X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FJSONFileTest.java;h=0fe721a879332e31d7861055676ed3ddd0c4e1e7;hb=aa218da8aa3bf61463d84e478b1ed498d7d964cb;hp=4cd5b54b8d0722beafd58d2364833bf00cf30e64;hpb=4306800413a28da102c15fe7301bcac7816445fe;p=jalview.git diff --git a/test/jalview/io/JSONFileTest.java b/test/jalview/io/JSONFileTest.java index 4cd5b54..0fe721a 100644 --- a/test/jalview/io/JSONFileTest.java +++ b/test/jalview/io/JSONFileTest.java @@ -22,7 +22,8 @@ package jalview.io; import static org.testng.AssertJUnit.assertNotNull; -import jalview.api.AlignExportSettingI; +import jalview.api.AlignExportSettingsI; +import jalview.datamodel.AlignExportSettingsAdapter; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; @@ -94,7 +95,7 @@ public class JSONFileTest private JSONFile jf; - private AlignExportSettingI exportSettings; + private AlignExportSettingsI exportSettings; @BeforeTest(alwaysRun = true) public void setup() throws Exception @@ -147,11 +148,10 @@ public class JSONFileTest grpSeqs.add(seqs[2]); grpSeqs.add(seqs[3]); grpSeqs.add(seqs[4]); - SequenceGroup seqGrp = new SequenceGroup(grpSeqs, - "JGroup:1883305585", + SequenceGroup seqGrp = new SequenceGroup(grpSeqs, "JGroup:1883305585", null, true, true, false, 21, 29); - ColourSchemeI scheme = ColourSchemeMapper.getJalviewColourScheme( - "zappo", seqGrp); + ColourSchemeI scheme = ColourSchemeMapper + .getJalviewColourScheme("zappo", seqGrp); seqGrp.cs.setColourScheme(scheme); seqGrp.setShowNonconserved(false); seqGrp.setDescription(null); @@ -208,44 +208,7 @@ public class JSONFileTest TEST_ANOT_HEIGHT = expectedAnnots.size(); TEST_CS_HEIGHT = expectedColSel.getNumberOfRegions(); - exportSettings = new AlignExportSettingI() - { - @Override - public boolean isExportHiddenSequences() - { - return true; - } - - @Override - public boolean isExportHiddenColumns() - { - return true; - } - - @Override - public boolean isExportGroups() - { - return true; - } - - @Override - public boolean isExportFeatures() - { - return true; - } - - @Override - public boolean isExportAnnotations() - { - return true; - } - - @Override - public boolean isCancelled() - { - return false; - } - }; + exportSettings = new AlignExportSettingsAdapter(true); AppletFormatAdapter formatAdapter = new AppletFormatAdapter(); try @@ -259,12 +222,13 @@ public class JSONFileTest AlignFrame.DEFAULT_HEIGHT); af.getViewport().setShowSequenceFeatures(jf.isShowSeqFeatures()); String colourSchemeName = jf.getGlobalColourScheme(); - ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme( - colourSchemeName, alignment); + ColourSchemeI cs = ColourSchemeMapper + .getJalviewColourScheme(colourSchemeName, alignment); af.changeColour(cs); af.getViewport().setFeaturesDisplayed(jf.getDisplayedFeatures()); - formatAdapter = new AppletFormatAdapter(af.alignPanel, exportSettings); + formatAdapter = new AppletFormatAdapter(af.alignPanel, + exportSettings); String jsonOutput = formatAdapter.formatSequences(FileFormat.Json, af.alignPanel.getAlignment(), false); @@ -272,7 +236,7 @@ public class JSONFileTest testAlignment = formatAdapter.readFile(jsonOutput, DataSourceType.PASTE, FileFormat.Json); testJsonFile = (JSONFile) formatAdapter.getAlignFile(); - // System.out.println(jsonOutput); + System.out.println(jsonOutput); } catch (IOException e) { e.printStackTrace(); @@ -381,11 +345,11 @@ public class JSONFileTest SequenceGroup sg = new SequenceGroup(); sg.addSequence(_alignment.getSequenceAt(0), false); sg.setColourScheme(null); - ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme( - ResidueColourScheme.NONE, _alignment); + ColourSchemeI cs = ColourSchemeMapper + .getJalviewColourScheme(ResidueColourScheme.NONE, _alignment); alignFrame.changeColour(cs); - alignFrame.getViewport().setFeaturesDisplayed( - bioJsonFile.getDisplayedFeatures()); + alignFrame.getViewport() + .setFeaturesDisplayed(bioJsonFile.getDisplayedFeatures()); formatAdapter = new AppletFormatAdapter(alignFrame.alignPanel, exportSettings); // export BioJSON string @@ -435,8 +399,9 @@ public class JSONFileTest for (AlignmentAnnotation annot : testAlignment.getAlignmentAnnotation()) { AlignmentAnnotation expectedAnnot = expectedAnnots.get(annot.label); - AssertJUnit.assertTrue("Failed AlignmentAnnotation Test for >>> " - + annot.label, isAnnotationMatched(expectedAnnot, annot)); + AssertJUnit.assertTrue( + "Failed AlignmentAnnotation Test for >>> " + annot.label, + isAnnotationMatched(expectedAnnot, annot)); passedCount++; } AssertJUnit.assertEquals("Some Sequences did not pass the test", @@ -473,8 +438,8 @@ public class JSONFileTest System.out.println("Testing >>> " + actualSeq.getName()); if (expectedSeq.getName().equals(actualSeq.getName()) - && expectedSeq.getSequenceAsString().equals( - actualSeq.getSequenceAsString()) + && expectedSeq.getSequenceAsString() + .equals(actualSeq.getSequenceAsString()) && expectedSeq.getStart() == actualSeq.getStart() && expectedSeq.getEnd() == actualSeq.getEnd() && featuresMatched(expectedSeq, actualSeq)) @@ -494,29 +459,29 @@ public class JSONFileTest + actualGrp.getColourText()); System.out.println(expectedGrp.getDisplayBoxes() + " | " + actualGrp.getDisplayBoxes()); - System.out.println(expectedGrp.isIgnoreGapsConsensus() + " | " - + actualGrp.isIgnoreGapsConsensus()); + System.out.println(expectedGrp.getIgnoreGapsConsensus() + " | " + + actualGrp.getIgnoreGapsConsensus()); System.out.println(expectedGrp.getSequences().size() + " | " + actualGrp.getSequences().size()); - System.out.println(expectedGrp.getStartRes() + " | " - + actualGrp.getStartRes()); - System.out.println(expectedGrp.getEndRes() + " | " - + actualGrp.getEndRes()); + System.out.println( + expectedGrp.getStartRes() + " | " + actualGrp.getStartRes()); + System.out.println( + expectedGrp.getEndRes() + " | " + actualGrp.getEndRes()); System.out.println(expectedGrp.cs.getColourScheme() + " | " + actualGrp.cs.getColourScheme()); - boolean colourSchemeMatches = (expectedGrp.cs.getColourScheme() == null && actualGrp.cs - .getColourScheme() == null) + boolean colourSchemeMatches = (expectedGrp.cs.getColourScheme() == null + && actualGrp.cs.getColourScheme() == null) || expectedGrp.cs.getColourScheme().getClass() .equals(actualGrp.cs.getColourScheme().getClass()); if (expectedGrp.getName().equals(actualGrp.getName()) && expectedGrp.getColourText() == actualGrp.getColourText() && expectedGrp.getDisplayBoxes() == actualGrp.getDisplayBoxes() - && expectedGrp.isIgnoreGapsConsensus() == actualGrp - .isIgnoreGapsConsensus() + && expectedGrp.getIgnoreGapsConsensus() == actualGrp + .getIgnoreGapsConsensus() && colourSchemeMatches - && expectedGrp.getSequences().size() == actualGrp - .getSequences().size() + && expectedGrp.getSequences().size() == actualGrp.getSequences() + .size() && expectedGrp.getStartRes() == actualGrp.getStartRes() && expectedGrp.getEndRes() == actualGrp.getEndRes()) { @@ -558,8 +523,8 @@ public class JSONFileTest */ if (!in.equals(out)) { - System.err.println("Mismatch of " + in.toString() + " " - + out.toString()); + System.err.println( + "Mismatch of " + in.toString() + " " + out.toString()); return false; } /* @@ -594,8 +559,8 @@ public class JSONFileTest { if (m1 != null || m2 != null) { - System.err - .println("only one SequenceFeature.otherDetails is not null"); + System.err.println( + "only one SequenceFeature.otherDetails is not null"); return false; } else @@ -615,8 +580,9 @@ public class JSONFileTest System.err.println(key + " in only one otherDetails"); return false; } - if (m1.get(key) == null && m2.get(key) != null || m1.get(key) != null - && m2.get(key) == null || !m1.get(key).equals(m2.get(key))) + if (m1.get(key) == null && m2.get(key) != null + || m1.get(key) != null && m2.get(key) == null + || !m1.get(key).equals(m2.get(key))) { System.err.println(key + " values in otherDetails don't match"); return false; @@ -636,8 +602,7 @@ public class JSONFileTest AlignmentI copy = new Alignment(testAlignment); SequenceGroup sg = testAlignment.getGroups().get(0); SequenceGroup copySg = new SequenceGroup(new ArrayList(), - sg.getName(), - null, sg.getDisplayBoxes(), sg.getDisplayText(), + sg.getName(), null, sg.getDisplayBoxes(), sg.getDisplayText(), sg.getColourText(), sg.getStartRes(), sg.getEndRes()); for (SequenceI seq : sg.getSequences()) { @@ -649,8 +614,8 @@ public class JSONFileTest AlignFrame af = new AlignFrame(copy, copy.getWidth(), copy.getHeight()); AppletFormatAdapter formatAdapter = new AppletFormatAdapter( af.alignPanel); - String jsonOutput = formatAdapter.formatSequences(FileFormat.Json, - copy, false); + String jsonOutput = formatAdapter.formatSequences(FileFormat.Json, copy, + false); formatAdapter = new AppletFormatAdapter(); AlignmentI newAlignment = formatAdapter.readFile(jsonOutput, DataSourceType.PASTE, FileFormat.Json);