{
final SequenceI jds = jal.getSequenceAt(i);
final SequenceI jdatasq = jds.getDatasetSequence() == null ? jds
- : jds
- .getDatasetSequence();
+ : jds.getDatasetSequence();
String id = seqHash(jds);
if (seqRefIds.get(id) != null)
if (jds.getSequenceFeatures() != null)
{
- jalview.datamodel.SequenceFeature[] sf = jds
- .getSequenceFeatures();
+ jalview.datamodel.SequenceFeature[] sf = jds.getSequenceFeatures();
int index = 0;
while (index < sf.length)
{
}
}
- // {
- // AlcodonFrame alc = new AlcodonFrame();
- // vamsasSet.addAlcodonFrame(alc);
- // for (int p = 0; p < acf.aaWidth; p++)
- // {
- // Alcodon cmap = new Alcodon();
- // if (acf.codons[p] != null)
- // {
- // // Null codons indicate a gapped column in the translated peptide
- // // alignment.
- // cmap.setPos1(acf.codons[p][0]);
- // cmap.setPos2(acf.codons[p][1]);
- // cmap.setPos3(acf.codons[p][2]);
- // }
- // alc.addAlcodon(cmap);
- // }
- // if (acf.getProtMappings() != null
- // && acf.getProtMappings().length > 0)
- // {
- // SequenceI[] dnas = acf.getdnaSeqs();
- // jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
- // for (int m = 0; m < pmaps.length; m++)
- // {
- // AlcodMap alcmap = new AlcodMap();
- // alcmap.setDnasq(seqHash(dnas[m]));
- // alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
- // false));
- // alc.addAlcodMap(alcmap);
- // }
- // }
+ // {
+ // AlcodonFrame alc = new AlcodonFrame();
+ // vamsasSet.addAlcodonFrame(alc);
+ // for (int p = 0; p < acf.aaWidth; p++)
+ // {
+ // Alcodon cmap = new Alcodon();
+ // if (acf.codons[p] != null)
+ // {
+ // // Null codons indicate a gapped column in the translated peptide
+ // // alignment.
+ // cmap.setPos1(acf.codons[p][0]);
+ // cmap.setPos2(acf.codons[p][1]);
+ // cmap.setPos3(acf.codons[p][2]);
+ // }
+ // alc.addAlcodon(cmap);
+ // }
+ // if (acf.getProtMappings() != null
+ // && acf.getProtMappings().length > 0)
+ // {
+ // SequenceI[] dnas = acf.getdnaSeqs();
+ // jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
+ // for (int m = 0; m < pmaps.length; m++)
+ // {
+ // AlcodMap alcmap = new AlcodMap();
+ // alcmap.setDnasq(seqHash(dnas[m]));
+ // alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
+ // false));
+ // alc.addAlcodMap(alcmap);
+ // }
+ // }
}
}
if (sg.cs instanceof jalview.schemes.UserColourScheme)
{
- jGroup.setColour(setUserColourScheme(sg.cs, userColours,
- jms));
+ jGroup.setColour(setUserColourScheme(sg.cs, userColours, jms));
}
else
{
- jGroup
- .setColour(ColourSchemeProperty.getColourName(sg.cs));
+ jGroup.setColour(ColourSchemeProperty.getColourName(sg.cs));
}
}
else if (sg.cs instanceof jalview.schemes.AnnotationColourGradient)
}
else if (sg.cs instanceof jalview.schemes.UserColourScheme)
{
- jGroup
- .setColour(setUserColourScheme(sg.cs, userColours, jms));
+ jGroup.setColour(setUserColourScheme(sg.cs, userColours, jms));
}
else
{
else
{
setting.setColour(ap.getSeqPanel().seqCanvas
- .getFeatureRenderer()
- .getColour(renderOrder[ro]).getRGB());
+ .getFeatureRenderer().getColour(renderOrder[ro])
+ .getRGB());
}
setting.setDisplay(av.getFeaturesDisplayed().isVisible(
final SequenceI jds, List<String> viewIds, AlignmentPanel ap,
boolean storeDataset)
{
+ if (Desktop.desktop == null)
+ {
+ return;
+ }
JInternalFrame[] frames = Desktop.desktop.getAllFrames();
for (int f = frames.length - 1; f > -1; f--)
{
{
String varnaStateFile = varna.getStateInfo(model.rna);
- jarEntryName = RNA_PREFIX + viewId + "_"
- + nextCounter();
+ jarEntryName = RNA_PREFIX + viewId + "_" + nextCounter();
copyFileToJar(jout, varnaStateFile, jarEntryName);
rnaSessions.put(model, jarEntryName);
}
private void storeAlignmentAnnotation(AlignmentAnnotation[] aa,
IdentityHashMap<SequenceGroup, String> groupRefs,
- AlignmentViewport av,
- Set<String> calcIdSet, boolean storeDS, SequenceSet vamsasSet)
+ AlignmentViewport av, Set<String> calcIdSet, boolean storeDS,
+ SequenceSet vamsasSet)
{
for (int i = 0; i < aa.length; i++)
