From 4884e25f5b34c098cbfe5f207b2a3d938c9b82c4 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@dundee.ac.uk>
Date: Fri, 23 Jan 2015 13:14:58 +0000
Subject: [PATCH] JAL-1628 tweak signature of core annotation printer for
 outputting hidden columns and view names via VIEW_HIDECOLS
 and VIEW_DEF

---
 help/html/features/annotationsFormat.html |   12 ++-
 src/jalview/io/AnnotationFile.java        |  117 ++++++++++++++++++++++++++---
 test/jalview/io/AnnotationFileIOTest.java |    5 +-
 3 files changed, 117 insertions(+), 17 deletions(-)

diff --git a/help/html/features/annotationsFormat.html b/help/html/features/annotationsFormat.html
index 90dfd9b..72691ce 100755
--- a/help/html/features/annotationsFormat.html
+++ b/help/html/features/annotationsFormat.html
@@ -60,7 +60,7 @@ ignored. The sections below describe the structure of an annotation file.
 <li><a href="#groupdefs">SEQUENCE_GROUP</a> to define groups of sequences for further annotation</li>
 <li><a href="#groupprops">PROPERTIES</a> to set visualisation properties for sequence groups</li>
 <li><a href="#seqgrprefs">SEQUENCE_REF and GROUP_REF</a> for attaching annotation to sequences and groups</li>
-		<li><a href="#refsandviews">VIEW_SETREF and HIDE_INSERTIONS</a>
+		<li><a href="#refsandviews">VIEW_SETREF, VIEW_HIDECOLS and HIDE_INSERTIONS</a>
 			for defining a reference sequence on the alignment and hiding regions
 			based on gaps in a reference sequence</li>
 	</ul>
@@ -168,7 +168,7 @@ of sequence IDs. </p>
 <tr><td width="50%">idColour</td><td>Colour for highlighting the Sequence ID labels for this group<br/>If <em>idColour</em> is given but <em>colour</em> is not, then idColor will also be used for the group background colour.</td></tr>
 <tr><td width="50%">showunconserved</td><td>Boolean (default false) indicating whether residues should only be shown that are different from current reference or consensus sequence</td></tr>
 <tr><td width="50%">hide</td><td>Boolean (default false) indicating whether the rows in this group should be marked as hidden.<br/><em>Note:</em> if the group is sequence associated (specified by SEQUENCE_REF), then all members will be hidden and marked as represented by the reference sequence.</td></tr>
-<tr><td width="50%">hidecols</td><td>Boolean (default false) indicating whether columns in this groushould be marked as hidden</td></tr></tbody>
+<!-- <tr><td width="50%">hidecols</td><td>Boolean (default false) indicating whether columns in this groushould be marked as hidden</td></tr> --></tbody>
 </table>
 
 <p><strong>Specifying colours in PROPERTIES key-value pairs</strong><br/>
@@ -206,7 +206,7 @@ Group association is turned off for subsequent annotation rows by:
 <pre>GROUP_REF&#9;<em>ALIGNMENT</em></pre>
 </p>
 <hr/>
-<p><strong><a name="refsandviews">VIEW_SETREF, and HIDE_INSERTIONS</a></strong><br/>
+<p><strong><a name="refsandviews">VIEW_SETREF, VIEW_HIDECOL and HIDE_INSERTIONS</a></strong><br/>
 Since Jalview 2.9, the Annotations file has also supported the definition of views on the alignment, and definition of hidden regions.</p>
 <!-- 	<p>
 		<em>VIEW_DEF</em> allows the current view to be named according to the
@@ -220,6 +220,12 @@ Since Jalview 2.9, the Annotations file has also supported the definition of vie
 		corresponding sequence as the <a href="../features/refsequence.html">reference
 			sequence</a> for the alignment.
 	</p>
+	<em>VIEW_HIDECOLS</em> takes either a single argument consisting of a
+	comma separated series of integer pairs like
+	<em>3-4</em>. These integer pairs define columns (starting from the
+	left-hand column 0) that should be marked as hidden in the alignment
+	view.
+	</p>
 	<p>
 		<em>HIDE_INSERTIONS</em> takes a either a single sequence ID or a
 		numeric index, or no arguments. This command marks all gapped
diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 6834e76..8dc84b8 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -99,7 +99,7 @@ public class AnnotationFile
   public String printAnnotations(AlignmentAnnotation[] annotations,
           List<SequenceGroup> list, Hashtable properties)
   {
-    return printAnnotations(annotations, list, properties, null);
+    return printAnnotations(annotations, list, properties, null, null, null);
 
