Highlight from alignment

[jalview.git] / src / jalview / gui / AnnotationPanel.java

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 4f984fd..d97c80f 100755 (executable)
--- 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);\r
     }\r
 \r
+    public AnnotationPanel(AlignViewport av)\r
+    {\r
+      this.av = av;\r
+    }\r
+\r
+\r
     /**\r
      * DOCUMENT ME!\r
      *\r
@@ -89,9 +95,10 @@ public class AnnotationPanel extends JPanel implements MouseListener,
     /**\r
      * DOCUMENT ME!\r
      */\r
-    public void adjustPanelHeight()\r
+    public int adjustPanelHeight()\r
     {\r
         // setHeight of panels\r
+        image = null;\r
         AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
         int height = 0;\r
 \r
@@ -135,6 +142,8 @@ public class AnnotationPanel extends JPanel implements MouseListener,
         }\r
 \r
         this.setPreferredSize(new Dimension(1, height));\r
+\r
+        return height;\r
     }\r
 \r
     /**\r
@@ -147,6 +156,8 @@ public class AnnotationPanel extends JPanel implements MouseListener,
         if (activeRow == -1)\r
         {\r
             AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
+            if(aa==null)\r
+              return;\r
 \r
             for (int j = 0; j < aa.length; j++)\r
             {\r
@@ -177,6 +188,8 @@ public class AnnotationPanel extends JPanel implements MouseListener,
         if (activeRow == -1)\r
         {\r
             AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
+            if(aa==null)\r
+              return;\r
 \r
             for (int j = 0; j < aa.length; j++)\r
             {\r
@@ -332,7 +345,10 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 \r
         for (int i = 0; i < aa.length; i++)\r
         {\r
-            height += aa[i].height;\r
+            if (aa[i].visible)\r
+            {\r
+              height += aa[i].height;\r
+            }\r
 \r
             if (evt.getY() < height)\r
             {\r
@@ -522,7 +538,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
       g.setColor(Color.white);\r
       g.fillRect(0, 0, getWidth(), getHeight());\r
 \r
-      if (fastPaint)\r
+      if (fastPaint && image!=null)\r
       {\r
         g.drawImage(image, 0, 0, this);\r
         fastPaint = false;\r
@@ -531,24 +547,18 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 \r
       imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;\r
 \r
-      if (image != null && imgWidth == image.getWidth())\r
+      if (image == null || imgWidth != image.getWidth())\r
       {\r
-        //This will be called by a mouse over, tool tip etc\r
-        // no need to redraw whole image\r
-        g.drawImage(image, 0, 0, this);\r
-        fastPaint = false;\r
-        return;\r
+        image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(),\r
+                                  BufferedImage.TYPE_INT_RGB);\r
+        gg = (Graphics2D) image.getGraphics();\r
+        gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
+                            RenderingHints.VALUE_ANTIALIAS_ON);\r
+\r
+        gg.setFont(av.getFont());\r
+        fm = gg.getFontMetrics();\r
       }\r
 \r
-      image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(),\r
-                                BufferedImage.TYPE_INT_RGB);\r
-      gg = (Graphics2D) image.getGraphics();\r
-      gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
-                          RenderingHints.VALUE_ANTIALIAS_ON);\r
-\r
-      gg.setFont(av.getFont());\r
-      fm = gg.getFontMetrics();\r
-\r
       drawComponent(gg, av.startRes, av.endRes + 1);\r
       g.drawImage(image, 0, 0, this);\r
     }\r
@@ -604,8 +614,14 @@ public class AnnotationPanel extends JPanel implements MouseListener,
      * @param startRes DOCUMENT ME!\r
      * @param endRes DOCUMENT ME!\r
      */\r
-    public void drawComponent(Graphics2D g, int startRes, int endRes)\r
+    public void drawComponent(Graphics g, int startRes, int endRes)\r
     {\r
+      g.setFont(av.getFont());\r
+\r
+      if (fm == null)\r
+        fm = g.getFontMetrics();\r
+\r
+\r
         g.setColor(Color.white);\r
         g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());\r
 \r
@@ -640,6 +656,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                 continue;\r
             }\r
 \r
+\r
             if (row.isGraph)\r
             {\r
                 // this is so that we draw the characters below the graph\r
@@ -847,19 +864,23 @@ public class AnnotationPanel extends JPanel implements MouseListener,
     }\r
 \r
     // used by overview window\r
-    public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y)\r
+    public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y, int sRes, int eRes)\r
     {\r
         g.setColor(Color.white);\r
         g.fillRect(0, 0, width, y);\r
         g.setColor(new Color(0, 0, 180));\r
 \r
-        int x = 0;\r
 \r
-        for (int j = 0; j < aa.annotations.length; j++)\r
+        int x = 0, height;\r
+\r
+        for (int j = sRes; j < eRes; j++)\r
         {\r
             g.setColor(new Color(0, 0, 180));\r
 \r
-            int height = (int) ((aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT);\r
+            height = (int) ((aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT);\r
+            if(height>y)\r
+              height = y;\r
+\r
             g.fillRect(x, y - height, av.charWidth, height);\r
             x += av.charWidth;\r
         }\r