From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 3 Feb 2006 17:39:03 +0000 (+0000)
Subject: Applet draws line graphs
X-Git-Tag: Root_VamJalview_2_07b+~184
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=9f7b5126265a85454dae0987f617771ed9b8f138;hp=59183747dbffe3ab6b141c5440d2f70799ae360b;p=jalview.git

Applet draws line graphs
---

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