getSelectionAsNewSequence added

[jalview.git] / src / jalview / io / FeaturesFile.java

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