From: Ben Soares Date: Thu, 24 Jan 2019 15:29:54 +0000 (+0000) Subject: JAL-3141 Eclipse re-formatting of file X-Git-Tag: Release_2_11_0~17^2~97^2~18 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=6db15a0553c0323a33121baad6d23ac9d8d4250b;p=jalview.git JAL-3141 Eclipse re-formatting of file --- diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java index 3f4ed71..d6df39a 100644 --- a/test/jalview/project/Jalview2xmlTests.java +++ b/test/jalview/project/Jalview2xmlTests.java @@ -109,35 +109,38 @@ public class Jalview2xmlTests extends Jalview2xmlBase assertNotNull(af, "Didn't read input file " + inFile); int olddsann = countDsAnn(af.getViewport()); assertTrue(olddsann > 0, "Didn't find any dataset annotations"); - af.changeColour_actionPerformed(JalviewColourScheme.RNAHelices - .toString()); + af.changeColour_actionPerformed( + JalviewColourScheme.RNAHelices.toString()); assertTrue( - af.getViewport().getGlobalColourScheme() instanceof RNAHelicesColour, + af.getViewport() + .getGlobalColourScheme() instanceof RNAHelicesColour, "Couldn't apply RNA helices colourscheme"); assertTrue(af.saveAlignment(tfile, FileFormat.Jalview), "Failed to store as a project."); af.closeMenuItem_actionPerformed(true); af = null; - af = new FileLoader() - .LoadFileWaitTillLoaded(tfile, DataSourceType.FILE); + af = new FileLoader().LoadFileWaitTillLoaded(tfile, + DataSourceType.FILE); assertNotNull(af, "Failed to import new project"); int newdsann = countDsAnn(af.getViewport()); assertEquals(olddsann, newdsann, "Differing numbers of dataset sequence annotation\nOriginally " + olddsann + " and now " + newdsann); - System.out - .println("Read in same number of annotations as originally present (" + System.out.println( + "Read in same number of annotations as originally present (" + olddsann + ")"); assertTrue( - af.getViewport().getGlobalColourScheme() instanceof RNAHelicesColour, + af.getViewport() + .getGlobalColourScheme() instanceof RNAHelicesColour, "RNA helices colourscheme was not applied on import."); } @Test(groups = { "Functional" }) public void testTCoffeeScores() throws Exception { - String inFile = "examples/uniref50.fa", inAnnot = "examples/uniref50.score_ascii"; + String inFile = "examples/uniref50.fa", + inAnnot = "examples/uniref50.score_ascii"; String tfile = File.createTempFile("JalviewTest", ".jvp") .getAbsolutePath(); AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile, @@ -146,28 +149,32 @@ public class Jalview2xmlTests extends Jalview2xmlBase af.loadJalviewDataFile(inAnnot, DataSourceType.FILE, null, null); assertSame(af.getViewport().getGlobalColourScheme().getClass(), TCoffeeColourScheme.class, "Didn't set T-coffee colourscheme"); - assertNotNull(ColourSchemeProperty.getColourScheme(af.getViewport() - .getAlignment(), af.getViewport().getGlobalColourScheme() - .getSchemeName()), "Recognise T-Coffee score from string"); + assertNotNull( + ColourSchemeProperty.getColourScheme( + af.getViewport().getAlignment(), + af.getViewport().getGlobalColourScheme() + .getSchemeName()), + "Recognise T-Coffee score from string"); assertTrue(af.saveAlignment(tfile, FileFormat.Jalview), "Failed to store as a project."); af.closeMenuItem_actionPerformed(true); af = null; - af = new FileLoader() - .LoadFileWaitTillLoaded(tfile, DataSourceType.FILE); + af = new FileLoader().LoadFileWaitTillLoaded(tfile, + DataSourceType.FILE); assertNotNull(af, "Failed to import new project"); assertSame(af.getViewport().getGlobalColourScheme().getClass(), TCoffeeColourScheme.class, "Didn't set T-coffee colourscheme for imported project."); - System.out - .println("T-Coffee score shading successfully recovered from project."); + System.out.println( + "T-Coffee score shading successfully recovered from project."); } @Test(groups = { "Functional" }) public void testColourByAnnotScores() throws Exception { - String inFile = "examples/uniref50.fa", inAnnot = "examples/testdata/uniref50_iupred.jva"; + String inFile = "examples/uniref50.fa", + inAnnot = "examples/testdata/uniref50_iupred.jva"; String tfile = File.createTempFile("JalviewTest", ".jvp") .getAbsolutePath(); AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile, @@ -178,12 +185,12 @@ public class Jalview2xmlTests extends Jalview2xmlBase .getSequenceAt(0).getAnnotation("IUPredWS (Short)"); assertTrue( - aa != null && aa.length > 0, + aa != null && aa.length > 0, "Didn't find any IUPred annotation to use to shade alignment."); AnnotationColourGradient cs = new AnnotationColourGradient(aa[0], null, AnnotationColourGradient.ABOVE_THRESHOLD); - AnnotationColourGradient