X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationPanel.java;h=9c45d5e57b00ac9ef805c741dd5606faa1a7fa6d;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=0fdeed67adfbf14f0806a60a1e6dc7deb22c452e;hpb=bf4d22102e92dc26cc62c532df539771bfd829a7;p=jalview.git

diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index 0fdeed6..9c45d5e 100755
--- a/src/jalview/appletgui/AnnotationPanel.java
+++ b/src/jalview/appletgui/AnnotationPanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -51,11 +51,18 @@ public class AnnotationPanel
 
   public static int GRAPH_HEIGHT = 40;
 
+  boolean MAC = false;
+
   public AnnotationPanel(AlignmentPanel ap)
   {
+    if (System.getProperty("os.name").startsWith("Mac"))
+    {
+      MAC = true;
+    }
+
     this.ap = ap;
     av = ap.av;
-    this.setLayout(null);
+    setLayout(null);
     adjustPanelHeight();
 
     addMouseMotionListener(new MouseMotionAdapter()
@@ -69,13 +76,11 @@ public class AnnotationPanel
     // ap.annotationScroller.getVAdjustable().addAdjustmentListener( this );
   }
 
-
   public AnnotationPanel(AlignViewport av)
   {
     this.av = av;
   }
 
-
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
     ap.alabels.setScrollOffset( -evt.getValue());
@@ -86,7 +91,6 @@ public class AnnotationPanel
     // setHeight of panels
     AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
 
-
     int height = 0;
     if (aa != null)
     {
@@ -108,7 +112,7 @@ public class AnnotationPanel
           aa[i].height += 16;
         }
 
-        if (aa[i].graph>0)
+        if (aa[i].graph > 0)
         {
           aa[i].height += GRAPH_HEIGHT;
         }
@@ -126,9 +130,6 @@ public class AnnotationPanel
     }
 
     this.setSize(getSize().width, height);
-    if(ap!=null)
-       ap.annotationScroller.setSize(getSize().width, height);
-
 
     repaint();
 
@@ -141,8 +142,10 @@ public class AnnotationPanel
     if (activeRow == -1)
     {
       AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
-      if(aa ==null)
+      if (aa == null)
+      {
         return;
+      }
 
       for (int j = 0; j < aa.length; j++)
       {
@@ -190,11 +193,19 @@ public class AnnotationPanel
     }
 
     int res = evt.getX() / av.getCharWidth() + av.getStartRes();
+
+    if (av.hasHiddenColumns)
+    {
+      res = av.getColumnSelection().adjustForHiddenColumns(res);
+    }
+
     if (row > -1 && res < aa[row].annotations.length && aa[row].annotations[res] != null)
     {
-      StringBuffer text = new StringBuffer("Sequence position " + (res + 1) +
-                                           "  " +
-                                           aa[row].annotations[res].description);
+      StringBuffer text = new StringBuffer("Sequence position " + (res + 1));
+      if (aa[row].annotations[res].description != null)
+      {
+        text.append("  " + aa[row].annotations[res].description);
+      }
       ap.alignFrame.statusBar.setText(text.toString());
     }
   }
@@ -206,9 +217,9 @@ public class AnnotationPanel
 
   public void paint(Graphics g)
   {
-    g.setColor(Color.white);
-    g.fillRect(0,0, getSize().width, getSize().height);
-    imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;
+
+    imgWidth = getSize().width;
+    //(av.endRes - av.startRes + 1) * av.charWidth;
 
     if (image == null || imgWidth != image.getWidth(this))
     {
@@ -226,7 +237,10 @@ public class AnnotationPanel
       return;
     }
 
+    gg.setColor(Color.white);
+    gg.fillRect(0, 0, getSize().width, getSize().height);
     drawComponent(gg, av.startRes, av.endRes + 1);
+
     g.drawImage(image, 0, 0, this);
   }
 
@@ -275,276 +289,364 @@ public class AnnotationPanel
   {
     g.setFont(av.getFont());
 
+    g.setColor(Color.white);
+    g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getSize().height);
+
     if (fm == null)
+    {
       fm = g.getFontMetrics();
+    }
 
