X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAnnotationFile.java;h=44c7f2e5efb53845de2b60d2c17bf48249c4c8bf;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=56040d9059083908a6063cddcb9ae66f6237b132;hpb=6a44f113099e7ee83deada4d8426cd98757c2425;p=jalview.git

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 56040d9..44c7f2e 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -1,51 +1,136 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * 
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
-
 package jalview.io;
 
 import java.io.*;
-import jalview.datamodel.*;
+import java.net.*;
 import java.util.*;
-import java.net.URL;
-import jalview.schemes.*;
-import jalview.analysis.Conservation;
 
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.schemes.*;
 
 public class AnnotationFile
 {
-  StringBuffer text = new StringBuffer(
-        "JALVIEW_ANNOTATION\n"
-        +"# Created: "
-      +new java.util.Date()+"\n\n");
+  public AnnotationFile()
+  {
+    init();
+  }
+
+  /**
+   * character used to write newlines
+   */
+  protected String newline = System.getProperty("line.separator");
+
+  /**
+   * set new line string and reset the output buffer
+   * 
+   * @param nl
+   */
+  public void setNewlineString(String nl)
+  {
+    newline = nl;
+    init();
+  }
+
+  public String getNewlineString()
+  {
+    return newline;
+  }
+
+  StringBuffer text;
+
+  private void init()
+  {
+    text = new StringBuffer("JALVIEW_ANNOTATION"+newline + "# Created: "
+            + new java.util.Date() + newline + newline);
+    refSeq = null;
+    refSeqId = null;
+  }
+
+  /**
+   * convenience method for pre-2.4 feature files which have no view, hidden
+   * columns or hidden row keywords.
+   * 
+   * @param annotations
+   * @param groups
+   * @param properties
+   * @return feature file as a string.
+   */
+  public String printAnnotations(AlignmentAnnotation[] annotations,
+          Vector groups, Hashtable properties)
+  {
+    return printAnnotations(annotations, groups, properties, null);
+
+  }
+
+  /**
+   * hold all the information about a particular view definition read from or
+   * written out in an annotations file.
+   */
+  public class ViewDef
+  {
+    public String viewname;
+
+    public HiddenSequences hidseqs;
+
+    public ColumnSelection hiddencols;
 
-  public String printAnnotations(AlignmentAnnotation [] annotations,
-                                Vector groups)
+    public Vector visibleGroups;
+
+    public Hashtable hiddenRepSeqs;
+
+    public ViewDef(String viewname, HiddenSequences hidseqs,
+            ColumnSelection hiddencols, Hashtable hiddenRepSeqs)
+    {
+      this.viewname = viewname;
+      this.hidseqs = hidseqs;
+      this.hiddencols = hiddencols;
+      this.hiddenRepSeqs = hiddenRepSeqs;
+    }
+  }
+
+  /**
+   * Prepare an annotation file given a set of annotations, groups, alignment
+   * properties and views.
+   * 
+   * @param annotations
+   * @param groups
+   * @param properties
+   * @param views
+   * @return annotation file
+   */
+  public String printAnnotations(AlignmentAnnotation[] annotations,
+          Vector groups, Hashtable properties, ViewDef[] views)
   {
-    if(annotations!=null)
+    // TODO: resolve views issue : annotationFile could contain visible region,
+    // or full data + hidden region specifications for a view.
+    if (annotations != null)
     {
+      boolean oneColour = true;
       AlignmentAnnotation row;
       String comma;
-      SequenceI seqref = null;
+      SequenceI refSeq = null;
+      SequenceGroup refGroup = null;
 
       StringBuffer colours = new StringBuffer();
       StringBuffer graphLine = new StringBuffer();
-
+      StringBuffer rowprops = new StringBuffer();
       Hashtable graphGroup = new Hashtable();
 
       java.awt.Color color;
@@ -54,103 +139,244 @@ public class AnnotationFile
       {
         row = annotations[i];
 
-        if (!row.visible)
+        if (!row.visible && !row.hasScore())
+        {
           continue;
+        }
 
         color = null;
+        oneColour = true;
 
         if (row.sequenceRef == null)
         {
-          if (seqref != null)
-            text.append("\nSEQUENCE_REF\tALIGNMENT\n");
+          if (refSeq != null)
+          {
+            text.append(newline);
+            text.append("SEQUENCE_REF\tALIGNMENT");
+            text.append(newline);
+          }
+
+          refSeq = null;
+        }
 
-          seqref = null;
+        else
+        {
+          if (refSeq == null || refSeq != row.sequenceRef)
+          {
+            refSeq = row.sequenceRef;
+            text.append(newline);
+            text.append("SEQUENCE_REF\t");
+            text.append(refSeq.getName());
+            text.append(newline);
+          }
+        }
+        // mark any group references for the row
+        if (row.groupRef == null)
+        {
+
+          if (refGroup != null)
+          {
+            text.append(newline);
+            text.append("GROUP_REF\tALIGNMENT");
+            text.append(newline);
+          }
+
+          refGroup = null;
+        }
+        else
+        {
+          if (refGroup == null || refGroup != row.groupRef)
+          {
+            refGroup = row.groupRef;
+            text.append(newline);
+            text.append("GROUP_REF\t");
+            text.append(refGroup.getName());
+            text.append(newline);
+          }
         }
 
-        else if (seqref == null || seqref != row.sequenceRef)
+        boolean hasGlyphs = row.hasIcons, hasLabels = row.hasText, hasValues = row.hasScore, hasText = false;
+        // lookahead to check what the annotation row object actually contains.
+        for (int j = 0; row.annotations != null
+                && j < row.annotations.length
+                && (!hasGlyphs || !hasLabels || !hasValues); j++)
         {
-          seqref = row.sequenceRef;
-          text.append("\nSEQUENCE_REF\t" + seqref.getName() + "\n");
+          if (row.annotations[j] != null)
+          {
+            hasLabels |= (row.annotations[j].displayCharacter != null
+                    && row.annotations[j].displayCharacter.length() > 0 && !row.annotations[j].displayCharacter
+                    .equals(" "));
+            hasGlyphs |= (row.annotations[j].secondaryStructure != 0 && row.annotations[j].secondaryStructure != ' ');
+            hasValues |= (row.annotations[j].value != Float.NaN); // NaNs can't
+            // be
+            // rendered..
+            hasText |= (row.annotations[j].description != null && row.annotations[j].description
+                    .length() > 0);
+          }
         }
 
