X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FAnnotationRenderer.java;h=5a53b717ef7e826cc228fe3fe50ebc5b5b20fb49;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=d0670c20d0b8fe2b646e1bbeaa1100ff43dba69d;hpb=a7a2f92e4f62caadd8992459f802753dc3170700;p=jalview.git

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index d0670c2..5a53b71 100644
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -1,9 +1,28 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.renderer;
 
 import jalview.analysis.AAFrequency;
 import jalview.analysis.StructureFrequency;
 import jalview.api.AlignViewportI;
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
 import jalview.schemes.ColourSchemeI;
 
@@ -17,19 +36,32 @@ import java.awt.Image;
 import java.awt.font.LineMetrics;
 import java.awt.geom.AffineTransform;
 import java.awt.image.ImageObserver;
+import java.util.BitSet;
 import java.util.Hashtable;
 
 import com.stevesoft.pat.Regex;
 
 public class AnnotationRenderer
 {
+  /**
+   * flag indicating if timing and redraw parameter info should be output
+   */
+  private final boolean debugRedraw;
 
   public AnnotationRenderer()
   {
-    // TODO Auto-generated constructor stub
+    this(false);
+  }
+  /**
+   * Create a new annotation Renderer
+   * @param debugRedraw flag indicating if timing and redraw parameter info should be output
+   */
+  public AnnotationRenderer(boolean debugRedraw)
+  {
+    this.debugRedraw=debugRedraw;
   }
 
-  public void drawStemAnnot(Graphics g, AlignmentAnnotation row,
+  public void drawStemAnnot(Graphics g, Annotation[] row_annotations,
           int lastSSX, int x, int y, int iconOffset, int startRes,
           int column, boolean validRes, boolean validEnd)
   {
@@ -39,21 +71,21 @@ public class AnnotationRenderer
     int x2 = (x * charWidth);
     Regex closeparen = new Regex("(\\))");
 
-    String dc = (column == 0 || row.annotations[column - 1] == null) ? ""
-            : row.annotations[column - 1].displayCharacter;
+    String dc = (column == 0 || row_annotations[column - 1] == null) ? ""
+            : row_annotations[column - 1].displayCharacter;
 
-    boolean diffupstream = sCol == 0 || row.annotations[sCol - 1] == null
-            || !dc.equals(row.annotations[sCol - 1].displayCharacter);
+    boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
+            || !dc.equals(row_annotations[sCol - 1].displayCharacter);
     boolean diffdownstream = !validRes || !validEnd
-            || row.annotations[column] == null
-            || !dc.equals(row.annotations[column].displayCharacter);
+            || row_annotations[column] == null
+            || !dc.equals(row_annotations[column].displayCharacter);
     // System.out.println("Column "+column+" diff up: "+diffupstream+" down:"+diffdownstream);
     // If a closing base pair half of the stem, display a backward arrow
     if (column > 0 && closeparen.search(dc))
     {
       if (diffupstream)
-      // if (validRes && column>1 && row.annotations[column-2]!=null &&
-      // dc.equals(row.annotations[column-2].displayCharacter))
+      // if (validRes && column>1 && row_annotations[column-2]!=null &&
+      // dc.equals(row_annotations[column-2].displayCharacter))
       {
         g.fillPolygon(new int[]
         { lastSSX + 5, lastSSX + 5, lastSSX }, new int[]
@@ -90,7 +122,7 @@ public class AnnotationRenderer
 
   private FontMetrics fm;
 
-  private boolean MAC = new jalview.util.Platform().isAMac();
+  private final boolean MAC = new jalview.util.Platform().isAMac();
 
