X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationPanel.java;h=614498c4bc1d684962a6e414de9a6cf1e35e0816;hb=8b875ed4be8113683a34f4d4df36b3a6bb1c556e;hp=a1597f8320f13dd1d98ac14c893a6796bc383359;hpb=ee53965807b83bf93a21cbc341cee9a9e005b2cb;p=jalview.git

diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index a1597f8..614498c 100755
--- a/src/jalview/appletgui/AnnotationPanel.java
+++ b/src/jalview/appletgui/AnnotationPanel.java
@@ -51,11 +51,16 @@ public class AnnotationPanel
 
   public static int GRAPH_HEIGHT = 40;
 
+  boolean MAC = false;
+
   public AnnotationPanel(AlignmentPanel ap)
   {
+    if (System.getProperty("os.name").startsWith("Mac"))
+      MAC = true;
+
     this.ap = ap;
     av = ap.av;
-    this.setLayout(null);
+    setLayout(null);
     adjustPanelHeight();
 
     addMouseMotionListener(new MouseMotionAdapter()
@@ -108,7 +113,7 @@ public class AnnotationPanel
           aa[i].height += 16;
         }
 
-        if (aa[i].isGraph)
+        if (aa[i].graph>0)
         {
           aa[i].height += GRAPH_HEIGHT;
         }
@@ -126,9 +131,6 @@ public class AnnotationPanel
     }
 
     this.setSize(getSize().width, height);
-    if(ap!=null)
-       ap.annotationScroller.setSize(getSize().width, height);
-
 
     repaint();
 
@@ -206,8 +208,8 @@ public class AnnotationPanel
 
   public void paint(Graphics g)
   {
-    g.setColor(Color.white);
-    g.fillRect(0,0, getSize().width, getSize().height);
+
+
     imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;
 
     if (image == null || imgWidth != image.getWidth(this))
@@ -227,6 +229,8 @@ public class AnnotationPanel
     }
 
     drawComponent(gg, av.startRes, av.endRes + 1);
+    g.setColor(Color.white);
+    g.fillRect(0, 0, getSize().width, getSize().height);
     g.drawImage(image, 0, 0, this);
   }
 
@@ -264,6 +268,13 @@ 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());
@@ -281,21 +292,24 @@ public class AnnotationPanel
           g.setColor(Color.white);
           g.fillRect(0, 0, getSize().width, getSize().height);
           g.setColor(Color.black);
-          g.drawString("Alignment has no annotations", 20, 15);
+          if(av.validCharWidth)
+            g.drawString("Alignment has no annotations", 20, 15);
 
           return;
       }
 
       AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
 
-      int j;
       int x = 0;
       int y = 0;
-      char[] lastSS = new char[aa.length];
-      int[] lastSSX = new int[aa.length];
+      char lastSS;
+      int lastSSX;
       int iconOffset = av.charHeight / 2;
       boolean validRes = false;
 
+      boolean [] graphGroupDrawn = new boolean[aa.length];
+
+
       //\u03B2 \u03B1
       for (int i = 0; i < aa.length; i++)
       {
@@ -306,9 +320,14 @@ public class AnnotationPanel
               continue;
           }
 
+          lastSS = ' ';
+          lastSSX = 0;
 
-          if (row.isGraph)
+          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;
 
@@ -327,10 +346,11 @@ public class AnnotationPanel
               iconOffset = 0;
           }
 
-          for (j = startRes; j < endRes; j++)
+          int column = startRes;
+          while(column < endRes)
           {
-              if ((row.annotations.length <= j) ||
-                      (row.annotations[j] == null))
+              if ((row.annotations.length <= column) ||
+                      (row.annotations[column] == null))
               {
                   validRes = false;
               }
@@ -339,50 +359,79 @@ public class AnnotationPanel
                   validRes = true;
               }
 
-              x = (j - startRes) * av.charWidth;
+              x = (column - startRes) * av.charWidth;
 
