X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAnnotationFile.java;h=ce1afc274bf08f745c6fabf3882aa7ff8ec8279f;hb=1660a4fe03b8dda74b008ae4de2d804f8044a463;hp=d004c1af0dfb429f97414e3a878d053a4bbaaf62;hpb=7dfbf441b22406f0575cd7db2a9cf351648a7838;p=jalview.git

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index d004c1a..ce1afc2 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -1,184 +1,466 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 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
  */
-
 package jalview.io;
 
 import java.io.*;
-import jalview.datamodel.*;
+import java.net.*;
 import java.util.*;
-import jalview.schemes.UserColourScheme;
-import java.net.URL;
 
+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");
+
+  /**
+   * 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);
+
+  }
 
-  public String printAnnotations(AlignmentAnnotation [] annotations)
+  /**
+   * hold all the information about a particular view definition read from or
+   * written out in an annotations file.
+   */
+  public class ViewDef
   {
-    StringBuffer text = new StringBuffer(
-      "JALVIEW_ANNOTATION\n"
-      +"# Created: "
-      +new java.util.Date()+"\n\n");
+    public String viewname;
 
-    AlignmentAnnotation row;
-    String comma;
-    String seqref = null;
+    public HiddenSequences hidseqs;
 
-    StringBuffer colours = new StringBuffer();
-    StringBuffer graphLine = new StringBuffer();
+    public ColumnSelection hiddencols;
 
-    Hashtable graphGroup = new Hashtable();
+    public Vector visibleGroups;
 
-    java.awt.Color color;
+    public Hashtable hiddenRepSeqs;
 
-    for(int i=0; i<annotations.length; i++)
+    public ViewDef(String viewname, HiddenSequences hidseqs,
+            ColumnSelection hiddencols, Hashtable hiddenRepSeqs)
     {
-      row = annotations[i];
-      color = null;
+      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)
+  {
+    // 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 refSeq = null;
 
-      if( row.sequenceRef == null)
-        seqref = null;
+      StringBuffer colours = new StringBuffer();
+      StringBuffer graphLine = new StringBuffer();
+      StringBuffer rowprops = new StringBuffer();
+      Hashtable graphGroup = new Hashtable();
 
-      else if (seqref == null
-           || !seqref.equals(row.sequenceRef.getName()))
+      java.awt.Color color;
+
+      for (int i = 0; i < annotations.length; i++)
       {
-        seqref = row.sequenceRef.getName();
-        text.append("\nSEQUENCE_REF\t" + seqref + "\n");
-      }
+        row = annotations[i];
+
+        if (!row.visible && !row.hasScore())
+        {
+          continue;
+        }
 
+        color = null;
+        oneColour = true;
 
-      if( row.graph == AlignmentAnnotation.NO_GRAPH)
-      {
+        if (row.sequenceRef == null)
+        {
+          if (refSeq != null)
+          {
+            text.append("\nSEQUENCE_REF\tALIGNMENT\n");
+          }
+
+          refSeq = null;
+        }
+
+        else if (refSeq == null || refSeq != row.sequenceRef)
+        {
+          refSeq = row.sequenceRef;
+          text.append("\nSEQUENCE_REF\t" + refSeq.getName() + "\n");
+        }
+        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++)
+        {
+          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");
-      }
-      else
-      {
-        if( row.graph == AlignmentAnnotation.BAR_GRAPH)
-          text.append("BAR_GRAPH\t");
-        else if(row.graph == AlignmentAnnotation.LINE_GRAPH)
-          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"
-                );
-
-          if(row.graphGroup>-1)
+          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");
+          }
+
+          if (row.graphGroup > -1)
           {
             String key = String.valueOf(row.graphGroup);
-            if(graphGroup.containsKey(key))
-              graphGroup.put(key, graphGroup.get(key)
-                             +"\t"+row.label);
+            if (graphGroup.containsKey(key))
+            {
+              graphGroup.put(key, graphGroup.get(key) + "\t" + row.label);
+            }
             else
+            {
               graphGroup.put(key, row.label);
+            }
           }
-      }
-
-      text.append(row.label+"\t");
+        }
 