if (groupIdr == null)
{
// make a locally unique String
- groupRefs.put(annotation.groupRef,
+ groupRefs.put(
+ annotation.groupRef,
groupIdr = ("" + System.currentTimeMillis()
- + annotation.groupRef.getName() + groupRefs.size()));
+ + annotation.groupRef.getName() + groupRefs
+ .size()));
}
an.setGroupRef(groupIdr.toString());
}
.entrySet())
{
AlignFrame af = candidate.getValue();
- if (!addedToSplitFrames.contains(af)) {
+ if (!addedToSplitFrames.contains(af))
+ {
Viewport view = candidate.getKey();
Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
view.getHeight());
// set visiblity for other annotation in this view
String annotationId = annotation.getId();
- if (annotationId != null
- && annotationIds.containsKey(annotationId))
+ if (annotationId != null && annotationIds.containsKey(annotationId))
{
AlignmentAnnotation jda = annotationIds.get(annotationId);
// in principle Visible should always be true for annotation displayed
SequenceGroup sg = new SequenceGroup(seqs, jGroup.getName(), cs,
jGroup.getDisplayBoxes(), jGroup.getDisplayText(),
- jGroup.getColourText(), jGroup.getStart(),
- jGroup.getEnd());
+ jGroup.getColourText(), jGroup.getStart(), jGroup.getEnd());
sg.setOutlineColour(new java.awt.Color(jGroup.getOutlineColour()));
if (jGroup.getId() != null && groupAnnotRefs.size() > 0)
{
// re-instate unique group/annotation row reference
- List<AlignmentAnnotation> jaal = groupAnnotRefs
- .get(jGroup.getId());
+ List<AlignmentAnnotation> jaal = groupAnnotRefs.get(jGroup
+ .getId());
if (jaal != null)
{
for (AlignmentAnnotation jaa : jaal)
if (addAnnotSchemeGroup)
{
// reconstruct the annotation colourscheme
- sg.cs = constructAnnotationColour(
- jGroup.getAnnotationColours(), null, al, jms, false);
+ sg.cs = constructAnnotationColour(jGroup.getAnnotationColours(),
+ null, al, jms, false);
}
}
}
for (int i = 0; i < jseq.getRnaViewerCount(); i++)
{
RnaViewer viewer = jseq.getRnaViewer(i);
- AppVarna appVarna = findOrCreateVarnaViewer(viewer, uniqueSetSuffix,
- ap);
+ AppVarna appVarna = findOrCreateVarnaViewer(viewer,
+ uniqueSetSuffix, ap);
for (int j = 0; j < viewer.getSecondaryStructureCount(); j++)
{
* viewer not found - make it
*/
RnaViewerModel model = new RnaViewerModel(postLoadId,
- viewer.getTitle(), viewer.getXpos(),
- viewer.getYpos(), viewer.getWidth(), viewer.getHeight(),
+ viewer.getTitle(), viewer.getXpos(), viewer.getYpos(),
+ viewer.getWidth(), viewer.getHeight(),
viewer.getDividerLocation());
AppVarna varna = new AppVarna(model, ap);
* @param af
* @param jprovider
*/
- protected void createChimeraViewer(Entry<String, StructureViewerModel> viewerData,
- AlignFrame af,
+ protected void createChimeraViewer(
+ Entry<String, StructureViewerModel> viewerData, AlignFrame af,
jarInputStreamProvider jprovider)
{
StructureViewerModel data = viewerData.getValue();
- String chimeraSessionFile = data.getStateData();
+ String chimeraSessionFile = data.getStateData();
/*
* Copy Chimera session from jar entry "viewer_"+viewId to a temporary file
String newViewId = viewerData.getKey();
ChimeraViewFrame cvf = new ChimeraViewFrame(chimeraSessionFile,
- af.alignPanel, pdbArray,
- seqsArray, colourByChimera, colourBySequence, newViewId);
+ af.alignPanel, pdbArray, seqsArray, colourByChimera,
+ colourBySequence, newViewId);
cvf.setSize(data.getWidth(), data.getHeight());
cvf.setLocation(data.getX(), data.getY());
}
newFileLoc.append(";");
}
- if (newFileLoc.length() > 0)
+ if (newFileLoc.length() == 0)
+ {
+ return;
+ }
+ int histbug = newFileLoc.indexOf("history = ");
+ if (histbug > -1)
{
- int histbug = newFileLoc.indexOf("history = ");
+ /*
+ * change "history = [true|false];" to "history = [1|0];"
+ */
histbug += 10;
int diff = histbug == -1 ? -1 : newFileLoc.indexOf(";", histbug);
String val = (diff == -1) ? null : newFileLoc
.substring(histbug, diff);
if (val != null && val.length() >= 4)
{
- if (val.contains("e"))
+ if (val.contains("e")) // eh? what can it be?
