From 08c8b9d76f478017bdb4fbd5bc1b4d0e16421de6 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 17 Aug 2016 12:30:57 +0100
Subject: [PATCH] JAL-2173 don't remove annotation from hidden columns

---
 src/jalview/appletgui/AnnotationPanel.java |   10 +++----
 src/jalview/gui/AnnotationPanel.java       |   45 ++++++++++++++++++----------
 2 files changed, 35 insertions(+), 20 deletions(-)

diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index dd652b1..1a5dc05 100755
--- a/src/jalview/appletgui/AnnotationPanel.java
+++ b/src/jalview/appletgui/AnnotationPanel.java
@@ -160,12 +160,12 @@ 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))
diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 398f57d..eec1881 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -289,9 +289,12 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
     if (evt.getActionCommand().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 (evt.getActionCommand().equals(LABEL))
@@ -423,9 +426,21 @@ 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
@@ -437,22 +452,22 @@ 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;
             }
           }
         }
@@ -460,13 +475,13 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         {
           if (last.length() > 0)
           {
-            collatedInput += " ";
+            collatedInput.append(" ");
           }
-          collatedInput += tlabel;
+          collatedInput.append(tlabel);
         }
       }
     }
-    return collatedInput;
+    return collatedInput.toString();
   }
 
   /**
-- 
1.7.10.2