X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFeaturesFile.java;h=b3d434efe6565676531f46294a63014243f1d128;hb=4f24ef0848cf3c43ba0467f31fce1baa5c57aad5;hp=a83dff8665787cf6bd93546f4624f5068b48904b;hpb=9922c9eec14599f6b141a8db8a3859cab7227ce0;p=jalview.git

diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index a83dff8..b3d434e 100755
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -65,12 +65,29 @@ public class FeaturesFile extends AlignFile
     }
 
     /**
-     * DOCUMENT ME!
+     * The Application can render HTML, but the applet will
+     * remove HTML tags and replace links with %LINK%
+     * Both need to read links in HTML however
+     *
+     * @throws IOException DOCUMENT ME!
+     */
+    public boolean parse(AlignmentI align,
+                         Hashtable colours,
+                         boolean removeHTML)
+    {
+      return parse(align, colours, null, removeHTML);
+    }
+    /**
+     * The Application can render HTML, but the applet will
+     * remove HTML tags and replace links with %LINK%
+     * Both need to read links in HTML however
      *
      * @throws IOException DOCUMENT ME!
      */
-    public boolean parse(AlignmentI align,  Hashtable colours)
-        throws IOException
+    public boolean parse(AlignmentI align,
+                         Hashtable colours,
+                         Hashtable featureLink,
+                         boolean removeHTML)
     {
       String line = null;
       try
@@ -82,7 +99,8 @@ public class FeaturesFile extends AlignFile
         float score;
         StringTokenizer st;
         SequenceFeature sf;
-        String featureGroup = null;
+        String featureGroup = null, groupLink = null;
+        Hashtable typeLink = new Hashtable();
 
         boolean GFFFile = true;
 
@@ -99,6 +117,11 @@ public class FeaturesFile extends AlignFile
             if (type.equalsIgnoreCase("startgroup"))
             {
               featureGroup = st.nextToken();
+              if (st.hasMoreElements())
+              {
+                groupLink = st.nextToken();
+                featureLink.put(featureGroup, groupLink);
+              }
             }
             else if (type.equalsIgnoreCase("endgroup"))
             {
@@ -106,11 +129,21 @@ public class FeaturesFile extends AlignFile
               //but at present theres no way of showing more than 1 group
               st.nextToken();
               featureGroup = null;
+              groupLink = null;
             }
             else
             {
               UserColourScheme ucs = new UserColourScheme(st.nextToken());
               colours.put(type, ucs.findColour("A"));
+              if (st.hasMoreElements())
+              {
+                String link = st.nextToken();
+                typeLink.put(type, link);
+                if(featureLink==null)
+                  featureLink = new Hashtable();
+                featureLink.put(type, link);
+              }
+
             }
             continue;
           }
@@ -132,7 +165,7 @@ public class FeaturesFile extends AlignFile
                 end = Integer.parseInt(st.nextToken());
                 try
                 {
-                  score = Float.parseFloat(st.nextToken());
+                  score =  new Float(st.nextToken()).floatValue();
                 }
                 catch (NumberFormatException ex)
                 {
@@ -201,7 +234,20 @@ public class FeaturesFile extends AlignFile
 
             sf = new SequenceFeature(type, desc, "", start, end, featureGroup);
 
-            seq.getDatasetSequence().addSequenceFeature(sf);
+            seq.addSequenceFeature(sf);
+
+            if(groupLink!=null && removeHTML)
+            {
+              sf.addLink(groupLink);
+              sf.description += "%LINK%";
+            }
+            if(typeLink.containsKey(type) && removeHTML)
+            {
+              sf.addLink(typeLink.get(type).toString());
+              sf.description += "%LINK%";
+            }
+
+            parseDescriptionHTML(sf, removeHTML);
 
             //If we got here, its not a GFFFile
             GFFFile = false;
@@ -212,14 +258,40 @@ public class FeaturesFile extends AlignFile
       {
         System.out.println(line);
         ex.printStackTrace();
-        System.out.println("Error parsing groups file: " + ex +"\n"+line);
+        System.out.println("Error parsing feature file: " + ex +"\n"+line);
         return false;
       }
 
       return true;
-
     }
 
+    void parseDescriptionHTML(SequenceFeature sf, boolean removeHTML)
+    {
+      StringBuffer sb = new StringBuffer();
+      StringTokenizer st = new StringTokenizer(sf.getDescription(), "<");
+      String token,  link;
+      while(st.hasMoreElements())
+      {
+        token = st.nextToken("<>");
+        if(token.equalsIgnoreCase("html") || token.startsWith("/"))
+          continue;
+
+        if(token.startsWith("a href="))
+        {
+          link = token.substring(token.indexOf("\"")+1, token.length()-1);
+          String label = st.nextToken("<>");
+          sf.addLink(label+"|"+link);
+          sb.append(label+"%LINK%");
+        }
+        else if(token.equalsIgnoreCase("br"))
+          sb.append("\n");
+        else
+          sb.append(token);
+      }
+
+      if(removeHTML)
+        sf.description = sb.toString();
+  }
 
     /**
      * DOCUMENT ME!
@@ -278,12 +350,15 @@ public class FeaturesFile extends AlignFile
 
         do
         {
-          if (groups.size() > 0)
+
+
+          if (groups.size() > 0 && groupIndex < groups.size())
           {
             group = groups.elementAt(groupIndex).toString();
             out.append("\nSTARTGROUP\t" + group + "\n");
           }
-
+          else
+            group = null;
 
           for (int i = 0; i < seqs.length; i++)
           {
@@ -295,7 +370,13 @@ public class FeaturesFile extends AlignFile
                 if (!visible.containsKey(next[j].type))
                   continue;
 
-                if (group != null && !next[j].featureGroup.equals(group))
+                if (group != null
+                    && (next[j].featureGroup==null
+                        || !next[j].featureGroup.equals(group))
+                  )
+                  continue;
+
+                if(group==null && next[j].featureGroup!=null)
                   continue;
 
                 if(next[j].description==null || next[j].description.equals(""))
@@ -312,14 +393,16 @@ public class FeaturesFile extends AlignFile
             }
           }
 
-          if(groups.size()>0)
+          if(group!=null)
           {
             out.append("ENDGROUP\t"+group+"\n");
+            groupIndex++;
           }
+          else
+            break;
 
-          groupIndex++;
         }
-        while(groupIndex < groups.size());
+        while(groupIndex < groups.size()+1);
 
 
       return out.toString();