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 61a3f8c..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;
@@ -290,9 +293,12 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     String action = evt.getActionCommand();
     if (action.equals(REMOVE))
     {
-      for (int sel : av.getColumnSelection().getSelected())
+      for (int index : av.getColumnSelection().getSelected())
       {
-        anot[sel] = null;
+        if (av.getColumnSelection().isVisible(index))
+        {
+          anot[index] = null;
+        }
       }
     }
     else if (action.equals(LABEL))
@@ -422,13 +428,27 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     return;
   }
 
-  private String collectAnnotVals(Annotation[] anot, String label2)
+  /**
+   * Returns any existing annotation concatenated as a string. For each
+   * annotation, takes the description, if any, else the secondary structure
+   * character (if type is HELIX, SHEET or STEM), else the display character (if
+   * type is LABEL).
+   * 
+   * @param anots
+   * @param type
+   * @return
+   */
+  private String collectAnnotVals(Annotation[] anots, String type)
   {
-    String collatedInput = "";
+    // TODO is this method wanted? why? 'last' is not used
+
+    StringBuilder collatedInput = new StringBuilder(64);
     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))
@@ -436,22 +456,22 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         continue;
       }
       String tlabel = null;
-      if (anot[index] != null)
+      if (anots[index] != null)
       { // LML added stem code
-        if (label2.equals(HELIX) || label2.equals(SHEET)
-                || label2.equals(STEM) || label2.equals(LABEL))
+        if (type.equals(HELIX) || type.equals(SHEET)
+                || type.equals(STEM) || type.equals(LABEL))
         {
-          tlabel = anot[index].description;
+          tlabel = anots[index].description;
           if (tlabel == null || tlabel.length() < 1)
           {
-            if (label2.equals(HELIX) || label2.equals(SHEET)
-                    || label2.equals(STEM))
+            if (type.equals(HELIX) || type.equals(SHEET)
+                    || type.equals(STEM))
             {
-              tlabel = "" + anot[index].secondaryStructure;
+              tlabel = "" + anots[index].secondaryStructure;
             }
             else
             {
-              tlabel = "" + anot[index].displayCharacter;
+              tlabel = "" + anots[index].displayCharacter;
             }
           }
         }
@@ -459,13 +479,13 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         {
           if (last.length() > 0)
           {
-            collatedInput += " ";
+            collatedInput.append(" ");
           }
-          collatedInput += tlabel;
+          collatedInput.append(tlabel);
         }
       }
     }
-    return collatedInput;
+    return collatedInput.toString();
   }
 
   /**
@@ -775,9 +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(")");
         }
       }
     }