X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationPanel.java;h=a1597f8320f13dd1d98ac14c893a6796bc383359;hb=436a05e4d6015e30a04bb0234cebd07210137df8;hp=ad4aeb80703f34c597cc168b60fb80ad719ea21a;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index ad4aeb8..a1597f8 100755
--- a/src/jalview/appletgui/AnnotationPanel.java
+++ b/src/jalview/appletgui/AnnotationPanel.java
@@ -69,15 +69,24 @@ public class AnnotationPanel
     // ap.annotationScroller.getVAdjustable().addAdjustmentListener( this );
   }
 
+
+  public AnnotationPanel(AlignViewport av)
+  {
+    this.av = av;
+  }
+
+
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
     ap.alabels.setScrollOffset( -evt.getValue());
   }
 
-  public void adjustPanelHeight()
+  public int adjustPanelHeight()
   {
     // setHeight of panels
     AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+
+
     int height = 0;
     if (aa != null)
     {
@@ -117,12 +126,14 @@ public class AnnotationPanel
     }
 
     this.setSize(getSize().width, height);
-    ap.annotationScroller.setSize(getSize().width, height);
+    if(ap!=null)
+       ap.annotationScroller.setSize(getSize().width, height);
 
-//  ap.annotationSpaceFillerHolder.setSize(d.width,annotationPanel.getSize().height);
 
     repaint();
 
+    return height;
+
   }
 
   public void addEditableColumn(int i)
@@ -130,6 +141,9 @@ public class AnnotationPanel
     if (activeRow == -1)
     {
       AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+      if(aa ==null)
+        return;
+
       for (int j = 0; j < aa.length; j++)
       {
         if (aa[j].editable)
@@ -192,6 +206,8 @@ 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))
@@ -212,7 +228,6 @@ public class AnnotationPanel
 
     drawComponent(gg, av.startRes, av.endRes + 1);
     g.drawImage(image, 0, 0, this);
-
   }
 
   public void fastPaint(int horizontal)
@@ -251,245 +266,253 @@ public class AnnotationPanel
 
   public void drawComponent(Graphics g, int startRes, int endRes)
   {
-    g.setColor(Color.white);
-    g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getSize().height);
-    if (av.alignment.getAlignmentAnnotation() == null ||
-        av.alignment.getAlignmentAnnotation().length < 1)
-    {
-      g.setColor(Color.white);
-      g.fillRect(0, 0, getSize().width, getSize().height);
-      g.setColor(Color.black);
-      g.drawString("Alignment has no annotations", 20, 15);
-      return;
-    }
+    g.setFont(av.getFont());
 
-    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+    if (fm == null)
+      fm = g.getFontMetrics();
 
-    int j, x = 0, y = 0;
-    char[] lastSS = new char[aa.length];
-    int[] lastSSX = new int[aa.length];
-    int iconOffset = av.charHeight / 2;
-    boolean validRes = false;
-    //\u03B2 \u03B1
 
-    for (int i = 0; i < aa.length; i++)
-    {
-      AlignmentAnnotation row = aa[i];
-      if (!row.visible)
-      {
-        continue;
-      }
+      g.setColor(Color.white);
+      g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getSize().height);
 
-      if (row.isGraph)
-      {
-        // this is so that we draw the characters below the graph
-        y += row.height;
-        if (row.hasText)
-        {
-          y -= av.charHeight;
-        }
-      }
-      if (row.hasText)
-      {
-        iconOffset = av.charHeight / 2;
-      }
-      else
+      if ((av.alignment.getAlignmentAnnotation() == null) ||
+              (av.alignment.getAlignmentAnnotation().length < 1))
       {
-        iconOffset = 0;
+          g.setColor(Color.white);
+          g.fillRect(0, 0, getSize().width, getSize().height);
+          g.setColor(Color.black);
+          g.drawString("Alignment has no annotations", 20, 15);
+
+          return;
       }
 
-      for (j = startRes; j < endRes; j++)
-      {
-        if (row.annotations.length <= j || row.annotations[j] == null)
-        {
-          validRes = false;
-        }
-        else
-        {
-          validRes = true;
-        }
+      AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
 
-        x = (j - startRes) * av.charWidth;
+      int j;
+      int x = 0;
+      int y = 0;
+      char[] lastSS = new char[aa.length];
+      int[] lastSSX = new int[aa.length];
+      int iconOffset = av.charHeight / 2;
+      boolean validRes = false;
 
-        if (activeRow == i)
-        {
+      //\u03B2 \u03B1
+      for (int i = 0; i < aa.length; i++)
+      {
+          AlignmentAnnotation row = aa[i];
+
+          if (!row.visible)
+          {
+              continue;
+          }
 
-          g.setColor(Color.red);
 
-          if (activeRes != null)
+          if (row.isGraph)
           {
-            for (int n = 0; n < activeRes.size(); n++)
-            {
-              int v = Integer.parseInt(activeRes.elementAt(n).toString());
-              if (v == j)
+              // this is so that we draw the characters below the graph
+              y += row.height;
+
+              if (row.hasText)
               {
-                g.fillRect( (j - startRes) * av.charWidth, y, av.charWidth,
-                           row.height);
+                  y -= av.charHeight;
               }
-            }
           }
-        }
 
