Added nicer header formatting for MSFfile output.

diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java
index 3c18432..63827a1 100755 (executable)
--- a/src/jalview/io/MSFfile.java
+++ b/src/jalview/io/MSFfile.java
@@ -145,39 +145,58 @@ public class MSFfile extends AlignFile {
   }\r
 \r
   public static String print(SequenceI[] s) {\r
-    StringBuffer out = new StringBuffer("PileUp\n\n");\r
+    return print(s, false);\r
+  }\r
+  public static String print(SequenceI[] s, boolean is_NA) {\r
+    StringBuffer out = new StringBuffer("!!"+(is_NA ? "NA":"AA")+"_MULTIPLE_ALIGNMENT 1.0\n\n"); // TODO: JBPNote : Jalview doesn't remember NA or AA yet.\r
 \r
     int max = 0;\r
     int maxid = 0;\r
-\r
     int i = 0;\r
     String big = "";\r
+\r
     while (i < s.length && s[i] != null) {\r
-      big += s[i].getSequence();\r
+      String sq;\r
+      big += (sq=s[i].getSequence());\r
+      if (sq.length() > max) {\r
+        max = sq.length();\r
+      }\r
       i++;\r
     }\r
+    Format maxLenpad = new Format("%"+(new String(""+max)).length()+"d");\r
+    Format maxChkpad = new Format("%"+(new String("1"+max)).length()+"d");\r
     i = 0;\r
-    int bigcheck = checkSum(big);\r
-\r
-    out.append("   MSF: " + s[0].getSequence().length() + "   Type: P    Check:  " + bigcheck + "   ..\n\n\n");\r
-\r
+    long bigcheck = checkSum(big);\r
+    long maxNB=0;\r
+    out.append("   MSF: " + s[0].getSequence().length() + "   Type: "+(is_NA?"N":"P")+"    Check:  " + bigcheck + "   ..\n\n\n");\r
+    String nameBlock[] = new String[s.length];\r
+    String idBlock[] = new String[s.length];\r
     while (i < s.length && s[i] != null) {\r
       String seq = s[i].getSequence();\r
       String name =  s[i].getName()+ "/" + s[i].getStart() + "-" + s[i].getEnd();\r
       int check = checkSum(s[i].getSequence());\r
-      out.append(" Name: " + name + " oo  Len:  " + s[i].getSequence().length() + "  Check:  " + check + "  Weight:  1.00\n");\r
-      if (seq.length() > max) {\r
-        max = seq.length();\r
-      }\r
+      nameBlock[i]=new String("  Name: "+name+" ");\r
+      idBlock[i] = new String("Len: " + maxLenpad.form(s[i].getSequence().length()) + "  Check:" + maxChkpad.form(check) + "  Weight: 1.00\n");\r
+\r
       if (name.length() > maxid) {\r
         maxid = name.length();\r
       }\r
+      if (nameBlock[i].length()>maxNB) {\r
+        maxNB=nameBlock[i].length();\r
+      }\r
+\r
       i++;\r
     }\r
-\r
     if (maxid < 10) {\r
       maxid = 10;\r
     }\r
+    if (maxNB<15) {\r
+      maxNB=15;\r
+    }\r
+    Format nbFormat = new Format("%-"+maxNB+"s");\r
+    for (i=0;i<s.length && s[i]!=null;i++) {\r
+      out.append(nbFormat.form(nameBlock[i])+idBlock[i]);\r
+    }\r
     maxid++;\r
     out.append( "\n\n//\n\n");\r
 \r