   boolean av_renderHistogram = true, av_renderProfile = true,
           av_normaliseProfile = false;
@@ -123,7 +155,23 @@ public class AnnotationRenderer
    * width of image to render in panel
    */
   private int imgWidth;
-
+  /**
+   * offset to beginning of visible area
+   */
+  private int sOffset;
+  /**
+   * offset to end of visible area
+   */
+  private int visHeight;
+  /**
+   * indicate if the renderer should only render the visible portion of the annotation given the current view settings
+   */
+  private boolean useClip=true;
+  /**
+   * master flag indicating if renderer should ever try to clip. not enabled for jalview 2.8.1 
+   */
+  private boolean canClip=false;
+  
   // public void updateFromAnnotationPanel(FontMetrics annotFM, AlignViewportI
   // av)
   public void updateFromAwtRenderPanel(AwtRenderPanelI annotPanel,
@@ -133,6 +181,22 @@ public class AnnotationRenderer
     annotationPanel = annotPanel;
     fadedImage = annotPanel.getFadedImage();
     imgWidth = annotPanel.getFadedImageWidth();
+    // visible area for rendering
+    int[] bounds=annotPanel.getVisibleVRange();
+    if (bounds!=null)
+    {
+      sOffset = bounds[0];
+      visHeight = bounds[1];
+      if (visHeight==0)
+      {
+        useClip=false;
+      } else {
+        useClip=canClip;
+      }
+    } else {
+      useClip=false;
+    }
+
     updateFromAlignViewport(av);
   }
 
@@ -177,7 +241,7 @@ public class AnnotationRenderer
       }
       // TODO extend annotation row to enable dynamic and static profile data to
       // be stored
-      if (aa.groupRef == null && aa.sequenceRef == null && av_renderProfile)
+      if (aa.groupRef == null && aa.sequenceRef == null)
       {
         return AAFrequency.extractProfile(hconsensus[column],
                 av_ignoreGapsConsensus);
@@ -199,7 +263,7 @@ public class AnnotationRenderer
         // to
         // be stored
         if (aa.groupRef == null && aa.sequenceRef == null
-                && av_renderProfile && hStrucConsensus != null
+                && hStrucConsensus != null
                 && hStrucConsensus.length > column)
         {
           return StructureFrequency.extractProfile(hStrucConsensus[column],
@@ -211,27 +275,39 @@ public class AnnotationRenderer
   }
 
   /**
-   * DOCUMENT ME!
+   * Render the annotation rows associated with an alignment.
    * 
-   * @param annotationPanel
-   *          TODO
+   * @param annotPanel
+   *          container frame
+   * @param av
+   *          data and view settings to render
    * @param g
-   *          DOCUMENT ME!
+   *          destination for graphics
+   * @param activeRow
+   *          row where a mouse event occured (or -1)
    * @param startRes
-   *          DOCUMENT ME!
+   *          first column that will be drawn
    * @param endRes
-   *          DOCUMENT ME!
+   *          last column that will be drawn
+   * @return true if the fadedImage was used for any alignment annotation rows
+   *         currently being calculated
    */
-  public void drawComponent(AwtRenderPanelI annotPanel, AlignViewportI av,
-          Graphics g, int activeRow, int startRes, int endRes)
+  public boolean drawComponent(AwtRenderPanelI annotPanel,
+          AlignViewportI av, Graphics g, int activeRow, int startRes,
+          int endRes)
   {
+    long stime=System.currentTimeMillis();
+    boolean usedFaded = false;
     // NOTES:
     // AnnotationPanel needs to implement: ImageObserver, access to
     // AlignViewport
     updateFromAwtRenderPanel(annotPanel, av);
     fm = g.getFontMetrics();
     AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
-
+    if (aa==null)
+    {
+      return false;
+    }
     int x = 0, y = 0;
     int column = 0;
     char lastSS;
@@ -243,16 +319,42 @@ public class AnnotationRenderer
     boolean centreColLabels, centreColLabelsDef = av
             .getCentreColumnLabels();
     boolean scaleColLabel = false;
-    boolean[] graphGroupDrawn = new boolean[aa.length];
+    AlignmentAnnotation consensusAnnot=av.getAlignmentConsensusAnnotation(),structConsensusAnnot=av.getAlignmentStrucConsensusAnnotation();
+    boolean renderHistogram = true, renderProfile = true, normaliseProfile = false;
+
+    BitSet graphGroupDrawn = new BitSet();
     int charOffset = 0; // offset for a label
     float fmWidth, fmScaling = 1f; // scaling for a label to fit it into a
     // column.
     Font ofont = g.getFont();
     // \u03B2 \u03B1
+    // debug ints
+    int yfrom=0,f_i=0,yto=0,f_to=0;
+    boolean clipst=false,clipend=false;
     for (int i = 0; i < aa.length; i++)
     {
       AlignmentAnnotation row = aa[i];
-
+      {
+        // check if this is a consensus annotation row and set the display settings appropriately
+        // TODO: generalise this to have render styles for consensus/profile
+        // data
+        if (row.groupRef != null && row == row.groupRef.getConsensus())
+        {
+          renderHistogram = row.groupRef.isShowConsensusHistogram();
+          renderProfile = row.groupRef.isShowSequenceLogo();
+          normaliseProfile = row.groupRef.isNormaliseSequenceLogo();
+        }
+        else if (row == consensusAnnot || row == structConsensusAnnot)
+        {
+          renderHistogram = av_renderHistogram;
+          renderProfile = av_renderProfile;
+          normaliseProfile = av_normaliseProfile;
+        } else {
+          renderHistogram = true;
+          // don't need to set render/normaliseProfile since they are not currently used in any other annotation track renderer
+        }
+      }
+      Annotation[] row_annotations = row.annotations;
       if (!row.visible)
       {
         continue;
@@ -262,10 +364,20 @@ public class AnnotationRenderer
       scaleColLabel = row.scaleColLabel;
       lastSS = ' ';
       lastSSX = 0;
+      
+      if (!useClip || ((y-charHeight)<visHeight && (y+row.height+charHeight*2)>=sOffset)) 
+      {// if_in_visible_region
+        if (!clipst)
+        {
+          clipst=true;
+          yfrom=y;
+          f_i=i;
+        }
+        yto = y;
+        f_to=i;
       if (row.graph > 0)
       {
-        if (row.graphGroup > -1 && graphGroupDrawn[row.graphGroup])
-        {
+        if (row.graphGroup > -1 && graphGroupDrawn.get(row.graphGroup)) {
           continue;
         }
 
