Merge branch 'bug/JAL-247pngShowHiddenSeqMarks' into trialMerge

[jalview.git] / src / jalview / gui / SeqCanvas.java

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 7ecedf4..b6b0d29 100755 (executable)
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -151,7 +151,6 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
     for (ScaleMark mark : marks)
     {
       int mpos = mark.column; // (i - startx - 1)
-//      System.out.println("n " + mpos +  " "  + ypos);
       if (mpos < 0)
       {
         continue;
@@ -199,9 +198,6 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
     int startX = startx;
     int endX = endx;
     
-    //System.out.println("v " + startx +  " "  + endx + " " + ypos);
-
-
     if (av.hasHiddenColumns())
     {
       HiddenColumns hiddenColumns = av.getAlignment().getHiddenColumns();
@@ -237,6 +233,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
         }
       }
 
+      
       /*
        * white fill the space for the scale
        */
@@ -245,7 +242,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
       // fillRect origin is top left of rectangle
       g.fillRect(0, y - charHeight, left ? labelWidthWest : labelWidthEast,
               charHeight + 1);
- 
+
       if (value != -1)
       {
         /*
@@ -259,11 +256,9 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
         int xOffset = labelSpace - labelLength;
         g.setColor(Color.black);
         g.drawString(valueAsString, xOffset, y);
-        
-        //System.out.println("v " + valueAsString + " " + xOffset +  " "  + y);
-
       }
     }
+
   }
 
   /**
@@ -672,7 +667,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
     calculateWrappedGeometry(canvasWidth, canvasHeight);
 
     /*
-     * draw one width at a time (including any scales or annotation shown),
+     * draw one width at a time (excluding any scales or annotation shown),
      * until we have run out of either alignment or vertical space available
      */
     int ypos = wrappedSpaceAboveAlignment;
@@ -723,7 +718,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
      */
     wrappedRepeatHeightPx = wrappedSpaceAboveAlignment;
     // add sequences
-    wrappedRepeatHeightPx += av.getRanges().getViewportHeight()
+    wrappedRepeatHeightPx += av.getAlignment().getHeight()
             * charHeight;
     // add annotations panel height if shown
     wrappedRepeatHeightPx += getAnnotationHeight();
@@ -787,12 +782,25 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
     int xOffset = labelWidthWest
             + ((startColumn - ranges.getStartRes()) % viewportWidth)
             * charWidth;
+
+    // BH 2018 note: I have switched to using Graphics.create() here because it is 
+    // more reliable (and simpler) to reset. The difference seems to be that SwingJS 
+    // automatically sets a clipping region on an image to be the image dimensions, whereas
+    // Java sets no clip for an image. (A bug? Go figure!)
+    // Since we are using an off-screen BufferedImage here, the result is that g.getClip()
+    // returns non-null in JavaScript but not Java. 
+    //
+    // Anyway, this works and, I suggest, is better design anyway. 
+    // 
+    // Graphics g = gg.create();
+    // mc 30/08/18 undone because gnu.jpdf.PDFGraphics doesn't handle
+    // get/setTransform
+
     g.translate(xOffset, 0);
 
     // When printing we have an extra clipped region,
     // the Printable page which we need to account for here
     Shape clip = g.getClip();
-
     if (clip == null)
     {
       g.setClip(0, 0, viewportWidth * charWidth, canvasHeight);
@@ -803,6 +811,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
               viewportWidth * charWidth, (int) clip.getBounds().getHeight());
     }
 
+
     /*
      * white fill the region to be drawn (so incremental fast paint doesn't
      * scribble over an existing image)
@@ -828,8 +837,9 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
               startColumn, endx + 1);
       g.translate(0, -cHeight - ypos - 3);
     }
-    g.setClip(clip);
+    // g.dispose();
     g.translate(-xOffset, 0);
+//    g.setClip(clip);
   }
 
   /**
@@ -844,6 +854,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
     int charWidth = av.getCharWidth();
 
     g.setFont(av.getFont());
+
     g.setColor(Color.black);
 
     int ypos = wrappedSpaceAboveAlignment;
@@ -866,7 +877,6 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
       {
         int x = labelWidthWest + viewportWidth * charWidth;
         
-        //System.out.println("shifting " + x);
         g.translate(x, 0);
         drawVerticalScale(g, startCol, endColumn, ypos, false);
         g.translate(-x, 0);