X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Frbvi%2Fchimera%2FJalviewChimeraView.java;h=d397a6bd40231f9246ee6e06de556634a4c7822d;hb=8b795f97aa57877aee49a46778283706dbf3e71b;hp=d85bb104a1055c5d55373b03216deecb661853d1;hpb=5965127c38ff1a35d10d806c4b4537cdc1e39579;p=jalview.git diff --git a/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java b/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java index d85bb10..d397a6b 100644 --- a/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java +++ b/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java @@ -25,6 +25,16 @@ import static org.testng.Assert.assertFalse; import static org.testng.Assert.assertNotNull; import static org.testng.Assert.assertTrue; +import java.io.File; +import java.io.IOException; +import java.util.List; +import java.util.Vector; + +import org.testng.annotations.AfterClass; +import org.testng.annotations.AfterMethod; +import org.testng.annotations.BeforeClass; +import org.testng.annotations.Test; + import jalview.api.FeatureRenderer; import jalview.api.structures.JalviewStructureDisplayI; import jalview.bin.Cache; @@ -39,24 +49,15 @@ import jalview.gui.JvOptionPane; import jalview.gui.Preferences; import jalview.gui.StructureViewer; import jalview.gui.StructureViewer.ViewerType; +import jalview.io.DataSourceType; import jalview.io.FileLoader; +import jalview.structure.StructureCommand; import jalview.structure.StructureMapping; import jalview.structure.StructureSelectionManager; import jalview.ws.sifts.SiftsClient; import jalview.ws.sifts.SiftsException; import jalview.ws.sifts.SiftsSettings; -import java.io.File; -import java.io.IOException; -import java.util.List; -import java.util.Vector; -import jalview.io.DataSourceType; - -import org.testng.annotations.AfterClass; -import org.testng.annotations.AfterMethod; -import org.testng.annotations.BeforeClass; -import org.testng.annotations.Test; - @Test(singleThreaded = true) public class JalviewChimeraView { @@ -148,7 +149,7 @@ public class JalviewChimeraView } } - assertTrue(binding.isChimeraRunning(), "Failed to start Chimera"); + assertTrue(binding.isViewerRunning(), "Failed to start Chimera"); assertEquals(chimeraViewer.getBinding().getPdbCount(), 1); chimeraViewer.closeViewer(true); @@ -208,7 +209,7 @@ public class JalviewChimeraView } } while (!binding.isFinishedInit()); - assertTrue(binding.isChimeraRunning(), "Failed to launch Chimera"); + assertTrue(binding.isViewerRunning(), "Failed to launch Chimera"); assertEquals(binding.getPdbCount(), 1); @@ -217,7 +218,7 @@ public class JalviewChimeraView * (or possibly 52-145 to 1-94 - see JAL-2319) */ StructureSelectionManager ssm = binding.getSsm(); - String pdbFile = binding.getPdbFile()[0]; + String pdbFile = binding.getStructureFiles()[0]; StructureMapping[] mappings = ssm.getMapping(pdbFile); assertTrue(mappings[0].getMappingDetailsOutput().contains("SIFTS"), "Failed to perform SIFTS mapping"); @@ -290,7 +291,8 @@ public class JalviewChimeraView /* * ask Chimera for its residue attribute names */ - List reply = binding.sendChimeraCommand("list resattr", true); + List reply = binding + .executeCommand(new StructureCommand("list resattr"), true); // prefixed and sanitised attribute names for Jalview features: assertTrue(reply.contains("resattr jv_domain")); assertTrue(reply.contains("resattr jv_metal_ion_binding_site")); @@ -306,8 +308,9 @@ public class JalviewChimeraView * ask Chimera for residues with an attribute * 91 and 96 on sequence --> residues 40 and 45 on chains A and B */ - reply = binding.sendChimeraCommand( - "list resi att jv_metal_ion_binding_site", true); + reply = binding.executeCommand( + new StructureCommand("list resi att jv_metal_ion_binding_site"), + true); assertEquals(reply.size(), 4); assertTrue(reply .contains("residue id #0:40.A jv_metal_ion_binding_site \"Iron-Sulfur (2Fe-2S)\" index 40")); @@ -322,7 +325,8 @@ public class JalviewChimeraView * check attributes with score values * sequence positions 62 and 65 --> residues 11 and 14 on chains A and B */ - reply = binding.sendChimeraCommand("list resi att jv_kd", true); + reply = binding.executeCommand( + new StructureCommand("list resi att jv_kd"), true); assertEquals(reply.size(), 4); assertTrue(reply.contains("residue id #0:11.A jv_kd -2.1 index 11")); assertTrue(reply.contains("residue id #0:14.A jv_kd 3.6 index 14")); @@ -332,8 +336,9 @@ public class JalviewChimeraView /* * list residues with positive kd score */ - reply = binding.sendChimeraCommand( - "list resi spec :*/jv_kd>0 attr jv_kd", true); + reply = binding.executeCommand( + new StructureCommand("list resi spec :*/jv_kd>0 attr jv_kd"), + true); assertEquals(reply.size(), 2); assertTrue(reply.contains("residue id #0:14.A jv_kd 3.6 index 14")); assertTrue(reply.contains("residue id #0:14.B jv_kd 3.6 index 14")); @@ -397,13 +402,13 @@ public class JalviewChimeraView } } while (!binding.isFinishedInit()); - assertTrue(binding.isChimeraRunning(), "Failed to launch Chimera"); + assertTrue(binding.isViewerRunning(), "Failed to launch Chimera"); assertEquals(binding.getPdbCount(), 1); /* - * 'perform' menu action to copy visible features to - * attributes in Chimera + * 'perform' menu action to copy Chimera attributes + * to features in Jalview */ // TODO rename and pull up method to binding interface // once functionality is added for Jmol as well @@ -440,15 +445,13 @@ public class JalviewChimeraView binding.copyStructureAttributesToFeatures("phi", af.getViewport() .getAlignPanel()); fr.setVisible("phi"); - List fs = fr.findFeaturesAtRes(fer2Arath, 54); - assertEquals(fs.size(), 3); - assertEquals(fs.get(0).getType(), "RESNUM"); - assertEquals(fs.get(1).getType(), "phi"); - assertEquals(fs.get(2).getType(), "phi"); - assertEquals(fs.get(1).getDescription(), "A"); // chain - assertEquals(fs.get(2).getDescription(), "B"); - assertEquals(fs.get(1).getScore(), -131.0713f, 0.001f); - assertEquals(fs.get(2).getScore(), -127.39512, 0.001f); + List fs = fer2Arath.getFeatures().findFeatures(54, 54, + "phi"); + assertEquals(fs.size(), 2); + assertTrue(fs.contains(new SequenceFeature("phi", "A", 54, 54, + -131.0713f, "Chimera"))); + assertTrue(fs.contains(new SequenceFeature("phi", "B", 54, 54, + -127.39512f, "Chimera"))); /* * tear down - also in AfterMethod @@ -470,10 +473,11 @@ public class JalviewChimeraView int res, String featureType) { String where = "at position " + res; - List fs = fr.findFeaturesAtRes(seq, res); - assertEquals(fs.size(), 2, where); - assertEquals(fs.get(0).getType(), "RESNUM", where); - SequenceFeature sf = fs.get(1); + List fs = seq.getFeatures().findFeatures(res, res, + featureType); + + assertEquals(fs.size(), 1, where); + SequenceFeature sf = fs.get(0); assertEquals(sf.getType(), featureType, where); assertEquals(sf.getFeatureGroup(), "Chimera", where); assertEquals(sf.getDescription(), "True", where);