JAL-2171 default SS symbol to existing (if present)

diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index dd652b1..823bbfd 100755 (executable)
--- a/src/jalview/appletgui/AnnotationPanel.java
+++ b/src/jalview/appletgui/AnnotationPanel.java
@@ -241,9 +241,11 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
       else if (evt.getActionCommand().equals(STEM))
       {
         type = 'S';
-        symbol = "\u03C3";
+        symbol = "(";// "\u03C3"; sigma
       }
 
+      symbol = getCurrentAnnotationCharacter(anot, symbol);
+
       if (!aa[activeRow].hasIcons)
       {
         aa[activeRow].hasIcons = true;
@@ -346,7 +348,8 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
     if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK
             && activeRow != -1)
     {
-      if (av.getColumnSelection() == null)
+      if (av.getColumnSelection() == null
+              || av.getColumnSelection().isEmpty())
       {
         return;
       }
@@ -354,10 +357,8 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
       PopupMenu pop = new PopupMenu(
               MessageManager.getString("label.structure_type"));
       MenuItem item;
-      /*
-       * Just display the needed structure options
-       */
-      if (av.getAlignment().isNucleotide() == true)
+
+      if (av.getAlignment().isNucleotide())
       {
         item = new MenuItem(STEM);
         item.addActionListener(this);
@@ -724,4 +725,38 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
       return null;
     }
   }
+
+  /**
+   * Returns the current annotation symbol (if any) within the visible selected
+   * columns (first symbol found left to right in selection). If none is found,
+   * the supplied default value is returned.
+   * 
+   * @param annotations
+   * @param defaultValue
+   * @return
+   */
+  String getCurrentAnnotationCharacter(Annotation[] annotations,
+          String defaultValue)
+  {
+    String result = defaultValue;
+    for (int index : av.getColumnSelection().getSelected())
+    {
+      if (!av.getColumnSelection().isVisible(index))
+      {
+        continue;
+      }
+  
+      Annotation annotation = annotations[index];
+      if (annotation != null)
+      {
+        String displayed = annotation.displayCharacter;
+        if (displayed != null && displayed.length() > 0)
+        {
+          result = displayed.substring(0, 1);
+          break;
+        }
+      }
+    }
+    return result;
+  }
 }

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 398f57d..91d4a5c 100755 (executable)
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -355,7 +355,7 @@ 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))
       {
@@ -364,14 +364,14 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       else if (evt.getActionCommand().equals(SHEET))
       {
         type = 'E';
-        symbol = "\u03B2";
+        symbol = "\u03B2"; // beta
       }
 
       // Added by LML to color stems
       else if (evt.getActionCommand().equals(STEM))
       {
         type = 'S';
-        symbol = "\u03C3";
+        symbol = "(";// "\u03C3"; // sigma
       }
 
       if (!aa[activeRow].hasIcons)
@@ -379,6 +379,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         aa[activeRow].hasIcons = true;
       }
 
+      symbol = getCurrentAnnotationCharacter(anot, symbol);
+
       String label = JOptionPane.showInputDialog(MessageManager
               .getString("label.enter_label_for_the_structure"), symbol);
 
@@ -423,6 +425,40 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     return;
   }
 
+  /**
+   * Returns the current annotation symbol (if any) within the visible selected
+   * columns (first symbol found left to right in selection). If none is found,
+   * the supplied default value is returned.
+   * 
+   * @param annotations
+   * @param defaultValue
+   * @return
+   */
+  String getCurrentAnnotationCharacter(Annotation[] annotations,
+          String defaultValue)
+  {
+    String result = defaultValue;
+    for (int index : av.getColumnSelection().getSelected())
+    {
+      if (!av.getColumnSelection().isVisible(index))
+      {
+        continue;
+      }
+
+      Annotation annotation = annotations[index];
+      if (annotation != null)
+      {
+        String displayed = annotation.displayCharacter;
+        if (displayed != null && displayed.length() > 0)
+        {
+          result = displayed.substring(0, 1);
+          break;
+        }
+      }
+    }
+    return result;
+  }
+
   private String collectAnnotVals(Annotation[] anot, String label2)
   {
     String collatedInput = "";
@@ -514,7 +550,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
     if (evt.isPopupTrigger() && activeRow != -1)
     {
-      if (av.getColumnSelection() == null)
+      if (av.getColumnSelection() == null
+              || av.getColumnSelection().isEmpty())
       {
         return;
       }
@@ -525,7 +562,7 @@ 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);
@@ -554,11 +591,6 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       return;
     }
 
-    if (aa == null)
-    {
-      return;
-    }
-
     ap.getScalePanel().mousePressed(evt);
 
   }