-
+    if ( (av.alignment.getAlignmentAnnotation() == null) ||
+        (av.alignment.getAlignmentAnnotation().length < 1))
+    {
       g.setColor(Color.white);
-      g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getSize().height);
-
-      if ((av.alignment.getAlignmentAnnotation() == null) ||
-              (av.alignment.getAlignmentAnnotation().length < 1))
+      g.fillRect(0, 0, getSize().width, getSize().height);
+      g.setColor(Color.black);
+      if (av.validCharWidth)
       {
-          g.setColor(Color.white);
-          g.fillRect(0, 0, getSize().width, getSize().height);
-          g.setColor(Color.black);
-          g.drawString("Alignment has no annotations", 20, 15);
-
-          return;
+        g.drawString("Alignment has no annotations", 20, 15);
       }
 
-      AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+      return;
+    }
+
+    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
 
-      int j;
-      int x = 0;
-      int y = 0;
-      char[] lastSS = new char[aa.length];
-      int[] lastSSX = new int[aa.length];
-      int iconOffset = av.charHeight / 2;
-      boolean validRes = false;
+    int x = 0;
+    int y = 0;
+    int column = 0;
+    char lastSS;
+    int lastSSX;
+    int iconOffset = av.charHeight / 2;
+    boolean validRes = false;
 
-      boolean [] graphGroupDrawn = new boolean[aa.length];
+    boolean[] graphGroupDrawn = new boolean[aa.length];
 
+    //\u03B2 \u03B1
+    for (int i = 0; i < aa.length; i++)
+    {
+      AlignmentAnnotation row = aa[i];
 
-      //\u03B2 \u03B1
-      for (int i = 0; i < aa.length; i++)
+      if (!row.visible)
       {
-          AlignmentAnnotation row = aa[i];
+        continue;
+      }
 
-          if (!row.visible)
-          {
-              continue;
-          }
+      lastSS = ' ';
+      lastSSX = 0;
 
+      if (row.graph > 0)
+      {
+        if (row.graphGroup > -1 && graphGroupDrawn[row.graphGroup])
+        {
+          continue;
+        }
 
+        // this is so that we draw the characters below the graph
+        y += row.height;
 
-          if (row.graph>0)
-          {
-              if(row.graphGroup>-1 && graphGroupDrawn[ row.graphGroup ] )
-                continue;
+        if (row.hasText)
+        {
+          y -= av.charHeight;
+        }
+      }
 
-              // this is so that we draw the characters below the graph
-              y += row.height;
+      if (row.hasText)
+      {
+        iconOffset = av.charHeight / 2;
+      }
+      else
+      {
+        iconOffset = 0;
+      }
 
-              if (row.hasText)
-              {
-                  y -= av.charHeight;
-              }
+      x = 0;
+      while (x < endRes - startRes)
+      {
+        if (av.hasHiddenColumns)
+        {
+          column = av.getColumnSelection().adjustForHiddenColumns(startRes + x);
+          if (column > row.annotations.length - 1)
+          {
+            break;
           }
+        }
+        else
+        {
+          column = startRes + x;
+        }
 
-          if (row.hasText)
+        if ( (row.annotations.length <= column) ||
+            (row.annotations[column] == null))
+        {
+          validRes = false;
+        }
+        else
+        {
+          validRes = true;
+        }
+
+        if (av.validCharWidth && validRes &&
+            (row.annotations[column].displayCharacter.length() > 0))
+        {
+          int charOffset = (av.charWidth -
+                            fm.charWidth(row.annotations[column].
+                                         displayCharacter.charAt(
+                                             0))) / 2;
+          g.setColor(row.annotations[column].colour);
+
+          if (column == 0 || row.graph > 0)
           {
-              iconOffset = av.charHeight / 2;
+            g.drawString(row.annotations[column].displayCharacter,
+                         (x * av.charWidth) + charOffset,
+                         y + iconOffset + 3);
           }
-          else
+          else if (
+              row.annotations[column - 1] == null
+              || (!row.annotations[column].displayCharacter.equals(
+                  row.annotations[column - 1].displayCharacter)
+                  ||
+                  (row.annotations[column].displayCharacter.length() < 2 &&
+                   row.annotations[column].secondaryStructure == ' ')))
           {
-              iconOffset = 0;
+            g.drawString(row.annotations[column].displayCharacter,
+                         (x * av.charWidth) + charOffset,
+                         y + iconOffset + 3);
           }
+        }
 