         if (row.graph == AlignmentAnnotation.NO_GRAPH)
         {
           text.append("NO_GRAPH\t");
+          hasValues = false; // only secondary structure
+          // hasLabels = false; // and annotation description string.
         }
         else
         {
           if (row.graph == AlignmentAnnotation.BAR_GRAPH)
+          {
             text.append("BAR_GRAPH\t");
+            hasGlyphs = false; // no secondary structure
+
+          }
           else if (row.graph == AlignmentAnnotation.LINE_GRAPH)
+          {
+            hasGlyphs = false; // no secondary structure
             text.append("LINE_GRAPH\t");
+          }
 
           if (row.getThreshold() != null)
-            graphLine.append("GRAPHLINE\t"
-                             + row.label + "\t"
-                             + row.getThreshold().value + "\t"
-                             + row.getThreshold().label + "\t"
-                             + jalview.util.Format.getHexString(
-                                 row.getThreshold().colour) + "\n"
-                );
+          {
+            graphLine.append("GRAPHLINE\t");
+            graphLine.append(row.label);
+            graphLine.append("\t");
+            graphLine.append(row.getThreshold().value);
+            graphLine.append("\t");
+            graphLine.append(row.getThreshold().label);
+            graphLine.append("\t");
+            graphLine.append(jalview.util.Format.getHexString(row
+                    .getThreshold().colour));
+            graphLine.append(newline);
+          }
 
           if (row.graphGroup > -1)
           {
             String key = String.valueOf(row.graphGroup);
             if (graphGroup.containsKey(key))
-              graphGroup.put(key, graphGroup.get(key)
-                             + "\t" + row.label);
+            {
+              graphGroup.put(key, graphGroup.get(key) + "\t" + row.label);
+            }
             else
+            {
               graphGroup.put(key, row.label);
+            }
           }
         }
 
         text.append(row.label + "\t");
         if (row.description != null)
+        {
           text.append(row.description + "\t");
-
-        for (int j = 0; j < row.annotations.length; j++)
+        }
+        for (int j = 0; row.annotations != null
+                && j < row.annotations.length; j++)
         {
-          if (seqref != null &&
-              jalview.util.Comparison.isGap(seqref.getCharAt(j)))
+          if (refSeq != null
+                  && jalview.util.Comparison.isGap(refSeq.getCharAt(j)))
+          {
             continue;
+          }
 
           if (row.annotations[j] != null)
           {
             comma = "";
-            if (row.annotations[j].secondaryStructure != ' ')
+            if (hasGlyphs) // could be also hasGlyphs || ...
             {
-              text.append(comma + row.annotations[j].secondaryStructure);
+
+              text.append(comma);
+              if (row.annotations[j].secondaryStructure != ' ')
+              {
+                // only write out the field if its not whitespace.
+                text.append(row.annotations[j].secondaryStructure);
+              }
               comma = ",";
             }
-            if (row.annotations[j].displayCharacter.length() > 0
-                && !row.annotations[j].displayCharacter.equals(" "))
+            if (hasValues)
             {
-              text.append(comma + row.annotations[j].displayCharacter);
+              if (row.annotations[j].value != Float.NaN)
+              {
+                text.append(comma + row.annotations[j].value);
+              }
+              else
+              {
+                System.err.println("Skipping NaN - not valid value.");
+                text.append(comma + 0f);// row.annotations[j].value);
+              }
               comma = ",";
             }
+            if (hasLabels)
+            {
+              // TODO: labels are emitted after values for bar graphs.
+              if // empty labels are allowed, so
+              (row.annotations[j].displayCharacter != null
+                      && row.annotations[j].displayCharacter.length() > 0
+                      && !row.annotations[j].displayCharacter.equals(" "))
+              {
+                text.append(comma + row.annotations[j].displayCharacter);
+                comma = ",";
+              }
+            }
+            if (hasText)
+            {
+              if (row.annotations[j].description != null
+                      && row.annotations[j].description.length() > 0
+                      && !row.annotations[j].description
+                              .equals(row.annotations[j].displayCharacter))
+              {
+                text.append(comma + row.annotations[j].description);
+                comma = ",";
+              }
+            }
+            if (color != null && !color.equals(row.annotations[j].colour))
+            {
+              oneColour = false;
+            }
+
+            color = row.annotations[j].colour;
 
-            if (row.annotations[j] != null)
+            if (row.annotations[j].colour != null
+                    && row.annotations[j].colour != java.awt.Color.black)
             {
-              color = row.annotations[j].colour;
-              if (row.annotations[j].value != 0f)
-                text.append(comma + row.annotations[j].value);
+              text.append(comma
+                      + "["
+                      + jalview.util.Format
+                              .getHexString(row.annotations[j].colour)
+                      + "]");
+              comma = ",";
             }
           }
           text.append("|");
         }
 
-        text.append("\n");
+        if (row.hasScore())
+          text.append("\t" + row.score);
+
+        text.append(newline);
 
-        if (color != null && color != java.awt.Color.black)
+        if (color != null && color != java.awt.Color.black && oneColour)
         {
-          colours.append("COLOUR\t"
-                         + row.label + "\t"
-                         + jalview.util.Format.getHexString(color) + "\n");
+          colours.append("COLOUR\t");
+          colours.append(row.label);
+          colours.append("\t");
+          colours.append(jalview.util.Format.getHexString(color));
+          colours.append(newline);
+        }
+        if (row.scaleColLabel || row.showAllColLabels
+                || row.centreColLabels)
+        {
+          rowprops.append("ROWPROPERTIES\t");
+          rowprops.append(row.label);
+          rowprops.append("\tscaletofit=");
+          rowprops.append(row.scaleColLabel);
+          rowprops.append("\tshowalllabs=");
+          rowprops.append(row.showAllColLabels);
+          rowprops.append("\tcentrelabs=");
+          rowprops.append(row.centreColLabels);
+          rowprops.append(newline);
         }
-
       }
 
-      text.append("\n");
+      text.append(newline);
 
       text.append(colours.toString());
       text.append(graphLine.toString());
@@ -160,79 +386,171 @@ public class AnnotationFile
         Enumeration en = graphGroup.elements();
         while (en.hasMoreElements())
         {
-          text.append(en.nextElement() + "\n");
+          text.append(en.nextElement());
+          text.append(newline);
         }
       }
+      text.append(rowprops.toString());
     }
 
