X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FAnnotationPanel.java;h=172211e6af687d2ee78785488ba8cbbef85b8479;hb=1b1a1007c534a02fdbae76df0c084f215c7c4c21;hp=f7ba2fe79beab8c3057252b4d012c5b0e2a260bc;hpb=21930635bd32076820fe0f474bd8f8f89b84dff2;p=jalview.git

diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index f7ba2fe..172211e 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) 2006 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 +51,16 @@ 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()
@@ -69,15 +74,24 @@ 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());
   }
 
-  public void adjustPanelHeight()
+  public int adjustPanelHeight()
   {
     // setHeight of panels
     AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+
+
     int height = 0;
     if (aa != null)
     {
@@ -99,7 +113,7 @@ public class AnnotationPanel
           aa[i].height += 16;
         }
 
-        if (aa[i].isGraph)
+        if (aa[i].graph>0)
         {
           aa[i].height += GRAPH_HEIGHT;
         }
@@ -117,12 +131,11 @@ public class AnnotationPanel
     }
 
     this.setSize(getSize().width, height);
-    ap.annotationScroller.setSize(getSize().width, height);
-
-//  ap.annotationSpaceFillerHolder.setSize(d.width,annotationPanel.getSize().height);
 
     repaint();
 
+    return height;
+
   }
 
   public void addEditableColumn(int i)
@@ -179,13 +192,17 @@ public class AnnotationPanel
     }
 
     int res = evt.getX() / av.getCharWidth() + av.getStartRes();
-    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);
-      ap.alignFrame.statusBar.setText(text.toString());
-    }
+
+    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));
+          if (aa[row].annotations[res].description != null)
+            text.append("  " + aa[row].annotations[res].description);
+          ap.alignFrame.statusBar.setText(text.toString());
+        }
   }
 
   public void update(Graphics g)
@@ -195,9 +212,9 @@ 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))
     {
@@ -217,7 +234,6 @@ public class AnnotationPanel
 
     drawComponent(gg, av.startRes, av.endRes + 1);
     g.drawImage(image, 0, 0, this);
-
   }
 
   public void fastPaint(int horizontal)
@@ -254,231 +270,492 @@ public class AnnotationPanel
     repaint();
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param g DOCUMENT ME!
+   * @param startRes DOCUMENT ME!
+   * @param endRes DOCUMENT ME!
+   */
   public void drawComponent(Graphics g, int startRes, int endRes)
   {
-    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.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.setFont(av.getFont());
 
-    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+    if (fm == null)
+      fm = g.getFontMetrics();
 
-    int j, x = 0, y = 0;
-    char[] lastSS = new char[aa.length];
-    int[] lastSSX = new int[aa.length];
-    int iconOffset = av.charHeight / 2;
-    boolean validRes = false;
-    //\u03B2 \u03B1
 
-    for (int i = 0; i < aa.length; i++)
-    {
-      AlignmentAnnotation row = aa[i];
-      if (!row.visible)
-      {
-        continue;
-      }
+      g.setColor(Color.white);
+      g.fillRect(0, 0, getSize().width, getSize().height);
 
-      if (row.isGraph)
+      if ((av.alignment.getAlignmentAnnotation() == null) ||
+              (av.alignment.getAlignmentAnnotation().length < 1))
       {
-        // this is so that we draw the characters below the graph
-        y += row.height;
-        if (row.hasText)
-        {
-          y -= av.charHeight;
-        }
-      }
-      if (row.hasText)
-      {
-        iconOffset = av.charHeight / 2;
-      }
-      else
-      {
-        iconOffset = 0;
+          g.setColor(Color.white);
+          g.fillRect(0, 0, getSize().width, getSize().height);
+          g.setColor(Color.black);
+          if(av.validCharWidth)
+            g.drawString("Alignment has no annotations", 20, 15);
+
+          return;
       }
 
-      for (j = startRes; j < endRes; j++)
-      {
-        if (row.annotations.length <= j || row.annotations[j] == null)
-        {
-          validRes = false;
-        }
-        else
-        {
-          validRes = true;
-        }
+      AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
 
-        x = (j - startRes) * av.charWidth;
+      int x = 0;
+      int y = 0;
+      int column=0;
+      char lastSS;
+      int lastSSX;
+      int iconOffset = av.charHeight / 2;
+      boolean validRes = false;
 
-        if (activeRow == i)
-        {
+      boolean [] graphGroupDrawn = new boolean[aa.length];
 
