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 eec1881..6a621ff 100755 (executable)
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -26,6 +26,7 @@ import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.SequenceI;
 import jalview.renderer.AnnotationRenderer;
 import jalview.renderer.AwtRenderPanelI;
+import jalview.schemes.ResidueProperties;
 import jalview.util.Comparison;
 import jalview.util.MessageManager;
 
@@ -48,6 +49,8 @@ import java.awt.event.MouseMotionListener;
 import java.awt.event.MouseWheelEvent;
 import java.awt.event.MouseWheelListener;
 import java.awt.image.BufferedImage;
+import java.util.Collections;
+import java.util.List;
 
 import javax.swing.JColorChooser;
 import javax.swing.JMenuItem;
@@ -287,7 +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())
       {
@@ -297,7 +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,
@@ -322,10 +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
         {
@@ -333,7 +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"),
@@ -358,23 +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)
@@ -393,7 +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;
         }
@@ -444,7 +446,9 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     String last = "";
     ColumnSelection viscols = av.getColumnSelection();
     // TODO: refactor and save av.getColumnSelection for efficiency
-    for (int index : viscols.getSelected())
+    List<Integer> selected = viscols.getSelected();
+    Collections.sort(selected);
+    for (int index : selected)
     {
       // always check for current display state - just in case
       if (!viscols.isVisible(index))
@@ -529,7 +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;
       }
@@ -540,7 +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);
@@ -569,11 +574,6 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       return;
     }
 
-    if (aa == null)
-    {
-      return;
-    }
-
     ap.getScalePanel().mousePressed(evt);
 
   }
@@ -795,9 +795,24 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         char residue = seqref.getCharAt(column);
         if (!Comparison.isGap(residue))
         {
+          text.append(" ");
+          String name;
+          if (av.getAlignment().isNucleotide())
+          {
+            name = ResidueProperties.nucleotideName.get(String
+                    .valueOf(residue));
+            text.append(" Nucleotide: ").append(
+                    name != null ? name : residue);
+          }
+          else
+          {
+            name = 'X' == residue ? "X" : ('*' == residue ? "STOP"
+                    : ResidueProperties.aa2Triplet.get(String
+                            .valueOf(residue)));
+            text.append(" Residue: ").append(name != null ? name : residue);
+          }
           int residuePos = seqref.findPosition(column);
-          text.append(": ").append(residue).append(" (")
-                  .append(residuePos).append(")");
+          text.append(" (").append(residuePos).append(")");
         }
       }
     }