X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAnnotationFile.java;h=7f71df18f9bb06686b879766426cde6203dd9dec;hb=67b2671b1ded591a6f8eb7f13d319e58f993df77;hp=d9fd871cf31c7332667ddf8525aaa69e334b3a6d;hpb=574045b24991af25bbb25526fbb9abd3b92c3fac;p=jalview.git

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index d9fd871..7f71df1 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 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
@@ -60,13 +60,15 @@ public class AnnotationFile
     public ColumnSelection hiddencols;
 
     public Vector visibleGroups;
-
+    public Hashtable hiddenRepSeqs;
+    
     public ViewDef(String viewname, HiddenSequences hidseqs,
-            ColumnSelection hiddencols)
+            ColumnSelection hiddencols, Hashtable hiddenRepSeqs)
     {
       this.viewname = viewname;
       this.hidseqs = hidseqs;
       this.hiddencols = hiddencols;
+      this.hiddenRepSeqs = hiddenRepSeqs;
     }
   }
 
@@ -259,6 +261,7 @@ public class AnnotationFile
         String key = en.nextElement().toString();
         text.append("\t" + key + "=" + properties.get(key));
       }
+      // TODO: output alignment visualization settings here if required
 
     }
 
@@ -268,12 +271,23 @@ public class AnnotationFile
   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");
@@ -305,7 +319,7 @@ public class AnnotationFile
       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="
@@ -318,14 +332,26 @@ public class AnnotationFile
       }
       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");
 
     }
@@ -413,6 +439,7 @@ 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;
         }
@@ -752,13 +779,33 @@ public class AnnotationFile
 
     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 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"))
@@ -810,6 +857,7 @@ 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)
@@ -891,6 +939,10 @@ 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());
@@ -917,6 +969,16 @@ public class AnnotationFile
           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)