X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=a88aa4a4ee30b6e5ea5920c84140c92bd5af46dc;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=755b85a1888eeb41bba73b90b44de3f7a217180c;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 755b85a..a88aa4a 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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.
  * 
@@ -26,7 +26,10 @@ import java.util.Hashtable;
 
 import javax.swing.*;
 
+import com.stevesoft.pat.Regex;
+
 import jalview.analysis.AAFrequency;
+import jalview.analysis.StructureFrequency;
 import jalview.datamodel.*;
 import jalview.schemes.ColourSchemeI;
 
@@ -43,6 +46,11 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 
   final String SHEET = "Sheet";
 
+  /**
+   * For RNA secondary structure "stems" aka helices
+   */
+  final String STEM = "RNA Helix";
+
   final String LABEL = "Label";
 
   final String REMOVE = "Remove Annotation";
@@ -53,6 +61,8 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 
   final Color SHEET_COLOUR = Color.green.darker().darker();
 
+  final Color STEM_COLOUR = Color.blue.darker();
+
   /** DOCUMENT ME!! */
   AlignViewport av;
 
@@ -85,6 +95,11 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 
   boolean MAC = false;
 
+  // for editing cursor
+  int cursorX = 0;
+
+  int cursorY = 0;
+
   /**
    * Creates a new AnnotationPanel object.
    * 
@@ -132,6 +147,25 @@ public class AnnotationPanel extends JPanel implements MouseListener,
    */
   public int adjustPanelHeight()
   {
+    int height = calcPanelHeight();
+    this.setPreferredSize(new Dimension(1, height));
+    if (ap != null)
+    {
+      // revalidate only when the alignment panel is fully constructed
+      ap.validate();
+    }
+
+    return height;
+  }
+
+  /**
+   * calculate the height for visible annotation, revalidating bounds where
+   * necessary ABSTRACT GUI METHOD
+   * 
+   * @return total height of annotation
+   */
+  public int calcPanelHeight()
+  {
     // setHeight of panels
     AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
     int height = 0;
@@ -175,18 +209,11 @@ public class AnnotationPanel extends JPanel implements MouseListener,
         height += aa[i].height;
       }
     }
-    else
+    if (height == 0)
     {
+      // set minimum
       height = 20;
     }
-
-    this.setPreferredSize(new Dimension(1, height));
-    if (ap != null)
-    {
-      // revalidate only when the alignment panel is fully constructed
-      ap.validate();
-    }
-
     return height;
   }
 
@@ -199,6 +226,10 @@ public class AnnotationPanel extends JPanel implements MouseListener,
   public void actionPerformed(ActionEvent evt)
   {
     AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+    if (aa == null)
+    {
+      return;
+    }
     Annotation[] anot = aa[activeRow].annotations;
 
     if (anot.length < av.getColumnSelection().getMax())
@@ -288,6 +319,13 @@ public class AnnotationPanel extends JPanel implements MouseListener,
         symbol = "\u03B2";
       }
 
+      // Added by LML to color stems
+      else if (evt.getActionCommand().equals(STEM))
+      {
+        type = 'S';
+        symbol = "\u03C3";
+      }
+
       if (!aa[activeRow].hasIcons)
       {
         aa[activeRow].hasIcons = true;
@@ -342,14 +380,15 @@ public class AnnotationPanel extends JPanel implements MouseListener,
         continue;
       String tlabel = null;
       if (anot[index] != null)
-      {
+      { // LML added stem code
         if (label2.equals(HELIX) || label2.equals(SHEET)
-                || label2.equals(LABEL))
+                || label2.equals(STEM) || label2.equals(LABEL))
         {
           tlabel = anot[index].description;
           if (tlabel == null || tlabel.length() < 1)
           {
-            if (label2.equals(HELIX) || label2.equals(SHEET))
+            if (label2.equals(HELIX) || label2.equals(SHEET)
+                    || label2.equals(STEM))
             {
               tlabel = "" + anot[index].secondaryStructure;
             }
@@ -422,12 +461,25 @@ public class AnnotationPanel extends JPanel implements MouseListener,
       }
 
