From 48d729681b0bf78441514aff3d084d16d86e876a Mon Sep 17 00:00:00 2001 From: TZVanaalten Date: Fri, 25 Aug 2017 14:52:18 +0100 Subject: [PATCH] Revert "jal-2629 fix for hmmbuild failing due to whitespace in the name" This reverts commit b0516b5aff64734bd343fe5b2178f64677c02863. --- src/jalview/hmmer/HMMBuildThread.java | 14 ++++---------- 1 file changed, 4 insertions(+), 10 deletions(-) diff --git a/src/jalview/hmmer/HMMBuildThread.java b/src/jalview/hmmer/HMMBuildThread.java index d5e938a..faba183 100644 --- a/src/jalview/hmmer/HMMBuildThread.java +++ b/src/jalview/hmmer/HMMBuildThread.java @@ -36,7 +36,6 @@ public class HMMBuildThread implements Runnable SequenceGroup group; List params; - boolean multiJob; boolean forGroup = false; @@ -96,14 +95,12 @@ public class HMMBuildThread implements Runnable { alignment = viewport.getAlignment(); groups.addAll(viewport.getAlignment().getGroups()); - multiJob = true; break; } else if ("All groups".equals(value)) { alignment = null; groups = viewport.getAlignment().getGroups(); - multiJob = true; break; } else if ("Selected group".equals(value)) @@ -298,11 +295,7 @@ public class HMMBuildThread implements Runnable switch (argName) { case "HMM Name": - if (!multiJob) - { - name = arg.getValue(); - name = name.trim(); - } + name = arg.getValue(); break; case "Use Reference Annotation": command += "--hand "; @@ -313,6 +306,8 @@ public class HMMBuildThread implements Runnable } } + name = name.trim(); + if (name == null || "".equals(name)) { if (forGroup) @@ -332,8 +327,7 @@ public class HMMBuildThread implements Runnable } } - - command += "-n " + name.replace(' ', '_') + cmds.SPACE; + command += "-n " + name + cmds.SPACE; if (!alignment.isNucleotide()) { command += cmds.FORCEAMINO; // TODO check for rna -- 1.7.10.2