JAL-2089 patch broken merge to master for Release 2.10.0b1

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

diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index ee8c9ca..6012c1a 100755 (executable)
--- a/src/jalview/appletgui/AnnotationPanel.java
+++ b/src/jalview/appletgui/AnnotationPanel.java
@@ -25,6 +25,7 @@ import jalview.datamodel.Annotation;
 import jalview.datamodel.SequenceI;
 import jalview.renderer.AnnotationRenderer;
 import jalview.renderer.AwtRenderPanelI;
+import jalview.schemes.ResidueProperties;
 import jalview.util.Comparison;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
@@ -162,12 +163,12 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
 
     if (evt.getActionCommand().equals(REMOVE))
     {
-      for (int sel : av.getColumnSelection().getSelected())
+      for (int index : av.getColumnSelection().getSelected())
       {
-        // TODO: JAL-2001 check if applet has faulty 'REMOVE' selected columns
-        // of
-        // annotation if selection includes hidden columns
-        anot[sel] = null;
+        if (av.getColumnSelection().isVisible(index))
+        {
+          anot[index] = null;
+        }
       }
     }
     else if (evt.getActionCommand().equals(LABEL))
@@ -474,9 +475,10 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
       StringBuilder text = new StringBuilder();
       text.append(MessageManager.getString("label.column")).append(" ")
               .append(column + 1);
-      if (aa[row].annotations[column].description != null)
+      String description = aa[row].annotations[column].description;
+      if (description != null && description.length() > 0)
       {
-        text.append("  ").append(aa[row].annotations[column].description);
+        text.append("  ").append(description);
       }
 
       /*
@@ -495,9 +497,28 @@ public class AnnotationPanel extends Panel 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(")");
+            // int residuePos = seqref.findPosition(column);
+            // text.append(residue).append(" (")
+            // .append(residuePos).append(")");
           }
         }
       }