X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPfamFile.java;h=6b9dc3f6a53836eb4573858bd51115744436b138;hb=9f118a08c0f093fb30a51a2459e2609b3c959614;hp=59ffbaac3439852f5c19218832ebcc0078b0c067;hpb=ee198b3ca3687f18a2ee186f4e7c7330f4ea30f0;p=jalview.git

diff --git a/src/jalview/io/PfamFile.java b/src/jalview/io/PfamFile.java
index 59ffbaa..6b9dc3f 100755
--- a/src/jalview/io/PfamFile.java
+++ b/src/jalview/io/PfamFile.java
@@ -109,7 +109,7 @@ public class PfamFile extends AlignFile
       }
       if (spces + 1 < line.length())
       {
-        tempseq.append(line.substring(spces + 1));
+        tempseq.append(line.substring(spces + 1).trim());
       }
     }
 
@@ -117,23 +117,22 @@ public class PfamFile extends AlignFile
 
     if (noSeqs < 1)
     {
-      throw new IOException(
-              MessageManager.getString("exception.pfam_no_sequences_found"));
+      throw new IOException(MessageManager
+              .getString("exception.pfam_no_sequences_found"));
     }
 
     for (i = 0; i < headers.size(); i++)
     {
       if (seqhash.get(headers.get(i)) != null)
       {
-        if (maxLength < seqhash.get(headers.get(i)).toString()
-                .length())
+        if (maxLength < seqhash.get(headers.get(i)).toString().length())
         {
           maxLength = seqhash.get(headers.get(i)).toString().length();
         }
 
         Sequence newSeq = parseId(headers.get(i).toString());
-        newSeq.setSequence(seqhash.get(headers.get(i).toString())
-                .toString());
+        newSeq.setSequence(
+                seqhash.get(headers.get(i).toString()).toString());
         seqs.addElement(newSeq);
       }
       else
@@ -144,7 +143,8 @@ public class PfamFile extends AlignFile
     }
   }
 
-  public String print(SequenceI[] s)
+  @Override
+  public String print(SequenceI[] s, boolean jvsuffix)
   {
     StringBuffer out = new StringBuffer("");
 
@@ -155,12 +155,9 @@ public class PfamFile extends AlignFile
 
     while ((i < s.length) && (s[i] != null))
     {
-      String tmp = printId(s[i]);
+      String tmp = printId(s[i], jvsuffix);
 
-      if (s[i].getSequence().length > max)
-      {
-        max = s[i].getSequence().length;
-      }
+      max = Math.max(max, s[i].getLength());
 
       if (tmp.length() > maxid)
       {
@@ -179,7 +176,8 @@ public class PfamFile extends AlignFile
 
     while ((j < s.length) && (s[j] != null))
     {
-      out.append(new Format("%-" + maxid + "s").form(printId(s[j]) + " "));
+      out.append(new Format("%-" + maxid + "s")
+              .form(printId(s[j], jvsuffix) + " "));
 
       out.append(s[j].getSequenceAsString());
       out.append(newline);
@@ -190,10 +188,4 @@ public class PfamFile extends AlignFile
 
     return out.toString();
   }
-
-  @Override
-  public String print()
-  {
-    return print(getSeqsAsArray());
-  }
 }