@@ -288,10 +400,10 @@ public class AnnotationRenderer
         iconOffset = 0;
       }
 
-      if (aa[i].autoCalculated && av.isCalculationInProgress(aa[i]))
+      if (row.autoCalculated && av.isCalculationInProgress(row))
       {
         y += charHeight;
-
+        usedFaded = true;
         g.drawImage(fadedImage, 0, y - row.height, imgWidth, y, 0, y
                 - row.height, imgWidth, y, annotationPanel);
         g.setColor(Color.black);
@@ -329,7 +441,7 @@ public class AnnotationRenderer
         if (hasHiddenColumns)
         {
           column = columnSelection.adjustForHiddenColumns(startRes + x);
-          if (column > row.annotations.length - 1)
+          if (column > row_annotations.length - 1)
           {
             break;
           }
@@ -339,8 +451,8 @@ public class AnnotationRenderer
           column = startRes + x;
         }
 
-        if ((row.annotations == null) || (row.annotations.length <= column)
-                || (row.annotations[column] == null))
+        if ((row_annotations == null) || (row_annotations.length <= column)
+                || (row_annotations[column] == null))
         {
           validRes = false;
         }
@@ -375,16 +487,16 @@ public class AnnotationRenderer
           }
           if (validCharWidth
                   && validRes
-                  && row.annotations[column].displayCharacter != null
-                  && (row.annotations[column].displayCharacter.length() > 0))
+                  && row_annotations[column].displayCharacter != null
+                  && (row_annotations[column].displayCharacter.length() > 0))
           {
 
             if (centreColLabels || scaleColLabel)
             {
-              fmWidth = (float) fm.charsWidth(
-                      row.annotations[column].displayCharacter
+              fmWidth = fm.charsWidth(
+                      row_annotations[column].displayCharacter
                               .toCharArray(), 0,
-                      row.annotations[column].displayCharacter.length());
+                      row_annotations[column].displayCharacter.length());
 
               if (scaleColLabel)
               {
@@ -403,29 +515,29 @@ public class AnnotationRenderer
             }
             else
             {
-              fmWidth = (float) fm
-                      .charWidth(row.annotations[column].displayCharacter
+              fmWidth = fm
+                      .charWidth(row_annotations[column].displayCharacter
                               .charAt(0));
             }
             charOffset = (int) ((charWidth - fmWidth) / 2f);
 
