X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPfamFile.java;h=bc22fae2933693a7dec73c3ed1a5c81b12ad7a92;hb=c355d0f7a994d0d064078d363e612eb8c89581f1;hp=71cc7f04a200e542f82578addb08a7a93d598f15;hpb=abad83613306b9afe956746610e3d62b47c4c0fd;p=jalview.git

diff --git a/src/jalview/io/PfamFile.java b/src/jalview/io/PfamFile.java
index 71cc7f0..bc22fae 100755
--- a/src/jalview/io/PfamFile.java
+++ b/src/jalview/io/PfamFile.java
@@ -36,9 +36,10 @@ public class PfamFile extends AlignFile
   {
   }
 
-  public PfamFile(String inFile, String type) throws IOException
+  public PfamFile(String inFile, DataSourceType sourceType)
+          throws IOException
   {
-    super(inFile, type);
+    super(inFile, sourceType);
   }
 
   public PfamFile(FileParse source) throws IOException
@@ -108,7 +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());
       }
     }
 
@@ -124,8 +125,7 @@ public class PfamFile extends AlignFile
     {
       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();
         }
@@ -143,7 +143,8 @@ public class PfamFile extends AlignFile
     }
   }
 
-  public String print(SequenceI[] s)
+  @Override
+  public String print(SequenceI[] s, boolean jvsuffix)
   {
     StringBuffer out = new StringBuffer("");
 
@@ -154,7 +155,7 @@ 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)
       {
@@ -178,7 +179,8 @@ 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);
@@ -189,10 +191,4 @@ public class PfamFile extends AlignFile
 
     return out.toString();
   }
-
-  @Override
-  public String print()
-  {
-    return print(getSeqsAsArray());
-  }
 }