X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FMSFfile.java;h=df2bed2a185239ae054549dca4dd7d3ad3b9c7d0;hb=bb5a8705457b0a597b43e5699d6422770c3b5742;hp=7e46978b7390b0b31c0e7bb086963ebe7c807270;hpb=853624fb32058cccc544ae7d13af6ad4b0800b6c;p=jalview.git

diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java
index 7e46978..df2bed2 100755
--- a/src/jalview/io/MSFfile.java
+++ b/src/jalview/io/MSFfile.java
@@ -58,7 +58,7 @@ public class MSFfile extends AlignFile
    * @throws IOException
    *           DOCUMENT ME!
    */
-  public MSFfile(String inFile, String type) throws IOException
+  public MSFfile(String inFile, DataSourceType type) throws IOException
   {
     super(inFile, type);
   }
@@ -216,7 +216,8 @@ public class MSFfile extends AlignFile
    * 
    * @return DOCUMENT ME!
    */
-  public String print(SequenceI[] sqs)
+  @Override
+  public String print(SequenceI[] sqs, boolean jvSuffix)
   {
 
     boolean is_NA = Comparison.isNucleotide(sqs);
@@ -277,10 +278,10 @@ public class MSFfile extends AlignFile
       i++;
     }
 
-    Format maxLenpad = new Format("%" + (new String("" + max)).length()
-            + "d");
-    Format maxChkpad = new Format("%" + (new String("1" + max)).length()
-            + "d");
+    Format maxLenpad = new Format(
+            "%" + (new String("" + max)).length() + "d");
+    Format maxChkpad = new Format(
+            "%" + (new String("1" + max)).length() + "d");
     i = 0;
 
     int bigChecksum = 0;
@@ -293,7 +294,7 @@ public class MSFfile extends AlignFile
     }
 
     long maxNB = 0;
-    out.append("   MSF: " + s[0].getSequence().length + "   Type: "
+    out.append("   MSF: " + s[0].getLength() + "   Type: "
             + (is_NA ? "N" : "P") + "    Check:  " + (bigChecksum % 10000)
             + "   ..");
     out.append(newline);
@@ -307,11 +308,11 @@ public class MSFfile extends AlignFile
     while ((i < s.length) && (s[i] != null))
     {
 
-      nameBlock[i] = new String("  Name: " + printId(s[i]) + " ");
+      nameBlock[i] = new String("  Name: " + printId(s[i], jvSuffix) + " ");
 
-      idBlock[i] = new String("Len: "
-              + maxLenpad.form(s[i].getSequence().length) + "  Check: "
-              + maxChkpad.form(checksums[i]) + "  Weight: 1.00" + newline);
+      idBlock[i] = new String("Len: " + maxLenpad.form(s[i].getLength())
+              + "  Check: " + maxChkpad.form(checksums[i])
+              + "  Weight: 1.00" + newline);
 
       if (s[i].getName().length() > maxid)
       {
@@ -359,7 +360,7 @@ public class MSFfile extends AlignFile
 
       while ((j < s.length) && (s[j] != null))
       {
-        String name = printId(s[j]);
+        String name = printId(s[j], jvSuffix);
 
         out.append(new Format("%-" + maxid + "s").form(name + " "));
 
@@ -368,8 +369,9 @@ public class MSFfile extends AlignFile
           int start = (i * 50) + (k * 10);
           int end = start + 10;
 
-          if ((end < s[j].getSequence().length)
-                  && (start < s[j].getSequence().length))
+          int length = s[j].getLength();
+          if ((end < length)
+                  && (start < length))
           {
             out.append(s[j].getSequence(start, end));
 
@@ -384,7 +386,7 @@ public class MSFfile extends AlignFile
           }
           else
           {
-            if (start < s[j].getSequence().length)
+            if (start < length)
             {
               out.append(s[j].getSequenceAsString().substring(start));
               out.append(newline);
@@ -407,15 +409,4 @@ public class MSFfile extends AlignFile
 
     return out.toString();
   }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
-  @Override
-  public String print()
-  {
-    return print(getSeqsAsArray());
-  }
 }