-
-    if(groups!=null)
+    if (groups != null)
     {
       printGroups(groups);
     }
 
+    if (properties != null)
+    {
+      text.append(newline);
+      text.append(newline);
+      text.append("ALIGNMENT");
+      Enumeration en = properties.keys();
+      while (en.hasMoreElements())
+      {
+        String key = en.nextElement().toString();
+        text.append("\t");
+        text.append(key);
+        text.append("=");
+        text.append(properties.get(key));
+      }
+      // TODO: output alignment visualization settings here if required
+
+    }
+
     return text.toString();
   }
 
-
   public void printGroups(Vector sequenceGroups)
   {
     SequenceGroup sg;
+    SequenceI seqrep = null;
     for (int i = 0; i < sequenceGroups.size(); i++)
     {
       sg = (SequenceGroup) sequenceGroups.elementAt(i);
-      text.append("SEQUENCE_GROUP\t"
-                  + sg.getName() + "\t"
-                  + (sg.getStartRes()+1) + "\t"
-                  + (sg.getEndRes()+1)  + "\t" + "-1\t");
-      for(int s=0; s<sg.getSize(); s++)
+      if (!sg.hasSeqrep())
       {
-        text.append(sg.getSequenceAt(s).getName()+"\t");
+        text.append("SEQUENCE_GROUP\t" + sg.getName() + "\t"
+                + (sg.getStartRes() + 1) + "\t" + (sg.getEndRes() + 1)
+                + "\t" + "-1\t");
+        seqrep = null;
       }
-
-      text.append("\nPROPERTIES\t"+sg.getName()+"\t");
-
-      if(sg.getDescription()!=null)
-        text.append("description="+sg.getDescription()+"\t");
-      if(sg.cs!=null)
+      else
       {
-        text.append("colour="+ColourSchemeProperty.getColourName(sg.cs)+"\t");
-        if(sg.cs.getThreshold()!=0)
-          text.append("pidThreshold="+sg.cs.getThreshold());
-        if(sg.cs.conservationApplied())
-          text.append("consThreshold="+sg.cs.getConservationInc()+"\t");
+        seqrep = sg.getSeqrep();
+        text.append("SEQUENCE_REF\t");
+        text.append(seqrep.getName());
+        text.append(newline);
+        text.append("SEQUENCE_GROUP\t");
+        text.append(sg.getName());
+        text.append("\t");
+        text.append((seqrep.findPosition(sg.getStartRes())));
+        text.append("\t");
+        text.append((seqrep.findPosition(sg.getEndRes())));
+        text.append("\t");
+        text.append("-1\t");
       }
-      text.append("outlineColour="+
-                  jalview.util.Format.getHexString(sg.getOutlineColour())+"\t");
-
-      text.append("displayBoxes=" + sg.getDisplayBoxes() + "\t");
-      text.append("displayText=" + sg.getDisplayText() + "\t");
-      text.append("colourText=" + sg.getColourText() + "\t");
+      for (int s = 0; s < sg.getSize(); s++)
+      {
+        text.append(sg.getSequenceAt(s).getName());
+        text.append("\t");
+      }
+      text.append(newline);
+      text.append("PROPERTIES\t");
+      text.append(sg.getName());
+      text.append("\t");
 
+      if (sg.getDescription() != null)
+      {
+        text.append("description=");
+        text.append(sg.getDescription());
+        text.append("\t");
+      }
+      if (sg.cs != null)
+      {
+        text.append("colour=");
+        text.append(ColourSchemeProperty.getColourName(sg.cs));
+        text.append("\t");
+        if (sg.cs.getThreshold() != 0)
+        {
+          text.append("pidThreshold=");
+          text.append(sg.cs.getThreshold());
+        }
+        if (sg.cs.conservationApplied())
+        {
+          text.append("consThreshold=");
+          text.append(sg.cs.getConservationInc());
+          text.append("\t");
+        }
+      }
+      text.append("outlineColour=");
+      text.append(jalview.util.Format.getHexString(sg.getOutlineColour()));
+      text.append("\t");
+
+      text.append("displayBoxes=");
+      text.append(sg.getDisplayBoxes());
+      text.append("\t");
+      text.append("displayText=");
+      text.append(sg.getDisplayText());
+      text.append("\t");
+      text.append("colourText=");
+      text.append(sg.getColourText());
+      text.append("\t");
+      text.append("showUnconserved=");
+      text.append(sg.getShowNonconserved());
+      text.append("\t");
       if (sg.textColour != java.awt.Color.black)
-        text.append("textCol1=" +
-                    jalview.util.Format.getHexString(sg.textColour) + "\t");
+      {
+        text.append("textCol1=");
+        text.append(jalview.util.Format.getHexString(sg.textColour));
+        text.append("\t");
+      }
       if (sg.textColour2 != java.awt.Color.white)
-        text.append("textCol2=" +
-                    jalview.util.Format.getHexString(sg.textColour2) + "\t");
-      if(sg.thresholdTextColour!=0)
-      text.append("textColThreshold="+sg.thresholdTextColour);
-
-      text.append("\n\n");
+      {
+        text.append("textCol2=");
+        text.append(jalview.util.Format.getHexString(sg.textColour2));
+        text.append("\t");
+      }
+      if (sg.thresholdTextColour != 0)
+      {
+        text.append("textColThreshold=");
+        text.append(sg.thresholdTextColour);
+        text.append("\t");
+      }
+      if (sg.idColour != null)
+      {
+        text.append("idColour=");
+        text.append(jalview.util.Format.getHexString(sg.idColour));
+        text.append("\t");
+      }
+      if (sg.isHidereps())
+      {
+        text.append("hide=true\t");
+      }
+      if (sg.isHideCols())
+      {
+        text.append("hidecols=true\t");
+      }
+      if (seqrep != null)
+      {
+        // terminate the last line and clear the sequence ref for the group
+        text.append(newline);
+        text.append("SEQUENCE_REF");
+      }
+      text.append(newline);
+      text.append(newline);
 
