From 371c9b1f7571fc7cf9deb28d0120ba341d0b7f3d Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Thu, 31 Mar 2005 09:54:19 +0000
Subject: [PATCH] Added a flag to control if the "/<seq_start>-<seq_end>"
 field of SequenceI.Name is included in fastA format files.
 This is used in the Jemboss client.

---
 src/jalview/io/FastaFile.java |    9 +++++++--
 src/jalview/ws/Jemboss.java   |    8 ++++----
 2 files changed, 11 insertions(+), 6 deletions(-)

diff --git a/src/jalview/io/FastaFile.java b/src/jalview/io/FastaFile.java
index 9a6e060..586ede6 100755
--- a/src/jalview/io/FastaFile.java
+++ b/src/jalview/io/FastaFile.java
@@ -98,7 +98,12 @@ public class FastaFile extends AlignFile {
   public static String print(SequenceI[] s, int len) {
     return print(s,len,true);
   }
+
   public static String print(SequenceI[] s, int len,boolean gaps) {
+    return print(s,len,gaps,true);
+  }
+
+  public static String print(SequenceI[] s, int len,boolean gaps, boolean displayId) {
     StringBuffer out = new StringBuffer();
     int i = 0;
     while (i < s.length && s[i] != null) {
@@ -108,8 +113,8 @@ public class FastaFile extends AlignFile {
       } else {
         seq = AlignSeq.extractGaps("-. ",s[i].getSequence());
       }
-
-      out.append(">" + s[i].getName() + "/" + s[i].getStart() + "-" + s[i].getEnd() + "\n");
+      // used to always put this here: + "/" + s[i].getStart() + "-" + s[i].getEnd() +
+      out.append(">" + ((displayId) ? s[i].getDisplayId() : s[i].getName())+"\n");
 
       int nochunks = seq.length() / len + 1;
 
diff --git a/src/jalview/ws/Jemboss.java b/src/jalview/ws/Jemboss.java
index 336be27..a8bf163 100755
--- a/src/jalview/ws/Jemboss.java
+++ b/src/jalview/ws/Jemboss.java
@@ -134,12 +134,12 @@ public class Jemboss
     for (int i=0; i<sequences.length; i++) {
         myseq[i] = new Sequence(sequences[i]);
     }
-    // Uniqueify, and 
+    // Uniqueify, and
     Hashtable namemap = uniquify(myseq);
     // Load sequence file into hash
-    
+
     filesToMove.put("jalseqs.fasta",
-                    jalview.io.FastaFile.print(myseq,124,false).getBytes());
+                    jalview.io.FastaFile.print(myseq,124,false, false).getBytes());
 
     if(vamsas_server.getUseAuth() == true)
       if(vamsas_server.getServiceUserName() == null)
@@ -163,7 +163,7 @@ public class Jemboss
           String alfile = h.get(thiskey).toString();
           String format = IdentifyFile.Identify(alfile, "Paste");
           SequenceI[] alignment = null;
-          
+
           if (FormatProperties.contains(format))
             alignment = FormatAdapter.read(alfile, "Paste", format);
           else
-- 
1.7.10.2