From d70d7e5bc8da1189f44709b6ec59ea1e23f6f557 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 29 Jan 2007 17:39:59 +0000
Subject: [PATCH] SequenceGroup parsing added to annotation file

---
 src/jalview/io/AnnotationFile.java |  131 ++++++++++++++++++++++++++++++++++--
 1 file changed, 126 insertions(+), 5 deletions(-)

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 2291f39..a7c67cd 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -22,8 +22,8 @@ package jalview.io;
 import java.io.*;
 import jalview.datamodel.*;
 import java.util.*;
-import jalview.schemes.UserColourScheme;
 import java.net.URL;
+import jalview.schemes.*;
 
 
 public class AnnotationFile
@@ -164,6 +164,9 @@ public class AnnotationFile
     return text.toString();
   }
 
+
+  SequenceI refSeq = null;
+  Hashtable annotationsHash = new Hashtable();
   public boolean readAnnotationFile(AlignmentI al,
                                     String file,
                                     String protocol)
@@ -195,7 +198,6 @@ public class AnnotationFile
 
       String line, label, description, token;
       int graphStyle, index;
-      SequenceI refSeq = null;
       int refSeqIndex = 1;
       int existingAnnotations = 0;
       if(al.getAlignmentAnnotation()!=null)
@@ -242,20 +244,20 @@ public class AnnotationFile
           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{
@@ -274,6 +276,18 @@ public class AnnotationFile
           continue;
         }
 
+        else if(token.equalsIgnoreCase("SEQUENCE_GROUP"))
+        {
+          addGroup(al, st);
+          continue;
+        }
+
+        else if(token.equalsIgnoreCase("PROPERTIES"))
+        {
+          addProperties(al, st);
+          continue;
+        }
+
 
         graphStyle = AlignmentAnnotation.getGraphValueFromString(token);
         label = st.nextToken();
@@ -460,6 +474,113 @@ 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 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 );
+    }
+
+
+    al.addGroup(sg);
+    annotationsHash.put(sg.getName(), 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
+    SequenceGroup sg = (SequenceGroup)annotationsHash.get(st.nextToken());
+
+    if(sg!=null)
+    {
+      String keyValue, key, value;
+      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), false);//
+        else if (key.equalsIgnoreCase("outlineColour"))
+         {
+           sg.setOutlineColour(new UserColourScheme(value).findColour('A'));
+         }
+
+         //Boolean.valueOf(string).booleanValue();
+        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);
+
+      }
+    }
   }
 }
-- 
1.7.10.2