From 8cf069b967632cb55cc1a7e4799e677b0fa36101 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Tue, 2 Oct 2007 16:05:40 +0000
Subject: [PATCH] added colSel as a parameter formatAdaptor print function to
 allow editing of annotation embedded in output.

---
 src/jalview/gui/AlignFrame.java   |    4 ++--
 src/jalview/io/FormatAdapter.java |   15 +++++++++------
 2 files changed, 11 insertions(+), 8 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 1795c1a..05beb00 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -781,7 +781,7 @@ public class AlignFrame
       String output = f.formatSequences(
           format,
           (Alignment) viewport.alignment, // class cast exceptions will occur in the distant future
-          omitHidden, f.getCacheSuffixDefault(format));
+          omitHidden, f.getCacheSuffixDefault(format), viewport.colSel);
 
       if (output == null)
       {
@@ -853,7 +853,7 @@ public class AlignFrame
     cap.setText(new FormatAdapter().formatSequences(
         e.getActionCommand(),
         viewport.alignment,
-        omitHidden));
+        omitHidden, viewport.colSel));
   }
 
   /**
diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 6c40696..24c9109 100755
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -139,19 +139,20 @@ public class FormatAdapter
       return jalview.bin.Cache.getDefault(format.toUpperCase()+"_JVSUFFIX", true);
     return false;
   }
-  public String formatSequences(String format, AlignmentI alignment, String[] omitHidden)
+  public String formatSequences(String format, AlignmentI alignment, String[] omitHidden, ColumnSelection colSel)
   {
-    return formatSequences(format, alignment, omitHidden, getCacheSuffixDefault(format));
+    return formatSequences(format, alignment, omitHidden, getCacheSuffixDefault(format), colSel);
   }
     /**
    * hack function to replace seuqences with visible sequence strings before generating a
    * string of the alignment in the given format.
    * @param format
-   * @param alignment
-   * @param omitHidden sequence strings to write out in order of sequences in alignment
+     * @param alignment
+     * @param omitHidden sequence strings to write out in order of sequences in alignment
+     * @param colSel defines hidden columns that are edited out of annotation 
    * @return string representation of the alignment formatted as format
    */
-  public String formatSequences(String format, AlignmentI alignment, String[] omitHidden, boolean suffix)
+  public String formatSequences(String format, AlignmentI alignment, String[] omitHidden, boolean suffix, ColumnSelection colSel)
   {
     AlignFile afile = null;
     if (omitHidden!=null)
@@ -161,7 +162,9 @@ public class FormatAdapter
       AlignmentAnnotation[] ala = alignment.getAlignmentAnnotation();
       for (int i=0; i<ala.length; i++)
       {
-        alv.addAnnotation(new AlignmentAnnotation(ala[i]));
+        AlignmentAnnotation na = new AlignmentAnnotation(ala[i]);
+        colSel.makeVisibleAnnotation(na);
+        alv.addAnnotation(na);
       }
       return this.formatSequences(format, alv, suffix);
     }
-- 
1.7.10.2