1.1 enabled

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

diff --git a/src/jalview/io/BLCFile.java b/src/jalview/io/BLCFile.java
index 0edcb63..04867a2 100755 (executable)
--- a/src/jalview/io/BLCFile.java
+++ b/src/jalview/io/BLCFile.java
@@ -1,6 +1,6 @@
 /*\r
 * Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
 *\r
 * This program is free software; you can redistribute it and/or\r
 * modify it under the terms of the GNU General Public License\r
@@ -42,15 +42,6 @@ public class BLCFile extends AlignFile
     {\r
     }\r
 \r
-    /**\r
-     * Creates a new BLCFile object.\r
-     *\r
-     * @param inStr DOCUMENT ME!\r
-     */\r
-    public BLCFile(String inStr)\r
-    {\r
-        super(inStr);\r
-    }\r
 \r
     /**\r
      * Creates a new BLCFile object.\r
@@ -77,18 +68,13 @@ 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
         StringBuffer[] seqstrings;\r
-        Vector starts = new Vector();\r
-        Vector ends = new Vector();\r
 \r
         String line = null;\r
 \r
-        try\r
-        {\r
             do\r
             {\r
                 line = nextLine();\r
@@ -105,68 +91,18 @@ 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("1");\r
-                            ends.addElement("-1");\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("1");\r
-                            ends.addElement("-1");\r
-                        }\r
-                    }\r
+                  line = line.substring(abracket+1);\r
+\r
+                  Sequence seq = parseId(line);\r
+                  seqs.addElement(seq);\r
                 }\r
             }\r
             while (!idsFound);\r
 \r
             int starCol = line.indexOf("*");\r
-            seqstrings = new StringBuffer[ids.size()];\r
+            seqstrings = new StringBuffer[seqs.size()];\r
 \r
-            for (int i = 0; i < ids.size(); i++)\r
+            for (int i = 0; i < seqs.size(); i++)\r
             {\r
                 if (seqstrings[i] == null)\r
                 {\r
@@ -176,7 +112,7 @@ public class BLCFile extends AlignFile
 \r
             while ((line = nextLine()).indexOf("*") == -1)\r
             {\r
-                for (int i = 0; i < ids.size(); i++)\r
+                for (int i = 0; i < seqs.size(); i++)\r
                 {\r
                     if (line.length() > (i + starCol))\r
                     {\r
@@ -185,19 +121,20 @@ public class BLCFile extends AlignFile
                 }\r
             }\r
 \r
-            for (int i = 0; i < ids.size(); i++)\r
+            for (int i = 0; i < seqs.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
-                seqs.addElement(newSeq);\r
+              Sequence newSeq = (Sequence) seqs.elementAt(i);\r
+\r
+              if (!isValidProteinSequence(newSeq.getSequence()))\r
+              {\r
+                throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS\r
+                               +" : "+ newSeq.getName()\r
+                               +" : "+invalidCharacter);\r
+              }\r
+\r
+              newSeq.setSequence(seqstrings[i].toString());\r
             }\r
-        }\r
-        catch (Exception ex)\r
-        {\r
-            ex.printStackTrace();\r
-        }\r
+\r
     }\r
 \r
     /**\r
@@ -217,21 +154,30 @@ 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]));\r
+            if(s[i].getDescription()!=null)\r
+              out.append(" "+s[i].getDescription());\r
+\r
+            out.append("\n");\r
 \r
-            if (s[i].getSequence().length() > max)\r
+            if (s[i].getSequence().length > max)\r
             {\r
-                max = s[i].getSequence().length();\r
+                max = s[i].getSequence().length;\r
             }\r
 \r
             i++;\r
@@ -245,9 +191,9 @@ public class BLCFile extends AlignFile
 \r
             while ((i < s.length) && (s[i] != null))\r
             {\r
-                if (s[i].getSequence().length() > j)\r
+                if (s[i].getSequence().length > j)\r
                 {\r
-                    out.append(s[i].getSequence().substring(j, j + 1));\r
+                    out.append(s[i].getSequenceAsString(j, j + 1));\r
                 }\r
                 else\r
                 {\r