X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=8f72f71c336a6959e3f8862a3db2e6c12754e9ab;hb=848bef9fdc243cfab564acb0b82fc7ee3bcffe9f;hp=15bc284e428c62ad508cf4c6b17117dd6caae1e0;hpb=09bcf67a11fad002fc7c18aca46bf3672bb9f3ec;p=jalview.git

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 15bc284..8f72f71 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -76,6 +76,12 @@ public class AnnotationPanel extends JPanel implements MouseListener,
         ap.annotationScroller.getVerticalScrollBar().addAdjustmentListener(this);
     }
 
+    public AnnotationPanel(AlignViewport av)
+    {
+      this.av = av;
+    }
+
+
     /**
      * DOCUMENT ME!
      *
@@ -89,7 +95,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
     /**
      * DOCUMENT ME!
      */
-    public void adjustPanelHeight()
+    public int adjustPanelHeight()
     {
         // setHeight of panels
         image = null;
@@ -117,7 +123,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                     aa[i].height += 16;
                 }
 
-                if (aa[i].isGraph)
+                if (aa[i].graph>0)
                 {
                     aa[i].height += GRAPH_HEIGHT;
                 }
@@ -136,6 +142,8 @@ public class AnnotationPanel extends JPanel implements MouseListener,
         }
 
         this.setPreferredSize(new Dimension(1, height));
+
+        return height;
     }
 
     /**
@@ -606,10 +614,13 @@ public class AnnotationPanel extends JPanel implements MouseListener,
      * @param startRes DOCUMENT ME!
      * @param endRes DOCUMENT ME!
      */
-    public void drawComponent(Graphics2D g, int startRes, int endRes)
+    public void drawComponent(Graphics g, int startRes, int endRes)
     {
-		if(fm==null)
-			fm = g.getFontMetrics();
+      g.setFont(av.getFont());
+
+      if (fm == null)
+        fm = g.getFontMetrics();
+
 
         g.setColor(Color.white);
         g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());
@@ -646,7 +657,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
             }
 
 
-            if (row.isGraph)
+            if (row.graph>0)
             {
                 // this is so that we draw the characters below the graph
                 y += row.height;
@@ -708,7 +719,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                                 0))) / 2;
                     g.setColor(row.annotations[j].colour);
 
-                    if (j == 0 || row.isGraph)
+                    if (j == 0 || row.graph>0)
                     {
                         g.drawString(row.annotations[j].displayCharacter, x+charOffset,
                             y + iconOffset + 3);
@@ -773,33 +784,19 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                     }
                 }
 
-                if (validRes && row.isGraph)
+                if (validRes && row.graph>0)
                 {
-                    g.setColor(new Color(0, 0, 180));
+                    ///g.setColor(new Color(0, 0, 180));
 
-                    int height = (int) ((row.annotations[j].value / row.graphMax) * GRAPH_HEIGHT);
+                    if(row.graph== AlignmentAnnotation.LINE_GRAPH )
+                        drawLineGraph(g, row, j, j+1, x, y);
+                    else if(row.graph == AlignmentAnnotation.BAR_GRAPH )
+                       drawBarGraph(g, row, j, j+1, x, y);
 
-                    if (row.windowLength > 1)
-                    {
-                        int total = 0;
+                    //int height = (int) ((row.annotations[j].value / row.graphMax) * GRAPH_HEIGHT);
 
-                        for (int i2 = j - (row.windowLength / 2);
-                                i2 < (j + (row.windowLength / 2)); i2++)
-                        {
-                            if ((i2 < 0) || (i2 >= av.alignment.getWidth()))
-                            {
-                                continue;
-                            }
-
-                            total += row.annotations[i2].value;
-                        }
-
-                        total /= row.windowLength;
-                        height = (int) ((total / row.graphMax) * GRAPH_HEIGHT);
-                    }
-
-                    g.setColor(row.annotations[j].colour);
-                    g.fillRect(x, y - height, av.charWidth, height);
+                   // g.setColor(row.annotations[j].colour);
+                   // g.fillRect(x, y - height, av.charWidth, height);
                 }
             }
 
@@ -840,38 +837,73 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                 }
             }
 
-            if (row.isGraph && row.hasText)
+            if (row.graph>0 && row.hasText)
             {
                 y += av.charHeight;
             }
 
-            if (!row.isGraph)
+            if (row.graph==0)
             {
                 y += aa[i].height;
             }
         }
     }
 
-    // used by overview window
-    public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y, int sRes, int eRes)
+    public void drawLineGraph(Graphics g, AlignmentAnnotation aa, int sRes, int eRes, int x, int y)
     {
-        g.setColor(Color.white);
-        g.fillRect(0, 0, width, y);
-        g.setColor(new Color(0, 0, 180));
+      g.setColor(new Color(0, 0, 0));
+      if(sRes==0)
+        sRes++;
 
+      int y1=y, y2=y;
+      for (int j = sRes; j < eRes; j++)
+      {
+          if(aa.annotations[j-1]!=null)
+            y1 = y - (int) ((aa.annotations[j-1].value / aa.graphMax) * GRAPH_HEIGHT);
 
-        int x = 0, height;
+          if(aa.annotations[j]!=null)
+          y2 = y - (int) ((aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT);
 
-        for (int j = sRes; j < eRes; j++)
-        {
-            g.setColor(new Color(0, 0, 180));
+          g.drawLine(x-av.charWidth/2, y1, x+av.charWidth/2, y2);
 
-            height = (int) ((aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT);
-            if(height>y)
-              height = y;
+          x += av.charWidth;
+        }
+    }
 
-            g.fillRect(x, y - height, av.charWidth, height);
-            x += av.charWidth;
+    public void drawBarGraph(Graphics g, AlignmentAnnotation aa, int sRes, int eRes, int x, int y)
+    {
+      g.setColor(new Color(0, 0, 180));
+      int j, height=0;
+      for (j = sRes; j < eRes; j++)
+      {
+          g.setColor(aa.annotations[j].colour);
+          height = (int) ((aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT);
+
+          g.fillRect(x, y - height, av.charWidth, height);
+          x += av.charWidth;
         }
     }
+
+    // used by overview window
+    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));
+
+      int x = 0, height;
+
+      for (int j = sRes; j < eRes; j++)
+      {
+          g.setColor(new Color(0, 0, 180));
+
+          height = (int) ((aa.annotations[j].value / aa.graphMax) * y);
+          if(height>y)
+            height = y;
+
+          g.fillRect(x, y - height, av.charWidth, height);
+          x += av.charWidth;
+      }
+    }
+
 }