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;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
+import java.util.Iterator;
import java.util.List;
import java.util.Map;
private JSONFile jf;
- private AlignExportSettingI exportSettings;
+ private AlignExportSettingsI exportSettings;
@BeforeTest(alwaysRun = true)
public void setup() throws Exception
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);
TEST_SEQ_HEIGHT = expectedSeqs.size();
TEST_GRP_HEIGHT = expectedGrps.size();
TEST_ANOT_HEIGHT = expectedAnnots.size();
- TEST_CS_HEIGHT = expectedColSel.getSize();
+ 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
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);
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();
{
HiddenColumns cs = testJsonFile.getHiddenColumns();
Assert.assertNotNull(cs);
- Assert.assertNotNull(cs.getHiddenColumnsCopy());
- List<int[]> hiddenCols = cs.getHiddenColumnsCopy();
- Assert.assertEquals(hiddenCols.size(), TEST_CS_HEIGHT);
- Assert.assertEquals(hiddenCols.get(0), expectedColSel
- .getHiddenColumnsCopy().get(0),
+
+ Iterator<int[]> it = cs.iterator();
+ Iterator<int[]> colselit = expectedColSel.iterator();
+ Assert.assertTrue(it.hasNext());
+ Assert.assertEquals(cs.getNumberOfRegions(), TEST_CS_HEIGHT);
+ Assert.assertEquals(it.next(), colselit.next(),
"Mismatched hidden columns!");
}
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
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",
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))
+ 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.getIgnoreGapsConsensus() == actualGrp
.getIgnoreGapsConsensus()
&& colourSchemeMatches
- && expectedGrp.getSequences().size() == actualGrp
- .getSequences().size()
+ && expectedGrp.getSequences().size() == actualGrp.getSequences()
+ .size()
&& expectedGrp.getStartRes() == actualGrp.getStartRes()
&& expectedGrp.getEndRes() == actualGrp.getEndRes())
{
*/
if (!in.equals(out))
{
- System.err.println("Mismatch of " + in.toString() + " "
- + out.toString());
+ System.err.println(
+ "Mismatch of " + in.toString() + " " + out.toString());
return false;
}
/*
{
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
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;
AlignmentI copy = new Alignment(testAlignment);
SequenceGroup sg = testAlignment.getGroups().get(0);
SequenceGroup copySg = new SequenceGroup(new ArrayList<SequenceI>(),
- 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())
{
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);
git://source.jalview.org / jalview.git / blobdiff