-            if (row.annotations[column].colour == null)
+            if (row_annotations[column].colour == null)
               g.setColor(Color.black);
             else
-              g.setColor(row.annotations[column].colour);
+              g.setColor(row_annotations[column].colour);
 
             if (column == 0 || row.graph > 0)
             {
-              g.drawString(row.annotations[column].displayCharacter,
+              g.drawString(row_annotations[column].displayCharacter,
                       (x * charWidth) + charOffset, y + iconOffset);
             }
-            else if (row.annotations[column - 1] == null
+            else if (row_annotations[column - 1] == null
                     || (labelAllCols
-                            || !row.annotations[column].displayCharacter
-                                    .equals(row.annotations[column - 1].displayCharacter) || (row.annotations[column].displayCharacter
-                            .length() < 2 && row.annotations[column].secondaryStructure == ' ')))
+                            || !row_annotations[column].displayCharacter
+                                    .equals(row_annotations[column - 1].displayCharacter) || (row_annotations[column].displayCharacter
+                            .length() < 2 && row_annotations[column].secondaryStructure == ' ')))
             {
-              g.drawString(row.annotations[column].displayCharacter, x
+              g.drawString(row_annotations[column].displayCharacter, x
                       * charWidth + charOffset, y + iconOffset);
             }
             g.setFont(ofont);
@@ -433,12 +545,12 @@ public class AnnotationRenderer
         }
         if (row.hasIcons)
         {
-          char ss = validRes ? row.annotations[column].secondaryStructure
+          char ss = validRes ? row_annotations[column].secondaryStructure
                   : ' ';
           if (ss == 'S')
           {
             // distinguish between forward/backward base-pairing
-            if (row.annotations[column].displayCharacter.indexOf(')') > -1)
+            if (row_annotations[column].displayCharacter.indexOf(')') > -1)
             {
               ss = 's';
             }
@@ -450,19 +562,19 @@ public class AnnotationRenderer
               switch (lastSS)
               {
               case 'H':
-                drawHelixAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
-                        column, validRes, validEnd);
+                drawHelixAnnot(g, row_annotations, lastSSX, x, y,
+                        iconOffset, startRes, column, validRes, validEnd);
                 break;
 
               case 'E':
-                drawSheetAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
-                        column, validRes, validEnd);
+                drawSheetAnnot(g, row_annotations, lastSSX, x, y,
+                        iconOffset, startRes, column, validRes, validEnd);
                 break;
 
               case 'S': // Stem case for RNA secondary structure
               case 's': // and opposite direction
-                drawStemAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
-                        column, validRes, validEnd);
+                drawStemAnnot(g, row_annotations, lastSSX, x, y,
+                        iconOffset, startRes, column, validRes, validEnd);
                 break;
 
               default:
@@ -490,17 +602,17 @@ public class AnnotationRenderer
         column++;
         x++;
       }
-      if (column >= row.annotations.length)
+      if (column >= row_annotations.length)
       {
-        column = row.annotations.length - 1;
+        column = row_annotations.length - 1;
         validEnd = false;
       }
       else
       {
         validEnd = true;
       }
-      if ((row.annotations == null) || (row.annotations.length <= column)
-              || (row.annotations[column] == null))
+      if ((row_annotations == null) || (row_annotations.length <= column)
+              || (row_annotations[column] == null))
       {
         validRes = false;
       }
@@ -516,22 +628,22 @@ public class AnnotationRenderer
         switch (lastSS)
         {
         case 'H':
-          drawHelixAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
-                  column, validRes, validEnd);
+          drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
+                  startRes, column, validRes, validEnd);
           break;
 