 
-              if (validRes &&
-                      (row.annotations[j].displayCharacter.length() > 0))
+              if (av.validCharWidth && validRes &&
+                        (row.annotations[column].displayCharacter.length() > 0))
               {
-
-                  int charOffset = (av.charWidth -
-                      fm.charWidth(row.annotations[j].displayCharacter.charAt(
-                              0))) / 2;
-                  g.setColor(row.annotations[j].colour);
-
-                  if (j == 0 || row.isGraph)
-                  {
-                      g.drawString(row.annotations[j].displayCharacter, x+charOffset,
-                          y + iconOffset + 3);
-                  }
-                  else if (((row.annotations[j - 1] == null) ||
-                          (row.annotations[j].displayCharacter != row.annotations[j -
-                          1].displayCharacter)))
-                  {
-                      g.drawString(row.annotations[j].displayCharacter, x+charOffset,
-                          y + iconOffset + 3);
-                  }
+                int charOffset = (av.charWidth -
+                    fm.charWidth(row.annotations[column].displayCharacter.charAt(
+                            0))) / 2;
+                g.setColor(row.annotations[column].colour);
+
+                if (column == 0 || row.graph>0)
+                {
+                    g.drawString(row.annotations[column].displayCharacter, x+charOffset,
+                        y + iconOffset + 3);
+                }
+                else if (
+                    row.annotations[column - 1] == null
+                    ||(!row.annotations[column].displayCharacter.equals(
+                        row.annotations[column - 1].displayCharacter)
+                    ||
+              (row.annotations[column].displayCharacter.length() <2 &&
+               row.annotations[column].secondaryStructure==' ')))
+                {
+                    g.drawString(row.annotations[column].displayCharacter, x+charOffset,
+                        y + iconOffset + 3);
+                    }
               }
 
               if (row.hasIcons)
               {
                   if (!validRes ||
-                          (row.annotations[j].secondaryStructure != lastSS[i]))
+                          (row.annotations[column].secondaryStructure != lastSS))
                   {
-                      switch (lastSS[i])
+                      switch (lastSS)
                       {
                       case 'H':
-                          g.setColor(HELIX_COLOUR);
-                          g.fillRoundRect(lastSSX[i], y + 4 + iconOffset,
-                              x - lastSSX[i], 7, 8, 8);
-
+                        g.setColor(HELIX_COLOUR);
+                        if (MAC)
+                        {
+                          //Off by 1 offset when drawing rects and ovals
+                          //to offscreen image on the MAC
+                          g.fillRoundRect(lastSSX, y + 4 + iconOffset,
+                                          x - lastSSX, 7, 8, 8);
                           break;
+                        }
+
+                        int sCol = (lastSSX / av.charWidth) + startRes;
+                        int x1 = lastSSX;
+                        int x2 = x;
+
+                       if(sCol==0 ||
+                          row.annotations[sCol-1]==null ||
+                          row.annotations[sCol-1].secondaryStructure!='H')
+                       {
+                         g.fillArc(lastSSX, y+4+iconOffset, av.charWidth, 8, 90,180) ;
+                         x1 += av.charWidth/2;
+                       }
+
+                        if(row.annotations[column]==null ||
+                           row.annotations[column].secondaryStructure!='H')
+                        {
+                          g.fillArc(x-av.charWidth, y+4+iconOffset, av.charWidth, 8, 270,180);
+                          x2 -= av.charWidth/2;
+                        }
+
+                        g.fillRect(x1, y+4+iconOffset, x2-x1, 8);
+                            break;
 
                       case 'E':
                           g.setColor(SHEET_COLOUR);
-                          g.fillRect(lastSSX[i], y + 4 + iconOffset,
-                              x - lastSSX[i] - 4, 7);
+                          g.fillRect(lastSSX, y + 4 + iconOffset,
+                              x - lastSSX - 4, 7);
                           g.fillPolygon(new int[] { x - 4, x - 4, x },
                               new int[]
                               {
@@ -392,107 +441,275 @@ public class AnnotationPanel
 
                           break;
 
-                      case 'C':
-                          break;
 
                       default:
                           g.setColor(Color.gray);
-                          g.fillRect(lastSSX[i], y + 6 + iconOffset,
-                              x - lastSSX[i], 2);
+                          g.fillRect(lastSSX, y + 6 + iconOffset,
+                              x - lastSSX, 2);
 
                           break;
                       }
 
                       if (validRes)
                       {
-                          lastSS[i] = row.annotations[j].secondaryStructure;
+                          lastSS = row.annotations[column].secondaryStructure;
                       }
                       else
                       {
-                          lastSS[i] = ' ';
+                          lastSS = ' ';
                       }
 
-                      lastSSX[i] = x;
+                      lastSSX = x;
                   }
               }
 
-              if (validRes && row.isGraph)
-              {
-                  g.setColor(new Color(0, 0, 180));
-
-                  int height = (int) ((row.annotations[j].value / row.graphMax) * GRAPH_HEIGHT);
-
-                  if (row.windowLength > 1)
-                  {
-                      int total = 0;
-
-                      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);
-              }
+          column++;
           }
 
