JAL-2549 skip ‘Unrecognised Service’ which resolves to a null entry in the get suppor...

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

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 92e1dbc..919356f 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 2.9.0b2)
- * Copyright (C) 2015 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.
  * 
@@ -23,6 +23,7 @@ package jalview.gui;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SequenceI;
 import jalview.renderer.AnnotationRenderer;
 import jalview.renderer.AwtRenderPanelI;
@@ -55,7 +56,6 @@ 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;
@@ -291,7 +291,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     {
       for (int index : av.getColumnSelection().getSelected())
       {
-        if (av.getColumnSelection().isVisible(index))
+        if (av.getAlignment().getHiddenColumns().isVisible(index))
         {
           anot[index] = null;
         }
@@ -300,7 +300,7 @@ 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)
@@ -315,7 +315,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
       for (int index : av.getColumnSelection().getSelected())
       {
-        if (!av.getColumnSelection().isVisible(index))
+        if (!av.getAlignment().getHiddenColumns().isVisible(index))
         {
           continue;
         }
@@ -338,7 +338,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
       for (int index : av.getColumnSelection().getSelected())
       {
-        if (!av.getColumnSelection().isVisible(index))
+        if (!av.getAlignment().getHiddenColumns().isVisible(index))
         {
           continue;
         }
@@ -380,7 +380,7 @@ 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)
@@ -398,7 +398,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       }
       for (int index : av.getColumnSelection().getSelected())
       {
-        if (!av.getColumnSelection().isVisible(index))
+        if (!av.getAlignment().getHiddenColumns().isVisible(index))
         {
           continue;
         }
@@ -441,6 +441,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     StringBuilder collatedInput = new StringBuilder(64);
     String last = "";
     ColumnSelection viscols = av.getColumnSelection();
+    HiddenColumns hidden = av.getAlignment().getHiddenColumns();
 
     /*
      * the selection list (read-only view) is in selection order, not
@@ -451,7 +452,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     for (int index : selected)
     {
       // always check for current display state - just in case
-      if (!viscols.isVisible(index))
+      if (!hidden.isVisible(index))
       {
         continue;
       }
@@ -708,11 +709,13 @@ 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())
     {
-      column = av.getColumnSelection().adjustForHiddenColumns(column);
+      column = av.getAlignment().getHiddenColumns()
+              .adjustForHiddenColumns(column);
     }
 
     AlignmentAnnotation ann = aa[row];
@@ -905,7 +908,8 @@ 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;
@@ -946,7 +950,8 @@ 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);
   }
@@ -976,8 +981,8 @@ 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