         case 'E':
-          drawSheetAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
-                  column, validRes, validEnd);
+          drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
+                  startRes, column, validRes, validEnd);
           break;
         case 's':
         case 'S': // Stem case for RNA secondary structure
-          drawStemAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
-                  column, validRes, validEnd);
+          drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
+                  startRes, column, validRes, validEnd);
           break;
         default:
-          drawGlyphLine(g, row, lastSSX, x, y, iconOffset, startRes,
-                  column, validRes, validEnd);
+          drawGlyphLine(g, row_annotations, lastSSX, x, y, iconOffset,
+                  startRes, column, validRes, validEnd);
           break;
         }
       }
@@ -540,8 +652,9 @@ public class AnnotationRenderer
       {
         if (row.graph == AlignmentAnnotation.LINE_GRAPH)
         {
-          if (row.graphGroup > -1 && !graphGroupDrawn[row.graphGroup])
+          if (row.graphGroup > -1 && !graphGroupDrawn.get(row.graphGroup))
           {
+            // TODO: JAL-1291 revise rendering model so the graphGroup map is computed efficiently for all visible labels
             float groupmax = -999999, groupmin = 9999999;
             for (int gg = 0; gg < aa.length; gg++)
             {
@@ -554,7 +667,6 @@ public class AnnotationRenderer
               {
                 aa[gg].visible = false;
               }
-
               if (aa[gg].graphMax > groupmax)
               {
                 groupmax = aa[gg].graphMax;
@@ -569,26 +681,31 @@ public class AnnotationRenderer
             {
               if (aa[gg].graphGroup == row.graphGroup)
               {
-                drawLineGraph(g, aa[gg], startRes, endRes, y, groupmin,
-                        groupmax, row.graphHeight);
+                drawLineGraph(g, aa[gg], aa[gg].annotations, startRes,
+                        endRes, y, groupmin, groupmax, row.graphHeight);
               }
             }
 
-            graphGroupDrawn[row.graphGroup] = true;
+            graphGroupDrawn.set(row.graphGroup);
           }
           else
           {
-            drawLineGraph(g, row, startRes, endRes, y, row.graphMin,
-                    row.graphMax, row.graphHeight);
+            drawLineGraph(g, row, row_annotations, startRes, endRes, y,
+                    row.graphMin, row.graphMax, row.graphHeight);
           }
         }
         else if (row.graph == AlignmentAnnotation.BAR_GRAPH)
         {
-          drawBarGraph(g, row, startRes, endRes, row.graphMin,
-                  row.graphMax, y);
+          drawBarGraph(g, row, row_annotations, startRes, endRes,
+                  row.graphMin, row.graphMax, y, renderHistogram,renderProfile,normaliseProfile);
         }
       }
-
+    } else {
+      if (clipst && !clipend)
+      {
+        clipend = true;
+      }
+    }// end if_in_visible_region
       if (row.graph > 0 && row.hasText)
       {
         y += charHeight;
@@ -599,32 +716,54 @@ public class AnnotationRenderer
         y += aa[i].height;
       }
     }
+    if (debugRedraw)
+    {
+      if (canClip)
+      {
+        if (clipst)
+        {
+          System.err.println("Start clip at : " + yfrom + " (index " + f_i
+                  + ")");
+        }
+        if (clipend)
+        {
+          System.err.println("End clip at : " + yto + " (index " + f_to
+                  + ")");
+        }
+      }
+      ;
+      System.err.println("Annotation Rendering time:"
+              + (System.currentTimeMillis() - stime));
+    }
+    ;
+
+    return !usedFaded;
   }
 
-  private Color GLYPHLINE_COLOR = Color.gray;
+  private final Color GLYPHLINE_COLOR = Color.gray;
 
-  private Color SHEET_COLOUR = Color.green;
+  private final Color SHEET_COLOUR = Color.green;
 
-  private Color HELIX_COLOUR = Color.red;
+  private final Color HELIX_COLOUR = Color.red;
 
-  private Color STEM_COLOUR = Color.blue;
+  private final Color STEM_COLOUR = Color.blue;
 
-  public void drawGlyphLine(Graphics g, AlignmentAnnotation row,
-          int lastSSX, int x, int y, int iconOffset, int startRes,
-          int column, boolean validRes, boolean validEnd)
+  public void drawGlyphLine(Graphics g, Annotation[] row, int lastSSX,
+          int x, int y, int iconOffset, int startRes, int column,
+          boolean validRes, boolean validEnd)
   {
     g.setColor(GLYPHLINE_COLOR);
     g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth) - lastSSX, 2);
   }
 