-          for (j = startRes; j < endRes; j++)
+        if (row.hasIcons)
+        {
+          if (!validRes ||
+              (row.annotations[column].secondaryStructure != lastSS))
           {
-              if ((row.annotations.length <= j) ||
-                      (row.annotations[j] == null))
-              {
-                  validRes = false;
-              }
-              else
-              {
-                  validRes = true;
-              }
-
-              x = (j - startRes) * av.charWidth;
-
-              if (activeRow == i)
-              {
-                  g.setColor(Color.red);
-
-                  if (activeRes != null)
-                  {
-                      for (int n = 0; n < activeRes.size(); n++)
-                      {
-                          int v = Integer.parseInt(activeRes.elementAt(n).toString());
-
-                          if (v == j)
-                          {
-                              g.fillRect((j - startRes) * av.charWidth, y,
-                                  av.charWidth, row.height);
-                          }
-                      }
-                  }
-              }
-
-              if (validRes &&
-                      (row.annotations[j].displayCharacter.length() > 0))
-              {
-
-                  int charOffset = (av.charWidth -
-                      fm.charWidth(row.annotations[j].displayCharacter.charAt(
-                              0))) / 2;
-                  g.setColor(row.annotations[j].colour);
-
-                  if (j == 0 || row.graph>0)
-                  {
-                      g.drawString(row.annotations[j].displayCharacter, x+charOffset,
-                          y + iconOffset + 3);
-                  }
-                  else if (((row.annotations[j - 1] == null) ||
-                          (row.annotations[j].displayCharacter != row.annotations[j -
-                          1].displayCharacter)))
-                  {
-                      g.drawString(row.annotations[j].displayCharacter, x+charOffset,
-                          y + iconOffset + 3);
-                  }
-              }
+            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);
+                break;
 
-              if (row.hasIcons)
-              {
-                  if (!validRes ||
-                          (row.annotations[j].secondaryStructure != lastSS[i]))
-                  {
-                      switch (lastSS[i])
-                      {
-                      case 'H':
-                          g.setColor(HELIX_COLOUR);
-                          g.fillRoundRect(lastSSX[i], y + 4 + iconOffset,
-                              x - lastSSX[i], 7, 8, 8);
-
-                          break;
-
-                      case 'E':
-                          g.setColor(SHEET_COLOUR);
-                          g.fillRect(lastSSX[i], y + 4 + iconOffset,
-                              x - lastSSX[i] - 4, 7);
-                          g.fillPolygon(new int[] { x - 4, x - 4, x },
+              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);
+                              y + iconOffset, y + 14 + iconOffset,
+                              y + 8 + iconOffset
+                }, 3);
 
-                          break;
+                break;
 
+              default:
+                g.setColor(Color.gray);
+                g.fillRect(lastSSX, y + 6 + iconOffset,
+                           (x * av.charWidth) - lastSSX, 2);
+
+                break;
+            }
+
+            if (validRes)
+            {
+              lastSS = row.annotations[column].secondaryStructure;
+            }
+            else
+            {
+              lastSS = ' ';
+            }
+
+            lastSSX = (x * av.charWidth);
+          }
+        }
 
-                      default:
-                          g.setColor(Color.gray);
-                          g.fillRect(lastSSX[i], y + 6 + iconOffset,
-                              x - lastSSX[i], 2);
-
-                          break;
-                      }
+        column++;
+        x++;
+      }
 
-                      if (validRes)
-                      {
-                          lastSS[i] = row.annotations[j].secondaryStructure;
-                      }
-                      else
-                      {
-                          lastSS[i] = ' ';
-                      }
+      if (column >= row.annotations.length)
+      {
+        column = row.annotations.length - 1;
+      }
 
-                      lastSSX[i] = x;
-                  }
-              }
-          }
+      //  x ++;
 
