From b241835b6eaf567f77259226135f909887901e00 Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Tue, 3 May 2005 12:42:25 +0000 Subject: [PATCH] FormatAdapter readFile --- src/jalview/ws/Jemboss.java | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/src/jalview/ws/Jemboss.java b/src/jalview/ws/Jemboss.java index 7983262..3e01b77 100755 --- a/src/jalview/ws/Jemboss.java +++ b/src/jalview/ws/Jemboss.java @@ -154,11 +154,11 @@ public class Jemboss JembossRun thisrun = new JembossRun(embossCommand,"", filesToMove,vamsas_server); Hashtable h = thisrun.hash(); - Enumeration enum = h.keys(); + Enumeration enumerator = h.keys(); // Find the alignment generated and parse it - while (enum.hasMoreElements()) + while (enumerator.hasMoreElements()) { - String thiskey = (String)enum.nextElement().toString(); + String thiskey = (String)enumerator.nextElement().toString(); if (thiskey.endsWith(".aln")) { // FormatAdapter, and IdentifyFile use a protocol string @@ -167,8 +167,8 @@ public class Jemboss String format = IdentifyFile.Identify(alfile, "Paste"); SequenceI[] alignment = null; - if (FormatProperties.contains(format)) - alignment = FormatAdapter.read(alfile, "Paste", format); + if (FormatAdapter.formats.contains(format)) + alignment = FormatAdapter.readFile(alfile, "Paste", format); else System.out.println("jalview.Jemboss: Unknown format "+format+"\n"); if (alignment == null) -- 1.7.10.2