-          g.setColor(Color.red);
 
-          if (activeRes != null)
+      //\u03B2 \u03B1
+      for (int i = 0; i < aa.length; i++)
+      {
+          AlignmentAnnotation row = aa[i];
+
+          if (!row.visible)
           {
-            for (int n = 0; n < activeRes.size(); n++)
-            {
-              int v = Integer.parseInt(activeRes.elementAt(n).toString());
-              if (v == j)
+              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.hasText)
               {
-                g.fillRect( (j - startRes) * av.charWidth, y, av.charWidth,
-                           row.height);
+                  y -= av.charHeight;
               }
-            }
           }
-        }
 
-        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.isGraph)
+          if (row.hasText)
           {
-            if (row.annotations[0].secondaryStructure == 'H'
-                || row.annotations[0].secondaryStructure == 'E')
-            {
-              g.drawString(row.annotations[j].displayCharacter, x,
-                           y + iconOffset + 3);
-            }
+              iconOffset = av.charHeight / 2;
           }
-          else if ( (row.annotations[j].secondaryStructure == 'H'
-                     || row.annotations[j].secondaryStructure == 'E') &&
-                   (row.annotations[j - 1] == null ||
-                    row.annotations[j].secondaryStructure !=
-                    row.annotations[j - 1].secondaryStructure))
+          else
           {
-
-            g.drawString(row.annotations[j].displayCharacter, x + charOffset,
-                         y + iconOffset + 3);
+              iconOffset = 0;
           }
 
-          if (!row.hasIcons)
+           x = 0;
+          while(x < endRes-startRes)
           {
-            g.drawString(row.annotations[j].displayCharacter, x + charOffset,
-                         y + iconOffset + 3);
+            if (av.hasHiddenColumns)
+            {
+              column = av.getColumnSelection().adjustForHiddenColumns(startRes+x);
+              if (column > row.annotations.length-1)
+              {
+                break;
+              }
+            }
+            else
+                column = startRes+x;
+
+              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)
+                {
+                    g.drawString(row.annotations[column].displayCharacter,
+                                (x*av.charWidth)+charOffset,
+                        y + iconOffset + 3);
+                }
+                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==' ')))
+                {
+                    g.drawString(row.annotations[column].displayCharacter,
+                       (x*av.charWidth)+charOffset,
+                        y + iconOffset + 3);
+                    }
+              }
+
+              if (row.hasIcons)
+              {
+                  if (!validRes ||
+                          (row.annotations[column].secondaryStructure != lastSS))
+                  {
+                      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);
+                          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);
+
+                          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);
+                  }
+              }
+
+
+          column++;
+          x++;
           }
-        }
 
-        if (row.hasIcons)
-        {
-          if (!validRes || row.annotations[j].secondaryStructure != lastSS[i])
+          if(column>=row.annotations.length)
+              column = row.annotations.length-1;
+
+        //  x ++;
+
+          if (row.hasIcons)
           {
-            switch (lastSS[i])
+            switch (lastSS)
             {
               case 'H':
                 g.setColor(HELIX_COLOUR);
-                g.fillRoundRect(lastSSX[i], y + 4 + iconOffset, x - lastSSX[i],
-                                7, 8, 8);
+                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);
-                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 + 8 + iconOffset}, 3);
-                break;
-              case 'C':
+
+                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);
-                g.fillRect(lastSSX[i], y + 6 + iconOffset, x - lastSSX[i], 2);
-                break;
-            }
+                if(!av.wrapAlignment || endRes==av.endRes)
+                g.fillRect(lastSSX, y + 6 + iconOffset,
+                           (x*av.charWidth) - lastSSX, 2);
 
-            if (validRes)
-            {
-              lastSS[i] = row.annotations[j].secondaryStructure;
-            }
-            else
-            {
-              lastSS[i] = ' ';
+                break;
             }
-            lastSSX[i] = x;
           }
-        }
 
-        if (validRes && row.isGraph)
-        {
-          g.setColor(new Color(0, 0, 180));
-          int height = (int) ( (row.annotations[j].value / row.graphMax) *
-                              GRAPH_HEIGHT);
-
-          if (row.windowLength > 1)
+          if (row.graph>0)
           {
-            int total = 0;
-            for (int i2 = j - (row.windowLength / 2);
-                 i2 < j + (row.windowLength / 2); i2++)
-            {
-              if (i2 < 0 || i2 >= av.alignment.getWidth())
+              if(row.graph == AlignmentAnnotation.LINE_GRAPH )
               {
-                continue;
+                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  );
               }
+              else if(row.graph == AlignmentAnnotation.BAR_GRAPH )
+                 drawBarGraph(g, row, startRes, endRes,
+                              row.graphMin, row.graphMax, y);
+          }
 