-          x += av.charWidth;
+      if (row.hasIcons)
+      {
+        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);
+
+            break;
+
+          case 'E':
+            g.setColor(SHEET_COLOUR);
+
+            if (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 * av.charWidth - lastSSX, 7);
+            }
+            break;
+
+          default:
+            g.setColor(Color.gray);
+            if (!av.wrapAlignment || endRes == av.endRes)
+            {
+              g.fillRect(lastSSX, y + 6 + iconOffset,
+                         (x * av.charWidth) - lastSSX, 2);
+            }
+
+            break;
+        }
+      }
 
-          if (row.hasIcons)
+      if (row.graph > 0)
+      {
+        if (row.graph == AlignmentAnnotation.LINE_GRAPH)
+        {
+          if (row.graphGroup > -1 && !graphGroupDrawn[row.graphGroup])
           {
-              switch (lastSS[i])
+            float groupmax = -999999, groupmin = 9999999;
+            for (int gg = 0; gg < aa.length; gg++)
+            {
+              if (aa[gg].graphGroup != row.graphGroup)
               {
-              case 'H':
-                  g.setColor(HELIX_COLOUR);
-                  g.fillRoundRect(lastSSX[i], y + 4 + iconOffset,
-                      x - lastSSX[i], 7, 8, 8);
-
-                  break;
-
-              case 'E':
-                  g.setColor(SHEET_COLOUR);
-
-                  if (row.annotations.length > endRes
-                      && row.annotations[endRes].secondaryStructure != 'E')
-                  {
-                    g.fillRect(lastSSX[i], y + 4 + iconOffset,
-                               x - lastSSX[i] - 4, 7);
-                    g.fillPolygon(new int[]
-                                  {x - 4, x - 4, x},
-                                  new int[]
-                                  {
-                                  y + iconOffset, y + 14 + iconOffset,
-                                  y + 7 + iconOffset
-                    }, 3);
-                  }
-                  else
-                    g.fillRect(lastSSX[i], y + 4 + iconOffset,
-                               x - lastSSX[i], 7);
-
-                  break;
-
-              case 'C':
-                  break;
+                continue;
+              }
 
-              default:
-                  g.setColor(Color.gray);
-                  g.fillRect(lastSSX[i], y + 6 + iconOffset, x - lastSSX[i], 2);
+              if (aa[gg] != row)
+              {
+                aa[gg].visible = false;
+              }
 
-                  break;
+              if (aa[gg].graphMax > groupmax)
+              {
+                groupmax = aa[gg].graphMax;
               }
-          }
+              if (aa[gg].graphMin < groupmin)
+              {
+                groupmin = aa[gg].graphMin;
+              }
+            }
 
-          if (row.graph>0)
-          {
-              if(row.graph == AlignmentAnnotation.LINE_GRAPH )
+            for (int gg = 0; gg < aa.length; gg++)
+            {
+              if (aa[gg].graphGroup == row.graphGroup)
               {
-                if(row.graphGroup>-1 && !graphGroupDrawn[row.graphGroup])
-                 {
-                   float groupmax=-999999, groupmin=9999999;
-                   for(int gg=0; gg<aa.length; gg++)
-                   {
-                     if(aa[gg].graphGroup!=row.graphGroup)
-                       continue;
-
-                     if(aa[gg]!=row)
-                       aa[gg].visible = false;
-
-                     if(aa[gg].graphMax>groupmax)
-                       groupmax = aa[gg].graphMax;
-                     if(aa[gg].graphMin<groupmin)
-                       groupmin = aa[gg].graphMin;
-                   }
-
-                   for (int gg = 0; gg < aa.length; gg++)
-                   {
-                     if (aa[gg].graphGroup == row.graphGroup)
-                     {
-                       drawLineGraph(g, aa[gg], startRes, endRes, y,
-                                     groupmin, groupmax,
-                                     row.graphHeight);
-                     }
-                   }
-
-                   graphGroupDrawn[ row.graphGroup ] = true;
-                 }
-                 else
-                   drawLineGraph(g, row, startRes, endRes,
-                                 y, row.graphMin, row.graphMax, row.graphHeight  );
+                drawLineGraph(g, aa[gg], startRes, endRes, y,
+                              groupmin, groupmax,
+                              row.graphHeight);
               }
-              else if(row.graph == AlignmentAnnotation.BAR_GRAPH )
-                 drawBarGraph(g, row, startRes, endRes,
-                              row.graphMin, row.graphMax, y);
-          }
+            }
 
