JAL-967, JAL-1114, JAL-1115 - modified render and calculation api to work on bare...

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 375504d..7e77b0f 100755 (executable)
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -219,33 +219,40 @@ public class AAFrequency
     }
     for (int i = iStart; i < width; i++)
     {
-      if (i >= hconsensus.length)
+      Hashtable hci;
+      if (i >= hconsensus.length || ((hci=hconsensus[i])==null))
       {
         // happens if sequences calculated over were shorter than alignment
         // width
         consensus.annotations[i] = null;
         continue;
       }
+
       value = 0;
+      Float fv;
       if (ignoreGapsInConsensusCalculation)
       {
-        value = ((Float) hconsensus[i].get(AAFrequency.PID_NOGAPS))
-                .floatValue();
+        fv = (Float) hci.get(AAFrequency.PID_NOGAPS);
       }
       else
       {
-        value = ((Float) hconsensus[i].get(AAFrequency.PID_GAPS))
-                .floatValue();
+        fv = (Float) hci.get(AAFrequency.PID_GAPS);
       }
-
-      String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE).toString();
-      String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) + " ";
+      if (fv==null)
+      {
+        consensus.annotations[i] = null;
+        // data has changed below us .. give up and
+        continue;
+      }
+      value = fv.floatValue();
+      String maxRes = hci.get(AAFrequency.MAXRESIDUE).toString();
+      String mouseOver = hci.get(AAFrequency.MAXRESIDUE) + " ";
       if (maxRes.length() > 1)
       {
         mouseOver = "[" + maxRes + "] ";
         maxRes = "+";
       }
-      int[][] profile = (int[][]) hconsensus[i].get(AAFrequency.PROFILE);
+      int[][] profile = (int[][]) hci.get(AAFrequency.PROFILE);
       if (profile != null && includeAllConsSymbols)
       {
         mouseOver = "";

diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index 4b646c3..ba066a1 100755 (executable)
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -367,7 +367,7 @@ public class OverviewPanel extends Panel implements Runnable,
         lastcol = (int) (col * sampleCol);
         {
           mg.translate(col, sequencesHeight);
-          ap.annotationPanel.renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(),
+          ap.annotationPanel.renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(),av.getAlignmentConservationAnnotation().annotations,
                   (int) (sampleCol) + 1, graphHeight,
                   (int) (col * sampleCol), (int) (col * sampleCol) + 1);
           mg.translate(-col, -sequencesHeight);

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index c844315..475f0c7 100755 (executable)
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -1,18 +1,18 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
  * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- * 
+ *
  * 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 
+ * 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 
+ *
+ * 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/>.
  */
 package jalview.gui;
@@ -26,7 +26,7 @@ import javax.swing.*;
 
 /**
  * DOCUMENT ME!
- * 
+ *
  * @author $author$
  * @version $Revision$
  */
@@ -67,7 +67,7 @@ public class OverviewPanel extends JPanel implements Runnable
 
   /**
    * Creates a new OverviewPanel object.
-   * 
+   *
    * @param ap
    *          DOCUMENT ME!
    */
@@ -115,6 +115,7 @@ public class OverviewPanel extends JPanel implements Runnable
 
     addComponentListener(new ComponentAdapter()
     {
+      @Override
       public void componentResized(ComponentEvent evt)
       {
         if ((getWidth() != width)
@@ -127,6 +128,7 @@ public class OverviewPanel extends JPanel implements Runnable
 
     addMouseMotionListener(new MouseMotionAdapter()
     {
+      @Override
       public void mouseDragged(MouseEvent evt)
       {
         if (!av.wrapAlignment)
@@ -142,6 +144,7 @@ public class OverviewPanel extends JPanel implements Runnable
 
     addMouseListener(new MouseAdapter()
     {
+      @Override
       public void mousePressed(MouseEvent evt)
       {
         if (!av.wrapAlignment)
@@ -242,6 +245,7 @@ public class OverviewPanel extends JPanel implements Runnable
   /**
    * DOCUMENT ME!
    */
+  @Override
   public void run()
   {
     miniMe = null;
@@ -359,13 +363,13 @@ public class OverviewPanel extends JPanel implements Runnable
 
     if (av.getAlignmentConservationAnnotation()!= null)
     {
-      renderer.updateFromAlignViewport(av); 
+      renderer.updateFromAlignViewport(av);
       for (col = 0; col < width; col++)
       {
         lastcol = (int) (col * sampleCol);
         {
           mg.translate(col, sequencesHeight);
-          renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(),
+          renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(),av.getAlignmentConservationAnnotation().annotations,
                   (int) (sampleCol) + 1, graphHeight,
                   (int) (col * sampleCol), (int) (col * sampleCol) + 1);
           mg.translate(-col, -sequencesHeight);
@@ -438,10 +442,11 @@ public class OverviewPanel extends JPanel implements Runnable
 
   /**
    * DOCUMENT ME!
-   * 
+   *
    * @param g
    *          DOCUMENT ME!
    */
+  @Override
   public void paintComponent(Graphics g)
   {
     if (resizing)

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index ace94f4..cfdfdf6 100644 (file)
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -4,6 +4,7 @@ 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;
 
