X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationPanel.java;h=006d6438a94f4f74f0aaf90542dd14780fc029db;hb=559b96a91b710f3f2e116790c9cf7e3aa6c76766;hp=bcc2866b8aeda417dce20b472237a18c53fb2262;hpb=9f7b5126265a85454dae0987f617771ed9b8f138;p=jalview.git

diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index bcc2866..006d643 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()
@@ -126,9 +131,6 @@ public class AnnotationPanel
     }
 
     this.setSize(getSize().width, height);
-    if(ap!=null)
-       ap.annotationScroller.setSize(getSize().width, height);
-
 
     repaint();
 
@@ -190,6 +192,10 @@ public class AnnotationPanel
     }
 
     int res = evt.getX() / av.getCharWidth() + av.getStartRes();
+
+    if(av.hasHiddenColumns)
+          res = av.getColumnSelection().adjustForHiddenColumns(res);
+
     if (row > -1 && res < aa[row].annotations.length && aa[row].annotations[res] != null)
     {
       StringBuffer text = new StringBuffer("Sequence position " + (res + 1) +
@@ -206,8 +212,7 @@ 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 +232,8 @@ 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);
   }
 
@@ -288,18 +295,19 @@ 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];
+      int column=0;
+      char lastSS;
+      int lastSSX;
       int iconOffset = av.charHeight / 2;
       boolean validRes = false;
 
@@ -316,7 +324,8 @@ public class AnnotationPanel
               continue;
           }
 
-
+          lastSS = ' ';
+          lastSSX = 0;
 
           if (row.graph>0)
           {
@@ -341,81 +350,107 @@ public class AnnotationPanel
               iconOffset = 0;
           }
 
-          for (j = startRes; j < endRes; j++)
+           x = 0;
+          while(x < endRes-startRes)
           {
-              if ((row.annotations.length <= j) ||
-                      (row.annotations[j] == null))
+            if (av.hasHiddenColumns)
+            {
+              column = av.getColumnSelection().adjustForHiddenColumns(startRes+x);
+              if (column > row.annotations.length-1)
               {
-                  validRes = false;
+                break;
               }
-              else
-              {
-                  validRes = true;
-              }
-
-              x = (j - startRes) * av.charWidth;
+            }
+            else
+                column = startRes+x;
 
-              if (activeRow == i)
+              if ( (row.annotations.length <= column) ||
+                  (row.annotations[column] == null))
               {
-                  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);
-                          }
-                      }
-                  }
+                validRes = false;
               }
-
-              if (validRes &&
-                      (row.annotations[j].displayCharacter.length() > 0))
+              else
               {
+                validRes = true;
+              }
 
-                  int charOffset = (av.charWidth -
-                      fm.charWidth(row.annotations[j].displayCharacter.charAt(
-                              0))) / 2;
-                  g.setColor(row.annotations[j].colour);
 
-                  if (j == 0 || row.graph>0)
-                  {
-                      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 (av.validCharWidth && validRes &&
+                        (row.annotations[column].displayCharacter.length() > 0))
+              {
+                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*av.charWidth)+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*av.charWidth)+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*av.charWidth) - lastSSX, 7, 8, 8);
                           break;
+                        }
+
+                        int sCol = (lastSSX / av.charWidth) + startRes;
+                        int x1 = lastSSX;
+                        int x2 = (x*av.charWidth);
+
+                       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)-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 },
+                          g.fillRect(lastSSX, y + 4 + iconOffset,
+                              (x*av.charWidth) - lastSSX - 4, 7);
+                          g.fillPolygon(new int[] { (x*av.charWidth) - 4,
+                                        (x*av.charWidth) - 4,
+                                        (x*av.charWidth) },
                               new int[]
                               {
                                   y + iconOffset, y + 14 + iconOffset,
@@ -427,70 +462,108 @@ public class AnnotationPanel
 
                       default:
                           g.setColor(Color.gray);
-                          g.fillRect(lastSSX[i], y + 6 + iconOffset,
-                              x - lastSSX[i], 2);
+                          g.fillRect(lastSSX, y + 6 + iconOffset,
+                              (x*av.charWidth) - 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*av.charWidth);
                   }
               }
+
+
+          column++;
+          x++;
           }
 
-          x += av.charWidth;
+          if(column>=row.annotations.length)
+              column = row.annotations.length-1;
+
+        //  x ++;
 
           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*av.charWidth) - lastSSX, 7, 8, 8);
                   break;
+                }
 
-              case 'E':
-                  g.setColor(SHEET_COLOUR);
+                int sCol = (lastSSX / av.charWidth) + startRes;
+                int x1 = lastSSX;
+                int x2 = (x*av.charWidth);
 
-                  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);
+                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;
+                }
 
-                  break;
+                if (row.annotations[column] == null ||
+                    row.annotations[column].secondaryStructure != 'H')
+                {
+                  g.fillArc((x*av.charWidth) - av.charWidth,
+                            y + 4 + iconOffset, av.charWidth, 8, 270,
+                            180);
+                  x2 -= av.charWidth / 2;
+                }
 