-          if (row.graph>0 && row.hasText)
-          {
-              y += av.charHeight;
+            graphGroupDrawn[row.graphGroup] = true;
           }
-
-          if (row.graph==0)
+          else
           {
-              y += aa[i].height;
+            drawLineGraph(g, row, 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);
+        }
+      }
+
+      if (row.graph > 0 && row.hasText)
+      {
+        y += av.charHeight;
+      }
+
+      if (row.graph == 0)
+      {
+        y += aa[i].height;
       }
+    }
   }
 
   public void drawLineGraph(Graphics g, AlignmentAnnotation aa,
@@ -553,53 +655,81 @@ public class AnnotationPanel
                             float min, float max,
                             int graphHeight)
   {
-    if(sRes>aa.annotations.length)
+    if (sRes > aa.annotations.length)
+    {
       return;
+    }
 
     int x = 0;
 
     //Adjustment for fastpaint to left
-    if(eRes<av.endRes)
+    if (eRes < av.endRes)
+    {
       eRes++;
+    }
+
+    eRes = Math.min(eRes, aa.annotations.length);
 
-    if(sRes==0)
+    if (sRes == 0)
     {
       sRes++;
-      x+=av.charWidth;
+      x += av.charWidth;
     }
 
-    int y1=y, y2=y;
+    int y1 = y, y2 = y;
     float range = max - min;
 
     ////Draw origin
-    if(min<0)
-      y2 = (int)(y - (0-min / range)*graphHeight);
+    if (min < 0)
+    {
+      y2 = y - (int) ( (0 - min / range) * graphHeight);
+    }
 
     g.setColor(Color.gray);
-    g.drawLine(x-av.charWidth,y2,(eRes-sRes+1)*av.charWidth,y2);
+    g.drawLine(x - av.charWidth, y2, (eRes - sRes) * av.charWidth, y2);
 
+    eRes = Math.min(eRes, aa.annotations.length);
 
-    if(aa.threshold!=null)
-    {
-        g.setColor(aa.threshold.colour);
-        y2 = (int)(y - ((aa.threshold.value-min) / range)*graphHeight);
-        g.drawLine(x-av.charWidth,y2,(eRes-sRes+1)*av.charWidth,y2);
-    }
+    int column;
+    int aaMax = aa.annotations.length - 1;
 
-    eRes = Math.min(eRes, aa.annotations.length);
-    for (int j = sRes; j < eRes; j++)
+    while (x < eRes - sRes)
     {
-      if(aa.annotations[j]==null || aa.annotations[j-1]==null)
+      column = sRes + x;
+      if (av.hasHiddenColumns)
+      {
+        column = av.getColumnSelection().adjustForHiddenColumns(column);
+      }
+
+      if (column > aaMax)
+      {
+        break;
+      }
+
+      if (aa.annotations[column] == null || aa.annotations[column - 1] == null)
       {
-        x+=av.charWidth;
+        x++;
         continue;
       }
-        g.setColor(aa.annotations[j].colour);
-        y1 = y - (int) (((aa.annotations[j-1].value-min) / range) * graphHeight);
-        y2 = y - (int) (((aa.annotations[j].value-min) / range) * graphHeight);
-        g.drawLine(x-av.charWidth/2, y1, x+av.charWidth/2, y2);
-        x += av.charWidth;
-     }
+
+      g.setColor(aa.annotations[column].colour);
+      y1 = y -
+          (int) ( ( (aa.annotations[column - 1].value - min) / range) * graphHeight);
+      y2 = y -
+          (int) ( ( (aa.annotations[column].value - min) / range) * graphHeight);
+
+      g.drawLine(x * av.charWidth - av.charWidth / 2, y1,
+                 x * av.charWidth + av.charWidth / 2, y2);
+      x++;
+    }
+
+    if (aa.threshold != null)
+    {
+      g.setColor(aa.threshold.colour);
+
+      y2 = (int) (y - ( (aa.threshold.value - min) / range) * graphHeight);
+      g.drawLine(0, y2, (eRes - sRes) * av.charWidth, y2);
+    }
   }
 
   public void drawBarGraph(Graphics g, AlignmentAnnotation aa,
@@ -607,72 +737,93 @@ public class AnnotationPanel
                            float min, float max,
                            int y)
   {
-    if(sRes>aa.annotations.length)
+    if (sRes > aa.annotations.length)
+    {
       return;
+    }
+
+    eRes = Math.min(eRes, aa.annotations.length);
 
