From: Jim Procter Date: Tue, 15 Feb 2022 16:55:17 +0000 (+0000) Subject: JAL-1761 need to pass molecule type when generating superposition commands X-Git-Tag: Release_2_11_2_0~10^2~1 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=7af7ccb2d58a22ffabe1f3129d9f33348efb2534;p=jalview.git JAL-1761 need to pass molecule type when generating superposition commands --- diff --git a/test/jalview/ext/jmol/JmolCommandsTest.java b/test/jalview/ext/jmol/JmolCommandsTest.java index 21f7e19..64899d3 100644 --- a/test/jalview/ext/jmol/JmolCommandsTest.java +++ b/test/jalview/ext/jmol/JmolCommandsTest.java @@ -199,7 +199,7 @@ public class JmolCommandsTest toAlign.addRange("2", 20, 21, "B"); toAlign.addRange("2", 22, 22, "C"); List command = testee.superposeStructures(ref, - toAlign); + toAlign, false); // doesn't matter for Jmol whether nuc or protein assertEquals(command.size(), 1); String refSpec = "12-14:A/1.1|18:B/1.1|22-23:B/1.1"; String toAlignSpec = "15-17:B/2.1|20-21:B/2.1|22:C/2.1"; diff --git a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java index 6880985..a5933d2 100644 --- a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java +++ b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java @@ -203,7 +203,7 @@ public class ChimeraCommandsTest toAlign.addRange("2", 20, 21, "B"); toAlign.addRange("2", 22, 22, "C"); List command = testee.superposeStructures(ref, - toAlign); + toAlign, false); // qualifier to restrict match to CA and no altlocs String carbonAlphas = "@CA&~@.B-Z&~@.2-9"; String refSpec = "#1:12-14.A,18.B,22-23.B"; diff --git a/test/jalview/ext/rbvi/chimera/ChimeraXCommandsTest.java b/test/jalview/ext/rbvi/chimera/ChimeraXCommandsTest.java index 439401a..80bf042 100644 --- a/test/jalview/ext/rbvi/chimera/ChimeraXCommandsTest.java +++ b/test/jalview/ext/rbvi/chimera/ChimeraXCommandsTest.java @@ -187,7 +187,7 @@ public class ChimeraXCommandsTest toAlign.addRange("2", 20, 21, "B"); toAlign.addRange("2", 22, 22, "C"); List command = testee.superposeStructures(ref, - toAlign); + toAlign,false); assertEquals(command.size(), 1); String cmd = command.get(0).getCommand(); String refSpec = "#1/A:12-14/B:18,22-23";