-      for(int j=0; j<row.annotations.length; j++)
-      {
-        if(row.annotations[j]!=null)
+        text.append(row.label + "\t");
+        if (row.description != null)
         {
-          comma = "";
-          if (row.annotations[j].displayCharacter.length() > 0
-              && !row.annotations[j].displayCharacter.equals(" "))
-          {
-            text.append(row.annotations[j].displayCharacter);
-            comma = ",";
-          }
-          if (row.annotations[j].secondaryStructure!=' ')
+          text.append(row.description + "\t");
+        }
+        for (int j = 0; row.annotations != null
+                && j < row.annotations.length; j++)
+        {
+          if (refSeq != null
+                  && jalview.util.Comparison.isGap(refSeq.getCharAt(j)))
           {
-            text.append(comma + row.annotations[j].secondaryStructure);
-            comma = ",";
+            continue;
           }
-          if (row.annotations[j].value!=0f)
+
+          if (row.annotations[j] != null)
           {
+            comma = "";
+            if (row.annotations[j].secondaryStructure != ' ') // could be also hasGlyphs || ... 
+            {
+
+              text.append(comma + row.annotations[j].secondaryStructure);
+              comma = ",";
+            }
+            if (hasValues)
+            {
+              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;
-            text.append(comma + row.annotations[j].value);
+
+            if (row.annotations[j].colour != null
+                    && row.annotations[j].colour != java.awt.Color.black)
+            {
+              text.append(comma
+                      + "["
+                      + jalview.util.Format
+                              .getHexString(row.annotations[j].colour)
+                      + "]");
+              comma = ",";
+            }
           }
+          text.append("|");
+        }
+
+        if (row.hasScore())
+          text.append("\t" + row.score);
+
+        text.append("\n");
+
+        if (color != null && color != java.awt.Color.black && oneColour)
+        {
+          colours.append("COLOUR\t" + row.label + "\t"
+                  + jalview.util.Format.getHexString(color) + "\n");
+        }
+        if (row.scaleColLabel || row.showAllColLabels || row.centreColLabels)
+        {
+          rowprops.append("ROWPROPERTIES\t"+row.label);
+          rowprops.append("\tscaletofit="+row.scaleColLabel);
+          rowprops.append("\tshowalllabs="+row.showAllColLabels);
+          rowprops.append("\tcentrelabs="+row.centreColLabels);
+          rowprops.append("\n");
         }
-        text.append("|");
       }
 
       text.append("\n");
 
-      if(color!=null && color!=java.awt.Color.black)
+      text.append(colours.toString());
+      text.append(graphLine.toString());
+      if (graphGroup.size() > 0)
       {
-        colours.append("COLOUR\t"
-                       +row.label+"\t"
-                       +jalview.util.Format.getHexString(color)+"\n");
+        text.append("COMBINE\t");
+        Enumeration en = graphGroup.elements();
+        while (en.hasMoreElements())
+        {
+          text.append(en.nextElement() + "\n");
+        }
       }
-
+      text.append(rowprops.toString());
     }
 
-    text.append("\n");
+    if (groups != null)
+    {
+      printGroups(groups);
+    }
 
-    text.append(colours.toString());
-    text.append(graphLine.toString());
-    if(graphGroup.size()>0)
+    if (properties != null)
     {
-      text.append("COMBINE\t");
-      Enumeration en = graphGroup.elements();
-      while(en.hasMoreElements())
+      text.append("\n\nALIGNMENT");
+      Enumeration en = properties.keys();
+      while (en.hasMoreElements())
       {
-        text.append(en.nextElement()+"\n");
+        String key = en.nextElement().toString();
+        text.append("\t" + key + "=" + properties.get(key));
       }
+      // TODO: output alignment visualization settings here if required
+
     }
 