-              total += row.annotations[i2].value;
-            }
-
-            total /= row.windowLength;
-            height = (int) ( (total / row.graphMax) * GRAPH_HEIGHT);
+          if (row.graph>0 && row.hasText)
+          {
+              y += av.charHeight;
+          }
 
+          if (row.graph==0)
+          {
+              y += aa[i].height;
           }
-          g.setColor(row.annotations[j].colour);
-          g.fillRect(x, y - height, av.charWidth, height);
-        }
+      }
+  }
+
+  public void drawLineGraph(Graphics g, AlignmentAnnotation aa,
+                            int sRes, int eRes,
+                            int y,
+                            float min, float max,
+                            int graphHeight)
+  {
+    if(sRes>aa.annotations.length)
+      return;
+
+
+
+    int x = 0;
+
+    //Adjustment for fastpaint to left
+    if(eRes<av.endRes)
+      eRes++;
+
+    eRes = Math.min(eRes, aa.annotations.length);
+
+
+    if(sRes==0)
+    {
+      sRes++;
+      x+=av.charWidth;
+    }
 
+    int y1=y, y2=y;
+    float range = max - min;
+
+    ////Draw origin
+    if(min<0)
+      y2 = y - (int)((0-min / range)*graphHeight);
+
+    g.setColor(Color.gray);
+    g.drawLine(x-av.charWidth,y2,(eRes-sRes)*av.charWidth,y2);
+
+    eRes = Math.min(eRes, aa.annotations.length);
+
+    int column;
+    int aaMax = aa.annotations.length-1;
+
+    while( x < eRes - sRes )
+    {
+      column = sRes + x;
+      if(av.hasHiddenColumns)
+      {
+        column = av.getColumnSelection().adjustForHiddenColumns(column);
       }
 
-      x += av.charWidth;
+      if (column > aaMax)
+      {
+        break;
+      }
 
-      if (row.hasIcons)
+      if(aa.annotations[column]==null || aa.annotations[column-1]==null)
       {
-        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}
-                          , new int[]
-                          {y + iconOffset, y + 14 + iconOffset,
-                          y + 7 + iconOffset}
-                          , 3);
-            break;
-          case 'C':
-            break;
-          default:
-            g.setColor(Color.gray);
-            g.fillRect(lastSSX[i], y + 6 + iconOffset, x - lastSSX[i], 2);
-            break;
+        x++;
+        continue;
+      }
 
-        }
+        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,
+                           int sRes, int eRes,
+                           float min, float max,
+                           int y)
+  {
+    if(sRes>aa.annotations.length)
+      return;
+
+    eRes = Math.min(eRes, aa.annotations.length);
+
+    int x=0, y1=y, y2=y;
+
+    float range = max - min;
+
+    if(min<0)
+      y2 = y - (int)((0-min / (range))*aa.graphHeight);
+
+    g.setColor(Color.gray);
+
+    g.drawLine(x,y2,(eRes-sRes)*av.charWidth,y2);
+
+    int column;
+    int aaMax = aa.annotations.length-1;
+
+    while( x < eRes-sRes )
+    {
+      column = sRes + x;
+      if(av.hasHiddenColumns)
+      {
+        column = av.getColumnSelection().adjustForHiddenColumns(column);
       }
 
-      if (row.isGraph && row.hasText)
+      if(column > aaMax)
       {
-        y += av.charHeight;
+          break;
       }
-      if (!row.isGraph)
+
+      if (aa.annotations[column] == null)
       {
-        y += aa[i].height;
+        x ++;
+        continue;
       }
+
+        g.setColor(aa.annotations[column].colour);
+        y1 = y - (int) (((aa.annotations[column].value-min) / (range)) * aa.graphHeight);
+
+        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 ++ ;
+
     }
+    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
@@ -492,7 +769,7 @@ public class AnnotationPanel
 
       for (int j = sRes; j < eRes; j++)
       {
-          g.setColor(new Color(0, 0, 180));
+          g.setColor(aa.annotations[j].colour);
 
           height = (int) ((aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT);
           if(height>y)