JAL-1619 align the added sequences to match what they are added to

[jalview.git] / src / jalview / gui / AnnotationPanel.java

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 9f56206..c952c13 100755 (executable)
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -241,7 +241,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
     // update annotation label display
-    ap.alabels.setScrollOffset(-evt.getValue());
+    ap.getAlabels().setScrollOffset(-evt.getValue());
   }
 
   /**
@@ -566,7 +566,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       return;
     }
 
-    ap.scalePanel.mousePressed(evt);
+    ap.getScalePanel().mousePressed(evt);
 
   }
 
@@ -582,7 +582,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     graphStretch = -1;
     graphStretchY = -1;
     mouseDragging = false;
-    ap.scalePanel.mouseReleased(evt);
+    ap.getScalePanel().mouseReleased(evt);
   }
 
   /**
@@ -594,7 +594,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   @Override
   public void mouseEntered(MouseEvent evt)
   {
-    ap.scalePanel.mouseEntered(evt);
+    ap.getScalePanel().mouseEntered(evt);
   }
 
   /**
@@ -606,7 +606,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   @Override
   public void mouseExited(MouseEvent evt)
   {
-    ap.scalePanel.mouseExited(evt);
+    ap.getScalePanel().mouseExited(evt);
   }
 
   /**
@@ -632,7 +632,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     }
     else
     {
-      ap.scalePanel.mouseDragged(evt);
+      ap.getScalePanel().mouseDragged(evt);
     }
   }
 
@@ -757,10 +757,10 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   public void drawCursor(Graphics graphics, SequenceI seq, int res, int x1,
           int y1)
   {
-    int pady = av.charHeight / 5;
+    int pady = av.getCharHeight() / 5;
     int charOffset = 0;
     graphics.setColor(Color.black);
-    graphics.fillRect(x1, y1, av.charWidth, av.charHeight);
+    graphics.fillRect(x1, y1, av.getCharWidth(), av.getCharHeight());
 
     if (av.validCharWidth)
     {
@@ -768,9 +768,9 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
       char s = seq.getCharAt(res);
 
-      charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+      charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
       graphics.drawString(String.valueOf(s), charOffset + x1,
-              (y1 + av.charHeight) - pady);
+              (y1 + av.getCharHeight()) - pady);
     }
 
   }
@@ -799,7 +799,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         return;
       }
     }
-    imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;
+    imgWidth = (av.endRes - av.startRes + 1) * av.getCharWidth();
     if (imgWidth < 1)
     {
       return;
@@ -809,7 +809,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     {
       try
       {
-        image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(),
+        image = new BufferedImage(imgWidth, ap.getAnnotationPanel().getHeight(),
                 BufferedImage.TYPE_INT_RGB);
       } catch (OutOfMemoryError oom)
       {
@@ -867,7 +867,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       return;
     }
     long stime = System.currentTimeMillis();
-    gg.copyArea(0, 0, imgWidth, getHeight(), -horizontal * av.charWidth, 0);
+    gg.copyArea(0, 0, imgWidth, getHeight(),
+            -horizontal * av.getCharWidth(), 0);
     long mtime = System.currentTimeMillis();
     int sr = av.startRes;
     int er = av.endRes + 1;
@@ -875,7 +876,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
     if (horizontal > 0) // scrollbar pulled right, image to the left
     {
-      transX = (er - sr - horizontal) * av.charWidth;
+      transX = (er - sr - horizontal) * av.getCharWidth();
       sr = er - horizontal;
     }
     else if (horizontal < 0)
@@ -960,7 +961,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     }
 
     g.setColor(Color.white);
-    g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());
+    g.fillRect(0, 0, (endRes - startRes) * av.getCharWidth(), getHeight());
 
     g.setFont(av.getFont());
     if (fm == null)
@@ -1013,9 +1014,9 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   @Override
   public int[] getVisibleVRange()
   {
-    if (ap != null && ap.alabels != null)
+    if (ap != null && ap.getAlabels() != null)
     {
-      int sOffset = -ap.alabels.scrollOffset;
+      int sOffset = -ap.getAlabels().getScrollOffset();
       int visHeight = sOffset + ap.annotationSpaceFillerHolder.getHeight();
       bounds[0] = sOffset;
       bounds[1] = visHeight;