     }
   }
 
-
   SequenceI refSeq = null;
-  Hashtable annotationsHash = new Hashtable();
-  public boolean readAnnotationFile(AlignmentI al,
-                                    String file,
-                                    String protocol)
+
+  String refSeqId = null;
+
+  public boolean readAnnotationFile(AlignmentI al, String file,
+          String protocol)
   {
+    BufferedReader in = null;
     try
     {
-      BufferedReader in = null;
       if (protocol.equals(AppletFormatAdapter.FILE))
       {
         in = new BufferedReader(new FileReader(file));
@@ -242,7 +560,7 @@ public class AnnotationFile
         URL url = new URL(file);
         in = new BufferedReader(new InputStreamReader(url.openStream()));
       }
-     else if (protocol.equals(AppletFormatAdapter.PASTE))
+      else if (protocol.equals(AppletFormatAdapter.PASTE))
       {
         in = new BufferedReader(new StringReader(file));
       }
@@ -253,14 +571,57 @@ public class AnnotationFile
         {
           in = new BufferedReader(new java.io.InputStreamReader(is));
         }
+      }
+      if (in != null)
+      {
+        return parseAnnotationFrom(al, in);
+      }
+
+    } catch (Exception ex)
+    {
+      ex.printStackTrace();
+      System.out.println("Problem reading annotation file: " + ex);
+      return false;
     }
+    return false;
+  }
+
+  public boolean parseAnnotationFrom(AlignmentI al, BufferedReader in)
+          throws Exception
+  {
+    boolean modified = false;
+    String groupRef = null;
+    Hashtable groupRefRows = new Hashtable();
 
+    Hashtable autoAnnots = new Hashtable();
+    {
       String line, label, description, token;
       int graphStyle, index;
       int refSeqIndex = 1;
       int existingAnnotations = 0;
-      if(al.getAlignmentAnnotation()!=null)
-       existingAnnotations = al.getAlignmentAnnotation().length;
+      // when true - will add new rows regardless of whether they are duplicate
+      // auto-annotation like consensus or conservation graphs
+      boolean overrideAutoAnnot = false;
+      if (al.getAlignmentAnnotation() != null)
+      {
+        existingAnnotations = al.getAlignmentAnnotation().length;
+        if (existingAnnotations > 0)
+        {
+          AlignmentAnnotation[] aa = al.getAlignmentAnnotation();
+          for (int aai = 0; aai < aa.length; aai++)
+          {
+            if (aa[aai].autoCalculated)
+            {
+              // make a note of the name and description
+              autoAnnots.put(
+                      autoAnnotsKey(aa[aai], aa[aai].sequenceRef,
+                              (aa[aai].groupRef == null ? null
+                                      : aa[aai].groupRef.getName())),
+                      new Integer(1));
+            }
+          }
+        }
+      }
 
       int alWidth = al.getWidth();
 
@@ -270,10 +631,12 @@ public class AnnotationFile
 
       // First confirm this is an Annotation file
       boolean jvAnnotationFile = false;
-      while ( (line = in.readLine()) != null)
+      while ((line = in.readLine()) != null)
       {
-        if (line.indexOf("#") == 0 )
+        if (line.indexOf("#") == 0)
+        {
           continue;
+        }
 
         if (line.indexOf("JALVIEW_ANNOTATION") > -1)
         {
@@ -282,196 +645,440 @@ public class AnnotationFile
         }
       }
 
-      if(!jvAnnotationFile)
+      if (!jvAnnotationFile)
       {
         in.close();
         return false;
       }
 
-      while ( (line = in.readLine()) != null)
+      while ((line = in.readLine()) != null)
       {
-        if(line.indexOf("#")==0
-           || line.indexOf("JALVIEW_ANNOTATION")>-1
-           || line.length()==0)
+        if (line.indexOf("#") == 0
+                || line.indexOf("JALVIEW_ANNOTATION") > -1
+                || line.length() == 0)
+        {
           continue;
+        }
 
         st = new StringTokenizer(line, "\t");
         token = st.nextToken();
-        if(token.equalsIgnoreCase("COLOUR"))
+        if (token.equalsIgnoreCase("COLOUR"))
         {
+          // TODO: use graduated colour def'n here too
           colourAnnotations(al, st.nextToken(), st.nextToken());
+          modified = true;
           continue;
         }
 
-        else if(token.equalsIgnoreCase("COMBINE") )
+        else if (token.equalsIgnoreCase("COMBINE"))
         {
           combineAnnotations(al, st);
+          modified = true;
+          continue;
+        }
+        else if (token.equalsIgnoreCase("ROWPROPERTIES"))
+        {
+          addRowProperties(al, st);
+          modified = true;
           continue;
         }
-
         else if (token.equalsIgnoreCase("GRAPHLINE"))
         {
           addLine(al, st);
+          modified = true;
           continue;
         }
 
-
-        else if(token.equalsIgnoreCase("SEQUENCE_REF") )
+        else if (token.equalsIgnoreCase("SEQUENCE_REF"))
         {
-          refSeq = al.findName(st.nextToken());
-          try{
-            refSeqIndex = Integer.parseInt(st.nextToken());
-            if(refSeqIndex<1)
+          if (st.hasMoreTokens())
+          {
+            refSeq = al.findName(refSeqId = st.nextToken());
+            if (refSeq == null)
+            {
+              refSeqId = null;
+            }
+            try
+            {
+              refSeqIndex = Integer.parseInt(st.nextToken());
+              if (refSeqIndex < 1)
+              {
+                refSeqIndex = 1;
+                System.out
+                        .println("WARNING: SEQUENCE_REF index must be > 0 in AnnotationFile");
+              }
+            } catch (Exception ex)
             {
               refSeqIndex = 1;
-              System.out.println("WARNING: SEQUENCE_REF index must be > 0 in AnnotationFile");
             }
           }
-          catch(Exception ex)
+          else
           {
-            refSeqIndex = 1;
+            refSeq = null;
+            refSeqId = null;
           }
-
           continue;
         }
-
-        else if(token.equalsIgnoreCase("SEQUENCE_GROUP"))
+        else if (token.equalsIgnoreCase("GROUP_REF"))
+        {
+          // Group references could be forward or backwards, so they are
+          // resolved after the whole file is read in
+          groupRef = null;
+          if (st.hasMoreTokens())
+          {
+            groupRef = st.nextToken();
+            if (groupRef.length() < 1)
+            {
+              groupRef = null; // empty string
+            }
+            else
+            {
+              if (groupRefRows.get(groupRef) == null)
+              {
+                groupRefRows.put(groupRef, new Vector());
+              }
+            }
+          }
+          continue;
+        }
+        else if (token.equalsIgnoreCase("SEQUENCE_GROUP"))
         {
           addGroup(al, st);
           continue;
         }
 