-  public void drawSheetAnnot(Graphics g, AlignmentAnnotation row,
-          int lastSSX, int x, int y, int iconOffset, int startRes,
-          int column, boolean validRes, boolean validEnd)
+  public void drawSheetAnnot(Graphics g, Annotation[] row, int lastSSX,
+          int x, int y, int iconOffset, int startRes, int column,
+          boolean validRes, boolean validEnd)
   {
     g.setColor(SHEET_COLOUR);
 
-    if (!validEnd || !validRes || row.annotations[column] == null
-            || row.annotations[column].secondaryStructure != 'E')
+    if (!validEnd || !validRes || row == null || row[column] == null
+            || row[column].secondaryStructure != 'E')
     {
       g.fillRect(lastSSX, y + 4 + iconOffset,
               (x * charWidth) - lastSSX - 4, 7);
@@ -642,9 +781,9 @@ public class AnnotationRenderer
 
   }
 
-  public void drawHelixAnnot(Graphics g, AlignmentAnnotation row,
-          int lastSSX, int x, int y, int iconOffset, int startRes,
-          int column, boolean validRes, boolean validEnd)
+  public void drawHelixAnnot(Graphics g, Annotation[] row, int lastSSX,
+          int x, int y, int iconOffset, int startRes, int column,
+          boolean validRes, boolean validEnd)
   {
     g.setColor(HELIX_COLOUR);
 
@@ -658,8 +797,8 @@ public class AnnotationRenderer
       // Off by 1 offset when drawing rects and ovals
       // to offscreen image on the MAC
       g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1, 8, 8, 8);
-      if (sCol == 0 || row.annotations[sCol - 1] == null
-              || row.annotations[sCol - 1].secondaryStructure != 'H')
+      if (sCol == 0 || row[sCol - 1] == null
+              || row[sCol - 1].secondaryStructure != 'H')
       {
       }
       else
@@ -668,8 +807,8 @@ public class AnnotationRenderer
         g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1 - ofs + 1, 8,
                 0, 0);
       }
-      if (!validRes || row.annotations[column] == null
-              || row.annotations[column].secondaryStructure != 'H')
+      if (!validRes || row[column] == null
+              || row[column].secondaryStructure != 'H')
       {
 
       }
@@ -684,15 +823,15 @@ public class AnnotationRenderer
       return;
     }
 
-    if (sCol == 0 || row.annotations[sCol - 1] == null
-            || row.annotations[sCol - 1].secondaryStructure != 'H')
+    if (sCol == 0 || row[sCol - 1] == null
+            || row[sCol - 1].secondaryStructure != 'H')
     {
       g.fillArc(lastSSX, y + 4 + iconOffset, charWidth, 8, 90, 180);
       x1 += charWidth / 2;
     }
 
-    if (!validRes || row.annotations[column] == null
-            || row.annotations[column].secondaryStructure != 'H')
+    if (!validRes || row[column] == null
+            || row[column].secondaryStructure != 'H')
     {
       g.fillArc((x * charWidth) - charWidth, y + 4 + iconOffset, charWidth,
               8, 270, 180);
@@ -702,10 +841,11 @@ public class AnnotationRenderer
     g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
   }
 
-  public void drawLineGraph(Graphics g, AlignmentAnnotation aa, int sRes,
-          int eRes, int y, float min, float max, int graphHeight)
+  public void drawLineGraph(Graphics g, AlignmentAnnotation _aa,
+          Annotation[] aa_annotations, int sRes, int eRes, int y,
+          float min, float max, int graphHeight)
   {
-    if (sRes > aa.annotations.length)
+    if (sRes > aa_annotations.length)
     {
       return;
     }
@@ -718,7 +858,7 @@ public class AnnotationRenderer
       eRes++;
     }
 
-    eRes = Math.min(eRes, aa.annotations.length);
+    eRes = Math.min(eRes, aa_annotations.length);
 
     if (sRes == 0)
     {
@@ -737,10 +877,10 @@ public class AnnotationRenderer
     g.setColor(Color.gray);
     g.drawLine(x - charWidth, y2, (eRes - sRes + 1) * charWidth, y2);
 
