basic hack to get (almost) equal height density plot

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index a0e530c..5083ac8 100644 (file)
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -366,8 +366,7 @@ public class AnnotationRenderer
         }
         else
         {
-          return AAFrequency.extractProfile(
-hconsensus.get(column),
+          return AAFrequency.extractProfile(hconsensus.get(column),
                   av_ignoreGapsConsensus);
         }
       }
@@ -1030,9 +1029,18 @@ hconsensus.get(column),
           }
           else if (row.graph == AlignmentAnnotation.BAR_GRAPH)
           {
+            if (row.autoCalculated && row.label != null
+                    && row.label.startsWith("Consen"))
+            {
+              drawProfileDensity(g, row, row_annotations, startRes, endRes,
+                      row.graphMin, row.graphMax, y);
+            }
+            else
+            {
             drawBarGraph(g, row, row_annotations, startRes, endRes,
                     row.graphMin, row.graphMax, y, renderHistogram,
                     renderProfile, normaliseProfile);
+            }
           }
         }
       }
@@ -1619,4 +1627,129 @@ hconsensus.get(column),
 
     }
   }
+
+  void drawProfileDensity(Graphics g, AlignmentAnnotation _aa,
+          Annotation[] aa_annotations, int sRes, int eRes, float min,
+          float max, int y)
+  {
+    if (sRes > aa_annotations.length)
+    {
+      return;
+    }
+    Font ofont = g.getFont();
+    eRes = Math.min(eRes, aa_annotations.length);
+
+    int x = 0, y2 = y;
+
+
+
+    g.setColor(Color.pink);
+
+    g.drawLine(x, y2, (eRes - sRes) * charWidth, y2);
+
+    int column;
+    int aaMax = aa_annotations.length - 1;
+    while (x < eRes - sRes)
+    {
+      column = sRes + x;
+      if (hasHiddenColumns)
+      {
+        column = columnSelection.adjustForHiddenColumns(column);
+      }
+
+      if (column > aaMax)
+      {
+        break;
+      }
+
+      if (aa_annotations[column] == null)
+      {
+        x++;
+        continue;
+      }
+      if (aa_annotations[column].colour == null)
+      {
+        g.setColor(Color.black);
+      }
+      else
+      {
+        g.setColor(aa_annotations[column].colour);
+      }
+
+
+      /*
+       * {profile type, #values, total count, char1, pct1, char2, pct2...}
+       */
+      int profl[] = getProfileFor(_aa, column);
+
+      // just try to draw the logo if profl is not null
+      if (profl != null && profl[2] != 0)
+      {
+        boolean isStructureProfile = profl[0] == AlignmentAnnotation.STRUCTURE_PROFILE;
+        boolean isCdnaProfile = profl[0] == AlignmentAnnotation.CDNA_PROFILE;
+        float ht = y2; // - _aa.graphHeight;
+        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)];
+
+        double scale = _aa.graphHeight / (profl[1]);
+
+        /*
+         * Traverse the character(s)/percentage data in the array
+         */
+        int c = 3;
+        int valuesProcessed = 0;
+        // profl[1] is the number of values in the profile
+
+        while (valuesProcessed < profl[1])
+        {
+          if (isStructureProfile)
+          {
+            // todo can we encode a structure pair as an int, like codons?
+            dc[0] = (char) profl[c++];
+            dc[1] = (char) profl[c++];
+          }
+          else if (isCdnaProfile)
+          {
+            dc = CodingUtils.decodeCodon(profl[c++]);
+          }
+          else
+          {
+            dc[0] = (char) profl[c++];
+          }
+
+          ht -= scale;
+          // next profl[] position is profile % for the character(s)
+          // render boxes
+          g.setColor(jalview.util.ColorUtils.getGraduatedColour(profl[c++],
+                  0f, Color.gray, 100, Color.blue));
+          // g.setColor(profcolour.findColour(dc[0]).darker());
+
+          g.fillRect(x * charWidth, (int) ht, charWidth, (int) scale);
+          valuesProcessed++;
+        }
+        g.setFont(ofont);
+      }
+      x++;
+
+    }
+
+    // if (_aa.threshold != null)
+    // {
+    // g.setColor(_aa.threshold.colour);
+    // Graphics2D g2 = (Graphics2D) g;
+    // g2.setStroke(new BasicStroke(1, BasicStroke.CAP_SQUARE,
+    // BasicStroke.JOIN_ROUND, 3f, new float[] { 5f, 3f }, 0f));
+    //
+    // y2 = (int) (y - ((_aa.threshold.value - min) / range)
+    // * _aa.graphHeight);
+    // g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
+    // g2.setStroke(new BasicStroke());
+    // }
+  }
+
 }