       JPopupMenu pop = new JPopupMenu("Structure type");
-      JMenuItem item = new JMenuItem(HELIX);
-      item.addActionListener(this);
-      pop.add(item);
-      item = new JMenuItem(SHEET);
-      item.addActionListener(this);
-      pop.add(item);
+      JMenuItem item;
+      /*
+       * Just display the needed structure options
+       */
+      if (av.alignment.isNucleotide() == true)
+      {
+        item = new JMenuItem(STEM);
+        item.addActionListener(this);
+        pop.add(item);
+      }
+      else
+      {
+        item = new JMenuItem(HELIX);
+        item.addActionListener(this);
+        pop.add(item);
+        item = new JMenuItem(SHEET);
+        item.addActionListener(this);
+        pop.add(item);
+      }
       item = new JMenuItem(LABEL);
       item.addActionListener(this);
       pop.add(item);
@@ -620,6 +672,38 @@ public class AnnotationPanel extends JPanel implements MouseListener,
    */
   public void mouseClicked(MouseEvent evt)
   {
+    if (activeRow != -1)
+    {
+      AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+      AlignmentAnnotation anot = aa[activeRow];
+
+      if (anot.description.equals("secondary structure"))
+      {
+        // System.out.println(anot.description+" "+anot.getRNAStruc());
+      }
+    }
+  }
+
+  // TODO mouseClicked-content and drawCursor are quite experimental!
+  public void drawCursor(Graphics graphics, SequenceI seq, int res, int x1,
+          int y1)
+  {
+    int pady = av.charHeight / 5;
+    int charOffset = 0;
+    graphics.setColor(Color.black);
+    graphics.fillRect(x1, y1, av.charWidth, av.charHeight);
+
+    if (av.validCharWidth)
+    {
+      graphics.setColor(Color.white);
+
+      char s = seq.getCharAt(res);
+
+      charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+      graphics.drawString(String.valueOf(s), charOffset + x1,
+              (y1 + av.charHeight) - pady);
+    }
+
   }
 
   /**
@@ -796,7 +880,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
     boolean[] graphGroupDrawn = new boolean[aa.length];
     int charOffset = 0; // offset for a label
     float fmWidth, fmScaling = 1f; // scaling for a label to fit it into a
-                                   // column.
+    // column.
     Font ofont = g.getFont();
     // \u03B2 \u03B1
     for (int i = 0; i < aa.length; i++)
@@ -812,7 +896,6 @@ public class AnnotationPanel extends JPanel implements MouseListener,
       scaleColLabel = row.scaleColLabel;
       lastSS = ' ';
       lastSSX = 0;
-
       if (row.graph > 0)
       {
         if (row.graphGroup > -1 && graphGroupDrawn[row.graphGroup])
@@ -875,7 +958,9 @@ public class AnnotationPanel extends JPanel implements MouseListener,
         continue;
       }
 
-      x = 0;
+      // first pass sets up state for drawing continuation from left-hand column
+      // of startRes
+      x = (startRes == 0) ? 0 : -1;
       while (x < endRes - startRes)
       {
         if (av.hasHiddenColumns)
@@ -901,162 +986,144 @@ public class AnnotationPanel extends JPanel implements MouseListener,
         {
           validRes = true;
         }
-
-        if (activeRow == i)
+        if (x > -1)
         {
-          g.setColor(Color.red);
-
-          if (av.getColumnSelection() != null)
+          if (activeRow == i)
           {
-            for (int n = 0; n < av.getColumnSelection().size(); n++)
-            {
-              int v = av.getColumnSelection().columnAt(n);
+            g.setColor(Color.red);
 
-              if (v == column)
+            if (av.getColumnSelection() != null)
+            {
+              for (int n = 0; n < av.getColumnSelection().size(); n++)
               {
-                g
-                        .fillRect(x * av.charWidth, y, av.charWidth,
-                                av.charHeight);
+                int v = av.getColumnSelection().columnAt(n);
+
+                if (v == column)
+                {
+                  g.fillRect(x * av.charWidth, y, av.charWidth,
+                          av.charHeight);
+                }
               }
             }
           }
-        }
 
-        if (av.validCharWidth && validRes
-                && row.annotations[column].displayCharacter != null
-                && (row.annotations[column].displayCharacter.length() > 0))
-        {
-
-          if (centreColLabels || scaleColLabel)
+          if (av.validCharWidth
+                  && validRes
+                  && row.annotations[column].displayCharacter != null
+                  && (row.annotations[column].displayCharacter.length() > 0))
           {
-            fmWidth = (float) fm.charsWidth(
-                    row.annotations[column].displayCharacter.toCharArray(),
-                    0, row.annotations[column].displayCharacter.length());
 