     return text.toString();
   }
 
-  public boolean readAnnotationFile(AlignmentI al, String file)
+  public void printGroups(Vector sequenceGroups)
   {
-    try
+    SequenceGroup sg;
+    SequenceI seqrep = null;
+    for (int i = 0; i < sequenceGroups.size(); i++)
     {
-      BufferedReader in = null;
-      java.io.InputStream is = getClass().getResourceAsStream("/" + file);
-      if (is != null)
+      sg = (SequenceGroup) sequenceGroups.elementAt(i);
+      if (!sg.hasSeqrep())
       {
-        in = new BufferedReader(new java.io.InputStreamReader(is));
+        text.append("SEQUENCE_GROUP\t" + sg.getName() + "\t"
+                + (sg.getStartRes() + 1) + "\t" + (sg.getEndRes() + 1)
+                + "\t" + "-1\t");
+        seqrep = null;
       }
       else
       {
-        try
+        seqrep = sg.getSeqrep();
+        text.append("SEQUENCE_REF\t" + seqrep.getName() + "\n");
+        text.append("SEQUENCE_GROUP\t" + sg.getName() + "\t"
+                + (seqrep.findPosition(sg.getStartRes())) + "\t"
+                + (seqrep.findPosition(sg.getEndRes())) + "\t" + "-1\t");
+      }
+      for (int s = 0; s < sg.getSize(); s++)
+      {
+        text.append(sg.getSequenceAt(s).getName() + "\t");
+      }
+
+      text.append("\nPROPERTIES\t" + sg.getName() + "\t");
+
+      if (sg.getDescription() != null)
+      {
+        text.append("description=" + sg.getDescription() + "\t");
+      }
+      if (sg.cs != null)
+      {
+        text.append("colour=" + ColourSchemeProperty.getColourName(sg.cs)
+                + "\t");
+        if (sg.cs.getThreshold() != 0)
+        {
+          text.append("pidThreshold=" + sg.cs.getThreshold());
+        }
+        if (sg.cs.conservationApplied())
         {
-          URL url = new URL(file);
-          in = new BufferedReader(new InputStreamReader(url.openStream()));
+          text.append("consThreshold=" + sg.cs.getConservationInc() + "\t");
         }
-        catch (java.net.MalformedURLException ex)
+      }
+      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");
+      text.append("showUnconserved=" + sg.getShowunconserved() + "\t");
+      if (sg.textColour != java.awt.Color.black)
+      {
+        text.append("textCol1="
+                + jalview.util.Format.getHexString(sg.textColour) + "\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 + "\t");
+      }
+      if (sg.idColour != null)
+      {
+        text.append("idColour="
+                + jalview.util.Format.getHexString(sg.idColour) + "\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("\nSEQUENCE_REF");
+      }
+      text.append("\n\n");
+
+    }
+  }
+
+  SequenceI refSeq = null;
+
+  String refSeqId = null;
+
+  public boolean readAnnotationFile(AlignmentI al, String file,
+          String protocol)
+  {
+    try
+    {
+      BufferedReader in = null;
+      if (protocol.equals(AppletFormatAdapter.FILE))
+      {
+        in = new BufferedReader(new FileReader(file));
+      }
+      else if (protocol.equals(AppletFormatAdapter.URL))
+      {
+        URL url = new URL(file);
+        in = new BufferedReader(new InputStreamReader(url.openStream()));
+      }
+      else if (protocol.equals(AppletFormatAdapter.PASTE))
+      {
+        in = new BufferedReader(new StringReader(file));
+      }
+      else if (protocol.equals(AppletFormatAdapter.CLASSLOADER))
+      {
+        java.io.InputStream is = getClass().getResourceAsStream("/" + file);
+        if (is != null)
         {
-          in = new BufferedReader(new FileReader(file));
+          in = new BufferedReader(new java.io.InputStreamReader(is));
         }
       }
 
       String line, label, description, token;
       int graphStyle, index;
-      SequenceI refSeq = null;
       int refSeqIndex = 1;
       int existingAnnotations = 0;
-      if(al.getAlignmentAnnotation()!=null)
-       existingAnnotations = al.getAlignmentAnnotation().length;
+      if (al.getAlignmentAnnotation() != null)
+      {
+        existingAnnotations = al.getAlignmentAnnotation().length;
+      }
 
       int alWidth = al.getWidth();
 
@@ -188,10 +470,12 @@ 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)
         {
@@ -200,163 +484,325 @@ 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());
           continue;
         }
 
-        if(token.equalsIgnoreCase("COMBINE") )
+        else if (token.equalsIgnoreCase("COMBINE"))
         {
           combineAnnotations(al, st);
           continue;
         }
-
-        if (token.equalsIgnoreCase("GRAPHLINE"))
+        else if (token.equalsIgnoreCase("ROWPROPERTIES"))
+        {
+          addRowProperties(al, st);
+          continue;
+        }
+        else if (token.equalsIgnoreCase("GRAPHLINE"))
         {
           addLine(al, st);
           continue;
         }
 
-
-        if(token.equalsIgnoreCase("SEQUENCE_REF") )
+        else if (token.equalsIgnoreCase("SEQUENCE_REF"))
         {
-          refSeq = al.findName(st.nextToken());
-          try{
-            refSeqIndex = Integer.parseInt(st.nextToken());
+          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;
+            }
           }
-          catch(Exception ex)
+          else
           {
-            refSeqIndex = 1;
+            refSeq = null;
+            refSeqId = null;
           }
-
           continue;
         }
 
