From 17e147b95865a902e82368e4fc9a3bcf44d3d7ef Mon Sep 17 00:00:00 2001 From: gmungoc Date: Fri, 9 Aug 2019 08:48:53 +0100 Subject: [PATCH] JAL-3390 move StructureCommands to utils package --- src/jalview/ext/jmol/JalviewJmolBinding.java | 2 +- src/jalview/ext/jmol/JmolCommands.java | 2 +- src/jalview/ext/rbvi/chimera/ChimeraCommands.java | 1 + src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java | 1 + src/jalview/{ext/rbvi/chimera => util}/StructureCommands.java | 7 +++---- test/jalview/ext/jmol/JmolCommandsTest.java | 4 ++-- test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java | 1 + 7 files changed, 10 insertions(+), 8 deletions(-) rename src/jalview/{ext/rbvi/chimera => util}/StructureCommands.java (97%) diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java index 972f093..f0ae6dc 100644 --- a/src/jalview/ext/jmol/JalviewJmolBinding.java +++ b/src/jalview/ext/jmol/JalviewJmolBinding.java @@ -28,7 +28,6 @@ import jalview.datamodel.HiddenColumns; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; import jalview.ext.rbvi.chimera.AtomSpecModel; -import jalview.ext.rbvi.chimera.StructureCommands; import jalview.gui.IProgressIndicator; import jalview.io.DataSourceType; import jalview.io.StructureFile; @@ -38,6 +37,7 @@ import jalview.structure.AtomSpec; import jalview.structure.StructureSelectionManager; import jalview.structures.models.AAStructureBindingModel; import jalview.util.MessageManager; +import jalview.util.StructureCommands; import java.awt.Color; import java.awt.Container; diff --git a/src/jalview/ext/jmol/JmolCommands.java b/src/jalview/ext/jmol/JmolCommands.java index f0949b8..a900701 100644 --- a/src/jalview/ext/jmol/JmolCommands.java +++ b/src/jalview/ext/jmol/JmolCommands.java @@ -28,11 +28,11 @@ import jalview.datamodel.AlignmentI; import jalview.datamodel.HiddenColumns; import jalview.datamodel.SequenceI; import jalview.ext.rbvi.chimera.AtomSpecModel; -import jalview.ext.rbvi.chimera.StructureCommands; import jalview.renderer.seqfeatures.FeatureColourFinder; import jalview.structure.StructureMapping; import jalview.structure.StructureMappingcommandSet; import jalview.structure.StructureSelectionManager; +import jalview.util.StructureCommands; import java.awt.Color; import java.util.ArrayList; diff --git a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java index 8c00e74..bfec5b2 100644 --- a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java +++ b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java @@ -33,6 +33,7 @@ import jalview.structure.StructureMappingcommandSet; import jalview.structure.StructureSelectionManager; import jalview.structures.models.AAStructureBindingModel; import jalview.util.ColorUtils; +import jalview.util.StructureCommands; import java.awt.Color; import java.util.ArrayList; diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java index 2bb24d9..dd0a75e 100644 --- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java +++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java @@ -40,6 +40,7 @@ import jalview.structure.StructureMappingcommandSet; import jalview.structure.StructureSelectionManager; import jalview.structures.models.AAStructureBindingModel; import jalview.util.MessageManager; +import jalview.util.StructureCommands; import java.awt.Color; import java.io.File; diff --git a/src/jalview/ext/rbvi/chimera/StructureCommands.java b/src/jalview/util/StructureCommands.java similarity index 97% rename from src/jalview/ext/rbvi/chimera/StructureCommands.java rename to src/jalview/util/StructureCommands.java index 5f707ae..8e66da8 100644 --- a/src/jalview/ext/rbvi/chimera/StructureCommands.java +++ b/src/jalview/util/StructureCommands.java @@ -1,4 +1,4 @@ -package jalview.ext.rbvi.chimera; +package jalview.util; import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; @@ -7,11 +7,10 @@ import jalview.api.SequenceRenderer; import jalview.datamodel.AlignmentI; import jalview.datamodel.HiddenColumns; import jalview.datamodel.SequenceI; +import jalview.ext.rbvi.chimera.AtomSpecModel; import jalview.renderer.seqfeatures.FeatureColourFinder; import jalview.structure.StructureMapping; import jalview.structures.models.AAStructureBindingModel; -import jalview.util.Comparison; -import jalview.util.IntRangeComparator; import java.awt.Color; import java.util.Collections; @@ -44,7 +43,7 @@ public abstract class StructureCommands * @param endPos * @param chain */ - protected static void addAtomSpecRange(Map map, + public static void addAtomSpecRange(Map map, Object value, int model, int startPos, int endPos, String chain) { diff --git a/test/jalview/ext/jmol/JmolCommandsTest.java b/test/jalview/ext/jmol/JmolCommandsTest.java index e140fe1..45e66ce 100644 --- a/test/jalview/ext/jmol/JmolCommandsTest.java +++ b/test/jalview/ext/jmol/JmolCommandsTest.java @@ -32,7 +32,6 @@ import jalview.datamodel.HiddenColumns; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceI; import jalview.ext.rbvi.chimera.AtomSpecModel; -import jalview.ext.rbvi.chimera.StructureCommands; import jalview.gui.AlignFrame; import jalview.gui.JvOptionPane; import jalview.gui.SequenceRenderer; @@ -43,6 +42,7 @@ import jalview.structure.StructureMapping; import jalview.structure.StructureMappingcommandSet; import jalview.structure.StructureSelectionManager; import jalview.structures.models.AAStructureBindingModel; +import jalview.util.StructureCommands; import java.awt.Color; import java.util.HashMap; @@ -274,7 +274,7 @@ public class JmolCommandsTest } @Test(groups = "Functional") - public void testGetColourBySequenceCommand_mapVersion() + public void testGetColourBySequenceCommand() { /* * load these sequences, coloured by Strand propensity, diff --git a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java index 9adbd8e..fb8626c 100644 --- a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java +++ b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java @@ -40,6 +40,7 @@ import jalview.structure.AtomSpec; import jalview.structure.StructureMapping; import jalview.structure.StructureSelectionManager; import jalview.structures.models.AAStructureBindingModel; +import jalview.util.StructureCommands; import java.awt.Color; import java.util.HashMap; -- 1.7.10.2