{
if (val.trim().equals("true"))
{
newFileLoc.replace(histbug, diff, val);
}
}
+ }
- final String[] pdbf = pdbfilenames.toArray(new String[pdbfilenames
- .size()]);
- final String[] id = pdbids.toArray(new String[pdbids.size()]);
- final SequenceI[][] sq = seqmaps
- .toArray(new SequenceI[seqmaps.size()][]);
- final String fileloc = newFileLoc.toString();
- final String sviewid = viewerData.getKey();
- final AlignFrame alf = af;
- final Rectangle rect = new Rectangle(svattrib.getX(),
- svattrib.getY(), svattrib.getWidth(), svattrib.getHeight());
- try
+ final String[] pdbf = pdbfilenames.toArray(new String[pdbfilenames
+ .size()]);
+ final String[] id = pdbids.toArray(new String[pdbids.size()]);
+ final SequenceI[][] sq = seqmaps
+ .toArray(new SequenceI[seqmaps.size()][]);
+ final String fileloc = newFileLoc.toString();
+ final String sviewid = viewerData.getKey();
+ final AlignFrame alf = af;
+ final Rectangle rect = new Rectangle(svattrib.getX(), svattrib.getY(),
+ svattrib.getWidth(), svattrib.getHeight());
+ try
+ {
+ javax.swing.SwingUtilities.invokeAndWait(new Runnable()
{
- javax.swing.SwingUtilities.invokeAndWait(new Runnable()
+ @Override
+ public void run()
{
- @Override
- public void run()
+ JalviewStructureDisplayI sview = null;
+ try
{
- JalviewStructureDisplayI sview = null;
- try
- {
- sview = new StructureViewer(alf.alignPanel
- .getStructureSelectionManager()).createView(
- StructureViewer.ViewerType.JMOL, pdbf, id, sq,
- alf.alignPanel, svattrib, fileloc, rect, sviewid);
- addNewStructureViewer(sview);
- } catch (OutOfMemoryError ex)
+ sview = new StructureViewer(alf.alignPanel
+ .getStructureSelectionManager()).createView(
+ StructureViewer.ViewerType.JMOL, pdbf, id, sq,
+ alf.alignPanel, svattrib, fileloc, rect, sviewid);
+ addNewStructureViewer(sview);
+ } catch (OutOfMemoryError ex)
+ {
+ new OOMWarning("restoring structure view for PDB id " + id,
+ (OutOfMemoryError) ex.getCause());
+ if (sview != null && sview.isVisible())
{
- new OOMWarning("restoring structure view for PDB id " + id,
- (OutOfMemoryError) ex.getCause());
- if (sview != null && sview.isVisible())
- {
- sview.closeViewer(false);
- sview.setVisible(false);
- sview.dispose();
- }
+ sview.closeViewer(false);
+ sview.setVisible(false);
+ sview.dispose();
}
}
- });
- } catch (InvocationTargetException ex)
- {
- warn("Unexpected error when opening Jmol view.", ex);
+ }
+ });
+ } catch (InvocationTargetException ex)
+ {
+ warn("Unexpected error when opening Jmol view.", ex);
- } catch (InterruptedException e)
- {
- // e.printStackTrace();
- }
+ } catch (InterruptedException e)
+ {
+ // e.printStackTrace();
}
+
}
/**
}
}
af.setMenusFromViewport(af.viewport);
-
+
// TODO: we don't need to do this if the viewport is aready visible.