+        else if (token.equalsIgnoreCase("SEQUENCE_GROUP"))
+        {
+          addGroup(al, st);
+          continue;
+        }
 
-        graphStyle = AlignmentAnnotation.getGraphValueFromString(token);
-        label = description = st.nextToken();
+        else if (token.equalsIgnoreCase("PROPERTIES"))
+        {
+          addProperties(al, st);
+          continue;
+        }
 
-        line = st.nextToken();
+        else if (token.equalsIgnoreCase("BELOW_ALIGNMENT"))
+        {
+          setBelowAlignment(al, st);
+          continue;
+        }
+        else if (token.equalsIgnoreCase("ALIGNMENT"))
+        {
+          addAlignmentDetails(al, st);
+          continue;
+        }
 
-        st = new StringTokenizer(line, "|", true);
-        annotations = new Annotation[alWidth];
+        graphStyle = AlignmentAnnotation.getGraphValueFromString(token);
+        label = st.nextToken();
 
         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);
+        }
 
-       if(refSeq!=null)
-       {
-         annotation.createSequenceMapping(refSeq, refSeqIndex);
-         refSeq.addAlignmentAnnotation(annotation);
-       }
+        annotation = new AlignmentAnnotation(label, description,
+                (index == 0) ? null : annotations, 0, 0, graphStyle);
 
-       al.addAnnotation(annotation);
+        annotation.score = score;
 
-       al.setAnnotationIndex(annotation,  al.getAlignmentAnnotation().length - existingAnnotations-1);
+        if (refSeq != null)
+        {
+          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);
+            // and recover our virgin copy to use again if necessary.
+            annotation = ann;
+
+          } while (refSeqId != null
+                  && (referedSeq = al.findName(referedSeq, refSeqId, true)) != null);
+        }
+        else
+        {
+          al.addAnnotation(annotation);
+          al.setAnnotationIndex(annotation,
+                  al.getAlignmentAnnotation().length - existingAnnotations
+                          - 1);
+        }
       }
 
-    }catch(Exception ex)
+    } catch (Exception ex)
     {
       ex.printStackTrace();
-      System.out.println("Problem reading annotation file: "+ex);
+      System.out.println("Problem reading annotation file: " + ex);
       return false;
     }
     return true;
   }
 
-  Annotation parseAnnotation(String string)
+  Annotation parseAnnotation(String string, int graphStyle)
   {
-    String desc = "", 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;
+    while (st.hasMoreTokens())
     {
       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{
-          displayChar = token;
+        try
+        {
+          displayChar = token; 
+          // foo
           value = new Float(token).floatValue();
           parsedValue = true;
-        }catch(NumberFormatException ex){}
+          continue;
+        } catch (NumberFormatException ex)
+        {
+        }
       }
 
-      if(token.equals("H") || token.equals("E"))
+      if (hasSymbols && (token.equals("H") || token.equals("E") || 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.length()<1)
+      else if (desc == null)
+      {
         desc = token;
+      }
 
     }
+//    if (!dcset && string.charAt(string.length() - 1) == ',')
+//    {
+//      displayChar = " "; // empty display char symbol.
+//    }
+    if (displayChar != null && displayChar.length() > 1 && desc != null
+            && desc.length() == 1)
+    {
+      String tmp = displayChar;
+      displayChar = desc;
+      desc = tmp;
+    }
+    /*
+     * In principle, this code will ensure that the Annotation element generated
+     * is renderable by any of the applet or application rendering code but
+     * instead we check for null strings when the display character is rendered.
+     * if (displayChar==null) { displayChar=""; }
+     */
+    Annotation anot = new Annotation(displayChar, desc, ss, value);
 
-    return new Annotation(displayChar, desc, ss, value);
+    anot.colour = colour;
+
+    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)
-            annotations[j].colour = ucs.findColour("A");
+          if (annotations[j] != null)
+          {
+            annotations[j].colour = ucs.findColour('A');
+          }
         }
       }
     }
@@ -366,22 +812,22 @@ 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++)
+    // 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))
+      if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))
       {
-        graphGroup = al.getAlignmentAnnotation()[i].graphGroup +1;
+        graphGroup = al.getAlignmentAnnotation()[i].graphGroup + 1;
         al.getAlignmentAnnotation()[i].graphGroup = graphGroup;
         break;
       }
     }
 
-    //Now update groups
-    while(st.hasMoreTokens())
+    // Now update groups
+    while (st.hasMoreTokens())
     {
       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))
         {
@@ -406,18 +852,328 @@ public class AnnotationFile
       }
     }
 
