From d37cf2412f01d6cae5d62ae549ec534785e20ed4 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Sun, 19 Jun 2016 11:19:45 +0100 Subject: [PATCH 1/1] JAL-2110 test alcodonframes must be distinct --- test/jalview/gui/AlignViewportTest.java | 30 ++++++++++++++++++++++++++++-- 1 file changed, 28 insertions(+), 2 deletions(-) diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java index b39b2bd..dc9113c 100644 --- a/test/jalview/gui/AlignViewportTest.java +++ b/test/jalview/gui/AlignViewportTest.java @@ -36,6 +36,7 @@ import jalview.datamodel.SequenceI; import jalview.io.FileLoader; import jalview.io.FormatAdapter; import jalview.structure.StructureSelectionManager; +import jalview.util.MapList; import java.util.ArrayList; import java.util.List; @@ -133,8 +134,13 @@ public class AlignViewportTest AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded( ">Seq1\nCAGT\n", FormatAdapter.PASTE); + SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0); AlignedCodonFrame acf1 = new AlignedCodonFrame(); + acf1.addMap(s1, s1, new MapList(new int[] { 1, 4 }, new int[] { 1, 4 }, + 1, 1)); AlignedCodonFrame acf2 = new AlignedCodonFrame(); + acf2.addMap(s1, s1, new MapList(new int[] { 1, 4 }, new int[] { 4, 1 }, + 1, 1)); List mappings = new ArrayList(); mappings.add(acf1); @@ -178,10 +184,20 @@ public class AlignViewportTest ">Seq1\nRSVQ\n", FormatAdapter.PASTE); AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded( ">Seq2\nDGEL\n", FormatAdapter.PASTE); - + SequenceI cs1 = new Sequence("cseq1", "CCCGGGTTTAAA"); + SequenceI cs2 = new Sequence("cseq2", "CTTGAGTCTAGA"); + SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0); + SequenceI s2 = af2.getViewport().getAlignment().getSequenceAt(0); + // need to be distinct AlignedCodonFrame acf1 = new AlignedCodonFrame(); + acf1.addMap(cs1, s1, new MapList(new int[] { 1, 4 }, + new int[] { 1, 12 }, 1, 3)); AlignedCodonFrame acf2 = new AlignedCodonFrame(); + acf2.addMap(cs2, s2, new MapList(new int[] { 1, 4 }, + new int[] { 1, 12 }, 1, 3)); AlignedCodonFrame acf3 = new AlignedCodonFrame(); + acf3.addMap(cs2, cs2, new MapList(new int[] { 1, 12 }, new int[] { 1, + 12 }, 1, 1)); List mappings1 = new ArrayList(); mappings1.add(acf1); @@ -231,10 +247,20 @@ public class AlignViewportTest ">Seq1\nRSVQ\n", FormatAdapter.PASTE); AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded( ">Seq2\nDGEL\n", FormatAdapter.PASTE); - + SequenceI cs1 = new Sequence("cseq1", "CCCGGGTTTAAA"); + SequenceI cs2 = new Sequence("cseq2", "CTTGAGTCTAGA"); + SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0); + SequenceI s2 = af2.getViewport().getAlignment().getSequenceAt(0); + // need to be distinct AlignedCodonFrame acf1 = new AlignedCodonFrame(); + acf1.addMap(cs1, s1, new MapList(new int[] { 1, 4 }, + new int[] { 1, 12 }, 1, 3)); AlignedCodonFrame acf2 = new AlignedCodonFrame(); + acf2.addMap(cs2, s2, new MapList(new int[] { 1, 4 }, + new int[] { 1, 12 }, 1, 3)); AlignedCodonFrame acf3 = new AlignedCodonFrame(); + acf3.addMap(cs2, cs2, new MapList(new int[] { 1, 12 }, new int[] { 1, + 12 }, 1, 1)); List mappings1 = new ArrayList(); mappings1.add(acf1); -- 1.7.10.2