Applet draws line graphs

diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index a71e439..bcc2866 100755 (executable)
--- a/src/jalview/appletgui/AnnotationPanel.java
+++ b/src/jalview/appletgui/AnnotationPanel.java
@@ -264,6 +264,13 @@ public class AnnotationPanel
     repaint();\r
   }\r
 \r
+  /**\r
+   * DOCUMENT ME!\r
+   *\r
+   * @param g DOCUMENT ME!\r
+   * @param startRes DOCUMENT ME!\r
+   * @param endRes DOCUMENT ME!\r
+   */\r
   public void drawComponent(Graphics g, int startRes, int endRes)\r
   {\r
     g.setFont(av.getFont());\r
@@ -296,6 +303,9 @@ public class AnnotationPanel
       int iconOffset = av.charHeight / 2;\r
       boolean validRes = false;\r
 \r
+      boolean [] graphGroupDrawn = new boolean[aa.length];\r
+\r
+\r
       //\u03B2 \u03B1\r
       for (int i = 0; i < aa.length; i++)\r
       {\r
@@ -307,8 +317,12 @@ public class AnnotationPanel
           }\r
 \r
 \r
+\r
           if (row.graph>0)\r
           {\r
+              if(row.graphGroup>-1 && graphGroupDrawn[ row.graphGroup ] )\r
+                continue;\r
+\r
               // this is so that we draw the characters below the graph\r
               y += row.height;\r
 \r
@@ -341,6 +355,24 @@ public class AnnotationPanel
 \r
               x = (j - startRes) * av.charWidth;\r
 \r
+              if (activeRow == i)\r
+              {\r
+                  g.setColor(Color.red);\r
+\r
+                  if (activeRes != null)\r
+                  {\r
+                      for (int n = 0; n < activeRes.size(); n++)\r
+                      {\r
+                          int v = Integer.parseInt(activeRes.elementAt(n).toString());\r
+\r
+                          if (v == j)\r
+                          {\r
+                              g.fillRect((j - startRes) * av.charWidth, y,\r
+                                  av.charWidth, row.height);\r
+                          }\r
+                      }\r
+                  }\r
+              }\r
 \r
               if (validRes &&\r
                       (row.annotations[j].displayCharacter.length() > 0))\r
@@ -392,8 +424,6 @@ public class AnnotationPanel
 \r
                           break;\r
 \r
-                      case 'C':\r
-                          break;\r
 \r
                       default:\r
                           g.setColor(Color.gray);\r
@@ -415,16 +445,6 @@ public class AnnotationPanel
                       lastSSX[i] = x;\r
                   }\r
               }\r
-\r
-              if (validRes && row.graph>0)\r
-              {\r
-                  g.setColor(new Color(0, 0, 180));\r
-\r
-                  int height = (int) ((row.annotations[j].value / row.graphMax) * GRAPH_HEIGHT);\r
-\r
-                  g.setColor(row.annotations[j].colour);\r
-                  g.fillRect(x, y - height, av.charWidth, height);\r
-              }\r
           }\r
 \r
           x += av.charWidth;\r
@@ -442,14 +462,23 @@ public class AnnotationPanel
 \r
               case 'E':\r
                   g.setColor(SHEET_COLOUR);\r
-                  g.fillRect(lastSSX[i], y + 4 + iconOffset,\r
-                      x - lastSSX[i] - 4, 7);\r
-                  g.fillPolygon(new int[] { x - 4, x - 4, x },\r
-                      new int[]\r
-                      {\r
-                          y + iconOffset, y + 14 + iconOffset,\r
-                          y + 7 + iconOffset\r
-                      }, 3);\r
+\r
+                  if (row.annotations.length > endRes\r
+                      && row.annotations[endRes].secondaryStructure != 'E')\r
+                  {\r
+                    g.fillRect(lastSSX[i], y + 4 + iconOffset,\r
+                               x - lastSSX[i] - 4, 7);\r
+                    g.fillPolygon(new int[]\r
+                                  {x - 4, x - 4, x},\r
+                                  new int[]\r
+                                  {\r
+                                  y + iconOffset, y + 14 + iconOffset,\r
+                                  y + 7 + iconOffset\r
+                    }, 3);\r
+                  }\r
+                  else\r
+                    g.fillRect(lastSSX[i], y + 4 + iconOffset,\r
+                               x - lastSSX[i], 7);\r
 \r
                   break;\r
 \r
@@ -464,6 +493,48 @@ public class AnnotationPanel
               }\r
           }\r
 \r
+          if (row.graph>0)\r
+          {\r
+              if(row.graph == AlignmentAnnotation.LINE_GRAPH )\r
+              {\r
+                if(row.graphGroup>-1 && !graphGroupDrawn[row.graphGroup])\r
+                 {\r
+                   float groupmax=-999999, groupmin=9999999;\r
+                   for(int gg=0; gg<aa.length; gg++)\r
+                   {\r