+          if(column>=row.annotations.length)
+              column = row.annotations.length-1;
+
           x += av.charWidth;
 
           if (row.hasIcons)
           {
-              switch (lastSS[i])
+              switch (lastSS)
               {
               case 'H':
-                  g.setColor(HELIX_COLOUR);
-                  g.fillRoundRect(lastSSX[i], y + 4 + iconOffset,
-                      x - lastSSX[i], 7, 8, 8);
-
+                g.setColor(HELIX_COLOUR);
+                if (MAC)
+                {
+                  //Off by 1 offset when drawing rects and ovals
+                  //to offscreen image on the MAC
+                  g.fillRoundRect(lastSSX, y + 4 + iconOffset,
+                                  x - lastSSX, 7, 8, 8);
                   break;
+                }
+
+
+                int sCol = (lastSSX / av.charWidth) + startRes;
+                int x1 = lastSSX;
+                int x2 = x;
+
+               if(sCol==0 ||
+                  row.annotations[sCol-1]==null ||
+                  row.annotations[sCol-1].secondaryStructure!='H')
+               {
+                 g.fillArc(lastSSX, y+4+iconOffset, av.charWidth, 8, 90,180) ;
+                 x1 += av.charWidth/2;
+               }
+
+                if(row.annotations[column]==null ||
+                   row.annotations[column].secondaryStructure!='H')
+                {
+                  g.fillArc(x-av.charWidth, y+4+iconOffset, av.charWidth, 8, 270,180);
+                  x2 -= av.charWidth/2;
+                }
+
+                g.fillRect(x1, y+4+iconOffset, x2-x1, 8);
+
+                    break;
 
               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);
 
-                  break;
+                  if (row.annotations[endRes] ==null
+                        || row.annotations[endRes].secondaryStructure != 'E')
+                  {
+                    g.fillRect(lastSSX, y + 4 + iconOffset,
+                               x - lastSSX - 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, y + 4 + iconOffset,
+                               x - lastSSX, 7);
 
-              case 'C':
                   break;
 
+
               default:
                   g.setColor(Color.gray);
-                  g.fillRect(lastSSX[i], y + 6 + iconOffset, x - lastSSX[i], 2);
+                  g.fillRect(lastSSX, y + 6 + iconOffset, x - lastSSX, 2);
 
                   break;
               }
           }
 
-          if (row.isGraph && row.hasText)
+          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;
           }
 
-          if (!row.isGraph)
+          if (row.graph==0)
           {
               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++;
+
+    eRes = Math.min(eRes, aa.annotations.length);
+
+
+    if(sRes==0)
+    {
+      sRes++;
+      x+=av.charWidth;
+    }
+
+    int y1=y, y2=y;
+    float range = max - min;
+
+    ////Draw origin
+    if(min<0)
+      y2 = y - (int)((0-min / range)*graphHeight);
+
+    g.setColor(Color.gray);
+    g.drawLine(x-av.charWidth,y2,(eRes-sRes)*av.charWidth,y2);
+
+
+    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;
+     }
+
+
+     if(aa.threshold!=null)
+     {
+         g.setColor(aa.threshold.colour);
+         y2 = (int)(y - ((aa.threshold.value-min) / range)*aa.graphHeight);
+         g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2);
+     }
+
+  }
+
+  public void drawBarGraph(Graphics g, AlignmentAnnotation aa,
+                           int sRes, int eRes,
+                           float min, float max,
+                           int y)
+  {
+    if(sRes>aa.annotations.length)
+      return;
+
+
+    eRes = Math.min(eRes, aa.annotations.length);
+
+    int x=0, y1, y2;
+
+    float range = max - min;
+
+    y1 = y2 = y;
+
+    if(min<0)
+      y2 = y -(int)( (0-min / (range))*aa.graphHeight);
+
+    g.setColor(Color.gray);
+
+    g.drawLine(x,y2,(eRes-sRes)*av.charWidth,y2);
+
+    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;
+    }
+
+
+    if(aa.threshold!=null)
+    {
+        g.setColor(aa.threshold.colour);
+        y2 = (int)(y - ((aa.threshold.value-min) / range)*aa.graphHeight);
+        g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2);
+    }
+
+
   }
 
   // used by overview window
@@ -506,7 +723,7 @@ public class AnnotationPanel
 
       for (int j = sRes; j < eRes; j++)
       {
-          g.setColor(new Color(0, 0, 180));
+          g.setColor(aa.annotations[j].colour);
 
           height = (int) ((aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT);
           if(height>y)