-    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");
+      colour = ucs.findColour('A');
     }
 
     annotation.setThreshold(new GraphLine(value, label, colour));
+  }
 
+  void addGroup(AlignmentI al, StringTokenizer st)
+  {
+    SequenceGroup sg = new SequenceGroup();
+    sg.setName(st.nextToken());
+    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"))
+    {
+      while (st.hasMoreElements())
+      {
+        sg.addSequence(al.findName(st.nextToken()), false);
+      }
+    }
+    else
+    {
+      StringTokenizer st2 = new StringTokenizer(index, ",");
+
+      while (st2.hasMoreTokens())
+      {
+        String tmp = st2.nextToken();
+        if (tmp.equals("*"))
+        {
+          for (int i = 0; i < al.getHeight(); i++)
+          {
+            sg.addSequence(al.getSequenceAt(i), false);
+          }
+        }
+        else if (tmp.indexOf("-") >= 0)
+        {
+          StringTokenizer st3 = new StringTokenizer(tmp, "-");
+
+          int start = (Integer.parseInt(st3.nextToken()));
+          int end = (Integer.parseInt(st3.nextToken()));
+
+          if (end > start)
+          {
+            for (int i = start; i <= end; i++)
+            {
+              sg.addSequence(al.getSequenceAt(i - 1), false);
+            }
+          }
+        }
+        else
+        {
+          sg
+                  .addSequence(al.getSequenceAt(Integer.parseInt(tmp) - 1),
+                          false);
+        }
+      }
+    }
+
+    if (refSeq != null)
+    {
+      sg.setStartRes(refSeq.findIndex(sg.getStartRes() + 1) - 1);
+      sg.setEndRes(refSeq.findIndex(sg.getEndRes() + 1) - 1);
+      sg.setSeqrep(refSeq);
+    }
+
+    if (sg.getSize() > 0)
+    {
+      al.addGroup(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(); 
+        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
+    if (al.getGroups() == null)
+    {
+      return;
+    }
+    SequenceGroup 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;
+      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);
+
+        if (key.equalsIgnoreCase("description"))
+        {
+          sg.setDescription(value);
+        }
+        else if (key.equalsIgnoreCase("colour"))
+        {
+          sg.cs = ColourSchemeProperty.getColour(al, value);
+        }
+        else if (key.equalsIgnoreCase("pidThreshold"))
+        {
+          sg.cs.setThreshold(Integer.parseInt(value), true);
+
+        }
+        else if (key.equalsIgnoreCase("consThreshold"))
+        {
+          sg.cs.setConservationInc(Integer.parseInt(value));
+          Conservation c = new Conservation("Group",
+                  ResidueProperties.propHash, 3, sg.getSequences(null), sg
+                          .getStartRes(), sg.getEndRes() + 1);
+
+          c.calculate();
+          c.verdict(false, 25);
+
+          sg.cs.setConservation(c);
+
+        }
+        else if (key.equalsIgnoreCase("outlineColour"))
+        {
+          sg.setOutlineColour(new UserColourScheme(value).findColour('A'));
+        }
+        else if (key.equalsIgnoreCase("displayBoxes"))
+        {
+          sg.setDisplayBoxes(Boolean.valueOf(value).booleanValue());
+        }
+        else if (key.equalsIgnoreCase("showUnconserved"))
+        {
+          sg.setShowunconserved(Boolean.valueOf(value).booleanValue());
+        }
+        else if (key.equalsIgnoreCase("displayText"))
+        {
+          sg.setDisplayText(Boolean.valueOf(value).booleanValue());
+        }
+        else if (key.equalsIgnoreCase("colourText"))
+        {
+          sg.setColourText(Boolean.valueOf(value).booleanValue());
+        }
+        else if (key.equalsIgnoreCase("textCol1"))
+        {
+          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);
+        }
+        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;
+      }
+    }
+  }
+
+  void setBelowAlignment(AlignmentI al, StringTokenizer st)
+  {
+    String token;
+    AlignmentAnnotation aa;
+    while (st.hasMoreTokens())
+    {
+      token = st.nextToken();
+      for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
+      {
+        aa = al.getAlignmentAnnotation()[i];
+        if (aa.sequenceRef == refSeq && aa.label.equals(token))
+        {
+          aa.belowAlignment = true;
+        }
+      }
+    }
+  }
+
+  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("\n");
+        }
+        p = cp + 1;
+      } while (p > 0);
+    }
+    return sp.toString();
   }
 }