-    int x=0, y1, y2;
+    int x = 0, y1 = y, y2 = y;
 
     float range = max - min;
 
-    if(aa.threshold!=null)
+    if (min < 0)
     {
-        g.setColor(aa.threshold.colour);
-        y2 = (int)(y - ((aa.threshold.value-min) / range)*aa.graphHeight);
-        g.drawLine(x-av.charWidth,y2,(eRes-sRes+1)*av.charWidth,y2);
+      y2 = y - (int) ( (0 - min / (range)) * aa.graphHeight);
     }
 
-    y1 = y2 = y;
-
-    if(min<0)
-      y2 = (int)(y - (0-min / (range))*aa.graphHeight);
-
     g.setColor(Color.gray);
 
-    g.drawLine(x,y2,(eRes-sRes+1)*av.charWidth,y2);
+    g.drawLine(x, y2, (eRes - sRes) * av.charWidth, y2);
 
-    eRes = Math.min(eRes, aa.annotations.length-1);
+    int column;
+    int aaMax = aa.annotations.length - 1;
 
-
-    for (int j = sRes; j < eRes; j++)
+    while (x < eRes - sRes)
     {
+      column = sRes + x;
+      if (av.hasHiddenColumns)
+      {
+        column = av.getColumnSelection().adjustForHiddenColumns(column);
+      }
+
+      if (column > aaMax)
+      {
+        break;
+      }
 
-      if (aa.annotations[j] == null)
+      if (aa.annotations[column] == null)
       {
-        x += av.charWidth;
+        x++;
         continue;
       }
 
-        g.setColor(aa.annotations[j].colour);
-        y1 = y - (int) (((aa.annotations[j].value-min) / (range)) * aa.graphHeight);
+      g.setColor(aa.annotations[column].colour);
+      y1 = y -
+          (int) ( ( (aa.annotations[column].value - min) / (range)) * aa.graphHeight);
 
-        if(y1-y2>0)
-          g.fillRect(x, y2, av.charWidth, y1-y2 );
-        else
-          g.fillRect(x, y1, av.charWidth, y2-y1 );
+      if (y1 - y2 > 0)
+      {
+        g.fillRect(x * av.charWidth, y2, av.charWidth, y1 - y2);
+      }
+      else
+      {
+        g.fillRect(x * av.charWidth, y1, av.charWidth, y2 - y1);
+      }
 
-        x += av.charWidth;
-    }
+      x++;
 
+    }
+    if (aa.threshold != null)
+    {
+      g.setColor(aa.threshold.colour);
+      y2 = (int) (y - ( (aa.threshold.value - min) / range) * aa.graphHeight);
+      g.drawLine(0, y2, (eRes - sRes) * av.charWidth, y2);
+    }
   }
 
   // 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, int width, int y,
+                        int sRes, int eRes)
   {
-      g.setColor(Color.white);
-      g.fillRect(0, 0, width, y);
-      g.setColor(new Color(0, 0, 180));
+    g.setColor(Color.white);
+    g.fillRect(0, 0, width, y);
+    g.setColor(new Color(0, 0, 180));
 
-      int x = 0, height;
+    int x = 0, height;
 
-      for (int j = sRes; j < eRes; j++)
-      {
-          g.setColor(new Color(0, 0, 180));
+    for (int j = sRes; j < eRes; j++)
+    {
+      g.setColor(aa.annotations[j].colour);
 
-          height = (int) ((aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT);
-          if(height>y)
-              height = y;
-          g.fillRect(x, y - height, av.charWidth, height);
-          x += av.charWidth;
+      height = (int) ( (aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT);
+      if (height > y)
+      {
+        height = y;
       }
+      g.fillRect(x, y - height, av.charWidth, height);
+      x += av.charWidth;
     }
+  }
 }