-    eRes = Math.min(eRes, aa.annotations.length);
+    eRes = Math.min(eRes, aa_annotations.length);
 
     int column;
-    int aaMax = aa.annotations.length - 1;
+    int aaMax = aa_annotations.length - 1;
 
     while (x < eRes - sRes)
     {
@@ -755,51 +895,52 @@ public class AnnotationRenderer
         break;
       }
 
-      if (aa.annotations[column] == null
-              || aa.annotations[column - 1] == null)
+      if (aa_annotations[column] == null
+              || aa_annotations[column - 1] == null)
       {
         x++;
         continue;
       }
 
-      if (aa.annotations[column].colour == null)
+      if (aa_annotations[column].colour == null)
         g.setColor(Color.black);
       else
-        g.setColor(aa.annotations[column].colour);
+        g.setColor(aa_annotations[column].colour);
 
       y1 = y
-              - (int) (((aa.annotations[column - 1].value - min) / range) * graphHeight);
+              - (int) (((aa_annotations[column - 1].value - min) / range) * graphHeight);
       y2 = y
-              - (int) (((aa.annotations[column].value - min) / range) * graphHeight);
+              - (int) (((aa_annotations[column].value - min) / range) * graphHeight);
 
       g.drawLine(x * charWidth - charWidth / 2, y1, x * charWidth
               + charWidth / 2, y2);
       x++;
     }
 
-    if (aa.threshold != null)
+    if (_aa.threshold != null)
     {
-      g.setColor(aa.threshold.colour);
+      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) * graphHeight);
+      y2 = (int) (y - ((_aa.threshold.value - min) / range) * graphHeight);
       g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
       g2.setStroke(new BasicStroke());
     }
   }
 
-  public void drawBarGraph(Graphics g, AlignmentAnnotation aa, int sRes,
-          int eRes, float min, float max, int y)
+  public void drawBarGraph(Graphics g, AlignmentAnnotation _aa,
+          Annotation[] aa_annotations, int sRes, int eRes, float min,
+          float max, int y, boolean renderHistogram,boolean renderProfile,boolean normaliseProfile)
   {
-    if (sRes > aa.annotations.length)
+    if (sRes > aa_annotations.length)
     {
       return;
     }
     Font ofont = g.getFont();
-    eRes = Math.min(eRes, aa.annotations.length);
+    eRes = Math.min(eRes, aa_annotations.length);
 
     int x = 0, y1 = y, y2 = y;
 
@@ -807,7 +948,7 @@ public class AnnotationRenderer
 
     if (min < 0)
     {
-      y2 = y - (int) ((0 - min / (range)) * aa.graphHeight);
+      y2 = y - (int) ((0 - min / (range)) * _aa.graphHeight);
     }
 
     g.setColor(Color.gray);
@@ -815,24 +956,7 @@ public class AnnotationRenderer
     g.drawLine(x, y2, (eRes - sRes) * charWidth, y2);
 
     int column;
-    int aaMax = aa.annotations.length - 1;
-    boolean renderHistogram = true, renderProfile = true, normaliseProfile = false;
-    // if (aa.autoCalculated && aa.label.startsWith("Consensus"))
-    {
-      // TODO: generalise this to have render styles for consensus/profile data
-      if (aa.groupRef != null)
-      {
-        renderHistogram = aa.groupRef.isShowConsensusHistogram();
-        renderProfile = aa.groupRef.isShowSequenceLogo();
-        normaliseProfile = aa.groupRef.isNormaliseSequenceLogo();
-      }
-      else
-      {
-        renderHistogram = av_renderHistogram;
-        renderProfile = av_renderProfile;
-        normaliseProfile = av_normaliseProfile;
-      }
-    }
+    int aaMax = aa_annotations.length - 1;
     while (x < eRes - sRes)
     {
       column = sRes + x;
@@ -846,18 +970,18 @@ public class AnnotationRenderer
         break;
       }
 