   }
 
@@ -140,16 +140,56 @@ public class AnnotationFile
    * @return annotation file
    */
   public String printAnnotations(AlignmentAnnotation[] annotations,
-          List<SequenceGroup> list, Hashtable properties, ViewDef[] views)
+          List<SequenceGroup> list, Hashtable properties,
+          ColumnSelection cs, AlignmentI al, ViewDef view)
   {
-    // TODO: resolve views issue : annotationFile could contain visible region,
-    // or full data + hidden region specifications for a view.
-    if (views != null)
+    if (view != null)
     {
-      // are views defined and then annotation added to alignment or the other
-      // way around ?
-
+      if (view.viewname != null)
+      {
+        text.append("VIEW_DEF\t" + view.viewname + "\n");
+      }
+      if (list == null)
+      {
+        list = view.visibleGroups;
+      }
+      if (cs == null)
+      {
+        cs = view.hiddencols;
+      }
+      if (al == null)
+      {
+        // add hidden rep sequences.
+      }
+    }
+    // first target - store and restore all settings for a view.
+    if (al != null && al.hasSeqrep())
+    {
+      text.append("VIEW_SETREF\t" + al.getSeqrep().getName() + "\n");
     }
+    if (cs != null && cs.hasHiddenColumns())
+    {
+      text.append("VIEW_HIDECOLS\t");
+      List<int[]> hc = cs.getHiddenColumns();
+      boolean comma = false;
+      for (int[] r : hc)
+      {
+        if (!comma)
+        {
+          comma = true;
+        }
+        else
+        {
+          text.append(",");
+        }
+        text.append(r[0]);
+        text.append("-");
+        text.append(r[1]);
+      }
+      text.append("\n");
+    }
+    // TODO: allow efficient recovery of annotation data shown in several
+    // different views
     if (annotations != null)
     {
       boolean oneColour = true;
@@ -432,7 +472,8 @@ public class AnnotationFile
         text.append(properties.get(key));
       }
       // TODO: output alignment visualization settings here if required
-
+      // iterate through one or more views, defining, marking columns and rows as visible/hidden, and emmitting view properties.
+      // View specific annotation is 
     }
 
     return text.toString();
@@ -888,6 +929,12 @@ public class AnnotationFile
           modified = true;
           continue;
         }
+        // else if (token.equalsIgnoreCase("VIEW_DEF"))
+        // {
+        // addOrSetView(al,st);
+        // modified = true;
+        // continue;
+        // }
         else if (token.equalsIgnoreCase("VIEW_SETREF"))
         {
           if (refSeq != null)
@@ -897,6 +944,19 @@ public class AnnotationFile
           modified = true;
           continue;
         }
+        else if (token.equalsIgnoreCase("VIEW_HIDECOLS"))
+        {
+          if (st.hasMoreTokens())
+          {
+            if (colSel == null)
+            {
+              colSel = new ColumnSelection();
+            }
+            parseHideCols(colSel, st.nextToken());
+          }
+          modified = true;
+          continue;
+        }
         else if (token.equalsIgnoreCase("HIDE_INSERTIONS"))
         {
           SequenceI sr = refSeq == null ? al.getSeqrep() : refSeq;
@@ -1121,6 +1181,40 @@ public class AnnotationFile
     return modified;
   }
 
+  private void parseHideCols(ColumnSelection colSel, String nextToken)
+  {
+    StringTokenizer inval = new StringTokenizer(nextToken,",");
+    while (inval.hasMoreTokens())
+    {
+      String range = inval.nextToken().trim();
+      int from, to = range.indexOf("-");
+      if (to == -1)
+      {
+        from = to = Integer.parseInt(range);
+        if (from >= 0)
+        {
+          colSel.hideColumns(from, to);
+        }
+      }
+      else
+      {
+        from = Integer.parseInt(range.substring(0, to));
+        if (to < range.length() - 1)
+        {
+          to = Integer.parseInt(range.substring(to + 1));
+        }
+        else
+        {
+          to = from;
+        }
+        if (from > 0 && to >= from)
+        {
+          colSel.hideColumns(from, to);
+        }
+      }
+    }
+  }
+
   private Object autoAnnotsKey(AlignmentAnnotation annotation,
           SequenceI refSeq, String groupRef)
   {
@@ -1697,12 +1791,13 @@ public class AnnotationFile
     return printAnnotations(viewport.isShowAnnotation() ? viewport
             .getAlignment().getAlignmentAnnotation() : null, viewport
             .getAlignment().getGroups(), viewport.getAlignment()
-            .getProperties());
+            .getProperties(), viewport.getColumnSelection(),
+            viewport.getAlignment(), null);
   }
 
   public String printAnnotationsForAlignment(AlignmentI al)
   {
     return printAnnotations(al.getAlignmentAnnotation(), al.getGroups(),
-            al.getProperties());
+            al.getProperties(), null, al, null);
   }
 }
diff --git a/test/jalview/io/AnnotationFileIOTest.java b/test/jalview/io/AnnotationFileIOTest.java
index 3d4e841..56e6cda 100644
--- a/test/jalview/io/AnnotationFileIOTest.java
+++ b/test/jalview/io/AnnotationFileIOTest.java
@@ -115,13 +115,12 @@ public class AnnotationFileIOTest
               new AnnotationFile().readAnnotationFile(al, cs, af,
                       FormatAdapter.FILE));
 
-      ViewDef[] v = new ViewDef[1];
       AnnotationFile aff = new AnnotationFile();
-      v[0] = aff.new ViewDef(null, al.getHiddenSequences(), cs,
+      ViewDef v = aff.new ViewDef(null, al.getHiddenSequences(), cs,
               new Hashtable());
       String anfileout = new AnnotationFile().printAnnotations(
               al.getAlignmentAnnotation(), al.getGroups(),
-              al.getProperties(), v);
+              al.getProperties(), null, al, v);
       assertTrue(
               "Test "
                       + testname
-- 
1.7.10.2