/*
* Add the AlignFrame to the desktop (it may be 'gathered' later), unless it
}
}
}
-
+
return result;
}
import java.io.File;
import java.io.IOException;
import java.io.InputStreamReader;
+import java.util.ArrayList;
import org.testng.Assert;
import org.testng.FileAssert;
-import org.testng.annotations.AfterClass;
-import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeTest;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
public class CommandLineOperations
{
- @BeforeClass
- public static void setUpBeforeClass() throws Exception
- {
- }
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception
- {
- }
+ private ArrayList<String> successfulCMDs = new ArrayList<String>();
/***
* from
private static class Worker extends Thread
{
private final Process process;
-
+ private BufferedReader outputReader;
+ private BufferedReader errorReader;
private Integer exit;
private Worker(Process process)
return;
}
}
+
+ public BufferedReader getOutputReader()
+ {
+ return outputReader;
+ }
+
+ public void setOutputReader(BufferedReader outputReader)
+ {
+ this.outputReader = outputReader;
+ }
+
+ public BufferedReader getErrorReader()
+ {
+ return errorReader;
+ }
+
+ public void setErrorReader(BufferedReader errorReader)
+ {
+ this.errorReader = errorReader;
+ }
}
private Worker jalviewDesktopRunner(boolean withAwt, String cmd,
- int timeout) throws InterruptedException, IOException
+ int timeout)
{
String _cmd = "java "
+ (withAwt ? "-Djava.awt.headless=true" : "")
+ " -Djava.ext.dirs=./lib -classpath ./classes jalview.bin.Jalview ";
- System.out.println("############ Testing Jalview CMD: " + _cmd + cmd);
- Process ls2_proc = Runtime.getRuntime().exec(_cmd + cmd);
- BufferedReader outputReader = new BufferedReader(new InputStreamReader(
- ls2_proc.getInputStream()));
-
- BufferedReader errorReader = new BufferedReader(new InputStreamReader(
- ls2_proc.getErrorStream()));
- Worker worker = new Worker(ls2_proc);
- worker.start();
- worker.join(timeout);
- // System.out.println("Output: ");
- // String ln = null;
- // while ((ln = outputReader.readLine()) != null)
- // {
- // System.out.println(ln);
- // }
- //
- // System.out.println("Error: ");
- // while ((ln = errorReader.readLine()) != null)
- // {
- // System.out.println(ln);
- // }
+ System.out.println("CMD [" + cmd + "]");
+ Process ls2_proc = null;
+ Worker worker = null;
+ try
+ {
+ ls2_proc = Runtime.getRuntime().exec(_cmd + cmd);
+ } catch (IOException e1)
+ {
+ e1.printStackTrace();
+ }
+ if (ls2_proc != null)
+ {
+ BufferedReader outputReader = new BufferedReader(
+ new InputStreamReader(ls2_proc.getInputStream()));
+ BufferedReader errorReader = new BufferedReader(
+ new InputStreamReader(ls2_proc.getErrorStream()));
+ worker = new Worker(ls2_proc);
+ worker.start();
+ try
+ {
+ worker.join(timeout);
+ } catch (InterruptedException e)
+ {
+ // e.printStackTrace();
+ }
+ worker.setOutputReader(outputReader);
+ worker.setErrorReader(errorReader);
+ }
return worker;
}
- @BeforeTest
+ @BeforeTest(alwaysRun = true)
public void initialize()
{
new CommandLineOperations();
}
-
- @Test(groups =
- { "Functional" }, dataProvider = "headlessModeOutputParams")
- public void testHeadlessModeOutputs(String harg, String type,
- String fileName, boolean withAWT, int expectedMinFileSize)
+ @BeforeTest(alwaysRun = true)
+ public void setUpForHeadlessCommandLineInputOperations()
+ throws IOException
{
- String cmd = harg + type + " " + fileName;
- // System.out.println(">>>>>>>>>>>>>>>> Command : " + cmd);
- File file = new File(fileName);
- Worker worker = null;
- try
+ String cmds = "nodisplay -open examples/uniref50.fa -sortbytree -props FILE -colour zappo "
+ + "-jabaws http://www.compbio.dundee.ac.uk/jabaws -nosortbytree -dasserver nickname=www.test.com "
