From: jprocter <Jim Procter>
Date: Fri, 27 May 2005 11:47:10 +0000 (+0000)
Subject: Added nicer header formatting for MSFfile output.
X-Git-Tag: Release_2_0~160
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=f960a9572b838aa32b8618324a12e9e4767f98cf;p=jalview.git

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