-            if (scaleColLabel)
+            if (centreColLabels || scaleColLabel)
             {
-              // justify the label and scale to fit in column
-              if (fmWidth > av.charWidth)
+              fmWidth = (float) fm.charsWidth(
+                      row.annotations[column].displayCharacter
+                              .toCharArray(), 0,
+                      row.annotations[column].displayCharacter.length());
+
+              if (scaleColLabel)
               {
-                // scale only if the current font isn't already small enough
-                fmScaling = av.charWidth;
-                fmScaling /= fmWidth;
-                g.setFont(ofont.deriveFont(AffineTransform
-                        .getScaleInstance(fmScaling, 1.0)));
-                // and update the label's width to reflect the scaling.
-                fmWidth = av.charWidth;
+                // justify the label and scale to fit in column
+                if (fmWidth > av.charWidth)
+                {
+                  // scale only if the current font isn't already small enough
+                  fmScaling = av.charWidth;
+                  fmScaling /= fmWidth;
+                  g.setFont(ofont.deriveFont(AffineTransform
+                          .getScaleInstance(fmScaling, 1.0)));
+                  // and update the label's width to reflect the scaling.
+                  fmWidth = av.charWidth;
+                }
               }
             }
-          }
-          else
-          {
-            fmWidth = (float) fm
-                    .charWidth(row.annotations[column].displayCharacter
-                            .charAt(0));
-          }
-          charOffset = (int) ((av.charWidth - fmWidth) / 2f);
+            else
+            {
+              fmWidth = (float) fm
+                      .charWidth(row.annotations[column].displayCharacter
+                              .charAt(0));
+            }
+            charOffset = (int) ((av.charWidth - fmWidth) / 2f);
 
-          if (row.annotations[column].colour == null)
-            g.setColor(Color.black);
-          else
-            g.setColor(row.annotations[column].colour);
+            if (row.annotations[column].colour == null)
+              g.setColor(Color.black);
+            else
+              g.setColor(row.annotations[column].colour);
 
-          if (column == 0 || row.graph > 0)
-          {
-            g.drawString(row.annotations[column].displayCharacter,
-                    (x * av.charWidth) + charOffset, y + iconOffset);
-          }
-          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 == ' ')))
-          {
-            g.drawString(row.annotations[column].displayCharacter, x
-                    * av.charWidth + charOffset, y + iconOffset);
+            if (column == 0 || row.graph > 0)
+            {
+              g.drawString(row.annotations[column].displayCharacter,
+                      (x * av.charWidth) + charOffset, y + iconOffset);
+            }
+            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 == ' ')))
+            {
+              g.drawString(row.annotations[column].displayCharacter, x
+                      * av.charWidth + charOffset, y + iconOffset);
+            }
+            g.setFont(ofont);
           }
-          g.setFont(ofont);
         }
-
         if (row.hasIcons)
         {
-          if (!validRes
-                  || (row.annotations[column].secondaryStructure != lastSS))
+          char ss = validRes ? row.annotations[column].secondaryStructure
+                  : ' ';
+          if (ss == 'S')
           {
-            switch (lastSS)
+            // distinguish between forward/backward base-pairing
+            if (row.annotations[column].displayCharacter.indexOf(')') > -1)
             {
-            case 'H':
-              g.setColor(HELIX_COLOUR);
-              if (MAC)
+              ss = 's';
+            }
+          }
+          if (!validRes || (ss != lastSS))
+          {
+            if (x > -1)
+            {
+              switch (lastSS)
               {
-                // Off by 1 offset when drawing rects and ovals
-                // to offscreen image on the MAC
-                g.fillRoundRect(lastSSX, y + 4 + iconOffset,
-                        (x * av.charWidth) - lastSSX, 7, 8, 8);
+              case 'H':
+                drawHelixAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
+                        column, validRes, validEnd);
                 break;
-              }
-
-              int sCol = (lastSSX / av.charWidth) + startRes;
-              int x1 = lastSSX;
-              int x2 = (x * av.charWidth);
 
