X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=bffa89a77912a96d3dd507de08e0fdd39505c848;hb=c77ccc33971183dba9cb66b40886a6b61fe8eaa0;hp=5ae610fc6aa67fbcf2c2ab508feba80f2d5fc17b;hpb=f6235770cfcf11c4970e9dbe96ca293966611f24;p=jalview.git

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 5ae610f..bffa89a 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -128,10 +128,12 @@ public class AnnotationLabels extends JPanel implements MouseListener,
                 label = "";
             }
 
-            ap.av.alignment.addAnnotation(new AlignmentAnnotation(label,
+            AlignmentAnnotation newAnnotation = new AlignmentAnnotation(label,
                     "New description",
-                    new Annotation[ap.av.alignment.getWidth()]));
+                    new Annotation[ap.av.alignment.getWidth()]);
 
+            ap.av.alignment.addAnnotation(newAnnotation);
+            ap.av.alignment.setAnnotationIndex(newAnnotation, 0);
             dif = aa[aa.length - 1].height;
         }
         else if (evt.getActionCommand().equals(HIDE))
@@ -182,15 +184,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
 
 
         ap.annotationPanel.adjustPanelHeight();
-
-        Dimension d = ap.annotationScroller.getPreferredSize();
-        ap.annotationScroller.setPreferredSize(new Dimension(d.width,
-                d.height + dif));
-        d = ap.annotationSpaceFillerHolder.getPreferredSize();
-        ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension(d.width,
-                d.height + dif));
-
-        ap.addNotify();
+        ap.annotationScroller.validate();
+        ap.repaint();
     }
 
     /**
@@ -363,6 +358,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
          width = ap.calculateIdWidth().width + 4;
 
        Graphics2D g2 = (Graphics2D) g;
+       if(av.antiAlias)
         g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
             RenderingHints.VALUE_ANTIALIAS_ON);
 
@@ -390,8 +386,11 @@ public class AnnotationLabels extends JPanel implements MouseListener,
         g.setColor(Color.black);
 
         AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
-        int y = g.getFont().getSize();
+        int fontHeight = g.getFont().getSize();
+        int y = fontHeight;
         int x = 0;
+        int graphExtras = 0;
+
 
 
         if (aa != null)
@@ -405,15 +404,73 @@ public class AnnotationLabels extends JPanel implements MouseListener,
 
                 x = width - fm.stringWidth(aa[i].label) - 3;
 
-                if (aa[i].isGraph)
+                if (aa[i].graph>0)
                 {
+                    graphExtras = y;
+
                     y += (aa[i].height / 3);
+
+                    if(aa[i].graphGroup<0)
+                        graphExtras = y + fontHeight;
                 }
 
-                g.drawString(aa[i].label, x, y);
+                if(aa[i].graphGroup>-1)
+                {
+                  int groupSize = 0;
+                  for (int gg = 0; gg < aa.length; gg++)
+                  {
+                    if (aa[gg].graphGroup == aa[i].graphGroup)
+                      groupSize++;
+                  }
+
+                  if(groupSize * (fontHeight+8) < aa[i].height)
+                    graphExtras += (aa[i].height -( groupSize * (fontHeight+8)) )/2;
+
+                 for(int gg=0; gg<aa.length; gg++)
+                 {
+                   if(aa[gg].graphGroup==aa[i].graphGroup)
+                   {
+                     x = width - fm.stringWidth(aa[gg].label) - 3;
+                     g.drawString(aa[gg].label, x, graphExtras );
+                     if(aa[gg].annotations[0]!=null)
+                       g.setColor(aa[gg].annotations[0].colour);
+
+                     g.drawLine( x, graphExtras+3,
+                                 x+fm.stringWidth(aa[gg].label),
+                                 graphExtras+3);
+
+                     g.setColor(Color.black);
+                     graphExtras += fontHeight+8;
+                   }
+                 }
+                }
+                else
+                  g.drawString(aa[i].label, x, y);
 
-                if (aa[i].isGraph)
+                if (aa[i].graph>0)
                 {
+                /*  if (aa[i].graphLines != null)
+                  {
+                    for (int gl = 0; gl < aa[i].graphLines.size(); gl++)
+                    {
+                       x = width - fm.stringWidth(aa[i].getGraphLine(gl).label) - 3;
+                      g.drawString(aa[i].getGraphLine(gl).label, x, graphExtras);
+                      g.setColor(aa[i].getGraphLine(gl).colour);
+                      Graphics2D g2 = (Graphics2D) g;
+                      g2.setStroke(new BasicStroke(1,
+                          BasicStroke.CAP_SQUARE,
+                          BasicStroke.JOIN_ROUND, 3f,
+                          new float[]
+                          {5f, 3f}, 0f));
+
+                      graphExtras += 3;
+
+                      g.drawLine(x, graphExtras,
+                                 x+fm.stringWidth(aa[i].label),
+                                 graphExtras);
+                      g2.setStroke(new BasicStroke());
+                    }
+                  }*/
                     y += ((2 * aa[i].height) / 3);
                 }
                 else
@@ -427,7 +484,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
         {
             if (image != null)
             {
-                g.drawImage(image, 2, 0, this);
+                g.drawImage(image, 2, 0 - scrollOffset, this);
             }
         }