From f3133c4f086cbdf59a7ce7fe465d2a5fa4a0fd60 Mon Sep 17 00:00:00 2001 From: tva Date: Wed, 10 Jul 2019 15:12:58 +0100 Subject: [PATCH 1/1] JAL-2629 hmmsearch # of new sequences now only displayed when specified --- src/jalview/hmmer/HMMSearch.java | 19 +++++++++++++------ 1 file changed, 13 insertions(+), 6 deletions(-) diff --git a/src/jalview/hmmer/HMMSearch.java b/src/jalview/hmmer/HMMSearch.java index d2b469f..bf58a27 100644 --- a/src/jalview/hmmer/HMMSearch.java +++ b/src/jalview/hmmer/HMMSearch.java @@ -387,9 +387,12 @@ public class HMMSearch extends HmmerCommand Desktop.addInternalFrame(alignFrame, ttl, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); - int nNew = checkForNewSequences(); - JvOptionPane.showMessageDialog(af.alignPanel, nNew + " " - + MessageManager.getString("label.new_returned")); + if (returnNoOfNewSeqs) + { + int nNew = checkForNewSequences(); + JvOptionPane.showMessageDialog(af.alignPanel, nNew + " " + + MessageManager.getString("label.new_returned")); + } } @@ -417,6 +420,7 @@ public class HMMSearch extends HmmerCommand if (resultSeq.getName().equals(aliSeq.getName())) { nNew--; + break; } } } @@ -454,9 +458,12 @@ public class HMMSearch extends HmmerCommand HmmerCommand hmmalign = new HMMAlign(frame, alignArgs); hmmalign.run(); - int nNew = checkForNewSequences(); - JvOptionPane.showMessageDialog(frame.alignPanel, - nNew + " " + MessageManager.getString("label.new_returned")); + if (returnNoOfNewSeqs) + { + int nNew = checkForNewSequences(); + JvOptionPane.showMessageDialog(frame.alignPanel, + nNew + " " + MessageManager.getString("label.new_returned")); + } } /** -- 1.7.10.2