+ + "-features examples/testdata/plantfdx.features -annotations examples/testdata/plantfdx.annotations -tree examples/testdata/uniref50_test_tree";
+ Worker worker = jalviewDesktopRunner(true, cmds, 9000);
+ String ln = null;
+ while ((ln = worker.getOutputReader().readLine()) != null)
{
- worker = jalviewDesktopRunner(withAWT, cmd, 9000);
- } catch (InterruptedException e)
+ System.out.println(ln);
+ successfulCMDs.add(ln);
+ }
+ }
+
+ @BeforeTest(alwaysRun = true)
+ public void setUpForCommandLineInputOperations() throws IOException
+ {
+ String cmds = "-open examples/uniref50.fa -noquestionnaire -nousagestats";
+ Worker worker = jalviewDesktopRunner(false, cmds, 9000);
+ String ln = null;
+ int count = 0;
+ while ((ln = worker.getErrorReader().readLine()) != null)
{
- e.printStackTrace();
- } catch (IOException e)
+ System.out.println(ln);
+ successfulCMDs.add(ln);
+ if (++count > 5)
+ {
+ break;
+ }
+ }
+ if (worker != null && worker.exit == null)
{
- e.printStackTrace();
+ worker.interrupt();
+ Thread.currentThread().interrupt();
+ worker.process.destroy();
}
+ }
+
+ @Test(groups =
+ { "Functional" }, dataProvider = "allInputOpearationsData")
+ public void testAllInputOperations(String expectedString,
+ String failureMsg)
+ {
+ Assert.assertTrue(successfulCMDs.contains(expectedString), failureMsg);
+ }
+
+ @Test(groups =
+ { "Functional" }, dataProvider = "headlessModeOutputOperationsData")
+ public void testHeadlessModeOutputOperations(String harg, String type,
+ String fileName, boolean withAWT, int expectedMinFileSize,
+ int timeout)
+ {
+ String cmd = harg + type + " " + fileName;
+ // System.out.println(">>>>>>>>>>>>>>>> Command : " + cmd);
+ File file = new File(fileName);
+ Worker worker = jalviewDesktopRunner(withAWT, cmd, timeout);
FileAssert.assertFile(file, "Didn't create an output" + type
+ " file.[" + harg + "]");
worker.interrupt();
Thread.currentThread().interrupt();
worker.process.destroy();
- Assert.fail("Jalview did not exit after "
+ Assert.fail("Jalview did not exit after "
+ type
+ " generation (try running test again to verify - timeout at 9000ms). ["
+ harg + "]");
new File(fileName).delete();
}
- @DataProvider(name = "headlessModeOutputParams")
- public static Object[][] headlessModeOutput()
+
+ @DataProvider(name = "allInputOpearationsData")
+ public Object[][] getHeadlessModeInputParams()
+ {
+ return new Object[][]
+ {
+ // headless mode input operations
+ { "CMD [-color zappo] executed successfully!",
+ "Failed command : -color zappo" },
+ { "CMD [-props FILE] executed successfully!",
+ "Failed command : -props File" },
+ { "CMD [-sortbytree] executed successfully!",
+ "Failed command : -sortbytree" },
+ {
+ "CMD [-jabaws http://www.compbio.dundee.ac.uk/jabaws] executed successfully!",
+ "Failed command : -jabaws http://www.compbio.dundee.ac.uk/jabaws" },
+ { "CMD [-open examples/uniref50.fa] executed successfully!",
+ "Failed command : -open examples/uniref50.fa" },
+ { "CMD [-nosortbytree] executed successfully!",
+ "Failed command : -nosortbytree" },
+ { "CMD [-dasserver nickname=www.test.com] executed successfully!",
+ "Failed command : -dasserver nickname=www.test.com" },
+ {
+ "CMD [-features examples/testdata/plantfdx.features] executed successfully!",
+ "Failed command : -features examples/testdata/plantfdx.features" },
+ {
+ "CMD [-annotations examples/testdata/plantfdx.annotations] executed successfully!",
+ "Failed command : -annotations examples/testdata/plantfdx.annotations" },
+ {
+ "CMD [-tree examples/testdata/uniref50_test_tree] executed successfully!",
+ "Failed command : -tree examples/testdata/uniref50_test_tree" },
+ // non headless mode input operations
+ { "CMD [-nousagestats] executed successfully!",
+ "Failed command : -nousagestats" },
