X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAnnotationReader.java;h=cd7abfdf62b67fa32cfeb636477a5270cbd83ce2;hb=69e9cd54dcfd25dd3067f353bc53eb6b4d7e27af;hp=5ba1e266706813ff7691d30904969bfb20f1ef11;hpb=e9d286eaa2ec9b85d1d2634ba53401fa65cf21bc;p=jalview.git

diff --git a/src/jalview/io/AnnotationReader.java b/src/jalview/io/AnnotationReader.java
index 5ba1e26..cd7abfd 100755
--- a/src/jalview/io/AnnotationReader.java
+++ b/src/jalview/io/AnnotationReader.java
@@ -4,89 +4,43 @@ 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;
+      java.io.InputStream is = getClass().getResourceAsStream("/" + file);
+      if (is != null)
       {
-        lineNo++;
-        st = new StringTokenizer(line, "\t");
-        if (st.countTokens() == 2)
+        in = new BufferedReader(new java.io.InputStreamReader(is));
+      }
+      else
+      {
+        try
         {
-          type = st.nextToken();
-          UserColourScheme ucs = new UserColourScheme(st.nextToken());
-          fr.setColour(type, ucs.findColour("A"));
-          continue;
+          URL url = new URL(file);
+          in = new BufferedReader(new InputStreamReader(url.openStream()));
         }
-
-        while (st.hasMoreElements())
+        catch (java.net.MalformedURLException ex)
         {
-          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 = 1;
+      int existingAnnotations = 0;
+      if(al.getAlignmentAnnotation()!=null)
+       existingAnnotations = al.getAlignmentAnnotation().length;
 
+      int alWidth = al.getWidth();
 
       StringTokenizer st;
       Annotation[] annotations;
@@ -146,30 +100,34 @@ public class AnnotationReader
           try{
             refSeqIndex = Integer.parseInt(st.nextToken());
           }
-          catch(NumberFormatException ex)
+          catch(Exception ex)
           {
-            refSeqIndex = 0;
+            refSeqIndex = 1;
           }
 
           continue;
         }
 
+
         graphStyle = AlignmentAnnotation.getGraphValueFromString(token);
         label = description = st.nextToken();
 
         line = st.nextToken();
+
         st = new StringTokenizer(line, "|", true);
-        annotations = new Annotation[st.countTokens()];
+        annotations = new Annotation[alWidth];
+
         index = 0;
         boolean emptyColumn = true;
-        while (st.hasMoreElements())
+
+
+        while (st.hasMoreElements() && index<alWidth)
         {
           token = st.nextToken().trim();
-
           if(token.equals("|"))
           {
             if(emptyColumn)
-              annotations[index++] = parseAnnotation("");
+              index++;
 
             emptyColumn = true;
           }
@@ -187,12 +145,21 @@ public class AnnotationReader
                                           0,
                                           graphStyle);
 
-       al.addAnnotation(annotation, refSeq, refSeqIndex);
+       if(refSeq!=null)
+       {
+         annotation.createSequenceMapping(refSeq, refSeqIndex);
+         refSeq.addAlignmentAnnotation(annotation);
+       }
 
+       al.addAnnotation(annotation);
+
+       al.setAnnotationIndex(annotation,  al.getAlignmentAnnotation().length - existingAnnotations-1);
       }
+
     }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;
@@ -203,6 +170,7 @@ public class AnnotationReader
     String desc = "", displayChar="";
     char ss = ' '; // secondaryStructure
     float value = 0;
+    boolean parsedValue = false;
     StringTokenizer st = new StringTokenizer(string, ",");
     String token;
     while(st.hasMoreTokens())
@@ -211,29 +179,24 @@ public class AnnotationReader
       if(token.length()==0)
         continue;
 
-      if(value==0)
-      {  try{
-          value = Float.parseFloat(token);
+      if(!parsedValue)
+      {
+        try{
+          value = new Float(token).floatValue();
+          displayChar = token;
+          parsedValue = true;
         }catch(NumberFormatException ex){}
       }
 
-      if(token.length()==1)
+      if(token.equals("H") || token.equals("E"))
       {
         // Either this character represents a helix or sheet
         // or an integer which can be displayed
-        if(token.equals("H") || token.equals("E"))
-        {
-          ss = token.charAt(0);
-        }
-        else //if(value!=0)
-        {
-          displayChar = token;
-        }
+        ss = token.charAt(0);
       }
       else if(desc.length()<1)
         desc = token;
-      else
-        displayChar = token;
+
     }
 
     return new Annotation(displayChar, desc, ss, value);
@@ -303,8 +266,7 @@ 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())
@@ -313,7 +275,7 @@ public class AnnotationReader
       colour = ucs.findColour("A");
     }
 
-    annotation.addGraphLine(new GraphLine(value, label, colour));
+    annotation.setThreshold(new GraphLine(value, label, colour));
 
   }
 }