X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=84f3e6c56925862ad035d072827b838b98c3a074;hb=b0f76adef2787dd14566525e66a4073278e75d67;hp=0b2f6cc24dcaacaad9f3be57b2fe8d52a1cbc6fc;hpb=89f6349fbcbaadc2f330c0cc7f567f7f0e60f5c0;p=jalview.git

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 0b2f6cc..84f3e6c 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -55,7 +55,6 @@ import java.util.List;
 
 import javax.swing.JColorChooser;
 import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.JPopupMenu;
 import javax.swing.Scrollable;
@@ -300,7 +299,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     else if (action.equals(LABEL))
     {
       String exMesg = collectAnnotVals(anot, LABEL);
-      String label = JOptionPane.showInputDialog(this,
+      String label = JvOptionPane.showInputDialog(this,
               MessageManager.getString("label.enter_label"), exMesg);
 
       if (label == null)
@@ -380,7 +379,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         aa[activeRow].hasIcons = true;
       }
 
-      String label = JOptionPane.showInputDialog(MessageManager
+      String label = JvOptionPane.showInputDialog(MessageManager
               .getString("label.enter_label_for_the_structure"), symbol);
 
       if (label == null)
@@ -458,8 +457,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       String tlabel = null;
       if (anots[index] != null)
       { // LML added stem code
-        if (type.equals(HELIX) || type.equals(SHEET)
-                || type.equals(STEM) || type.equals(LABEL))
+        if (type.equals(HELIX) || type.equals(SHEET) || type.equals(STEM)
+                || type.equals(LABEL))
         {
           tlabel = anots[index].description;
           if (tlabel == null || tlabel.length() < 1)
@@ -708,7 +707,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       return;
     }
 
-    int column = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+    int column = (evt.getX() / av.getCharWidth())
+            + av.getRanges().getStartRes();
 
     if (av.hasHiddenColumns())
     {
@@ -814,8 +814,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       {
         text.append(", ")
                 .append(MessageManager.getString("label.sequence"))
-                .append(" ")
-                .append(seqIndex + 1);
+                .append(" ").append(seqIndex + 1);
         char residue = seqref.getCharAt(column);
         if (!Comparison.isGap(residue))
         {
@@ -906,7 +905,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         return;
       }
     }
-    imgWidth = (av.endRes - av.startRes + 1) * av.getCharWidth();
+    imgWidth = (av.getRanges().getEndRes() - av.getRanges().getStartRes() + 1)
+            * av.getCharWidth();
     if (imgWidth < 1)
     {
       return;
@@ -947,7 +947,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       imageFresh = true;
     }
 
-    drawComponent(gg, av.startRes, av.endRes + 1);
+    drawComponent(gg, av.getRanges().getStartRes(), av.getRanges()
+            .getEndRes() + 1);
     imageFresh = false;
     g.drawImage(image, 0, 0, this);
   }
@@ -977,8 +978,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     gg.copyArea(0, 0, imgWidth, getHeight(),
             -horizontal * av.getCharWidth(), 0);
     long mtime = System.currentTimeMillis();
-    int sr = av.startRes;
-    int er = av.endRes + 1;
+    int sr = av.getRanges().getStartRes();
+    int er = av.getRanges().getEndRes() + 1;
     int transX = 0;
 
     if (horizontal > 0) // scrollbar pulled right, image to the left