From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 3 Feb 2006 17:46:11 +0000 (+0000)
Subject: Many changes
X-Git-Tag: Root_VamJalview_2_07b+~172
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=3cf306f55e6e186f60de89f3e800c1cbc366be46;p=jalview.git

Many changes
---

diff --git a/src/jalview/io/AnnotationReader.java b/src/jalview/io/AnnotationReader.java
index 5ba1e26..9c6dc49 100755
--- a/src/jalview/io/AnnotationReader.java
+++ b/src/jalview/io/AnnotationReader.java
@@ -4,89 +4,34 @@ import java.io.*;
 import jalview.datamodel.*;
 import java.util.StringTokenizer;
 import jalview.schemes.UserColourScheme;
-import jalview.gui.FeatureRenderer;
+import java.net.URL;
 
 public class AnnotationReader
 {
-  public boolean readGroupsFile(FeatureRenderer fr, AlignmentI al, String file)
+  public boolean readAnnotationFile(AlignmentI al, String file)
   {
+
     try
     {
-      BufferedReader in = new BufferedReader(new FileReader(file));
-      SequenceI seq = null;
-      String line, type, desc, token;
 
-      int index, start, end;
-      StringTokenizer st;
-      SequenceFeature sf;
-      int lineNo = 0;
-      while ( (line = in.readLine()) != null)
+      BufferedReader in = null;
+      try{
+        URL url = new URL(file);
+        in = new BufferedReader(new InputStreamReader(url.openStream()));
+      }
+      catch(java.net.MalformedURLException ex)
       {
-        lineNo++;
-        st = new StringTokenizer(line, "\t");
-        if (st.countTokens() == 2)
-        {
-          type = st.nextToken();
-          UserColourScheme ucs = new UserColourScheme(st.nextToken());
-          fr.setColour(type, ucs.findColour("A"));
-          continue;
-        }
-
-        while (st.hasMoreElements())
-        {
-          desc = st.nextToken();
-          token = st.nextToken();
-          if (!token.equals("ID_NOT_SPECIFIED"))
-          {
-            index = al.findIndex(al.findName(token));
-            st.nextToken();
-          }
-          else
-          {
-            index = Integer.parseInt(st.nextToken());
-          }
-
-          start = Integer.parseInt(st.nextToken());
-          end = Integer.parseInt(st.nextToken());
-
-          seq = al.getSequenceAt(index);
-          start = seq.findIndex(start) - 1;
-          end = seq.findIndex(end) - 1;
-
-          type = st.nextToken();
-
-          if (fr.getColour(type) == null)
-          {
-            // Probably the old style groups file
-            UserColourScheme ucs = new UserColourScheme(type);
-            fr.setColour(type, ucs.findColour("A"));
-          }
-
-          sf = new SequenceFeature(type, desc, "", start, end);
-
-          seq.getDatasetSequence().addSequenceFeature(sf);
-        }
+        in = new BufferedReader(new FileReader(file));
       }
-    }
-    catch (Exception ex)
-    {
-      System.out.println("Error parsing groups file: " + ex);
-      return false;
-    }
 
-    return true;
-  }
 
-  public boolean readAnnotationFile(AlignmentI al, String file)
-  {
-    try
-    {
-      BufferedReader in = new BufferedReader(new FileReader(file));
       String line, label, description, token;
       int graphStyle, index;
       SequenceI refSeq = null;
-      int refSeqIndex = -1;
-
+      int refSeqIndex = 0;
+      int existingAnnotations = 0;
+      if(al.getAlignmentAnnotation()!=null)
+       existingAnnotations = al.getAlignmentAnnotation().length;
 
       StringTokenizer st;
       Annotation[] annotations;
@@ -146,7 +91,7 @@ public class AnnotationReader
           try{
             refSeqIndex = Integer.parseInt(st.nextToken());
           }
-          catch(NumberFormatException ex)
+          catch(Exception ex)
           {
             refSeqIndex = 0;
           }
@@ -159,8 +104,8 @@ public class AnnotationReader
 
         line = st.nextToken();
         st = new StringTokenizer(line, "|", true);
-        annotations = new Annotation[st.countTokens()];
-        index = 0;
+        annotations = new Annotation[st.countTokens()+refSeqIndex];
+        index = refSeqIndex;
         boolean emptyColumn = true;
         while (st.hasMoreElements())
         {
@@ -187,12 +132,17 @@ public class AnnotationReader
                                           0,
                                           graphStyle);
 
-       al.addAnnotation(annotation, refSeq, refSeqIndex);
-
+       annotation = al.addAnnotation(annotation, refSeq);
+       al.setAnnotationIndex(annotation,  al.getAlignmentAnnotation().length - existingAnnotations-1);
       }
+
+       al.adjustSequenceAnnotations();
+
+
     }catch(Exception ex)
-    {ex.printStackTrace();
-    //  System.out.println("Problem reading annotation file: "+ex);
+    {
+      ex.printStackTrace();
+      System.out.println("Problem reading annotation file: "+ex);
       return false;
     }
     return true;
@@ -213,7 +163,7 @@ public class AnnotationReader
 
       if(value==0)
       {  try{
-          value = Float.parseFloat(token);
+          value =  new Float(token).floatValue();
         }catch(NumberFormatException ex){}
       }
 
@@ -303,8 +253,7 @@ public class AnnotationReader
 
     if(annotation==null)
       return;
-
-    float value = Float.parseFloat(st.nextToken());
+    float value = new Float(st.nextToken()).floatValue();
     String label = st.hasMoreTokens() ?  st.nextToken() : null;
     java.awt.Color colour = null;
     if(st.hasMoreTokens())