X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAnnotationFile.java;h=288ce2fc0a14df4d30c7f285e800bf4146d6b604;hb=f683f4d6c8af43be0ffeb96513b52572619efed5;hp=2291f390ca0c509e85ac1891a0b5de97697d1fcc;hpb=75836e49226d034ba50dfec18ab75f8bf4f0b242;p=jalview.git

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 2291f39..288ce2f 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 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
@@ -20,150 +20,310 @@
 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
 {
-
-  public String printAnnotations(AlignmentAnnotation [] annotations)
-  {
-    StringBuffer text = new StringBuffer(
+  StringBuffer text = new StringBuffer(
       "JALVIEW_ANNOTATION\n"
-      +"# Created: "
-      +new java.util.Date()+"\n\n");
-
-    AlignmentAnnotation row;
-    String comma;
-    SequenceI seqref = null;
+      + "# 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);
 
-    StringBuffer colours = new StringBuffer();
-    StringBuffer graphLine = new StringBuffer();
+  }
+  /**
+   * 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 ViewDef(String viewname, HiddenSequences hidseqs,
+            ColumnSelection hiddencols)
+    {
+      this.viewname = viewname;
+      this.hidseqs = hidseqs;
+      this.hiddencols = hiddencols;
+    }
+  }
+  public String printAnnotations(AlignmentAnnotation[] annotations,
+          Vector groups,
+          Hashtable properties, ViewDef[] views)
+  {
+    if (annotations != null)
+    {
+      boolean oneColour = true;
+      AlignmentAnnotation row;
+      String comma;
+      SequenceI refSeq = null;
 
-    Hashtable graphGroup = new Hashtable();
+      StringBuffer colours = new StringBuffer();
+      StringBuffer graphLine = new StringBuffer();
 
-    java.awt.Color color;
+      Hashtable graphGroup = new Hashtable();
 
-    for(int i=0; i<annotations.length; i++)
-    {
-      row = annotations[i];
+      java.awt.Color color;
 
-      if(!row.visible)
-        continue;
+      for (int i = 0; i < annotations.length; i++)
+      {
+        row = annotations[i];
 
-      color = null;
+        if (!row.visible && !row.hasScore())
+        {
+          continue;
+        }
 
-      if( row.sequenceRef == null)
-      {
-        if(seqref!=null)
-          text.append("\nSEQUENCE_REF\tALIGNMENT\n");
+        color = null;
+        oneColour = true;
 
-        seqref = null;
-      }
+        if (row.sequenceRef == null)
+        {
+          if (refSeq != null)
+          {
+            text.append("\nSEQUENCE_REF\tALIGNMENT\n");
+          }
 
-      else if (seqref == null || seqref != row.sequenceRef)
-      {
-        seqref = row.sequenceRef;
-        text.append("\nSEQUENCE_REF\t" + seqref.getName() + "\n");
-      }
+          refSeq = null;
+        }
 
+        else if (refSeq == null || refSeq != row.sequenceRef)
+        {
+          refSeq = row.sequenceRef;
+          text.append("\nSEQUENCE_REF\t" + refSeq.getName() + "\n");
+        }
 
-      if( row.graph == AlignmentAnnotation.NO_GRAPH)
-      {
+        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");
+        }
+        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)
+          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"
+                                 row.getThreshold().colour) + "\n"
                 );
+          }
 
-          if(row.graphGroup>-1)
+          if (row.graphGroup > -1)
           {
             String key = String.valueOf(row.graphGroup);
-            if(graphGroup.containsKey(key))
+            if (graphGroup.containsKey(key))
+            {
               graphGroup.put(key, graphGroup.get(key)
-                             +"\t"+row.label);
+                             + "\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++)
-      {
-        if (seqref != null && jalview.util.Comparison.isGap(seqref.getCharAt(j)))
-          continue;
+        text.append(row.label + "\t");
+        if (row.description != null)
+        {
+          text.append(row.description + "\t");
+        }
 
-        if(row.annotations[j]!=null)
+        for (int j = 0; row.annotations!=null && j < row.annotations.length; j++)
         {
-          comma = "";
-          if (row.annotations[j].secondaryStructure!=' ')
+          if (refSeq != null &&
+              jalview.util.Comparison.isGap(refSeq.getCharAt(j)))
           {
-            text.append(comma + row.annotations[j].secondaryStructure);
-            comma = ",";
+            continue;
           }
-          if (row.annotations[j].displayCharacter.length() > 0
-                  && !row.annotations[j].displayCharacter.equals(" "))
+
+          if (row.annotations[j] != null)
+          {
+            comma = "";
+            if (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(" "))
+            {
+              text.append(comma + row.annotations[j].displayCharacter);
+              comma = ",";
+            }
+
+            if (row.annotations[j] != null)
+            {
+              if(color!=null && !color.equals(row.annotations[j].colour))
               {
-                text.append(comma + row.annotations[j].displayCharacter);
-                comma = ",";
+                oneColour = false;
               }
 
-          if (row.annotations[j]!=null)
-          {
-            color = row.annotations[j].colour;
-            if (row.annotations[j].value!=0f)
-              text.append(comma + row.annotations[j].value);
+              color = row.annotations[j].colour;
+              if (row.annotations[j].value != 0f && row.annotations[j].value!=Float.NaN) 
+              {
+                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)+"]");
+            }
           }
+          text.append("|");
         }
-        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");
+        }
+
       }
 
       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("\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();
+      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));
       }
-    }
 