-              if (sCol == 0
-                      || row.annotations[sCol - 1] == null
-                      || row.annotations[sCol - 1].secondaryStructure != 'H')
-              {
-                g.fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8, 90,
-                        180);
-                x1 += av.charWidth / 2;
-              }
-
-              if (!validRes || row.annotations[column] == null
-                      || row.annotations[column].secondaryStructure != 'H')
-              {
-                g.fillArc((x * av.charWidth) - av.charWidth, y + 4
-                        + iconOffset, av.charWidth, 8, 270, 180);
-                x2 -= av.charWidth / 2;
-              }
-
-              g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
-              break;
-
-            case 'E':
-              g.setColor(SHEET_COLOUR);
-              g.fillRect(lastSSX, y + 4 + iconOffset, (x * av.charWidth)
-                      - lastSSX - 4, 7);
-              g.fillPolygon(new int[]
-              { (x * av.charWidth) - 4, (x * av.charWidth) - 4,
-                  (x * av.charWidth) }, new int[]
-              { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset },
-                      3);
+              case 'E':
+                drawSheetAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
+                        column, validRes, validEnd);
+                break;
 
-              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);
+                break;
 
-            default:
-              g.setColor(Color.gray);
-              g.fillRect(lastSSX, y + 6 + iconOffset, (x * av.charWidth)
-                      - lastSSX, 2);
+              default:
+                g.setColor(Color.gray);
+                g.fillRect(lastSSX, y + 6 + iconOffset, (x * av.charWidth)
+                        - lastSSX, 2);
 
-              break;
+                break;
+              }
             }
-
             if (validRes)
             {
-              lastSS = row.annotations[column].secondaryStructure;
+              lastSS = ss;
             }
             else
             {
               lastSS = ' ';
             }
-
-            lastSSX = (x * av.charWidth);
+            if (x > -1)
+            {
+              lastSSX = (x * av.charWidth);
+            }
           }
         }
-
         column++;
         x++;
       }
-
       if (column >= row.annotations.length)
       {
         column = row.annotations.length - 1;
@@ -1074,66 +1141,22 @@ public class AnnotationPanel extends JPanel implements MouseListener,
         switch (lastSS)
         {
         case 'H':
-          g.setColor(HELIX_COLOUR);
-          if (MAC)
-          {
-            // Off by 1 offset when drawing rects and ovals
-            // to offscreen image on the MAC
-            g.fillRoundRect(lastSSX, y + 4 + iconOffset, (x * av.charWidth)
-                    - lastSSX, 7, 8, 8);
-            break;
-          }
-
-          int sCol = (lastSSX / av.charWidth) + startRes;
-          int x1 = lastSSX;
-          int x2 = (x * av.charWidth);
-
-          if (sCol == 0 || row.annotations[sCol - 1] == null
-                  || row.annotations[sCol - 1].secondaryStructure != 'H')
-          {
-            g
-                    .fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8,
-                            90, 180);
-            x1 += av.charWidth / 2;
-          }
-
-          if (row.annotations[column] == null
-                  || row.annotations[column].secondaryStructure != 'H')
-          {
-            g.fillArc((x * av.charWidth) - av.charWidth,
-                    y + 4 + iconOffset, av.charWidth, 8, 270, 180);
-            x2 -= av.charWidth / 2;
-          }
-
-          g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
-
+          drawHelixAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
+                  column, validRes, validEnd);
           break;
 
         case 'E':
-          g.setColor(SHEET_COLOUR);
-
-          if (!validEnd || row.annotations[endRes] == null
-                  || row.annotations[endRes].secondaryStructure != 'E')
-          {
-            g.fillRect(lastSSX, y + 4 + iconOffset, (x * av.charWidth)
-                    - lastSSX - 4, 7);
-            g.fillPolygon(new int[]
-            { (x * av.charWidth) - 4, (x * av.charWidth) - 4,
-                (x * av.charWidth) }, new int[]
-            { y + iconOffset, y + 14 + iconOffset, y + 7 + iconOffset }, 3);
-          }
-          else
-          {
-            g.fillRect(lastSSX, y + 4 + iconOffset, (x + 1) * av.charWidth
-                    - lastSSX, 7);
-          }
+          drawSheetAnnot(g, row, 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);
           break;
-
         default:
-          g.setColor(Color.gray);
-          g.fillRect(lastSSX, y + 6 + iconOffset, (x * av.charWidth)
-                  - lastSSX, 2);
-
+          drawGlyphLine(g, row, lastSSX, x, y, iconOffset, startRes,
+                  column, validRes, validEnd);
           break;
         }
       }
@@ -1203,6 +1226,157 @@ public class AnnotationPanel extends JPanel implements MouseListener,
     }
   }
 