-        else if(token.equalsIgnoreCase("PROPERTIES"))
+        else if (token.equalsIgnoreCase("PROPERTIES"))
         {
           addProperties(al, st);
+          modified = true;
           continue;
         }
 
+        else if (token.equalsIgnoreCase("BELOW_ALIGNMENT"))
+        {
+          setBelowAlignment(al, st);
+          modified = true;
+          continue;
+        }
+        else if (token.equalsIgnoreCase("ALIGNMENT"))
+        {
+          addAlignmentDetails(al, st);
+          modified = true;
+          continue;
+        }
 
+        // Parse out the annotation row
         graphStyle = AlignmentAnnotation.getGraphValueFromString(token);
         label = st.nextToken();
 
-        if(st.countTokens()>1)
-          description = st.nextToken();
-        else
-          description = null;
-
-        line = st.nextToken();
-
-        st = new StringTokenizer(line, "|", true);
-        annotations = new Annotation[alWidth];
-
         index = 0;
-        boolean emptyColumn = true;
-
+        annotations = new Annotation[alWidth];
+        description = null;
+        float score = Float.NaN;
 
-        while (st.hasMoreElements() && index<alWidth)
+        if (st.hasMoreTokens())
         {
-          token = st.nextToken().trim();
-          if(token.equals("|"))
+          line = st.nextToken();
+
+          if (line.indexOf("|") == -1)
           {
-            if(emptyColumn)
-              index++;
+            description = line;
+            if (st.hasMoreTokens())
+              line = st.nextToken();
+          }
 
-            emptyColumn = true;
+          if (st.hasMoreTokens())
+          {
+            // This must be the score
+            score = Float.valueOf(st.nextToken()).floatValue();
           }
-          else
+
+          st = new StringTokenizer(line, "|", true);
+
+          boolean emptyColumn = true;
+          boolean onlyOneElement = (st.countTokens() == 1);
+
+          while (st.hasMoreElements() && index < alWidth)
           {
-            annotations[index++] = parseAnnotation(token);
-            emptyColumn = false;
+            token = st.nextToken().trim();
+
+            if (onlyOneElement)
+            {
+              try
+              {
+                score = Float.valueOf(token).floatValue();
+                break;
+              } catch (NumberFormatException ex)
+              {
+              }
+            }
+
+            if (token.equals("|"))
+            {
+              if (emptyColumn)
+              {
+                index++;
+              }
+
+              emptyColumn = true;
+            }
+            else
+            {
+              annotations[index++] = parseAnnotation(token, graphStyle);
+              emptyColumn = false;
+            }
           }
+
         }
 
-       annotation = new AlignmentAnnotation(label,
-                                          description,
-                                          annotations,
-                                          0,
-                                          0,
-                                          graphStyle);
+        annotation = new AlignmentAnnotation(label, description,
+                (index == 0) ? null : annotations, 0, 0, graphStyle);
 
-       if(refSeq!=null)
-       {
-         annotation.createSequenceMapping(refSeq, refSeqIndex, false);
-         refSeq.addAlignmentAnnotation(annotation);
-       }
+        annotation.score = score;
+        if (!overrideAutoAnnot
+                && autoAnnots.containsKey(autoAnnotsKey(annotation, refSeq,
+                        groupRef)))
+        {
+          // skip - we've already got an automatic annotation of this type.
+          continue;
+        }
+        // otherwise add it!
+        if (refSeq != null)
+        {
 
-       al.addAnnotation(annotation);
+          annotation.belowAlignment = false;
+          // make a copy of refSeq so we can find other matches in the alignment
+          SequenceI referedSeq = refSeq;
+          do
+          {
+            // copy before we do any mapping business.
+            // TODO: verify that undo/redo with 1:many sequence associated
+            // annotations can be undone correctly
+            AlignmentAnnotation ann = new AlignmentAnnotation(annotation);
+            annotation
+                    .createSequenceMapping(referedSeq, refSeqIndex, false);
+            annotation.adjustForAlignment();
+            referedSeq.addAlignmentAnnotation(annotation);
+            al.addAnnotation(annotation);
+            al.setAnnotationIndex(annotation,
+                    al.getAlignmentAnnotation().length
+                            - existingAnnotations - 1);
+            if (groupRef != null)
+            {
+              ((Vector) groupRefRows.get(groupRef)).addElement(annotation);
+            }
+            // and recover our virgin copy to use again if necessary.
+            annotation = ann;
 
-       al.setAnnotationIndex(annotation,  al.getAlignmentAnnotation().length - existingAnnotations-1);
+          } while (refSeqId != null
+                  && (referedSeq = al.findName(referedSeq, refSeqId, true)) != null);
+        }
+        else
+        {
+          al.addAnnotation(annotation);
+          al.setAnnotationIndex(annotation,
+                  al.getAlignmentAnnotation().length - existingAnnotations
+                          - 1);
+          if (groupRef != null)
+          {
+            ((Vector) groupRefRows.get(groupRef)).addElement(annotation);
+          }
+        }
+        // and set modification flag
+        modified = true;
       }
+      // Finally, resolve the groupRefs
+      Enumeration en = groupRefRows.keys();
+      SequenceGroup theGroup = null;
 
-    }catch(Exception ex)
-    {
-      ex.printStackTrace();
-      System.out.println("Problem reading annotation file: "+ex);
-      return false;
+      while (en.hasMoreElements())
+      {
+        groupRef = (String) en.nextElement();
+        boolean matched = false;
+        // Resolve group: TODO: add a getGroupByName method to alignments
+        Vector grps = al.getGroups();
+        for (int g = 0, gSize = grps.size(); g < gSize; g++)
+        {
+          theGroup = (SequenceGroup) grps.elementAt(g);
+          if (theGroup.getName().equals(groupRef))
+          {
+            if (matched)
+            {
+              // TODO: specify and implement duplication of alignment annotation
+              // for multiple group references.
+              System.err
+                      .println("Ignoring 1:many group reference mappings for group name '"
+                              + groupRef + "'");
+            }
+            else
+            {
+              matched = true;
+              Vector rowset = (Vector) groupRefRows.get(groupRef);
+              if (rowset != null && rowset.size() > 0)
+              {
+                AlignmentAnnotation alan = null;
+                for (int elm = 0, elmSize = rowset.size(); elm < elmSize; elm++)
+                {
+                  alan = (AlignmentAnnotation) rowset.elementAt(elm);
+                  alan.groupRef = theGroup;
+                }
+              }
+            }
+          }
+        }
+        ((Vector) groupRefRows.get(groupRef)).removeAllElements();
+      }
     }
-    return true;
+    return modified;
+  }
+
+  private Object autoAnnotsKey(AlignmentAnnotation annotation,
+          SequenceI refSeq, String groupRef)
+  {
+    return annotation.graph + "\t" + annotation.label + "\t"
+            + annotation.description + "\t"
+            + (refSeq != null ? refSeq.getDisplayId(true) : "");
   }
 