-              case 'C':
-                  break;
+                g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
+
+                break;
+
+              case 'E':
+                g.setColor(SHEET_COLOUR);
+
+                if (row.annotations[endRes] == null
+                    || row.annotations[endRes].secondaryStructure != 'E')
+                {
+                  g.fillRect(lastSSX, y + 4 + iconOffset,
+                             (x*av.charWidth) - lastSSX - 4, 7);
+                  g.fillPolygon(new int[]
+                                {(x*av.charWidth) - 4,
+                                (x*av.charWidth) - 4,
+                               (x*av.charWidth)},
+                                new int[]
+                                {
+                                y + iconOffset, y + 14 + iconOffset,
+                                y + 7 + iconOffset
+                  }, 3);
+                }
+                else
+                 {
+                   g.fillRect(lastSSX, y + 4 + iconOffset,
+                              (x+1) * av.charWidth - lastSSX, 7);
+                 }
+                break;
 
               default:
-                  g.setColor(Color.gray);
-                  g.fillRect(lastSSX[i], y + 6 + iconOffset, x - lastSSX[i], 2);
+                g.setColor(Color.gray);
+                if(!av.wrapAlignment || endRes==av.endRes)
+                g.fillRect(lastSSX, y + 6 + iconOffset,
+                           (x*av.charWidth) - lastSSX, 2);
 
-                  break;
-              }
+                break;
+            }
           }
 
           if (row.graph>0)
@@ -556,12 +629,17 @@ public class AnnotationPanel
     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++;
@@ -573,36 +651,50 @@ public class AnnotationPanel
 
     ////Draw origin
     if(min<0)
-      y2 = (int)(y - (0-min / range)*graphHeight);
+      y2 = y - (int)((0-min / range)*graphHeight);
 
     g.setColor(Color.gray);
-    g.drawLine(x-av.charWidth,y2,(eRes-sRes+1)*av.charWidth,y2);
+    g.drawLine(x-av.charWidth,y2,(eRes-sRes)*av.charWidth,y2);
 
+    eRes = Math.min(eRes, aa.annotations.length);
 
-    if(aa.graphLines!=null)
+    int column;
+    int aaMax = aa.annotations.length-1;
+
+    while( x < eRes - sRes )
     {
-      for(int l=0; l<aa.graphLines.size(); l++)
+      column = sRes + x;
+      if(av.hasHiddenColumns)
       {
-        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);
+        column = av.getColumnSelection().adjustForHiddenColumns(column);
       }
-    }
 
-    eRes = Math.min(eRes, aa.annotations.length);
-    for (int j = sRes; j < eRes; j++)
-    {
-      if(aa.annotations[j]==null || aa.annotations[j-1]==null)
+      if (column > aaMax)
+      {
+        break;
+      }
+
+      if(aa.annotations[column]==null || aa.annotations[column-1]==null)
       {
-        x+=av.charWidth;
+        x++;
         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;
+
+        g.setColor(aa.annotations[column].colour);
+        y1 = y - (int) (((aa.annotations[column-1].value-min) / range) * graphHeight);
+        y2 = y - (int) (((aa.annotations[column].value-min) / range) * graphHeight);
+
+        g.drawLine(x*av.charWidth-av.charWidth/2, y1, x*av.charWidth+av.charWidth/2, y2);
+        x ++;
      }
+
+     if(aa.threshold!=null)
+     {
+         g.setColor(aa.threshold.colour);
+
+         y2 = (int)(y - ((aa.threshold.value-min) / range)*graphHeight);
+         g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2);
+    }
   }
 
   public void drawBarGraph(Graphics g, AlignmentAnnotation aa,
@@ -613,52 +705,58 @@ public class AnnotationPanel
     if(sRes>aa.annotations.length)
       return;
 
-    int x=0, y1, y2;
+    eRes = Math.min(eRes, aa.annotations.length);
 
-    float range = max - min;
+    int x=0, y1=y, y2=y;
 
-    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;
+    float range = max - min;
 
     if(min<0)
-      y2 = (int)(y - (0-min / (range))*aa.graphHeight);
+      y2 = y - (int)((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);
+    g.drawLine(x,y2,(eRes-sRes)*av.charWidth,y2);
 
+    int column;
+    int aaMax = aa.annotations.length-1;
 
-    for (int j = sRes; j < eRes; j++)
+    while( x < eRes-sRes )
     {
+      column = sRes + x;
+      if(av.hasHiddenColumns)
+      {
+        column = av.getColumnSelection().adjustForHiddenColumns(column);
+      }
+
+      if(column > aaMax)
+      {
+          break;
+      }
 
-      if (aa.annotations[j] == null)
+      if (aa.annotations[column] == null)
       {
-        x += av.charWidth;
+        x ++;
         continue;
       }
 
-        g.setColor(aa.annotations[j].colour);
-        y1 = y - (int) (((aa.annotations[j].value-min) / (range)) * aa.graphHeight);
+        g.setColor(aa.annotations[column].colour);
+        y1 = y - (int) (((aa.annotations[column].value-min) / (range)) * aa.graphHeight);
 
         if(y1-y2>0)
-          g.fillRect(x, y2, av.charWidth, y1-y2 );
+          g.fillRect(x*av.charWidth, y2, av.charWidth, y1-y2 );
         else
-          g.fillRect(x, y1, av.charWidth, y2-y1 );
+          g.fillRect(x*av.charWidth, y1, av.charWidth, y2-y1 );
 
-        x += av.charWidth;
-    }
+        x ++ ;
 
+    }
+    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
@@ -672,7 +770,7 @@ 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)