+  private void drawStemAnnot(Graphics g, AlignmentAnnotation row,
+          int lastSSX, int x, int y, int iconOffset, int startRes,
+          int column, boolean validRes, boolean validEnd)
+  {
+    g.setColor(STEM_COLOUR);
+    int sCol = (lastSSX / av.charWidth) + startRes;
+    int x1 = lastSSX;
+    int x2 = (x * av.charWidth);
+    Regex closeparen = new Regex("(\\))");
+
+    String dc = column == 0 ? ""
+            : row.annotations[column - 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);
+    // 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))
+      {
+        g.fillPolygon(new int[]
+        { lastSSX + 5, lastSSX + 5, lastSSX }, new int[]
+        { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
+        x1 += 5;
+      }
+      if (diffdownstream)
+      {
+        x2 -= 1;
+      }
+    }
+    else
+    {
+      // display a forward arrow
+      if (diffdownstream)
+      {
+        g.fillPolygon(new int[]
+        { x2 - 5, x2 - 5, x2 }, new int[]
+        { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
+        x2 -= 5;
+      }
+      if (diffupstream)
+      {
+        x1 += 1;
+      }
+    }
+    // draw arrow body
+    g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
+  }
+
+  private void drawGlyphLine(Graphics g, AlignmentAnnotation row,
+          int lastSSX, int x, int y, int iconOffset, int startRes,
+          int column, boolean validRes, boolean validEnd)
+  {
+    g.setColor(Color.gray);
+    g
+            .fillRect(lastSSX, y + 6 + iconOffset, (x * av.charWidth)
+                    - lastSSX, 2);
+  }
+
+  private void drawSheetAnnot(Graphics g, AlignmentAnnotation 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')
+    {
+      g.fillRect(lastSSX, y + 4 + iconOffset, (x * av.charWidth) - lastSSX
+              - 4, 7);
+      g.fillPolygon(
+              new int[]
+              { (x * av.charWidth) - 4, (x * av.charWidth) - 4,
+                  (x * av.charWidth) }, new int[]
+              { y + iconOffset, y + 14 + iconOffset, y + 7 + iconOffset },
+              3);
+    }
+    else
+    {
+      g.fillRect(lastSSX, y + 4 + iconOffset, (x + 1) * av.charWidth
+              - lastSSX, 7);
+    }
+
+  }
+
+  private void drawHelixAnnot(Graphics g, AlignmentAnnotation row,
+          int lastSSX, int x, int y, int iconOffset, int startRes,
+          int column, boolean validRes, boolean validEnd)
+  {
+    g.setColor(HELIX_COLOUR);
+
+    int sCol = (lastSSX / av.charWidth) + startRes;
+    int x1 = lastSSX;
+    int x2 = (x * av.charWidth);
+
+    if (MAC)
+    {
+      int ofs = av.charWidth / 2;
+      // 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')
+      {
+      }
+      else
+      {
+        // g.setColor(Color.orange);
+        g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1 - ofs + 1, 8,
+                0, 0);
+      }
+      if (!validRes || row.annotations[column] == null
+              || row.annotations[column].secondaryStructure != 'H')
+      {
+
+      }
+      else
+      {
+        // g.setColor(Color.magenta);
+        g.fillRoundRect(lastSSX + ofs, y + 4 + iconOffset, x2 - x1 - ofs
+                + 1, 8, 0, 0);
+
+      }
+
+      return;
+    }
+
+    if (sCol == 0 || row.annotations[sCol - 1] == null
+            || row.annotations[sCol - 1].secondaryStructure != 'H')
+    {
+      g.fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8, 90, 180);
+      x1 += av.charWidth / 2;
+    }
+
+    if (!validRes || row.annotations[column] == null
+            || row.annotations[column].secondaryStructure != 'H')
+    {
+      g.fillArc((x * av.charWidth) - av.charWidth, y + 4 + iconOffset,
+              av.charWidth, 8, 270, 180);
+      x2 -= av.charWidth / 2;
+    }
+
+    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)
   {
@@ -1375,48 +1549,79 @@ public class AnnotationPanel extends JPanel implements MouseListener,
         }
       }
       // draw profile if available
-      if (aa.annotations[column].value != 0 && renderProfile)
+      if (renderProfile && aa.annotations[column].value != 0)
       {
+
         int profl[] = getProfileFor(aa, column);
-        int ht = y1, htn = y2 - y1;// aa.graphHeight;
-        float wdth;
-        double ht2 = 0;
-        char[] dc = new char[1];
-        LineMetrics lm;
-        for (int c = 1; profl != null && c < profl[0];)
+        // just try to draw the logo if profl is not null
+        if (profl != null)
         {
-          dc[0] = (char) profl[c++];
-          wdth = av.charWidth;
-          wdth /= (float) fm.charsWidth(dc, 0, 1);
 