+    }
+    
     return text.toString();
   }
 
+  public void printGroups(Vector sequenceGroups)
+  {
+    SequenceGroup sg;
+    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++)
+      {
+        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())
+        {
+          text.append("consThreshold=" + sg.cs.getConservationInc() + "\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");
+
+      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);
+      }
+      if (sg.idColour!=null)
+      {
+        text.append("idColour="+jalview.util.Format.getHexString(sg.idColour)+"\t");
+      }
+
+      text.append("\n\n");
+
+    }
+  }
+
+  SequenceI refSeq = null;
+  String refSeqId = null;
   public boolean readAnnotationFile(AlignmentI al,
                                     String file,
                                     String protocol)
@@ -180,7 +340,7 @@ 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));
       }
@@ -191,15 +351,16 @@ public class AnnotationFile
         {
           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();
 
@@ -211,8 +372,10 @@ public class AnnotationFile
       boolean jvAnnotationFile = false;
       while ( (line = in.readLine()) != null)
       {
-        if (line.indexOf("#") == 0 )
+        if (line.indexOf("#") == 0)
+        {
           continue;
+        }
 
         if (line.indexOf("JALVIEW_ANNOTATION") > -1)
         {
@@ -221,7 +384,7 @@ public class AnnotationFile
         }
       }
 
-      if(!jvAnnotationFile)
+      if (!jvAnnotationFile)
       {
         in.close();
         return false;
@@ -229,108 +392,190 @@ public class AnnotationFile
 
       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"))
         {
           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("GRAPHLINE"))
         {
           addLine(al, st);
           continue;
         }
 
-
-        if(token.equalsIgnoreCase("SEQUENCE_REF") )
+        else if (token.equalsIgnoreCase("SEQUENCE_REF"))
         {
-          refSeq = al.findName(st.nextToken());
-          try{
+          if (st.hasMoreTokens())
+          {
+            refSeq = al.findName(refSeqId=st.nextToken());
+          if (refSeq==null)
+          {
+            refSeqId=null;
+          }
+          try
+          {
             refSeqIndex = Integer.parseInt(st.nextToken());
-            if(refSeqIndex<1)
+            if (refSeqIndex < 1)
             {
               refSeqIndex = 1;
-              System.out.println("WARNING: SEQUENCE_REF index must be > 0 in AnnotationFile");
+              System.out.println(
+                  "WARNING: SEQUENCE_REF index must be > 0 in AnnotationFile");
             }
           }
-          catch(Exception ex)
+          catch (Exception ex)
           {
             refSeqIndex = 1;
           }
+          } else {
+            refSeq = null;
+            refSeqId = null;
+          }
+          continue ;
+        }
 
+        else if (token.equalsIgnoreCase("SEQUENCE_GROUP"))
+        {
+          addGroup(al, st);
           continue;
         }
 
+        else if (token.equalsIgnoreCase("PROPERTIES"))
+        {
+          addProperties(al, st);
+          continue;
+        }
+
+        else if( token.equalsIgnoreCase("BELOW_ALIGNMENT"))
+        {
+          setBelowAlignment(al, st);
+          continue;
+        }
+        else if( token.equalsIgnoreCase("ALIGNMENT"))
+        {
+          addAlignmentDetails(al, st);
+          continue;
+        }
 
         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);
+              emptyColumn = false;
+            }
           }
-        }
 
-       annotation = new AlignmentAnnotation(label,
-                                          description,
-                                          annotations,
-                                          0,
-                                          0,
-                                          graphStyle);
+        }
 
-       if(refSeq!=null)
-       {
-         annotation.createSequenceMapping(refSeq, refSeqIndex, false);
-         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;
+          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(refSeq, refSeqIndex, false);
+            annotation.adjustForAlignment();
+            refSeq.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 && (refSeq=al.findName(refSeq, 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;
@@ -338,67 +583,103 @@ public class AnnotationFile
 
   Annotation parseAnnotation(String string)
   {
-    String desc = null, displayChar="";
+    String desc = null, displayChar = null;
     char ss = ' '; // secondaryStructure
     float value = 0;
     boolean parsedValue = 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));
+
+      string = string.substring(0,i)+string.substring(j+1);
+    }
+
     StringTokenizer st = new StringTokenizer(string, ",");
     String token;
-    while(st.hasMoreTokens())
+    while (st.hasMoreTokens())
     {
       token = st.nextToken().trim();
-      if(token.length()==0)
+      if (token.length() == 0)
+      {
         continue;
+      }
 
-      if(!parsedValue)
+      if (!parsedValue)
       {
-        try{
+        try
+        {
           displayChar = token;
           value = new Float(token).floatValue();
           parsedValue = true;
           continue;
-        }catch(NumberFormatException ex){}
+        }
+        catch (NumberFormatException ex)
+        {}
       }
 
-      if(token.equals("H") || token.equals("E"))
+      if (token.equals("H") || token.equals("E"))
       {
         // 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)
+      {
         desc = token;
+      }
 
     }
 
-    if(desc == null)
-      desc = value+"";
-
-    if(displayChar.length()>1 && desc.length()==1)
+    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)
+          if (annotations[j] != null)
+          {
             annotations[j].colour = ucs.findColour('A');
+          }
         }
       }
     }
@@ -409,21 +690,21 @@ 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++)
+    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())
+    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))
         {
@@ -448,18 +729,252 @@ 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');
     }
 
     annotation.setThreshold(new GraphLine(value, label, colour));
+  }
+
+  void addGroup(AlignmentI al, StringTokenizer st)
+  {
+    SequenceGroup sg = new SequenceGroup();
+    sg.setName(st.nextToken());
+    sg.setStartRes(Integer.parseInt(st.nextToken()) - 1);
+    sg.setEndRes(Integer.parseInt(st.nextToken()) - 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);
+    }
+
+    if (sg.getSize() > 0)
+    {
+      al.addGroup(sg);
+    }
+  }
+
+  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("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'));
+        }
+        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();
   }
 }