+ { "CMD [-noquestionnaire] executed successfully!",
+ "Failed command : -noquestionnaire nickname=www.test.com" }
+ };
+
+ }
+
+ @DataProvider(name = "headlessModeOutputOperationsData")
+ public static Object[][] getHeadlessModeOutputParams()
{
return new Object[][]
{
{ "nodisplay -open examples/uniref50.fa", " -eps",
- "test_uniref50_out.eps", true, 4096 },
+ "test_uniref50_out.eps", true, 4096, 4000 },
{ "nodisplay -open examples/uniref50.fa", " -eps",
- "test_uniref50_out.eps", false, 4096 },
- { "headless -open examples/uniref50.fa", " -eps",
- "test_uniref50_out.eps", true, 4096 },
- { "headless -open examples/uniref50.fa", " -eps",
- "test_uniref50_out.eps", false, 4096 },
+ "test_uniref50_out.eps", false, 4096, 4000 },
{ "nogui -open examples/uniref50.fa", " -eps",
- "test_uniref50_out.eps", true, 4096 },
+ "test_uniref50_out.eps", true, 4096, 4000 },
{ "nogui -open examples/uniref50.fa", " -eps",
- "test_uniref50_out.eps", false, 4096 },
- { "headless -open examples/uniref50.fa", " -svg",
- "test_uniref50_out.svg", true, 4096 },
+ "test_uniref50_out.eps", false, 4096, 4000 },
+ { "headless -open examples/uniref50.fa", " -eps",
+ "test_uniref50_out.eps", true, 4096, 4000 },
{ "headless -open examples/uniref50.fa", " -svg",
- "test_uniref50_out.svg", false, 4096 },
+ "test_uniref50_out.svg", false, 4096, 3000 },
{ "headless -open examples/uniref50.fa", " -png",
- "test_uniref50_out.png", true, 4096 },
- { "headless -open examples/uniref50.fa", " -png",
- "test_uniref50_out.png", false, 4096 },
- { "headless -open examples/uniref50.fa", " -html",
- "test_uniref50_out.html", true, 4096 },
+ "test_uniref50_out.png", true, 4096, 3000 },
{ "headless -open examples/uniref50.fa", " -html",
- "test_uniref50_out.html", false, 4096 },
+ "test_uniref50_out.html", true, 4096, 3000 },
{ "headless -open examples/uniref50.fa", " -fasta",
- "test_uniref50_out.mfa", true, 2096 },
- { "headless -open examples/uniref50.fa", " -fasta",
- "test_uniref50_out.mfa", false, 2096 },
- { "headless -open examples/uniref50.fa", " -clustal",
- "test_uniref50_out.aln", true, 2096 },
+ "test_uniref50_out.mfa", true, 2096, 3000 },
{ "headless -open examples/uniref50.fa", " -clustal",
- "test_uniref50_out.aln", false, 2096 },
- { "headless -open examples/uniref50.fa", " -msf",
- "test_uniref50_out.msf", true, 2096 },
+ "test_uniref50_out.aln", true, 2096, 3000 },
{ "headless -open examples/uniref50.fa", " -msf",
- "test_uniref50_out.msf", false, 2096 },
+ "test_uniref50_out.msf", true, 2096, 3000 },
{ "headless -open examples/uniref50.fa", " -pileup",
- "test_uniref50_out.aln", true, 2096 },
- { "headless -open examples/uniref50.fa", " -pileup",
- "test_uniref50_out.aln", false, 2096 },
- { "headless -open examples/uniref50.fa", " -pir",
- "test_uniref50_out.pir", true, 2096 },
+ "test_uniref50_out.aln", true, 2096, 3000 },
{ "headless -open examples/uniref50.fa", " -pir",
- "test_uniref50_out.pir", false, 2096 },
+ "test_uniref50_out.pir", true, 2096, 3000 },
{ "headless -open examples/uniref50.fa", " -pfam",
- "test_uniref50_out.pfam", true, 2096 },
- { "headless -open examples/uniref50.fa", " -pfam",
- "test_uniref50_out.pfam", false, 2096 },
- { "headless -open examples/uniref50.fa", " -blc",
- "test_uniref50_out.blc", true, 2096 },
+ "test_uniref50_out.pfam", true, 2096, 3000 },
{ "headless -open examples/uniref50.fa", " -blc",
- "test_uniref50_out.blc", false, 2096 },
- { "headless -open examples/uniref50.fa", " -jalview",
- "test_uniref50_out.jvp", true, 2096 },
+ "test_uniref50_out.blc", true, 2096, 3000 },
{ "headless -open examples/uniref50.fa", " -jalview",
- "test_uniref50_out.jvp", false, 2096 },
+ "test_uniref50_out.jvp", true, 2096, 3000 },
};
}
-
-
}
git://source.jalview.org / jalview.git / commitdiff