Added a flag to control if the "/<seq_start>-<seq_end>" field of

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

diff --git a/src/jalview/io/FastaFile.java b/src/jalview/io/FastaFile.java
index 9a6e060..586ede6 100755 (executable)
--- 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) {\r
     return print(s,len,true);\r
   }\r
+\r
   public static String print(SequenceI[] s, int len,boolean gaps) {\r
+    return print(s,len,gaps,true);\r
+  }\r
+\r
+  public static String print(SequenceI[] s, int len,boolean gaps, boolean displayId) {\r
     StringBuffer out = new StringBuffer();\r
     int i = 0;\r
     while (i < s.length && s[i] != null) {\r
@@ -108,8 +113,8 @@ public class FastaFile extends AlignFile {
       } else {\r
         seq = AlignSeq.extractGaps("-. ",s[i].getSequence());\r
       }\r
-\r
-      out.append(">" + s[i].getName() + "/" + s[i].getStart() + "-" + s[i].getEnd() + "\n");\r
+      // used to always put this here: + "/" + s[i].getStart() + "-" + s[i].getEnd() +\r
+      out.append(">" + ((displayId) ? s[i].getDisplayId() : s[i].getName())+"\n");\r
 \r
       int nochunks = seq.length() / len + 1;\r
 \r