From: Jim Procter Date: Thu, 23 Jul 2015 18:03:21 +0000 (+0100) Subject: Merge branch 'features/JAL-1759jmolUpdate' into develop X-Git-Tag: Release_2_10_0~562 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=5247711ab4a6453614e2a9fb9307e6bae6a7b4a9;hp=-c;p=jalview.git Merge branch 'features/JAL-1759jmolUpdate' into develop updates from revisions due to JAL-1805 --- 5247711ab4a6453614e2a9fb9307e6bae6a7b4a9 diff --combined src/jalview/gui/Jalview2XML.java index e4ec30b,107d9e3..3b90bf6 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@@ -676,8 -676,7 +676,7 @@@ public class Jalview2XM { 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) @@@ -736,8 -735,7 +735,7 @@@ if (jds.getSequenceFeatures() != null) { - jalview.datamodel.SequenceFeature[] sf = jds - .getSequenceFeatures(); + jalview.datamodel.SequenceFeature[] sf = jds.getSequenceFeatures(); int index = 0; while (index < sf.length) { @@@ -900,36 -898,36 +898,36 @@@ } } - // { - // 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); + // } + // } } } @@@ -1032,13 -1030,11 +1030,11 @@@ 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) @@@ -1050,8 -1046,7 +1046,7 @@@ } else if (sg.cs instanceof jalview.schemes.UserColourScheme) { - jGroup - .setColour(setUserColourScheme(sg.cs, userColours, jms)); + jGroup.setColour(setUserColourScheme(sg.cs, userColours, jms)); } else { @@@ -1211,8 -1206,8 +1206,8 @@@ else { setting.setColour(ap.getSeqPanel().seqCanvas - .getFeatureRenderer() - .getColour(renderOrder[ro]).getRGB()); + .getFeatureRenderer().getColour(renderOrder[ro]) + .getRGB()); } setting.setDisplay(av.getFeaturesDisplayed().isVisible( @@@ -1372,10 -1367,6 +1367,10 @@@ final SequenceI jds, List viewIds, AlignmentPanel ap, boolean storeDataset) { + if (Desktop.desktop == null) + { + return; + } JInternalFrame[] frames = Desktop.desktop.getAllFrames(); for (int f = frames.length - 1; f > -1; f--) { @@@ -1424,8 -1415,7 +1419,7 @@@ { String varnaStateFile = varna.getStateInfo(model.rna); - jarEntryName = RNA_PREFIX + viewId + "_" - + nextCounter(); + jarEntryName = RNA_PREFIX + viewId + "_" + nextCounter(); copyFileToJar(jout, varnaStateFile, jarEntryName); rnaSessions.put(model, jarEntryName); } @@@ -1608,8 -1598,8 +1602,8 @@@ private void storeAlignmentAnnotation(AlignmentAnnotation[] aa, IdentityHashMap groupRefs, - AlignmentViewport av, - Set calcIdSet, boolean storeDS, SequenceSet vamsasSet) + AlignmentViewport av, Set calcIdSet, boolean storeDS, + SequenceSet vamsasSet) { for (int i = 0; i < aa.length; i++) @@@ -1639,9 -1629,11 +1633,11 @@@ 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()); } @@@ -2419,7 -2411,8 +2415,8 @@@ .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()); @@@ -2892,8 -2885,7 +2889,7 @@@ // 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 @@@ -3127,8 -3119,7 +3123,7 @@@ 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())); @@@ -3167,8 -3158,8 +3162,8 @@@ if (jGroup.getId() != null && groupAnnotRefs.size() > 0) { // re-instate unique group/annotation row reference - List jaal = groupAnnotRefs - .get(jGroup.getId()); + List jaal = groupAnnotRefs.get(jGroup + .getId()); if (jaal != null) { for (AlignmentAnnotation jaa : jaal) @@@ -3196,8 -3187,8 +3191,8 @@@ if (addAnnotSchemeGroup) { // reconstruct the annotation colourscheme - sg.cs = constructAnnotationColour( - jGroup.getAnnotationColours(), null, al, jms, false); + sg.cs = constructAnnotationColour(jGroup.getAnnotationColours(), + null, al, jms, false); } } } @@@ -3329,8 -3320,8 +3324,8 @@@ 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++) { @@@ -3392,8 -3383,8 +3387,8 @@@ * 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); @@@ -3678,12 -3669,12 +3673,12 @@@ * @param af * @param jprovider */ - protected void createChimeraViewer(Entry viewerData, - AlignFrame af, + protected void createChimeraViewer( + Entry 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 @@@ -3720,8 -3711,8 +3715,8 @@@ 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()); } @@@ -3810,16 -3801,23 +3805,23 @@@ 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")) { @@@ -3832,54 -3830,55 +3834,55 @@@ 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(); } + } /** @@@ -4416,7 -4415,7 +4419,7 @@@ } } 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 @@@ -5321,7 -5320,7 +5324,7 @@@ } } } - + return result; } diff --combined test/MCview/PDBChainTest.java index fda4e1b,da49f22..b84ca28 --- a/test/MCview/PDBChainTest.java +++ b/test/MCview/PDBChainTest.java @@@ -31,7 -31,7 +31,7 @@@ public class PDBChainTes final Atom a4 = new Atom(2f, 1f, 7f); - @BeforeMethod(alwaysRun = true) - @BeforeMethod ++ @BeforeMethod(alwaysRun = true) public void setUp() { System.out.println("setup"); diff --combined test/jalview/bin/CommandLineOperations.java index adc24db,3582dc5..09650ea --- a/test/jalview/bin/CommandLineOperations.java +++ b/test/jalview/bin/CommandLineOperations.java @@@ -24,10 -24,11 +24,10 @@@ import java.io.BufferedReader 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; @@@ -35,7 -36,15 +35,7 @@@ public class CommandLineOperations { - @BeforeClass - public static void setUpBeforeClass() throws Exception - { - } - - @AfterClass - public static void tearDownAfterClass() throws Exception - { - } + private ArrayList successfulCMDs = new ArrayList(); /*** * from @@@ -48,8 -57,7 +48,8 @@@ private static class Worker extends Thread { private final Process process; - + private BufferedReader outputReader; + private BufferedReader errorReader; private Integer exit; private Worker(Process process) @@@ -67,130 -75,64 +67,129 @@@ 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 + "]"); @@@ -200,7 -142,7 +199,7 @@@ 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 + "]"); @@@ -208,83 -150,69 +207,83 @@@ 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 }, }; } - - }