X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FAnnotationPanel.java;h=006d6438a94f4f74f0aaf90542dd14780fc029db;hb=c42fcf7bf5cfcf51e67dd0f683edb9ab6683d157;hp=1bf3d38403b949f1de82d3b13d3ec92e5f40f138;hpb=2df9d1cb0e8975c84486ddc4728062e377adbb1f;p=jalview.git

diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index 1bf3d38..006d643 100755
--- a/src/jalview/appletgui/AnnotationPanel.java
+++ b/src/jalview/appletgui/AnnotationPanel.java
@@ -192,6 +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) +
@@ -209,7 +213,6 @@ public class AnnotationPanel
   public void paint(Graphics g)
   {
 
-
     imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;
 
     if (image == null || imgWidth != image.getWidth(this))
@@ -302,6 +305,7 @@ public class AnnotationPanel
 
       int x = 0;
       int y = 0;
+      int column=0;
       char lastSS;
       int lastSSX;
       int iconOffset = av.charHeight / 2;
@@ -346,21 +350,30 @@ public class AnnotationPanel
               iconOffset = 0;
           }
 
-          int column = startRes;
-          while(column < endRes)
+           x = 0;
+          while(x < endRes-startRes)
           {
-              if ((row.annotations.length <= column) ||
-                      (row.annotations[column] == null))
+            if (av.hasHiddenColumns)
+            {
+              column = av.getColumnSelection().adjustForHiddenColumns(startRes+x);
+              if (column > row.annotations.length-1)
+              {
+                break;
+              }
+            }
+            else
+                column = startRes+x;
+
+              if ( (row.annotations.length <= column) ||
+                  (row.annotations[column] == null))
               {
-                  validRes = false;
+                validRes = false;
               }
               else
               {
-                  validRes = true;
+                validRes = true;
               }
 
-              x = (column - startRes) * av.charWidth;
-
 
               if (av.validCharWidth && validRes &&
                         (row.annotations[column].displayCharacter.length() > 0))
@@ -372,7 +385,8 @@ public class AnnotationPanel
 
                 if (column == 0 || row.graph>0)
                 {
-                    g.drawString(row.annotations[column].displayCharacter, x+charOffset,
+                    g.drawString(row.annotations[column].displayCharacter,
+                                (x*av.charWidth)+charOffset,
                         y + iconOffset + 3);
                 }
                 else if (
@@ -383,7 +397,8 @@ public class AnnotationPanel
               (row.annotations[column].displayCharacter.length() <2 &&
                row.annotations[column].secondaryStructure==' ')))
                 {
-                    g.drawString(row.annotations[column].displayCharacter, x+charOffset,
+                    g.drawString(row.annotations[column].displayCharacter,
+                       (x*av.charWidth)+charOffset,
                         y + iconOffset + 3);
                     }
               }
@@ -402,13 +417,13 @@ public class AnnotationPanel
                           //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);
+                                          (x*av.charWidth) - lastSSX, 7, 8, 8);
                           break;
                         }
 
                         int sCol = (lastSSX / av.charWidth) + startRes;
                         int x1 = lastSSX;
-                        int x2 = x;
+                        int x2 = (x*av.charWidth);
 
                        if(sCol==0 ||
                           row.annotations[sCol-1]==null ||
@@ -421,7 +436,8 @@ public class AnnotationPanel
                         if(row.annotations[column]==null ||
                            row.annotations[column].secondaryStructure!='H')
                         {
-                          g.fillArc(x-av.charWidth, y+4+iconOffset, av.charWidth, 8, 270,180);
+                          g.fillArc((x*av.charWidth)-av.charWidth,
+                                    y+4+iconOffset, av.charWidth, 8, 270,180);
                           x2 -= av.charWidth/2;
                         }
 
@@ -431,8 +447,10 @@ public class AnnotationPanel
                       case 'E':
                           g.setColor(SHEET_COLOUR);
                           g.fillRect(lastSSX, y + 4 + iconOffset,
-                              x - lastSSX - 4, 7);
-                          g.fillPolygon(new int[] { x - 4, x - 4, x },
+                              (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,
@@ -445,7 +463,7 @@ public class AnnotationPanel
                       default:
                           g.setColor(Color.gray);
                           g.fillRect(lastSSX, y + 6 + iconOffset,
-                              x - lastSSX, 2);
+                              (x*av.charWidth) - lastSSX, 2);
 
                           break;
                       }
@@ -459,20 +477,24 @@ public class AnnotationPanel
                           lastSS = ' ';
                       }
 
-                      lastSSX = 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)
-              {
+            switch (lastSS)
+            {
               case 'H':
                 g.setColor(HELIX_COLOUR);
                 if (MAC)
@@ -480,63 +502,68 @@ public class AnnotationPanel
                   //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);
+                                  (x*av.charWidth) - 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')
+                int x2 = (x*av.charWidth);
+
+                if (sCol == 0 ||
+                    row.annotations[sCol - 1] == null ||
+                    row.annotations[sCol - 1].secondaryStructure != 'H')
                 {
-                  g.fillArc(x-av.charWidth, y+4+iconOffset, av.charWidth, 8, 270,180);
-                  x2 -= av.charWidth/2;
+                  g.fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8, 90, 180);
+                  x1 += av.charWidth / 2;
                 }
 
-                g.fillRect(x1, y+4+iconOffset, x2-x1, 8);
-
-                    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 'E':
-                  g.setColor(SHEET_COLOUR);
+                g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
 
-                  if (row.annotations.length > endRes
-                      && 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);
+                break;
 
-                  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, y + 6 + iconOffset, x - lastSSX, 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)
@@ -624,34 +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)*av.charWidth,y2);
 
+    eRes = Math.min(eRes, aa.annotations.length);
+
+    int column;
+    int aaMax = aa.annotations.length-1;
 
-    for (int j = sRes; j < eRes; j++)
+    while( x < eRes - sRes )
     {
-      if(aa.annotations[j]==null || aa.annotations[j-1]==null)
+      column = sRes + x;
+      if(av.hasHiddenColumns)
       {
-        x+=av.charWidth;
+        column = av.getColumnSelection().adjustForHiddenColumns(column);
+      }
+
+      if (column > aaMax)
+      {
+        break;
+      }
+
+      if(aa.annotations[column]==null || aa.annotations[column-1]==null)
+      {
+        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)*aa.graphHeight);
-         g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2);
-     }
 
+         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,
@@ -662,51 +705,58 @@ public class AnnotationPanel
     if(sRes>aa.annotations.length)
       return;
 
-
     eRes = Math.min(eRes, aa.annotations.length);
 
-    int x=0, y1, y2;
+    int x=0, y1=y, y2=y;
 
     float range = max - min;
 
-    y1 = y2 = y;
-
     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)*av.charWidth,y2);
 
-    for (int j = sRes; j < eRes; j++)
+    int column;
+    int aaMax = aa.annotations.length-1;
+
+    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 );
-
-        x += av.charWidth;
-    }
+          g.fillRect(x*av.charWidth, y1, av.charWidth, y2-y1 );
 
+        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