X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=86d5c6dacbec1fdb25a40cead49521e1ceb6d244;hb=266c4e2544701f88a8d21294b4a4f4cc42cf76cc;hp=895d1961daa58d379fea51acfa8db05bd4cdfdb5;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 895d196..86d5c6d 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -200,6 +200,9 @@ public class AnnotationPanel
       {
         int index = av.getColumnSelection().columnAt(i);
 
+        if(!av.colSel.isVisible(index))
+          continue;
+
         if (anot[index] == null)
         {
           anot[index] = new Annotation(label, "", ' ', 0);
@@ -218,6 +221,9 @@ public class AnnotationPanel
       {
         int index = av.getColumnSelection().columnAt(i);
 
+        if(!av.colSel.isVisible(index))
+          continue;
+
         if (anot[index] == null)
         {
           anot[index] = new Annotation("", "", ' ', 0);
@@ -264,6 +270,9 @@ public class AnnotationPanel
       {
         int index = av.getColumnSelection().columnAt(i);
 
+        if(!av.colSel.isVisible(index))
+          continue;
+
         if (anot[index] == null)
         {
           anot[index] = new Annotation(label, "", type, 0);
@@ -354,36 +363,7 @@ public class AnnotationPanel
       return;
     }
 
-    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
-
-    if (av.hasHiddenColumns)
-    {
-      res = av.getColumnSelection().adjustForHiddenColumns(res);
-    }
-
-    min = res;
-    max = res;
-
-    if (av.getColumnSelection().contains(res))
-    {
-      av.getColumnSelection().removeElement(res);
-    }
-    else
-    {
-      av.getColumnSelection().addElement(res);
-      SequenceGroup sg = new SequenceGroup();
-
-      for (int i = 0; i < av.alignment.getSequences().size(); i++)
-      {
-        sg.addSequence(av.alignment.getSequenceAt(i), false);
-      }
-
-      sg.setStartRes(res);
-      sg.setEndRes(res);
-      av.setSelectionGroup(sg);
-    }
-
-    ap.repaint();
+    ap.scalePanel.mousePressed(evt);
 
   }
 
@@ -397,6 +377,7 @@ public class AnnotationPanel
     graphStretch = -1;
     graphStretchY = -1;
     mouseDragging = false;
+    ap.scalePanel.mouseReleased(evt);
   }
 
   /**
@@ -406,10 +387,7 @@ public class AnnotationPanel
    */
   public void mouseEntered(MouseEvent evt)
   {
-    if (mouseDragging)
-    {
-      ap.seqPanel.scrollCanvas(null);
-    }
+     ap.scalePanel.mouseEntered(evt);
   }
 
   /**
@@ -419,10 +397,7 @@ public class AnnotationPanel
    */
   public void mouseExited(MouseEvent evt)
   {
-    if (mouseDragging)
-    {
-      ap.seqPanel.scrollCanvas(evt);
-    }
+    ap.scalePanel.mouseExited(evt);
   }
 
   /**
@@ -442,62 +417,11 @@ public class AnnotationPanel
       }
       graphStretchY = evt.getY();
       adjustPanelHeight();
-      ap.repaint();
+      ap.paintAlignment(true);
     }
     else
     {
-      mouseDragging = true;
-
-      int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
-
-      if (av.hasHiddenColumns)
-      {
-        res = av.getColumnSelection().adjustForHiddenColumns(res);
-      }
-
-      SequenceGroup sg = av.getSelectionGroup();
-
-      if (res < min)
-      {
-        min = res;
-      }
-
-      if (res > max)
-      {
-        max = res;
-      }
-
-      if (sg != null)
-      {
-        if (!av.getColumnSelection().contains(res))
-        {
-          av.getColumnSelection().addElement(res);
-        }
-
-        if (res > sg.getStartRes())
-        {
-          sg.setEndRes(res);
-        }
-        else if (res < sg.getStartRes())
-        {
-          sg.setStartRes(res);
-        }
-
-        for (int i = min; i <= max; i++)
-        {
-          if ( (i < sg.getStartRes()) || (i > sg.getEndRes()))
-          {
-            av.getColumnSelection().removeElement(i);
-          }
-          else
-          {
-            av.getColumnSelection().addElement(i);
-          }
-        }
-
-        ap.repaint();
-      }
-
+      ap.scalePanel.mouseDragged(evt);
     }
   }
 
@@ -763,11 +687,11 @@ public class AnnotationPanel
 
     AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
 
-    int x = 0, y = 0;
+    int x = 0, y=0;
     int column = 0;
     char lastSS;
     int lastSSX;
-    int iconOffset = av.charHeight / 2;
+    int iconOffset = 0;
     boolean validRes = false;
 
     boolean[] graphGroupDrawn = new boolean[aa.length];
@@ -797,9 +721,20 @@ public class AnnotationPanel
 
         if (row.hasText)
         {
+          iconOffset =av.charHeight -fm.getDescent();
           y -= av.charHeight;
         }
       }
+      else if (row.hasText)
+      {
+        iconOffset = av.charHeight -fm.getDescent();
+
+      }
+      else
+      {
+        iconOffset = 0;
+      }
+
 
       if (av.updatingConsensus && aa[i] == av.consensus)
       {
@@ -839,14 +774,7 @@ public class AnnotationPanel
         continue;
       }
 
-      if (row.hasText)
-      {
-        iconOffset = av.charHeight / 2 + 4;
-      }
-      else
-      {
-        iconOffset = 0;
-      }
+
 
       x = 0;
       while (x < endRes - startRes)
@@ -893,15 +821,20 @@ public class AnnotationPanel
           }
         }
 
-        if (av.validCharWidth && validRes &&
-            (row.annotations[column].displayCharacter.length() > 0))
+        if (av.validCharWidth && validRes
+            && row.annotations[column].displayCharacter != null
+            && (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 (row.annotations[column].colour == null)
+            g.setColor(Color.black);
+          else
+            g.setColor(row.annotations[column].colour);
 
           if (column == 0 || row.graph > 0)
           {
@@ -1215,7 +1148,11 @@ public class AnnotationPanel
         continue;
       }
 
-      g.setColor(aa.annotations[column].colour);
+      if (aa.annotations[column].colour == null)
+        g.setColor(Color.black);
+      else
+        g.setColor(aa.annotations[column].colour);
+
       y1 = y -
           (int) ( ( (aa.annotations[column - 1].value - min) / range) * graphHeight);
       y2 = y -
@@ -1289,7 +1226,11 @@ public class AnnotationPanel
         continue;
       }
 
-      g.setColor(aa.annotations[column].colour);
+      if (aa.annotations[column].colour == null)
+        g.setColor(Color.black);
+      else
+        g.setColor(aa.annotations[column].colour);
+
       y1 = y -
           (int) ( ( (aa.annotations[column].value - min) / (range)) * aa.graphHeight);
 
@@ -1336,7 +1277,10 @@ public class AnnotationPanel
     {
       if (aa.annotations[j] != null)
       {
-        g.setColor(aa.annotations[j].colour);
+        if (aa.annotations[j].colour == null)
+          g.setColor(Color.black);
+        else
+          g.setColor(aa.annotations[j].colour);
 
         height = (int) ( (aa.annotations[j].value / aa.graphMax) * y);
         if (height > y)