Merge branch 'develop' into features/JAL-2446NCList

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

diff --git a/src/jalview/io/PfamFile.java b/src/jalview/io/PfamFile.java
index c6c10bd..9f152cc 100755 (executable)
--- 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());
       }
     }
 
@@ -125,8 +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();
         }
@@ -158,10 +157,7 @@ public class PfamFile extends AlignFile
     {
       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)
       {