vamsasDemo new branch

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

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index d22dc12..630dc6c 100755 (executable)
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -39,6 +39,8 @@ 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
      * Creates a new AlignFile object.\r
@@ -149,4 +151,99 @@ public abstract class AlignFile extends FileParse
      * Print out in alignment file format the Sequences in the seqs Vector.\r
      */\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
+     *\r
+     * @String id Id to be parsed\r
+     */\r
+    Sequence parseId(String id)\r
+    {\r
+      Sequence seq = new Sequence("","");\r
+      int space = id.indexOf(" ");\r
+      if(space>-1)\r
+      {\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
+      {\r
+        seq.addDBRef( new DBRefEntry( st.nextToken(), "0", st.nextToken()));\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
+    /**\r
+     * Creates the output id.\r
+     * Adds prefix Uniprot format source|id\r
+     * And suffix Jalview /start-end\r
+     *\r
+     * @String id Id to be parsed\r
+     */\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
+    }\r
+\r
 }\r