X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FAnnotationFile.java;h=00b7ead85bde0ac4d6b5c104d33c3752c971904f;hb=96f41aa46d3e568f8734834ab36fdc9ad8e54ac1;hp=ef95458ad161bce16e3f3c2caac44cbc3bbbed7c;hpb=6951479b7dc56bd022ce2c370b7f88b5571004fd;p=jalview.git

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index ef95458..00b7ead 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -1,22 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 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.*;
@@ -29,23 +28,72 @@ import jalview.schemes.*;
 
 public class AnnotationFile
 {
-  StringBuffer text = new StringBuffer(
-      "JALVIEW_ANNOTATION\n"
-      + "# Created: "
-      + new java.util.Date() + "\n\n");
+  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);
+
+  }
+
+  /**
+   * 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 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)
+          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 seqref = null;
+      SequenceI refSeq = null;
 
       StringBuffer colours = new StringBuffer();
       StringBuffer graphLine = new StringBuffer();
-
+      StringBuffer rowprops = new StringBuffer();
       Hashtable graphGroup = new Hashtable();
 
       java.awt.Color color;
@@ -54,53 +102,81 @@ public class AnnotationFile
       {
         row = annotations[i];
 
-        if (!row.visible && row.annotations!=null)
+        if (!row.visible && !row.hasScore())
         {
           continue;
         }
 
         color = null;
+        oneColour = true;
 
         if (row.sequenceRef == null)
         {
-          if (seqref != null)
+          if (refSeq != null)
           {
             text.append("\nSEQUENCE_REF\tALIGNMENT\n");
           }
 
-          seqref = null;
+          refSeq = null;
         }
 
-        else if (seqref == null || seqref != row.sequenceRef)
+        else if (refSeq == null || refSeq != row.sequenceRef)
+        {
+          refSeq = row.sequenceRef;
+          text.append("\nSEQUENCE_REF\t" + refSeq.getName() + "\n");
+        }
+        boolean hasGlyphs = false, hasLabels = false, hasValues = false, 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"
+                            + row.label
+                            + "\t"
+                            + row.getThreshold().value
+                            + "\t"
+                            + row.getThreshold().label
+                            + "\t"
+                            + jalview.util.Format.getHexString(row
+                                    .getThreshold().colour) + "\n");
           }
 
           if (row.graphGroup > -1)
@@ -108,8 +184,7 @@ public class AnnotationFile
             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
             {
@@ -123,11 +198,11 @@ public class AnnotationFile
         {
           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;
           }
@@ -135,40 +210,87 @@ public class AnnotationFile
           if (row.annotations[j] != null)
           {
             comma = "";
-            if (row.annotations[j].secondaryStructure != ' ')
+            if (hasGlyphs && row.annotations[j].secondaryStructure != ' ')
             {
+
               text.append(comma + row.annotations[j].secondaryStructure);
               comma = ",";
             }
-            if (row.annotations[j].displayCharacter!=null
-                && 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 (row.annotations[j] != null)
+            if (hasLabels)
             {
-              color = row.annotations[j].colour;
-              if (row.annotations[j].value != 0f)
+              // 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].value);
+                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].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)
+        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" + 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("\n");
@@ -184,6 +306,7 @@ public class AnnotationFile
           text.append(en.nextElement() + "\n");
         }
       }
+      text.append(rowprops.toString());
     }
 
     if (groups != null)
@@ -191,19 +314,44 @@ public class AnnotationFile
       printGroups(groups);
     }
 
+    if (properties != null)
+    {
+      text.append("\n\nALIGNMENT");
+      Enumeration en = properties.keys();
+      while (en.hasMoreElements())
+      {
+        String key = en.nextElement().toString();
+        text.append("\t" + key + "=" + 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");
+      if (!sg.hasSeqrep())
+      {
+        text.append("SEQUENCE_GROUP\t" + sg.getName() + "\t"
+                + (sg.getStartRes() + 1) + "\t" + (sg.getEndRes() + 1)
+                + "\t" + "-1\t");
+        seqrep = null;
+      }
+      else
+      {
+        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");
@@ -217,8 +365,8 @@ public class AnnotationFile
       }
       if (sg.cs != null)
       {
-        text.append("colour=" + ColourSchemeProperty.getColourName(sg.cs) +
-                    "\t");
+        text.append("colour=" + ColourSchemeProperty.getColourName(sg.cs)
+                + "\t");
         if (sg.cs.getThreshold() != 0)
         {
           text.append("pidThreshold=" + sg.cs.getThreshold());
@@ -228,38 +376,57 @@ public class AnnotationFile
           text.append("consThreshold=" + sg.cs.getConservationInc() + "\t");
         }
       }
-      text.append("outlineColour=" +
-                  jalview.util.Format.getHexString(sg.getOutlineColour()) +
-                  "\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");
-
+      text.append("showUnconserved=" + sg.getShowunconserved() + "\t");
       if (sg.textColour != java.awt.Color.black)
       {
-        text.append("textCol1=" +
-                    jalview.util.Format.getHexString(sg.textColour) + "\t");
+        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");
+        text.append("textCol2="
+                + jalview.util.Format.getHexString(sg.textColour2) + "\t");
       }
       if (sg.thresholdTextColour != 0)
       {
-        text.append("textColThreshold=" + sg.thresholdTextColour);
+        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;
-  public boolean readAnnotationFile(AlignmentI al,
-                                    String file,
-                                    String protocol)
+
+  String refSeqId = null;
+
+  public boolean readAnnotationFile(AlignmentI al, String file,
+          String protocol)
   {
     try
     {
@@ -303,7 +470,7 @@ 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)
         {
@@ -323,11 +490,11 @@ public class AnnotationFile
         return false;
       }
 