+                     if(aa[gg].graphGroup!=row.graphGroup)\r
+                       continue;\r
+\r
+                     if(aa[gg]!=row)\r
+                       aa[gg].visible = false;\r
+\r
+                     if(aa[gg].graphMax>groupmax)\r
+                       groupmax = aa[gg].graphMax;\r
+                     if(aa[gg].graphMin<groupmin)\r
+                       groupmin = aa[gg].graphMin;\r
+                   }\r
+\r
+                   for (int gg = 0; gg < aa.length; gg++)\r
+                   {\r
+                     if (aa[gg].graphGroup == row.graphGroup)\r
+                     {\r
+                       drawLineGraph(g, aa[gg], startRes, endRes, y,\r
+                                     groupmin, groupmax,\r
+                                     row.graphHeight);\r
+                     }\r
+                   }\r
+\r
+                   graphGroupDrawn[ row.graphGroup ] = true;\r
+                 }\r
+                 else\r
+                   drawLineGraph(g, row, startRes, endRes,\r
+                                 y, row.graphMin, row.graphMax, row.graphHeight  );\r
+              }\r
+              else if(row.graph == AlignmentAnnotation.BAR_GRAPH )\r
+                 drawBarGraph(g, row, startRes, endRes,\r
+                              row.graphMin, row.graphMax, y);\r
+          }\r
+\r
           if (row.graph>0 && row.hasText)\r
           {\r
               y += av.charHeight;\r
@@ -473,7 +544,121 @@ public class AnnotationPanel
           {\r
               y += aa[i].height;\r
           }\r
-        }\r
+      }\r
+  }\r
+\r
+  public void drawLineGraph(Graphics g, AlignmentAnnotation aa,\r
+                            int sRes, int eRes,\r
+                            int y,\r
+                            float min, float max,\r
+                            int graphHeight)\r
+  {\r
+    if(sRes>aa.annotations.length)\r
+      return;\r
+\r
+    int x = 0;\r
+\r
+    //Adjustment for fastpaint to left\r
+    if(eRes<av.endRes)\r
+      eRes++;\r
+\r
+    if(sRes==0)\r
+    {\r
+      sRes++;\r
+      x+=av.charWidth;\r
+    }\r
+\r
+    int y1=y, y2=y;\r
+    float range = max - min;\r
+\r
+    ////Draw origin\r
+    if(min<0)\r
+      y2 = (int)(y - (0-min / range)*graphHeight);\r
+\r
+    g.setColor(Color.gray);\r
+    g.drawLine(x-av.charWidth,y2,(eRes-sRes+1)*av.charWidth,y2);\r
+\r
+\r
+    if(aa.graphLines!=null)\r
+    {\r
+      for(int l=0; l<aa.graphLines.size(); l++)\r
+      {\r
+        g.setColor(aa.getGraphLine(l).colour);\r
+        y2 = (int)(y - ((aa.getGraphLine(l).value-min) / range)*graphHeight);\r
+        g.drawLine(x-av.charWidth,y2,(eRes-sRes+1)*av.charWidth,y2);\r
+      }\r
+    }\r
+\r
+    eRes = Math.min(eRes, aa.annotations.length);\r
+    for (int j = sRes; j < eRes; j++)\r
+    {\r
+      if(aa.annotations[j]==null || aa.annotations[j-1]==null)\r
+      {\r
+        x+=av.charWidth;\r
+        continue;\r
+      }\r
+        g.setColor(aa.annotations[j].colour);\r
+        y1 = y - (int) (((aa.annotations[j-1].value-min) / range) * graphHeight);\r
+        y2 = y - (int) (((aa.annotations[j].value-min) / range) * graphHeight);\r
+        g.drawLine(x-av.charWidth/2, y1, x+av.charWidth/2, y2);\r
+        x += av.charWidth;\r
+     }\r
+  }\r
+\r
+  public void drawBarGraph(Graphics g, AlignmentAnnotation aa,\r
+                           int sRes, int eRes,\r
+                           float min, float max,\r
+                           int y)\r
+  {\r
+    if(sRes>aa.annotations.length)\r
+      return;\r
+\r
+    int x=0, y1, y2;\r
+\r
+    float range = max - min;\r
+\r
+    if(aa.graphLines!=null)\r
+    {\r
+      for(int l=0; l<aa.graphLines.size(); l++)\r
+      {\r
+        g.setColor(aa.getGraphLine(l).colour);\r
+        y2 = (int)(y - ((aa.getGraphLine(l).value-min) / range)*aa.graphHeight);\r
+        g.drawLine(x-av.charWidth,y2,(eRes-sRes+1)*av.charWidth,y2);\r
+       }\r
+    }\r
+\r
+    y1 = y2 = y;\r
+\r
+    if(min<0)\r
+      y2 = (int)(y - (0-min / (range))*aa.graphHeight);\r
+\r
+    g.setColor(Color.gray);\r
+\r
+    g.drawLine(x,y2,(eRes-sRes+1)*av.charWidth,y2);\r
+\r
+    eRes = Math.min(eRes, aa.annotations.length-1);\r
+\r
+\r
+    for (int j = sRes; j < eRes; j++)\r
+    {\r
+\r
+      if (aa.annotations[j] == null)\r
+      {\r
+        x += av.charWidth;\r
+        continue;\r
+      }\r
+\r
+        g.setColor(aa.annotations[j].colour);\r
+        y1 = y - (int) (((aa.annotations[j].value-min) / (range)) * aa.graphHeight);\r
+\r
+        if(y1-y2>0)\r
+          g.fillRect(x, y2, av.charWidth, y1-y2 );\r
+        else\r
+          g.fillRect(x, y1, av.charWidth, y2-y1 );\r
+\r
+        x += av.charWidth;\r
+    }\r
+\r
   }\r
 \r
   // used by overview window\r