gcs = new AnnotationColourGradient(aa[0], - null, AnnotationColourGradient.BELOW_THRESHOLD); + AnnotationColourGradient gcs = new AnnotationColourGradient(aa[0], null, + AnnotationColourGradient.BELOW_THRESHOLD); cs.setSeqAssociated(true); gcs.setSeqAssociated(true); af.changeColour(cs); @@ -199,15 +206,15 @@ public class Jalview2xmlTests extends Jalview2xmlBase "Failed to store as a project."); af.closeMenuItem_actionPerformed(true); af = null; - af = new FileLoader() - .LoadFileWaitTillLoaded(tfile, DataSourceType.FILE); + af = new FileLoader().LoadFileWaitTillLoaded(tfile, + DataSourceType.FILE); assertNotNull(af, "Failed to import new project"); // check for group and alignment colourschemes ColourSchemeI _rcs = af.getViewport().getGlobalColourScheme(); - ColourSchemeI _rgcs = af.getViewport().getAlignment().getGroups() - .get(0).getColourScheme(); + ColourSchemeI _rgcs = af.getViewport().getAlignment().getGroups().get(0) + .getColourScheme(); assertNotNull(_rcs, "Didn't recover global colourscheme"); assertTrue(_rcs instanceof AnnotationColourGradient, "Didn't recover annotation colour global scheme"); @@ -217,8 +224,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase boolean diffseqcols = false, diffgseqcols = false; SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray(); - for (int p = 0, pSize = af.getViewport().getAlignment().getWidth(); p < pSize - && (!diffseqcols || !diffgseqcols); p++) + for (int p = 0, pSize = af.getViewport().getAlignment() + .getWidth(); p < pSize && (!diffseqcols || !diffgseqcols); p++) { if (_rcs.findColour(sqs[0].getCharAt(p), p, sqs[0], null, 0f) != _rcs .findColour(sqs[5].getCharAt(p), p, sqs[5], null, 0f)) @@ -227,8 +234,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase } } assertTrue(diffseqcols, "Got Different sequence colours"); - System.out - .println("Per sequence colourscheme (Background) successfully applied and recovered."); + System.out.println( + "Per sequence colourscheme (Background) successfully applied and recovered."); assertNotNull(_rgcs, "Didn't recover group colourscheme"); assertTrue(_rgcs instanceof AnnotationColourGradient, @@ -237,25 +244,26 @@ public class Jalview2xmlTests extends Jalview2xmlBase assertTrue(__rcs.isSeqAssociated(), "Group Annotation colourscheme wasn't sequence associated"); - for (int p = 0, pSize = af.getViewport().getAlignment().getWidth(); p < pSize - && (!diffseqcols || !diffgseqcols); p++) + for (int p = 0, pSize = af.getViewport().getAlignment() + .getWidth(); p < pSize && (!diffseqcols || !diffgseqcols); p++) { - if (_rgcs.findColour(sqs[1].getCharAt(p), p, sqs[1], null, 0f) != _rgcs - .findColour(sqs[2].getCharAt(p), p, sqs[2], null, 0f)) + if (_rgcs.findColour(sqs[1].getCharAt(p), p, sqs[1], null, + 0f) != _rgcs.findColour(sqs[2].getCharAt(p), p, sqs[2], null, + 0f)) { diffgseqcols = true; } } assertTrue(diffgseqcols, "Got Different group sequence colours"); - System.out - .println("Per sequence (Group) colourscheme successfully applied and recovered."); + System.out.println( + "Per sequence (Group) colourscheme successfully applied and recovered."); } @Test(groups = { "Functional" }) public void gatherViewsHere() throws Exception { - int origCount = Desktop.getAlignFrames() == null ? 0 : Desktop - .getAlignFrames().length; + int origCount = Desktop.getAlignFrames() == null ? 0 + : Desktop.getAlignFrames().length; AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( "examples/exampleFile_2_7.jar", DataSourceType.FILE); assertNotNull(af, "Didn't read in the example file correctly."); @@ -336,14 +344,14 @@ public class Jalview2xmlTests extends Jalview2xmlBase sq.findPosition(p); try { - assertTrue( - (alaa.annotations[p] == null && refan.annotations[p] == null) - || alaa.annotations[p].value == refan.annotations[p].value, + assertTrue((alaa.annotations[p] == null + && refan.annotations[p] == null) + || alaa.annotations[p].value == refan.annotations[p].value, "Mismatch at alignment position " + p); } catch (NullPointerException q) { - Assert.fail("Mismatch of alignment annotations at position " - + p + " Ref seq ann: " + refan.annotations[p] + Assert.fail("Mismatch of alignment annotations at position " + p + + " Ref seq ann: " + refan.annotations[p] + " alignment " + alaa.annotations[p]); } } @@ -378,10 +386,10 @@ public class Jalview2xmlTests extends Jalview2xmlBase