-      while ( (line = in.readLine()) != null)
+      while ((line = in.readLine()) != null)
       {
         if (line.indexOf("#") == 0
-            || line.indexOf("JALVIEW_ANNOTATION") > -1
-            || line.length() == 0)
+                || line.indexOf("JALVIEW_ANNOTATION") > -1
+                || line.length() == 0)
         {
           continue;
         }
@@ -336,6 +503,7 @@ public class AnnotationFile
         token = st.nextToken();
         if (token.equalsIgnoreCase("COLOUR"))
         {
+          // TODO: use graduated colour def'n here too
           colourAnnotations(al, st.nextToken(), st.nextToken());
           continue;
         }
@@ -345,7 +513,11 @@ public class AnnotationFile
           combineAnnotations(al, st);
           continue;
         }
-
+        else if (token.equalsIgnoreCase("ROWPROPERTIES"))
+        {
+          addRowProperties(al, st);
+          continue;
+        }
         else if (token.equalsIgnoreCase("GRAPHLINE"))
         {
           addLine(al, st);
@@ -354,23 +526,33 @@ public class AnnotationFile
 
         else if (token.equalsIgnoreCase("SEQUENCE_REF"))
         {
-          refSeq = al.findName(st.nextToken());
-          try
+          if (st.hasMoreTokens())
           {
-            refSeqIndex = Integer.parseInt(st.nextToken());
-            if (refSeqIndex < 1)
+            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 ;
+          continue;
         }
 
         else if (token.equalsIgnoreCase("SEQUENCE_GROUP"))
@@ -385,68 +567,120 @@ public class AnnotationFile
           continue;
         }
 
-        graphStyle = AlignmentAnnotation.getGraphValueFromString(token);
-        label = st.nextToken();
-
-        if (st.countTokens() > 1)
+        else if (token.equalsIgnoreCase("BELOW_ALIGNMENT"))
         {
-          description = st.nextToken();
+          setBelowAlignment(al, st);
+          continue;
         }
-        else
+        else if (token.equalsIgnoreCase("ALIGNMENT"))
         {
-          description = null;
+          addAlignmentDetails(al, st);
+          continue;
         }
 
-        line = st.nextToken();
-
-        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);
+        annotation = new AlignmentAnnotation(label, description,
+                (index == 0) ? null : annotations, 0, 0, graphStyle);
+
+        annotation.score = score;
 
         if (refSeq != null)
         {
-          annotation.createSequenceMapping(refSeq, refSeqIndex, false);
-          annotation.adjustForAlignment();
-          refSeq.addAlignmentAnnotation(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);
+            // 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);
         }
-
-        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);
@@ -455,36 +689,66 @@ public class AnnotationFile
     return 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;
+    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)
       {
         try
         {
-          displayChar = token;
+          displayChar = token; 
+          // foo
           value = new Float(token).floatValue();
           parsedValue = true;
           continue;
+        } catch (NumberFormatException ex)
+        {
         }
-        catch (NumberFormatException ex)
-        {}
       }
 
-      if (token.equals("H") || token.equals("E"))
+      if (hasSymbols && (token.equals("H") || token.equals("E")))
       {
         // Either this character represents a helix or sheet
         // or an integer which can be displayed
@@ -500,20 +764,28 @@ public class AnnotationFile
       }
 
     }
-
-    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 && 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);
+
+    anot.colour = colour;
 
-    return new Annotation(displayChar, desc, ss, value);
+    return anot;
   }
 
   void colourAnnotations(AlignmentI al, String label, String colour)
@@ -540,7 +812,7 @@ public class AnnotationFile
   {
     int graphGroup = -1;
     String group = st.nextToken();
-    //First make sure we are not overwriting the graphIndex
+    // 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))
@@ -551,7 +823,7 @@ public class AnnotationFile
       }
     }
 
-    //Now update groups
+    // Now update groups
     while (st.hasMoreTokens())
     {
       group = st.nextToken();
@@ -600,8 +872,36 @@ 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"))
@@ -642,7 +942,9 @@ public class AnnotationFile
         }
         else
         {
-          sg.addSequence(al.getSequenceAt(Integer.parseInt(tmp) - 1), false);
+          sg
+                  .addSequence(al.getSequenceAt(Integer.parseInt(tmp) - 1),
+                          false);
         }
       }
     }
@@ -651,6 +953,7 @@ public class AnnotationFile
     {
       sg.setStartRes(refSeq.findIndex(sg.getStartRes() + 1) - 1);
       sg.setEndRes(refSeq.findIndex(sg.getEndRes() + 1) - 1);
+      sg.setSeqrep(refSeq);
     }
 
     if (sg.getSize() > 0)
@@ -659,12 +962,41 @@ public class AnnotationFile
     }
   }
 
+  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
+    // 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;
@@ -690,6 +1022,8 @@ public class AnnotationFile
     if (sg != null)
     {
       String keyValue, key, value;
+      ColourSchemeI def = sg.cs;
+      sg.cs = null;
       while (st.hasMoreTokens())
       {
         keyValue = st.nextToken();
@@ -713,10 +1047,8 @@ 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);
@@ -732,6 +1064,10 @@ public class AnnotationFile
         {
           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());
@@ -752,9 +1088,92 @@ public class AnnotationFile
         {
           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();
   }
 }