.drawArc(a, b, c, d, e, f);
-    }
   }
 
   private void drawLine(Graphics g, Stroke s, int a, int b, int c, int d)
@@ -1899,7 +1886,7 @@ public class AnnotationRenderer
 
   private void setAntialias(Graphics g)
   {
-    if (isVectorRendition())
+    if (isVectorRendering())
     {
       // no need to antialias vector drawings
       return;
@@ -1914,7 +1901,7 @@ public class AnnotationRenderer
 
   private void unsetAntialias(Graphics g)
   {
-    if (isVectorRendition())
+    if (isVectorRendering())
     {
       // no need to antialias vector drawings
       return;
@@ -1924,13 +1911,13 @@ public class AnnotationRenderer
             RenderingHints.VALUE_ANTIALIAS_OFF);
   }
 
-  public void setVectorRendition(boolean b)
+  public void setVectorRendering(boolean b)
   {
-    vectorRendition = b;
+    renderingVectors = b;
   }
 
-  public boolean isVectorRendition()
+  public boolean isVectorRendering()
   {
-    return vectorRendition;
+    return renderingVectors;
   }
 }