AssertJUnit.assertFalse(structureStyle.sameStyle(groupStyle)); groups.getAlignViewport().setViewStyle(structureStyle); - AssertJUnit.assertFalse(groupStyle.sameStyle(groups.getAlignViewport() - .getViewStyle())); - Assert.assertTrue(structureStyle.sameStyle(groups.getAlignViewport() - .getViewStyle())); + AssertJUnit.assertFalse( + groupStyle.sameStyle(groups.getAlignViewport().getViewStyle())); + Assert.assertTrue(structureStyle + .sameStyle(groups.getAlignViewport().getViewStyle())); } @@ -402,9 +410,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase // check FileLoader returned a reference to the one alignFrame that is // actually on the Desktop - assertSame( - af, - Desktop.getAlignFrameFor(af.getViewport()), + assertSame(af, Desktop.getAlignFrameFor(af.getViewport()), "Jalview2XML.loadAlignFrame() didn't return correct AlignFrame reference for multiple view window"); Desktop.explodeViews(af); @@ -431,11 +437,12 @@ public class Jalview2xmlTests extends Jalview2xmlBase af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), DataSourceType.FILE); Assert.assertNotNull(af); + Assert.assertEquals(Desktop.getAlignFrames().length, + Desktop.getAlignmentPanels( + af.getViewport().getSequenceSetId()).length); Assert.assertEquals( - Desktop.getAlignFrames().length, - Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length); - Assert.assertEquals( - Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length, + Desktop.getAlignmentPanels( + af.getViewport().getSequenceSetId()).length, oldviews); } @@ -537,8 +544,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase assertTrue(Jalview2XML.isVersionStringLaterThan(null, "Test")); assertTrue(Jalview2XML.isVersionStringLaterThan(null, "TEST")); assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "Test")); - assertTrue(Jalview2XML - .isVersionStringLaterThan(null, "Automated Build")); + assertTrue( + Jalview2XML.isVersionStringLaterThan(null, "Automated Build")); assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "Automated Build")); assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", @@ -647,8 +654,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase n++; } - File tfile = File - .createTempFile("testStoreAndRecoverGroupReps", ".jvp"); + File tfile = File.createTempFile("testStoreAndRecoverGroupReps", + ".jvp"); try { new Jalview2XML(false).saveState(tfile); @@ -687,9 +694,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase */ List hidden = hiddenSeqNames.get(ap.getViewName()); HiddenSequences hs = alignment.getHiddenSequences(); - assertEquals( - hidden.size(), - hs.getSize(), + assertEquals(hidden.size(), hs.getSize(), "wrong number of restored hidden sequences in " + ap.getViewName()); } @@ -731,14 +736,18 @@ public class Jalview2xmlTests extends Jalview2xmlBase pdbEntries[1] = new PDBEntry("3W5V", "B", Type.PDB, testFile); pdbEntries[2] = new PDBEntry("3W5V", "C", Type.PDB, testFile); pdbEntries[3] = new PDBEntry("3W5V", "D", Type.PDB, testFile); - Assert.assertEquals(seqs[0].getDatasetSequence().getAllPDBEntries() - .get(0), pdbEntries[0]); - Assert.assertEquals(seqs[1].getDatasetSequence().getAllPDBEntries() - .get(0), pdbEntries[1]); - Assert.assertEquals(seqs[2].getDatasetSequence().getAllPDBEntries() - .get(0), pdbEntries[2]); - Assert.assertEquals(seqs[3].getDatasetSequence().getAllPDBEntries() - .get(0), pdbEntries[3]); + Assert.assertEquals( + seqs[0].getDatasetSequence().getAllPDBEntries().get(0), + pdbEntries[0]); + Assert.assertEquals( + seqs[1].getDatasetSequence().getAllPDBEntries().get(0), + pdbEntries[1]); + Assert.assertEquals( + seqs[2].getDatasetSequence().getAllPDBEntries().get(0), + pdbEntries[2]); + Assert.assertEquals( + seqs[3].getDatasetSequence().getAllPDBEntries().get(0), + pdbEntries[3]); File tfile = File.createTempFile("testStoreAndRecoverPDBEntry", ".jvp"); try @@ -834,8 +843,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase sg.setEndRes(25); av.setSelectionGroup(sg); PopupMenu popupMenu = new PopupMenu(af.alignPanel, null, null); - popupMenu.changeColour_actionPerformed(JalviewColourScheme.Strand - .toString()); + popupMenu.changeColour_actionPerformed( + JalviewColourScheme.Strand.toString()); assertTrue(sg.getColourScheme() instanceof StrandColourScheme); assertEquals(al.getGroups().size(), 1); assertSame(al.getGroups().get(0), sg); @@ -978,8 +987,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase */ af.closeMenuItem_actionPerformed(true); af = null; - af = new FileLoader() - .LoadFileWaitTillLoaded(filePath, DataSourceType.FILE); + af = new FileLoader().LoadFileWaitTillLoaded(filePath, + DataSourceType.FILE); assertNotNull(af, "Failed to import new project"); /*