fileFormat enum wip changes

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

diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java
index 431544b..1f28f49 100755 (executable)
--- a/src/jalview/io/MSFfile.java
+++ b/src/jalview/io/MSFfile.java
@@ -22,6 +22,7 @@ package jalview.io;
 
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
 import jalview.util.Format;
 
 import java.io.IOException;
@@ -202,22 +203,13 @@ public class MSFfile extends AlignFile
     return check % 10000;
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param s
-   *          DOCUMENT ME!
-   * @param is_NA
-   *          DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
-  public String print(SequenceI[] seqs)
+  @Override
+  public String print(SequenceI[] sqs, boolean jvsuffix)
   {
 
-    boolean is_NA = jalview.util.Comparison.isNucleotide(seqs);
+    boolean is_NA = Comparison.isNucleotide(sqs);
 
-    SequenceI[] s = new SequenceI[seqs.length];
+    SequenceI[] s = new SequenceI[sqs.length];
 
     StringBuffer out = new StringBuffer("!!" + (is_NA ? "NA" : "AA")
             + "_MULTIPLE_ALIGNMENT 1.0");
@@ -228,11 +220,11 @@ public class MSFfile extends AlignFile
     int maxid = 0;
     int i = 0;
 
-    while ((i < seqs.length) && (seqs[i] != null))
+    while ((i < sqs.length) && (sqs[i] != null))
     {
       // Replace all internal gaps with . and external spaces with ~
-      s[i] = new Sequence(seqs[i].getName(), seqs[i].getSequenceAsString()
-              .replace('-', '.'), seqs[i].getStart(), seqs[i].getEnd());
+      s[i] = new Sequence(sqs[i].getName(), sqs[i].getSequenceAsString()
+              .replace('-', '.'), sqs[i].getStart(), sqs[i].getEnd());
 
       StringBuffer sb = new StringBuffer();
       sb.append(s[i].getSequence());
@@ -301,7 +293,7 @@ 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: "
@@ -353,7 +345,7 @@ 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 + " "));
 
@@ -401,15 +393,4 @@ public class MSFfile extends AlignFile
 
     return out.toString();
   }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
-  @Override
-  public String print()
-  {
-    return print(getSeqsAsArray());
-  }
 }