-  Annotation parseAnnotation(String string)
+  Annotation parseAnnotation(String string, int graphStyle)
   {
-    String desc = null, displayChar="";
+    boolean hasSymbols = (graphStyle == AlignmentAnnotation.NO_GRAPH); // don't
+    // do the
+    // glyph
+    // test
+    // if we
+    // don't
+    // want
+    // secondary
+    // structure
+    String desc = null, displayChar = null;
     char ss = ' '; // secondaryStructure
     float value = 0;
-    boolean parsedValue = false;
-    StringTokenizer st = new StringTokenizer(string, ",");
+    boolean parsedValue = false, dcset = false;
+
+    // find colour here
+    java.awt.Color colour = null;
+    int i = string.indexOf("[");
+    int j = string.indexOf("]");
+    if (i > -1 && j > -1)
+    {
+      UserColourScheme ucs = new UserColourScheme();
+
+      colour = ucs.getColourFromString(string.substring(i + 1, j));
+      if (i > 0 && string.charAt(i - 1) == ',')
+      {
+        // clip the preceding comma as well
+        i--;
+      }
+      string = string.substring(0, i) + string.substring(j + 1);
+    }
+
+    StringTokenizer st = new StringTokenizer(string, ",", true);
     String token;
-    while(st.hasMoreTokens())
+    boolean seenContent = false;
+    int pass = 0;
+    while (st.hasMoreTokens())
     {
+      pass++;
       token = st.nextToken().trim();
-      if(token.length()==0)
+      if (token.equals(","))
+      {
+        if (!seenContent && parsedValue && !dcset)
+        {
+          // allow the value below the bar/line to be empty
+          dcset = true;
+          displayChar = " ";
+        }
+        seenContent = false;
         continue;
+      }
+      else
+      {
+        seenContent = true;
+      }
 
-      if(!parsedValue)
+      if (!parsedValue)
       {
-        try{
+        try
+        {
           displayChar = token;
+          // foo
           value = new Float(token).floatValue();
           parsedValue = true;
           continue;
-        }catch(NumberFormatException ex){}
+        } catch (NumberFormatException ex)
+        {
+        }
       }
-
-      if(token.equals("H") || token.equals("E"))
+      else
+      {
+        if (token.length() == 1)
+        {
+          displayChar = token;
+        }
+      }
+      if (hasSymbols
+              && (token.equals("H") || token.equals("E") || token.equals("S") || token
+                      .equals(" ")))
       {
         // Either this character represents a helix or sheet
         // or an integer which can be displayed
         ss = token.charAt(0);
-        if(displayChar.equals(token.substring(0,1)))
+        if (displayChar.equals(token.substring(0, 1)))
+        {
           displayChar = "";
+        }
       }
-      else if(desc==null)
+      else if (desc == null || (parsedValue && pass > 2))
+      {
         desc = token;
+      }
 
     }
-
-    if(desc == null)
-      desc = value+"";
-
-    if(displayChar.length()>1 && desc.length()==1)
+    // if (!dcset && string.charAt(string.length() - 1) == ',')
+    // {
+    // displayChar = " "; // empty display char symbol.
+    // }
+    if (displayChar != null && desc != null && desc.length() == 1)
     {
-      String tmp = displayChar;
-      displayChar = desc;
-      desc = tmp;
+      if (displayChar.length() > 1)
+      {
+        // switch desc and displayChar - legacy support
+        String tmp = displayChar;
+        displayChar = desc;
+        desc = tmp;
+      }
+      else
+      {
+        if (displayChar.equals(desc))
+        {
+          // duplicate label - hangover from the 'robust parser' above
+          desc = null;
+        }
+      }
     }
+    Annotation anot = new Annotation(displayChar, desc, ss, value);
+
+    anot.colour = colour;
 
-    return new Annotation(displayChar, desc, ss, value);
+    return anot;
   }
 
   void colourAnnotations(AlignmentI al, String label, String colour)
   {
     UserColourScheme ucs = new UserColourScheme(colour);
     Annotation[] annotations;
-    for(int i=0; i<al.getAlignmentAnnotation().length; i++)
+    for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
     {
-      if(al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(label))
+      if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(label))
       {
         annotations = al.getAlignmentAnnotation()[i].annotations;
-        for(int j=0; j<annotations.length; j++)
+        for (int j = 0; j < annotations.length; j++)
         {
-          if(annotations[j]!=null)
+          if (annotations[j] != null)
+          {
             annotations[j].colour = ucs.findColour('A');
+          }
         }
       }
     }
@@ -481,52 +1088,64 @@ public class AnnotationFile
   {
     int graphGroup = -1;
     String group = st.nextToken();
-    //First make sure we are not overwriting the graphIndex
-    for(int i=0; i<al.getAlignmentAnnotation().length; i++)
-    {
-      if(al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))
-      {
-        graphGroup = al.getAlignmentAnnotation()[i].graphGroup +1;
-        al.getAlignmentAnnotation()[i].graphGroup = graphGroup;
-        break;
-      }
-    }
-
-    //Now update groups
-    while(st.hasMoreTokens())
+    // First make sure we are not overwriting the graphIndex
+    if (al.getAlignmentAnnotation() != null)
     {
-      group = st.nextToken();
-      for(int i=0; i<al.getAlignmentAnnotation().length; i++)
+      for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
       {
         if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))
         {
+          graphGroup = al.getAlignmentAnnotation()[i].graphGroup + 1;
           al.getAlignmentAnnotation()[i].graphGroup = graphGroup;
           break;
         }
       }
+
+      // Now update groups
+      while (st.hasMoreTokens())
+      {
+        group = st.nextToken();
+        for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
+        {
+          if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))
+          {
+            al.getAlignmentAnnotation()[i].graphGroup = graphGroup;
+            break;
+          }
+        }
+      }
+    }
+    else
+    {
+      System.err
+              .println("Couldn't combine annotations. None are added to alignment yet!");
     }
   }
 
