From: hansonr <hansonr@stolaf.edu>
Date: Wed, 27 Jun 2018 10:14:00 +0000 (+0100)
Subject: Consensus LOGO done
X-Git-Tag: Release_2_11_4_0~45^2~18^2~635
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=d6fde28142adb033d7421566a281e347a1b9e1eb;p=jalview.git

Consensus LOGO done
---

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index adca17e..f883b13 100644
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -1298,6 +1298,7 @@ public class AnnotationRenderer
     }
   }
 
+  @SuppressWarnings("unused")
   void drawBarGraph(Graphics g, AlignmentAnnotation _aa,
           Annotation[] aa_annotations, int sRes, int eRes, float min,
           float max, int y, boolean renderHistogram, boolean renderProfile,
@@ -1382,63 +1383,58 @@ public class AnnotationRenderer
           boolean isCdnaProfile = profl[0] == AlignmentAnnotation.CDNA_PROFILE;
           float ht = normaliseProfile ? y - _aa.graphHeight : y1;
           double htn = normaliseProfile ? _aa.graphHeight : (y2 - y1);// aa.graphHeight;
-          double hght;
-          float wdth;
-          double ht2 = 0;
-          char[] dc;
 
           /**
            * Render a single base for a sequence profile, a base pair for
            * structure profile, and a triplet for a cdna profile
            */
-          dc = new char[isStructureProfile ? 2 : (isCdnaProfile ? 3 : 1)];
+          char[] dc = new char[isStructureProfile ? 2
+                  : (isCdnaProfile ? 3 : 1)];
+
+          // lm is not necessary - we can just use fm - could be off by no more
+          // than 0.5 px
+          // LineMetrics lm = g.getFontMetrics(ofont).getLineMetrics("Q", g);
+          // System.out.println(asc + " " + dec + " " + (asc - lm.getAscent())
+          // + " " + (dec - lm.getDescent()));
+
+          double asc = fm.getAscent();
+          double dec = fm.getDescent();
+          double fht = fm.getHeight();
 
-          LineMetrics lm = g.getFontMetrics(ofont).getLineMetrics("Q", g);
           double scale = 1f / (normaliseProfile ? profl[2] : 100f);
-          float ofontHeight = 1f / lm.getAscent();// magnify to fill box
-          double scl = 0.0;
+          // float ofontHeight = 1f / fm.getAscent();// magnify to fill box
 
           /*
            * Traverse the character(s)/percentage data in the array
            */
-          int c = 3;
-          int valuesProcessed = 0;
+
+          float ht2 = ht;
+
           // profl[1] is the number of values in the profile
-          while (valuesProcessed < profl[1])
+          for (int i = 0, c = 3, last = profl[1]; i < last; i++)
           {
+
+            String s;
             if (isStructureProfile)
             {
               // todo can we encode a structure pair as an int, like codons?
               dc[0] = (char) profl[c++];
               dc[1] = (char) profl[c++];
+              s = new String(dc);
             }
             else if (isCdnaProfile)
             {
-              dc = CodingUtils.decodeCodon(profl[c++]);
+              CodingUtils.decodeCodon2(profl[c++], dc);
+              s = new String(dc);
             }
             else
             {
               dc[0] = (char) profl[c++];
+              s = new String(dc);
             }
-
-            wdth = charWidth;
-            wdth /= fm.charsWidth(dc, 0, dc.length);
-
-            ht += scl;
             // next profl[] position is profile % for the character(s)
-            scl = htn * scale * profl[c++];
-            lm = ofont.getLineMetrics(dc, 0, 1,
-                    g.getFontMetrics().getFontRenderContext());
-            Font font = ofont.deriveFont(AffineTransform
-                    .getScaleInstance(wdth, scl / lm.getAscent()));
-            g.setFont(font);
-            lm = g.getFontMetrics().getLineMetrics(dc, 0, 1, g);
-
-            // 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 newHeight = htn * scale * profl[c++];
 
             /*
              * Set character colour as per alignment colour scheme; use the
@@ -1448,7 +1444,7 @@ public class AnnotationRenderer
             if (isCdnaProfile)
             {
               final String codonTranslation = ResidueProperties
-                      .codonTranslate(new String(dc));
+                      .codonTranslate(s);
               colour = profcolour.findColour(codonTranslation.charAt(0),
                       column, null);
             }
@@ -1458,11 +1454,43 @@ public class AnnotationRenderer
             }
             g.setColor(colour == Color.white ? Color.lightGray : colour);
 
-            hght = (ht + (scl - lm.getDescent()
-                    - lm.getBaselineOffsets()[lm.getBaselineIndex()]));
+            // 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());
 
-            g.drawChars(dc, 0, dc.length, x * charWidth, (int) hght);
-            valuesProcessed++;
+            double sx = 1f * charWidth / fm.charsWidth(dc, 0, dc.length);            
+            double sy = newHeight / asc;
+            double newAsc = asc * sy; 
+            double newDec = dec * sy;
+            // it is not necessary to recalculated lm for the new font.
+            // note: lm.getBaselineOffsets()[lm.getBaselineIndex()]) must be 0
+            // by definition. Was:
+            // int hght = (int) (ht + (newAsc - newDec - lm.getBaselineOffsets()[lm.getBaselineIndex()]));
+
+            // original:
+
+             if (/** @j2sNative false && */ true) {
+               int hght = (int) (ht + (newAsc - newDec)); // Q: why " - newDec " ? (0,0) is on the font baseline, I think
+               Font font = ofont.deriveFont(AffineTransform.getScaleInstance(sx, sy));
+               g.setFont(font);
+               g.drawChars(dc, 0, dc.length, x * charWidth, hght);
+               ht += newHeight;
+             } else {
+              // SwingJS does not implement font.deriveFont() 
+              // this is off by a very small amount. 
+              int hght2 = (int) (ht2 + newAsc);               
+              Graphics2D gg = (Graphics2D) g.create();
+              gg.setFont(ofont);
+              gg.transform(AffineTransform.getScaleInstance(sx, sy));
+              //System.out.println("sx " + sx + " sy " + sy + " " + hght + " " + lm.getDescent() + " " + dec + " " + newDec + " " + lm.getAscent() + " " + asc + " " + newAsc);
+              gg.drawString(s, (int) (x * charWidth / sx),
+                      (int) (hght2 / sy));
+              gg.dispose();
+              ht2 += newHeight;
+            }
+            
           }
           g.setFont(ofont);
         }
@@ -1475,7 +1503,7 @@ public class AnnotationRenderer
       Graphics2D g2 = (Graphics2D) g;
       g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
               BasicStroke.JOIN_ROUND, 3f, new float[]
-              { 5f, 3f }, 0f));
+      { 5f, 3f }, 0f));
 
       y2 = (int) (y
               - ((_aa.threshold.value - min) / range) * _aa.graphHeight);