From: gmungoc Date: Sat, 9 Jul 2016 06:12:09 +0000 (+0100) Subject: Merge branch 'develop' into features/JAL-2110_crossRefDuplications X-Git-Tag: Release_2_10_0~140^2~5^2~10 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=4eb1ed22600411fe5b6e9ac93084b45429ccfad6;hp=-c;p=jalview.git Merge branch 'develop' into features/JAL-2110_crossRefDuplications --- 4eb1ed22600411fe5b6e9ac93084b45429ccfad6 diff --combined test/jalview/gui/AlignViewportTest.java index dc9113c,c956da1..2b72914 --- a/test/jalview/gui/AlignViewportTest.java +++ b/test/jalview/gui/AlignViewportTest.java @@@ -36,7 -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; @@@ -77,12 -76,12 +77,12 @@@ public class AlignViewportTes /* * Set up sequence pdb ids */ - PDBEntry pdb1 = new PDBEntry("1ABC", "A", Type.PDB, "1ABC.pdb"); - PDBEntry pdb2 = new PDBEntry("2ABC", "A", Type.PDB, "2ABC.pdb"); - PDBEntry pdb3 = new PDBEntry("3ABC", "A", Type.PDB, "3ABC.pdb"); + PDBEntry pdb1 = new PDBEntry("1ABC", "B", Type.PDB, "1ABC.pdb"); + PDBEntry pdb2 = new PDBEntry("2ABC", "C", Type.PDB, "2ABC.pdb"); + PDBEntry pdb3 = new PDBEntry("3ABC", "D", Type.PDB, "3ABC.pdb"); /* - * seq1 and seq3 refer to 1ABC, seq2 to 2ABC, none to 3ABC + * seq1 and seq3 refer to 1abcB, seq2 to 2abcC, none to 3abcD */ al.getSequenceAt(0).getDatasetSequence() .addPDBId(new PDBEntry("1ABC", "B", Type.PDB, "1ABC.pdb")); @@@ -134,13 -133,8 +134,13 @@@ 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); @@@ -184,20 -178,10 +184,20 @@@ ">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); @@@ -247,20 -231,10 +247,20 @@@ ">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); diff --combined test/jalview/structure/StructureSelectionManagerTest.java index d07f919,16f56a6..2074fb4 --- a/test/jalview/structure/StructureSelectionManagerTest.java +++ b/test/jalview/structure/StructureSelectionManagerTest.java @@@ -29,7 -29,6 +29,7 @@@ import jalview.datamodel.SequenceFeatur import jalview.datamodel.SequenceI; import jalview.io.FormatAdapter; import jalview.io.StructureFile; +import jalview.util.MapList; import java.util.ArrayList; import java.util.List; @@@ -44,7 -43,7 +44,7 @@@ public class StructureSelectionManagerT @BeforeMethod(alwaysRun = true) public void setUp() { - StructureViewSettings.setShowSeqFeatures(true); + StructureImportSettings.setShowSeqFeatures(true); ssm = new StructureSelectionManager(); } @@@ -52,11 -51,7 +52,11 @@@ public void testRegisterMapping() { AlignedCodonFrame acf1 = new AlignedCodonFrame(); + acf1.addMap(new Sequence("s1", "ttt"), new Sequence("p1", "p"), + new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1)); AlignedCodonFrame acf2 = new AlignedCodonFrame(); + acf2.addMap(new Sequence("s2", "ttt"), new Sequence("p2", "p"), + new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1)); ssm.registerMapping(acf1); assertEquals(1, ssm.getSequenceMappings().size()); @@@ -80,14 -75,8 +80,14 @@@ public void testRegisterMappings() { AlignedCodonFrame acf1 = new AlignedCodonFrame(); + acf1.addMap(new Sequence("s1", "ttt"), new Sequence("p1", "p"), + new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1)); AlignedCodonFrame acf2 = new AlignedCodonFrame(); + acf2.addMap(new Sequence("s2", "ttt"), new Sequence("p2", "p"), + new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1)); AlignedCodonFrame acf3 = new AlignedCodonFrame(); + acf3.addMap(new Sequence("s3", "ttt"), new Sequence("p3", "p"), + new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1)); List set1 = new ArrayList(); set1.add(acf1);