-        if (validRes && row.annotations[j].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)
+          if (row.hasText)
           {
-            if (row.annotations[0].secondaryStructure == 'H'
-                || row.annotations[0].secondaryStructure == 'E')
-            {
-              g.drawString(row.annotations[j].displayCharacter, x,
-                           y + iconOffset + 2);
-            }
+              iconOffset = av.charHeight / 2;
           }
-          else if ( (row.annotations[j].secondaryStructure == 'H'
-                     || row.annotations[j].secondaryStructure == 'E') &&
-                   (row.annotations[j - 1] == null ||
-                    row.annotations[j].secondaryStructure !=
-                    row.annotations[j - 1].secondaryStructure))
+          else
           {
-
-            g.drawString(row.annotations[j].displayCharacter, x + charOffset,
-                         y + iconOffset + 2);
+              iconOffset = 0;
           }
 
-          if (!row.hasIcons)
+          for (j = startRes; j < endRes; j++)
           {
-            g.drawString(row.annotations[j].displayCharacter, x + charOffset,
-                         y + iconOffset + 2);
-          }
-        }
+              if ((row.annotations.length <= j) ||
+                      (row.annotations[j] == null))
+              {
+                  validRes = false;
+              }
+              else
+              {
+                  validRes = true;
+              }
 
-        if (row.hasIcons)
-        {
-          if (!validRes || row.annotations[j].secondaryStructure != lastSS[i])
-          {
-            switch (lastSS[i])
-            {
-              case 'H':
-                g.setColor(HELIX_COLOUR);
-                g.fillRoundRect(lastSSX[i], y + 4 + iconOffset, x - lastSSX[i],
-                                7, 8, 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 + 8 + iconOffset}, 3);
-                break;
-              case 'C':
-                break;
-              default:
-                g.setColor(Color.gray);
-                g.fillRect(lastSSX[i], y + 6 + iconOffset, x - lastSSX[i], 2);
-                break;
-            }
-
-            if (validRes)
-            {
-              lastSS[i] = row.annotations[j].secondaryStructure;
-            }
-            else
-            {
-              lastSS[i] = ' ';
-            }
-            lastSSX[i] = x;
-          }
-        }
+              x = (j - startRes) * av.charWidth;
 
-        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())
+              if (validRes &&
+                      (row.annotations[j].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);
+                  }
+              }
+
+              if (row.hasIcons)
               {
-                continue;
+                  if (!validRes ||
+                          (row.annotations[j].secondaryStructure != lastSS[i]))
+                  {
+                      switch (lastSS[i])
+                      {
+                      case 'H':
+                          g.setColor(HELIX_COLOUR);
+                          g.fillRoundRect(lastSSX[i], y + 4 + iconOffset,
+                              x - lastSSX[i], 7, 8, 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 + 8 + iconOffset
+                              }, 3);
+
+                          break;
+
+                      case 'C':
+                          break;
+
+                      default:
+                          g.setColor(Color.gray);
+                          g.fillRect(lastSSX[i], y + 6 + iconOffset,
+                              x - lastSSX[i], 2);
+
+                          break;
+                      }
+
+                      if (validRes)
+                      {
+                          lastSS[i] = row.annotations[j].secondaryStructure;
+                      }
+                      else
+                      {
+                          lastSS[i] = ' ';
+                      }
+
+                      lastSSX[i] = x;
+                  }
               }
 
-              total += row.annotations[i2].value;
-            }
+              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.windowLength;
-            height = (int) ( (total / row.graphMax) * GRAPH_HEIGHT);
+                          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);
-        }
 
-      }
+          x += av.charWidth;
 
-      x += av.charWidth;
+          if (row.hasIcons)
+          {
+              switch (lastSS[i])
+              {
+              case 'H':
+                  g.setColor(HELIX_COLOUR);
+                  g.fillRoundRect(lastSSX[i], y + 4 + iconOffset,
+                      x - lastSSX[i], 7, 8, 8);
 
-      if (row.hasIcons)
-      {
-        switch (lastSS[i])
-        {
-          case 'H':
-            g.setColor(HELIX_COLOUR);
-            g.fillRoundRect(lastSSX[i], y + 4 + iconOffset, x - lastSSX[i], 7,
-                            8, 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;
-          case 'C':
-            break;
-          default:
-            g.setColor(Color.gray);
-            g.fillRect(lastSSX[i], y + 6 + iconOffset, x - lastSSX[i], 2);
-            break;
+                  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.isGraph && row.hasText)
-      {
-        y += av.charHeight;
-      }
-      if (!row.isGraph)
-      {
-        y += aa[i].height;
-      }
-    }
+              case 'C':
+                  break;
+
+              default:
+                  g.setColor(Color.gray);
+                  g.fillRect(lastSSX[i], y + 6 + iconOffset, x - lastSSX[i], 2);
+
+                  break;
+              }
+          }
+
+          if (row.isGraph && row.hasText)
+          {
+              y += av.charHeight;
+          }
+
+          if (!row.isGraph)
+          {
+              y += aa[i].height;
+          }
+        }
   }
 
   // used by overview window
-  public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y)
+  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;
-    for (int j = 0; j < aa.annotations.length; j++)
-    {
+      g.setColor(Color.white);
+      g.fillRect(0, 0, width, y);
       g.setColor(new Color(0, 0, 180));
-      int height = (int) ( (aa.annotations[j].value / aa.graphMax) *
-                          GRAPH_HEIGHT);
-      g.fillRect(x, y - height, av.charWidth, height);
-      x += av.charWidth;
+
+      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) * GRAPH_HEIGHT);
+          if(height>y)
+              height = y;
+          g.fillRect(x, y - height, av.charWidth, height);
+          x += av.charWidth;
+      }
     }
-  }
 }