-          if (c > 2)
+          int ht = y1, htn = y2 - y1;// aa.graphHeight;
+          float wdth;
+          double ht2 = 0;
+          char[] dc;
+
+          /**
+           * profl.length == 51 indicates that the profile of a secondary
+           * structure conservation row was accesed.
+           * Therefore dc gets length 2, to have space for a basepair instead of
+           * just a single nucleotide
+           */
+          if (profl.length == 51)
           {
-            ht += (int) ht2;
+            dc = new char[2];
           }
+          else
           {
-            // if (aa.annotations[column].value==0) {
-            // g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(wdth,
-            // (ht2=(aa.graphHeight*0.1/av.charHeight)))));
-            // ht = y2-(int)ht2;
-            // } else {
-            g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(
-                    wdth, (ht2 = (htn * ((double) profl[c++]) / 100.0))
-                            / av.charHeight)));
-            lm = g.getFontMetrics().getLineMetrics(dc, 0, 1, g);
-            // htn -=ht2;
-            // }
-            g.setColor(profcolour.findColour(dc[0])); // (av.globalColourScheme!=null)
-                                                      // ? );// try to get a
-                                                      // colourscheme for the
-                                                      // group(aa.groupRef.cs==null)
-                                                      // ? av.textColour2 :
-                                                      // cs.findColour(dc));
-            g.drawChars(dc, 0, 1, x * av.charWidth, (int) (ht + lm
-                    .getHeight()));
-            // ht+=g.getFontMetrics().getAscent()-g.getFontMetrics().getDescent();
+            dc = new char[1];
           }
+
+          LineMetrics lm;
+          for (int c = 1; profl != null && c < profl[0];)
+          {
+            dc[0] = (char) profl[c++];
+
+            if (aa.label.startsWith("StrucConsensus"))
+            {
+              dc[1] = (char) profl[c++];
+            }
+            
+            wdth = av.charWidth;
+            wdth /= (float) fm.charsWidth(dc, 0, dc.length);
+
+            if (c > 2)
+            {
+              ht += (int) ht2;
+            }
+            {
+              // if (aa.annotations[column].value==0) {
+              // g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(wdth,
+              // (ht2=(aa.graphHeight*0.1/av.charHeight)))));
+              // ht = y2-(int)ht2;
+              // } else {
+              g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(
+                      wdth, (ht2 = (htn * ((double) profl[c++]) / 100.0))
+                              / av.charHeight)));
+              lm = g.getFontMetrics().getLineMetrics(dc, 0, 1, g);
+              // htn -=ht2;
+              // }
+              g.setColor(profcolour.findColour(dc[0])); // (av.globalColourScheme!=null)
+              // ? );// try to get a
+              // colourscheme for the
+              // group(aa.groupRef.cs==null)
+              // ? av.textColour2 :
+              // cs.findColour(dc));
+              // System.out.println(dc[0]);
+
+              g.drawChars(dc, 0, dc.length, x * av.charWidth,
+                      (int) (ht + lm.getHeight()));
+
+              // ht+=g.getFontMetrics().getAscent()-g.getFontMetrics().getDescent();
+            }
+          }
+          g.setFont(ofont);
         }
-        g.setFont(ofont);
       }
       x++;
     }
@@ -1454,6 +1659,29 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                 .getIgnoreGapsConsensus());
       }
     }
+    else
+    {
+      if (aa.autoCalculated && aa.label.startsWith("StrucConsensus"))
+      {
+        if (aa.groupRef != null && aa.groupRef.consensusData != null
+                && aa.groupRef.isShowSequenceLogo())
+        {
+          //TODO check what happens for group selections
+          return StructureFrequency.extractProfile(
+                  aa.groupRef.consensusData[column], aa.groupRef
+                          .getIgnoreGapsConsensus());
+        }
+        // TODO extend annotation row to enable dynamic and static profile data
+        // to
+        // be stored
+        if (aa.groupRef == null && aa.sequenceRef == null
+                && av.isShowSequenceLogo())
+        {
+          return StructureFrequency.extractProfile(av.hStrucConsensus[column],
+                  av.getIgnoreGapsConsensus());
+        }
+      }
+    }
     return null;
   }