Don't parse input id, leave it as it is

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

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 630dc6c..f933961 100755 (executable)
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -39,7 +39,6 @@ public abstract class AlignFile extends FileParse
     Vector headers;\r
     long start;\r
     long end;\r
-    boolean dbPrefix = false;\r
     boolean jvSuffix = true;\r
 \r
     /**\r
@@ -152,67 +151,31 @@ public abstract class AlignFile extends FileParse
      */\r
     public abstract String print();\r
 \r
-    public void addDBPrefix(boolean b)\r
-    {\r
-      dbPrefix = b;\r
-    }\r
-\r
     public void addJVSuffix(boolean b)\r
     {\r
       jvSuffix = b;\r
     }\r
 \r
     /**\r
-     * A general parser for ids. Will look for dbrefs in\r
-     * Uniprot format source|id\r
-     * And also Jalview /start-end\r
+     * A general parser for ids.\r
      *\r
      * @String id Id to be parsed\r
      */\r
     Sequence parseId(String id)\r
     {\r
-      Sequence seq = new Sequence("","");\r
+      Sequence seq = null;\r
+      id = id.trim();\r
       int space = id.indexOf(" ");\r
       if(space>-1)\r
       {\r
+        seq = new Sequence(id.substring(0, space),"");\r
         seq.setDescription(id.substring(space+1));\r
-        id = id.substring(0, space);\r
       }\r
-\r
-      // Read in any DB refs first\r
-      StringTokenizer st;\r
-      st = new StringTokenizer(id, "|");\r
-\r
-      while (st.countTokens()>2)\r
+      else\r
       {\r
-        seq.addDBRef( new DBRefEntry( st.nextToken(), "0", st.nextToken()));\r
+        seq = new Sequence(id, "");\r
       }\r
 \r
-      if(st.hasMoreTokens())\r
-        id = st.nextToken();\r
-\r
-\r
-      // Remove /start-end from sequence\r
-      if (id.indexOf("/") > 0)\r
-      {\r
-        st = new StringTokenizer(id, "/");\r
-\r
-        if (st.countTokens() == 2)\r
-        {\r
-          id = st.nextToken();\r
-\r
-          String tmp = st.nextToken();\r
-\r
-          st = new StringTokenizer(tmp, "-");\r
-\r
-          if (st.countTokens() == 2)\r
-          {\r
-            seq.setStart( Integer.valueOf(st.nextToken()).intValue() );\r
-            seq.setEnd( Integer.valueOf(st.nextToken()).intValue() );\r
-          }\r
-        }\r
-      }\r
-      seq.setName(id);\r
       return seq;\r
     }\r
 \r
@@ -225,25 +188,7 @@ public abstract class AlignFile extends FileParse
      */\r
     String printId(SequenceI seq)\r
     {\r
-      StringBuffer result = new StringBuffer();\r
-      if(dbPrefix && seq.getDBRef()!=null)\r
-      {\r
-        Vector dbrefs = seq.getDBRef();\r
-        for(int i=0; i<dbrefs.size(); i++)\r
-        {\r
-          DBRefEntry entry = (DBRefEntry)dbrefs.elementAt(i);\r
-          result.append(entry.getSource()+"|"+entry.getAccessionId()+"|");\r
-        }\r
-      }\r
-\r
-      result.append(seq.getName());\r
-\r
-      if(jvSuffix)\r
-      {\r
-        result.append("/"+seq.getStart()+"-"+seq.getEnd());\r
-      }\r
-\r
-      return result.toString();\r
+     return seq.getDisplayId(jvSuffix);\r
     }\r
 \r
 }\r