@@ -29,7 +30,7 @@ public class AnnotationRenderer
     // TODO Auto-generated constructor stub
   }
 
-  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 +40,21 @@ 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[]
@@ -252,7 +253,7 @@ public class AnnotationRenderer
     for (int i = 0; i < aa.length; i++)
     {
       AlignmentAnnotation row = aa[i];
-
+      Annotation[] row_annotations=row.annotations;
       if (!row.visible)
       {
         continue;
@@ -329,7 +330,7 @@ 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 +340,8 @@ 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 +376,16 @@ 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 +404,29 @@ 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 +434,12 @@ 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';
             }
@@ -450,18 +451,18 @@ public class AnnotationRenderer
               switch (lastSS)
               {
               case 'H':
-                drawHelixAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
+                drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
                         column, validRes, validEnd);
                 break;
 
               case 'E':
-                drawSheetAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
+                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,
+                drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
                         column, validRes, validEnd);
                 break;
 
@@ -490,17 +491,17 @@ 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;
       }
@@ -516,21 +517,21 @@ public class AnnotationRenderer
         switch (lastSS)
         {
         case 'H':
-          drawHelixAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
+          drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
                   column, validRes, validEnd);
           break;
 
         case 'E':
-          drawSheetAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
+          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,
+          drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
                   column, validRes, validEnd);
           break;
         default:
-          drawGlyphLine(g, row, lastSSX, x, y, iconOffset, startRes,
+          drawGlyphLine(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
                   column, validRes, validEnd);
           break;
         }
@@ -569,7 +570,7 @@ public class AnnotationRenderer
             {
               if (aa[gg].graphGroup == row.graphGroup)
               {
-                drawLineGraph(g, aa[gg], startRes, endRes, y, groupmin,
+                drawLineGraph(g, aa[gg], aa[gg].annotations, startRes, endRes, y, groupmin,
                         groupmax, row.graphHeight);
               }
             }
@@ -578,13 +579,13 @@ public class AnnotationRenderer
           }
           else
           {
-            drawLineGraph(g, row, startRes, endRes, y, row.graphMin,
+            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,
+          drawBarGraph(g, row, row_annotations, startRes, endRes, row.graphMin,
                   row.graphMax, y);
         }
       }
@@ -609,7 +610,7 @@ public class AnnotationRenderer
 
   private Color STEM_COLOUR = Color.blue;
 
-  public void drawGlyphLine(Graphics g, AlignmentAnnotation row,
+  public void drawGlyphLine(Graphics g, Annotation[] row,
           int lastSSX, int x, int y, int iconOffset, int startRes,
           int column, boolean validRes, boolean validEnd)
   {
@@ -617,14 +618,14 @@ public class AnnotationRenderer
     g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth) - lastSSX, 2);
   }
 
-  public void drawSheetAnnot(Graphics g, AlignmentAnnotation row,
+  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);
@@ -642,7 +643,7 @@ public class AnnotationRenderer
 
   }
 
-  public void drawHelixAnnot(Graphics g, AlignmentAnnotation row,
+  public void drawHelixAnnot(Graphics g, Annotation[] row,
           int lastSSX, int x, int y, int iconOffset, int startRes,
           int column, boolean validRes, boolean validEnd)
   {
@@ -658,8 +659,8 @@ 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 +669,8 @@ 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 +685,15 @@ 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 +703,10 @@ public class AnnotationRenderer
     g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
   }
 
-  public void drawLineGraph(Graphics g, AlignmentAnnotation aa, int sRes,
+  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 +719,7 @@ public class AnnotationRenderer
       eRes++;
     }
 
-    eRes = Math.min(eRes, aa.annotations.length);
+    eRes = Math.min(eRes, aa_annotations.length);
 
     if (sRes == 0)
     {
@@ -737,10 +738,10 @@ 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 +756,51 @@ 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,
+  public void drawBarGraph(Graphics g, AlignmentAnnotation _aa, Annotation[] aa_annotations, int sRes,
           int eRes, float min, float max, int y)
   {
-    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 +808,7 @@ 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);
@@ -815,16 +816,16 @@ public class AnnotationRenderer
     g.drawLine(x, y2, (eRes - sRes) * charWidth, y2);
 
     int column;
-    int aaMax = aa.annotations.length - 1;
+    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)
+      if (_aa.groupRef != null)
       {
-        renderHistogram = aa.groupRef.isShowConsensusHistogram();
-        renderProfile = aa.groupRef.isShowSequenceLogo();
-        normaliseProfile = aa.groupRef.isNormaliseSequenceLogo();
+        renderHistogram = _aa.groupRef.isShowConsensusHistogram();
+        renderProfile = _aa.groupRef.isShowSequenceLogo();
+        normaliseProfile = _aa.groupRef.isNormaliseSequenceLogo();
       }
       else
       {
@@ -846,18 +847,18 @@ 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)
       {
@@ -874,12 +875,12 @@ public class AnnotationRenderer
       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 +907,17 @@ 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(
@@ -941,25 +942,25 @@ 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,
+  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 +969,14 @@ 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;