   void addLine(AlignmentI al, StringTokenizer st)
   {
     String group = st.nextToken();
-    AlignmentAnnotation annotation = null;
-
-    for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
+    AlignmentAnnotation annotation = null, alannot[] = al
+            .getAlignmentAnnotation();
+    if (alannot != null)
     {
-      if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))
+      for (int i = 0; i < alannot.length; i++)
       {
-        annotation = al.getAlignmentAnnotation()[i];
-        break;
+        if (alannot[i].label.equalsIgnoreCase(group))
+        {
+          annotation = alannot[i];
+          break;
+        }
       }
     }
-
-    if(annotation==null)
+    if (annotation == null)
+    {
       return;
+    }
     float value = new Float(st.nextToken()).floatValue();
-    String label = st.hasMoreTokens() ?  st.nextToken() : null;
+    String label = st.hasMoreTokens() ? st.nextToken() : null;
     java.awt.Color colour = null;
-    if(st.hasMoreTokens())
+    if (st.hasMoreTokens())
     {
       UserColourScheme ucs = new UserColourScheme(st.nextToken());
       colour = ucs.findColour('A');
@@ -539,11 +1158,39 @@ public class AnnotationFile
   {
     SequenceGroup sg = new SequenceGroup();
     sg.setName(st.nextToken());
-    sg.setStartRes(Integer.parseInt(st.nextToken())-1);
-    sg.setEndRes(Integer.parseInt(st.nextToken())-1);
+    String rng = "";
+    try
+    {
+      rng = st.nextToken();
+      if (rng.length() > 0 && !rng.startsWith("*"))
+      {
+        sg.setStartRes(Integer.parseInt(rng) - 1);
+      }
+      else
+      {
+        sg.setStartRes(0);
+      }
+      rng = st.nextToken();
+      if (rng.length() > 0 && !rng.startsWith("*"))
+      {
+        sg.setEndRes(Integer.parseInt(rng) - 1);
+      }
+      else
+      {
+        sg.setEndRes(al.getWidth() - 1);
+      }
+    } catch (Exception e)
+    {
+      System.err
+              .println("Couldn't parse Group Start or End Field as '*' or a valid column or sequence index: '"
+                      + rng + "' - assuming alignment width for group.");
+      // assume group is full width
+      sg.setStartRes(0);
+      sg.setEndRes(al.getWidth() - 1);
+    }
 
     String index = st.nextToken();
-    if(index.equals("-1"))
+    if (index.equals("-1"))
     {
       while (st.hasMoreElements())
       {
@@ -572,50 +1219,117 @@ public class AnnotationFile
           int end = (Integer.parseInt(st3.nextToken()));
 
           if (end > start)
+          {
             for (int i = start; i <= end; i++)
-              sg.addSequence(al.getSequenceAt(i-1), false);
+            {
+              sg.addSequence(al.getSequenceAt(i - 1), false);
+            }
+          }
         }
         else
         {
-          sg.addSequence(al.getSequenceAt(Integer.parseInt(tmp)-1 ), false);
+          sg.addSequence(al.getSequenceAt(Integer.parseInt(tmp) - 1), false);
         }
       }
     }
 
-    if(refSeq!=null)
+    if (refSeq != null)
     {
-      sg.setStartRes( refSeq.findIndex( sg.getStartRes()+1 )-1 );
-      sg.setEndRes(   refSeq.findIndex( sg.getEndRes() +1) -1 );
+      sg.setStartRes(refSeq.findIndex(sg.getStartRes() + 1) - 1);
+      sg.setEndRes(refSeq.findIndex(sg.getEndRes() + 1) - 1);
+      sg.setSeqrep(refSeq);
     }
 
-    if(sg.getSize()>0)
+    if (sg.getSize() > 0)
     {
       al.addGroup(sg);
-      annotationsHash.put(sg.getName(), sg);
+    }
+  }
+
+  void addRowProperties(AlignmentI al, StringTokenizer st)
+  {
+    String label = st.nextToken(), keyValue, key, value;
+    boolean scaletofit = false, centerlab = false, showalllabs = false;
+    while (st.hasMoreTokens())
+    {
+      keyValue = st.nextToken();
+      key = keyValue.substring(0, keyValue.indexOf("="));
+      value = keyValue.substring(keyValue.indexOf("=") + 1);
+      if (key.equalsIgnoreCase("scaletofit"))
+      {
+        scaletofit = Boolean.valueOf(value).booleanValue();
+      }
+      if (key.equalsIgnoreCase("showalllabs"))
+      {
+        showalllabs = Boolean.valueOf(value).booleanValue();
+      }
+      if (key.equalsIgnoreCase("centrelabs"))
+      {
+        centerlab = Boolean.valueOf(value).booleanValue();
+      }
+      AlignmentAnnotation[] alr = al.getAlignmentAnnotation();
+      if (alr != null)
+      {
+        for (int i = 0; i < alr.length; i++)
+        {
+          if (alr[i].label.equalsIgnoreCase(label))
+          {
+            alr[i].centreColLabels = centerlab;
+            alr[i].scaleColLabel = scaletofit;
+            alr[i].showAllColLabels = showalllabs;
+          }
+        }
+      }
     }
   }
 
   void addProperties(AlignmentI al, StringTokenizer st)
   {
 
-    //So far we have only added groups to the annotationHash,
-    //the idea is in the future properties can be added to
-    //alignments, other annotations etc
-    SequenceGroup sg = (SequenceGroup)annotationsHash.get(st.nextToken());
+    // So far we have only added groups to the annotationHash,
+    // the idea is in the future properties can be added to
+    // alignments, other annotations etc
+    if (al.getGroups() == null)
+    {
+      return;
+    }
+    SequenceGroup sg = null;
 
