Merge branch 'develop' into bug/JAL-1841rnaSecStr

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

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 3c9a13e..6a621ff 100755 (executable)
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -290,7 +290,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       aa[activeRow].annotations = anot;
     }
 
-    if (evt.getActionCommand().equals(REMOVE))
+    String action = evt.getActionCommand();
+    if (action.equals(REMOVE))
     {
       for (int index : av.getColumnSelection().getSelected())
       {
@@ -300,7 +301,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         }
       }
     }
-    else if (evt.getActionCommand().equals(LABEL))
+    else if (action.equals(LABEL))
     {
       String exMesg = collectAnnotVals(anot, LABEL);
       String label = JOptionPane.showInputDialog(this,
@@ -325,10 +326,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
         if (anot[index] == null)
         {
-          anot[index] = new Annotation(label, "", ' ', 0); // TODO: verify that
-          // null exceptions
-          // aren't raised
-          // elsewhere.
+          anot[index] = new Annotation(label, "", ' ', 0);
         }
         else
         {
@@ -336,7 +334,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         }
       }
     }
-    else if (evt.getActionCommand().equals(COLOUR))
+    else if (action.equals(COLOUR))
     {
       Color col = JColorChooser.showDialog(this,
               MessageManager.getString("label.select_foreground_colour"),
@@ -361,23 +359,24 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     // HELIX, SHEET or STEM
     {
       char type = 0;
-      String symbol = "\u03B1";
+      String symbol = "\u03B1"; // alpha
 
-      if (evt.getActionCommand().equals(HELIX))
+      if (action.equals(HELIX))
       {
         type = 'H';
       }
-      else if (evt.getActionCommand().equals(SHEET))
+      else if (action.equals(SHEET))
       {
         type = 'E';
-        symbol = "\u03B2";
+        symbol = "\u03B2"; // beta
       }
 
       // Added by LML to color stems
-      else if (evt.getActionCommand().equals(STEM))
+      else if (action.equals(STEM))
       {
         type = 'S';
-        symbol = "\u03C3";
+        int column = av.getColumnSelection().getSelectedRanges().get(0)[0];
+        symbol = aa[activeRow].getDefaultRnaHelixSymbol(column);
       }
 
       if (!aa[activeRow].hasIcons)
@@ -396,7 +395,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       if ((label.length() > 0) && !aa[activeRow].hasText)
       {
         aa[activeRow].hasText = true;
-        if (evt.getActionCommand().equals(STEM))
+        if (action.equals(STEM))
         {
           aa[activeRow].showAllColLabels = true;
         }
@@ -534,7 +533,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
     if (evt.isPopupTrigger() && activeRow != -1)
     {
-      if (av.getColumnSelection() == null)
+      if (av.getColumnSelection() == null
+              || av.getColumnSelection().isEmpty())
       {
         return;
       }
@@ -545,7 +545,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       /*
        * Just display the needed structure options
        */
-      if (av.getAlignment().isNucleotide() == true)
+      if (av.getAlignment().isNucleotide())
       {
         item = new JMenuItem(STEM);
         item.addActionListener(this);
@@ -574,11 +574,6 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       return;
     }
 
-    if (aa == null)
-    {
-      return;
-    }
-
     ap.getScalePanel().mousePressed(evt);
 
   }