-      if (aa.annotations[column] == null)
+      if (aa_annotations[column] == null)
       {
         x++;
         continue;
       }
-      if (aa.annotations[column].colour == null)
+      if (aa_annotations[column].colour == null)
         g.setColor(Color.black);
       else
-        g.setColor(aa.annotations[column].colour);
+        g.setColor(aa_annotations[column].colour);
 
       y1 = y
-              - (int) (((aa.annotations[column].value - min) / (range)) * aa.graphHeight);
+              - (int) (((aa_annotations[column].value - min) / (range)) * _aa.graphHeight);
 
       if (renderHistogram)
       {
@@ -871,15 +995,15 @@ public class AnnotationRenderer
         }
       }
       // draw profile if available
-      if (renderProfile && aa.annotations[column].value != 0)
+      if (renderProfile)
       {
 
-        int profl[] = getProfileFor(aa, column);
+        int profl[] = getProfileFor(_aa, column);
         // just try to draw the logo if profl is not null
         if (profl != null && profl[1] != 0)
         {
-          float ht = normaliseProfile ? y - aa.graphHeight : y1;
-          double htn = normaliseProfile ? aa.graphHeight : (y2 - y1);// aa.graphHeight;
+          float ht = normaliseProfile ? y - _aa.graphHeight : y1;
+          double htn = normaliseProfile ? _aa.graphHeight : (y2 - y1);// aa.graphHeight;
           double hght;
           float wdth;
           double ht2 = 0;
@@ -906,17 +1030,17 @@ public class AnnotationRenderer
           {
             dc[0] = (char) profl[c++];
 
-            if (aa.label.startsWith("StrucConsensus"))
+            if (_aa.label.startsWith("StrucConsensus"))
             {
               dc[1] = (char) profl[c++];
             }
 
             wdth = charWidth;
-            wdth /= (float) fm.charsWidth(dc, 0, dc.length);
+            wdth /= fm.charsWidth(dc, 0, dc.length);
 
             ht += scl;
             {
-              scl = ((double) htn) * scale * ((double) profl[c++]);
+              scl = htn * scale * profl[c++];
               lm = ofont.getLineMetrics(dc, 0, 1, g.getFontMetrics()
                       .getFontRenderContext());
               g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(
@@ -928,7 +1052,7 @@ public class AnnotationRenderer
               // g.drawRect(x*av.charWidth, (int)ht, av.charWidth,
               // (int)(scl));
               // g.setColor(profcolour.findColour(dc[0]).darker());
-              g.setColor(profcolour.findColour(dc[0]));
+              g.setColor(profcolour.findColour(dc[0], column, null));
 
               hght = (ht + (scl - lm.getDescent() - lm.getBaselineOffsets()[lm
                       .getBaselineIndex()]));
@@ -941,25 +1065,26 @@ public class AnnotationRenderer
       }
       x++;
     }
-    if (aa.threshold != null)
+    if (_aa.threshold != null)
     {
-      g.setColor(aa.threshold.colour);
+      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);
+      y2 = (int) (y - ((_aa.threshold.value - min) / range)
+              * _aa.graphHeight);
       g.drawLine(0, y2, (eRes - sRes) * charWidth, y2);
       g2.setStroke(new BasicStroke());
     }
   }
 
   // used by overview window
-  public void drawGraph(Graphics g, AlignmentAnnotation aa, int width,
-          int y, int sRes, int eRes)
+  public void drawGraph(Graphics g, AlignmentAnnotation _aa,
+          Annotation[] aa_annotations, int width, int y, int sRes, int eRes)
   {
-    eRes = Math.min(eRes, aa.annotations.length);
+    eRes = Math.min(eRes, aa_annotations.length);
     g.setColor(Color.white);
     g.fillRect(0, 0, width, y);
     g.setColor(new Color(0, 0, 180));
@@ -968,14 +1093,14 @@ public class AnnotationRenderer
 
     for (int j = sRes; j < eRes; j++)
     {
-      if (aa.annotations[j] != null)
+      if (aa_annotations[j] != null)
       {
-        if (aa.annotations[j].colour == null)
+        if (aa_annotations[j].colour == null)
           g.setColor(Color.black);
         else
-          g.setColor(aa.annotations[j].colour);
+          g.setColor(aa_annotations[j].colour);
 
-        height = (int) ((aa.annotations[j].value / aa.graphMax) * y);
+        height = (int) ((aa_annotations[j].value / _aa.graphMax) * y);
         if (height > y)
         {
           height = y;