P1 changed to N1

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

diff --git a/src/jalview/io/BLCFile.java b/src/jalview/io/BLCFile.java
index 074e6ce..56d40f9 100755 (executable)
--- a/src/jalview/io/BLCFile.java
+++ b/src/jalview/io/BLCFile.java
@@ -77,7 +77,7 @@ public class BLCFile extends AlignFile
     /**\r
      * DOCUMENT ME!\r
      */\r
-    public void parse()\r
+    public void parse() throws IOException\r
     {\r
         boolean idsFound = false;\r
         Vector ids = new Vector();\r
@@ -87,8 +87,6 @@ public class BLCFile extends AlignFile
 \r
         String line = null;\r
 \r
-        try\r
-        {\r
             do\r
             {\r
                 line = nextLine();\r
@@ -105,60 +103,19 @@ public class BLCFile extends AlignFile
 \r
                 if (abracket > -1)\r
                 {\r
-                    if (line.indexOf(" ") > -1) //\r
-                    {\r
-                        ///Colur it be this format?\r
-                        //>54402046         0             1   137   137:\r
-                        // or this??\r
-                        //     1   >L1H14       30539  343\r
-                        try\r
-                        {\r
-                            ids.addElement(line.substring(abracket + 1,\r
-                                    line.indexOf(" ", abracket + 1)));\r
-\r
-                            // remove p Value\r
-                            line = line.substring(abracket + 1);\r
-                            line = line.substring(line.indexOf(" ") + 1);\r
-                            line = line.trim();\r
-                            line = line.substring(line.indexOf(" ") + 1);\r
-                            line = line.trim();\r
-\r
-                            int value = Integer.parseInt(line.substring(0,\r
-                                        line.indexOf(" ")));\r
-                            starts.addElement(value + "");\r
-                            line = line.substring(line.indexOf(" ") + 1);\r
-                            line = line.trim();\r
-                            value = Integer.parseInt(line.substring(0,\r
-                                        line.indexOf(" ")));\r
-                            ends.addElement(value + "");\r
-                        }\r
-                        catch (Exception ex)\r
-                        {\r
-                            System.err.println("Error during blockfile read.");\r
-                            ex.printStackTrace();\r
-                            starts.addElement("0");\r
-                            ends.addElement("0");\r
-                        }\r
-                    }\r
-                    else\r
-                    {\r
-                        if (line.indexOf("/") > -1)\r
-                        {\r
-                            ids.addElement(line.substring(abracket + 1,\r
-                                    line.indexOf("/")));\r
-                            line = line.substring(line.indexOf("/") + 1);\r
-                            starts.addElement(line.substring(0,\r
-                                    line.indexOf("-")));\r
-                            ends.addElement(line.substring(line.indexOf("-") +\r
-                                    1));\r
-                        }\r
-                        else\r
-                        {\r
-                            ids.addElement(line.substring(abracket + 1));\r
-                            starts.addElement("0");\r
-                            ends.addElement("0");\r
-                        }\r
-                    }\r
+                  if (line.indexOf(" ") > -1) //\r
+                  {\r
+                    line = line.substring(abracket + 1,\r
+                                          line.indexOf(" ", abracket + 1));\r
+                  }\r
+                  else\r
+                    line = line.substring(abracket+1);\r
+\r
+\r
+                  Sequence seq = parseId(line);\r
+                  ids.addElement(seq.getName());\r
+                  starts.addElement(seq.getStart() + "");\r
+                  ends.addElement(seq.getEnd() + "");\r
                 }\r
             }\r
             while (!idsFound);\r
@@ -187,17 +144,23 @@ public class BLCFile extends AlignFile
 \r
             for (int i = 0; i < ids.size(); i++)\r
             {\r
-                Sequence newSeq = new Sequence(ids.elementAt(i).toString(),\r
-                        seqstrings[i].toString(),\r
-                        Integer.parseInt(starts.elementAt(i).toString()),\r
-                        Integer.parseInt(ends.elementAt(i).toString()));\r
+              Sequence newSeq = new Sequence(ids.elementAt(i).toString(),\r
+                                             seqstrings[i].toString(),\r
+                                             Integer.parseInt(starts.elementAt(i).\r
+                                                              toString()),\r
+                                             Integer.parseInt(ends.elementAt(i).toString()));\r
+\r
+              if (!isValidProteinSequence(newSeq.getSequence()))\r
+              {\r
+                throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS\r
+                               +" : "+ newSeq.getName()\r
+                               +" : "+invalidCharacter);\r
+\r
+              }\r
+\r
                 seqs.addElement(newSeq);\r
             }\r
-        }\r
-        catch (Exception ex)\r
-        {\r
-            ex.printStackTrace();\r
-        }\r
+\r
     }\r
 \r
     /**\r
@@ -217,17 +180,22 @@ public class BLCFile extends AlignFile
      *\r
      * @return DOCUMENT ME!\r
      */\r
-    public static String print(SequenceI[] s)\r
+    public String print(SequenceI[] s)\r
     {\r
         StringBuffer out = new StringBuffer();\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
         int i = 0;\r
         int max = -1;\r
 \r
         while ((i < s.length) && (s[i] != null))\r
         {\r
-            out.append(">" + s[i].getName() + "/" + s[i].getStart() + "-" +\r
-                s[i].getEnd() + "\n");\r
+            out.append(">" + printId(s[i]) +"\n");\r
 \r
             if (s[i].getSequence().length() > max)\r
             {\r