X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FBLCFile.java;h=624e134a0632d2a0f8f8e8c91df1726af590c707;hb=3d9d1f6c1c1da3b2657f9ebb95430d0bc8dde873;hp=ceeac648b12964b1f95944155d17f63cfe101e18;hpb=174230b4233d9ce80f94527768d2cd2f76da11ab;p=jalview.git

diff --git a/src/jalview/io/BLCFile.java b/src/jalview/io/BLCFile.java
index ceeac64..624e134 100755
--- a/src/jalview/io/BLCFile.java
+++ b/src/jalview/io/BLCFile.java
@@ -71,10 +71,7 @@ public class BLCFile extends AlignFile
     public void parse() throws IOException
     {
         boolean idsFound = false;
-        Vector ids = new Vector();
         StringBuffer[] seqstrings;
-        Vector starts = new Vector();
-        Vector ends = new Vector();
 
         String line = null;
 
@@ -94,27 +91,18 @@ public class BLCFile extends AlignFile
 
                 if (abracket > -1)
                 {
-                  if (line.indexOf(" ") > -1) //
-                  {
-                    line = line.substring(abracket + 1,
-                                          line.indexOf(" ", abracket + 1));
-                  }
-                  else
-                    line = line.substring(abracket+1);
-
+                  line = line.substring(abracket+1);
 
                   Sequence seq = parseId(line);
-                  ids.addElement(seq.getName());
-                  starts.addElement(seq.getStart() + "");
-                  ends.addElement(seq.getEnd() + "");
+                  seqs.addElement(seq);
                 }
             }
             while (!idsFound);
 
             int starCol = line.indexOf("*");
-            seqstrings = new StringBuffer[ids.size()];
+            seqstrings = new StringBuffer[seqs.size()];
 
-            for (int i = 0; i < ids.size(); i++)
+            for (int i = 0; i < seqs.size(); i++)
             {
                 if (seqstrings[i] == null)
                 {
@@ -124,7 +112,7 @@ public class BLCFile extends AlignFile
 
             while ((line = nextLine()).indexOf("*") == -1)
             {
-                for (int i = 0; i < ids.size(); i++)
+                for (int i = 0; i < seqs.size(); i++)
                 {
                     if (line.length() > (i + starCol))
                     {
@@ -133,23 +121,11 @@ public class BLCFile extends AlignFile
                 }
             }
 
-            for (int i = 0; i < ids.size(); i++)
+            for (int i = 0; i < seqs.size(); i++)
             {
-              Sequence newSeq = new Sequence(ids.elementAt(i).toString(),
-                                             seqstrings[i].toString(),
-                                             Integer.parseInt(starts.elementAt(i).
-                                                              toString()),
-                                             Integer.parseInt(ends.elementAt(i).toString()));
-
-              if (!isValidProteinSequence(newSeq.getSequence()))
-              {
-                throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS
-                               +" : "+ newSeq.getName()
-                               +" : "+invalidCharacter);
-
-              }
+              Sequence newSeq = (Sequence) seqs.elementAt(i);
 
-                seqs.addElement(newSeq);
+              newSeq.setSequence(seqstrings[i].toString());
             }
 
     }
@@ -186,11 +162,15 @@ public class BLCFile extends AlignFile
 
         while ((i < s.length) && (s[i] != null))
         {
-            out.append(">" + printId(s[i]) +"\n");
+            out.append(">" + printId(s[i]));
+            if(s[i].getDescription()!=null)
+              out.append(" "+s[i].getDescription());
+
+            out.append("\n");
 
-            if (s[i].getSequence().length() > max)
+            if (s[i].getSequence().length > max)
             {
-                max = s[i].getSequence().length();
+                max = s[i].getSequence().length;
             }
 
             i++;
@@ -204,9 +184,9 @@ public class BLCFile extends AlignFile
 
             while ((i < s.length) && (s[i] != null))
             {
-                if (s[i].getSequence().length() > j)
+                if (s[i].getSequence().length > j)
                 {
-                    out.append(s[i].getSequence().substring(j, j + 1));
+                    out.append(s[i].getSequenceAsString(j, j + 1));
                 }
                 else
                 {