-    if(sg!=null)
+    String name = st.nextToken();
+
+    Vector groups = al.getGroups();
+    for (int i = 0; i < groups.size(); i++)
+    {
+      sg = (SequenceGroup) groups.elementAt(i);
+      if (sg.getName().equals(name))
+      {
+        break;
+      }
+      else
+      {
+        sg = null;
+      }
+    }
+
+    if (sg != null)
     {
       String keyValue, key, value;
-      while(st.hasMoreTokens())
+      ColourSchemeI def = sg.cs;
+      sg.cs = null;
+      while (st.hasMoreTokens())
       {
         keyValue = st.nextToken();
-        key = keyValue.substring(0,keyValue.indexOf("="));
-        value=keyValue.substring(keyValue.indexOf("=")+1);
+        key = keyValue.substring(0, keyValue.indexOf("="));
+        value = keyValue.substring(keyValue.indexOf("=") + 1);
 
-        if(key.equalsIgnoreCase("description"))
+        if (key.equalsIgnoreCase("description"))
+        {
           sg.setDescription(value);
-        else if(key.equalsIgnoreCase("colour"))
+        }
+        else if (key.equalsIgnoreCase("colour"))
+        {
           sg.cs = ColourSchemeProperty.getColour(al, value);
+        }
         else if (key.equalsIgnoreCase("pidThreshold"))
         {
           sg.cs.setThreshold(Integer.parseInt(value), true);
@@ -625,40 +1339,149 @@ public class AnnotationFile
         {
           sg.cs.setConservationInc(Integer.parseInt(value));
           Conservation c = new Conservation("Group",
-                    ResidueProperties.propHash, 3,
-                    sg.getSequences(null),
-                    sg.getStartRes(),
-                    sg.getEndRes() + 1);
+                  ResidueProperties.propHash, 3, sg.getSequences(null),
+                  sg.getStartRes(), sg.getEndRes() + 1);
 
-            c.calculate();
-            c.verdict(false, 25);
+          c.calculate();
+          c.verdict(false, 25);
 
-            sg.cs.setConservation(c);
+          sg.cs.setConservation(c);
 
         }
         else if (key.equalsIgnoreCase("outlineColour"))
-         {
-           sg.setOutlineColour(new UserColourScheme(value).findColour('A'));
-         }
+        {
+          sg.setOutlineColour(new UserColourScheme(value).findColour('A'));
+        }
         else if (key.equalsIgnoreCase("displayBoxes"))
-         sg.setDisplayBoxes( Boolean.valueOf(value).booleanValue() );
+        {
+          sg.setDisplayBoxes(Boolean.valueOf(value).booleanValue());
+        }
+        else if (key.equalsIgnoreCase("showUnconserved"))
+        {
+          sg.setShowNonconserved(Boolean.valueOf(value).booleanValue());
+        }
         else if (key.equalsIgnoreCase("displayText"))
-         sg.setDisplayText( Boolean.valueOf(value).booleanValue() );
+        {
+          sg.setDisplayText(Boolean.valueOf(value).booleanValue());
+        }
         else if (key.equalsIgnoreCase("colourText"))
-         sg.setColourText( Boolean.valueOf(value).booleanValue() );
+        {
+          sg.setColourText(Boolean.valueOf(value).booleanValue());
+        }
         else if (key.equalsIgnoreCase("textCol1"))
-         {
-           sg.textColour = new UserColourScheme(value).findColour('A');
-         }
+        {
+          sg.textColour = new UserColourScheme(value).findColour('A');
+        }
         else if (key.equalsIgnoreCase("textCol2"))
         {
           sg.textColour2 = new UserColourScheme(value).findColour('A');
         }
         else if (key.equalsIgnoreCase("textColThreshold"))
-         sg.thresholdTextColour = Integer.parseInt(value);
+        {
+          sg.thresholdTextColour = Integer.parseInt(value);
+        }
+        else if (key.equalsIgnoreCase("idColour"))
+        {
+          // consider warning if colour doesn't resolve to a real colour
+          sg.setIdColour((def = new UserColourScheme(value))
+                  .findColour('A'));
+        }
+        else if (key.equalsIgnoreCase("hide"))
+        {
+          // see bug https://mantis.lifesci.dundee.ac.uk/view.php?id=25847
+          sg.setHidereps(true);
+        }
+        else if (key.equalsIgnoreCase("hidecols"))
+        {
+          // see bug https://mantis.lifesci.dundee.ac.uk/view.php?id=25847
+          sg.setHideCols(true);
+        }
+        sg.recalcConservation();
+      }
+      if (sg.cs == null)
+      {
+        sg.cs = def;
+      }
+    }
+  }
 
-       sg.recalcConservation();
+  void setBelowAlignment(AlignmentI al, StringTokenizer st)
+  {
+    String token;
+    AlignmentAnnotation aa, ala[] = al.getAlignmentAnnotation();
+    if (ala == null)
+    {
+      System.err
+              .print("Warning - no annotation to set below for sequence associated annotation:");
+    }
+    while (st.hasMoreTokens())
+    {
+      token = st.nextToken();
+      if (ala == null)
+      {
+        System.err.print(" " + token);
+      }
+      else
+      {
+        for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
+        {
+          aa = al.getAlignmentAnnotation()[i];
+          if (aa.sequenceRef == refSeq && aa.label.equals(token))
+          {
+            aa.belowAlignment = true;
+          }
+        }
       }
     }
+    if (ala == null)
+    {
+      System.err.print("\n");
+    }
+  }
+
+  void addAlignmentDetails(AlignmentI al, StringTokenizer st)
+  {
+    String keyValue, key, value;
+    while (st.hasMoreTokens())
+    {
+      keyValue = st.nextToken();
+      key = keyValue.substring(0, keyValue.indexOf("="));
+      value = keyValue.substring(keyValue.indexOf("=") + 1);
+      al.setProperty(key, value);
+    }
+  }
+
+  /**
+   * Write annotations as a CSV file of the form 'label, value, value, ...' for
+   * each row.
+   * 
+   * @param annotations
+   * @return CSV file as a string.
+   */
+  public String printCSVAnnotations(AlignmentAnnotation[] annotations)
+  {
+    StringBuffer sp = new StringBuffer();
+    for (int i = 0; i < annotations.length; i++)
+    {
+      String atos = annotations[i].toString();
+      int p = 0;
+      do
+      {
+        int cp = atos.indexOf("\n", p);
+        sp.append(annotations[i].label);
+        sp.append(",");
+        if (cp > p)
+        {
+          sp.append(atos.substring(p, cp + 1));
+        }
+        else
+        {
+          sp.append(atos.substring(p));
+          sp.append(newline);
+        }
+        p = cp + 1;
+      } while (p > 0);
+    }
+    return sp.toString();
   }
 }