import java.util.AbstractMap;
import java.util.ArrayList;
import java.util.Arrays;
-import java.util.Collections;
+import java.util.EnumSet;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import jalview.analysis.AlignmentUtils;
import jalview.bin.argparser.Arg;
import jalview.bin.argparser.ArgParser;
+import jalview.bin.argparser.ArgParser.Position;
import jalview.bin.argparser.ArgValue;
import jalview.bin.argparser.ArgValues;
import jalview.bin.argparser.ArgValuesMap;
import jalview.bin.argparser.SubVals;
-import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.datamodel.annotations.AlphaFoldAnnotationRowBuilder;
import jalview.gui.Preferences;
import jalview.gui.StructureChooser;
import jalview.gui.StructureViewer;
+import jalview.gui.StructureViewer.ViewerType;
import jalview.io.AppletFormatAdapter;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
import jalview.io.FileLoader;
import jalview.io.HtmlSvgOutput;
import jalview.io.IdentifyFile;
-import jalview.schemes.AnnotationColourGradient;
import jalview.structure.StructureImportSettings.TFType;
import jalview.structure.StructureSelectionManager;
import jalview.util.HttpUtils;
import jalview.util.MessageManager;
import jalview.util.Platform;
-import mc_view.PDBChain;
public class Commands
{
{
/*
* this approach isn't working yet // get default annotations before opening
- * AlignFrame if (m.get(Arg.SSANNOTATION) != null) {
- * Console.debug("##### SSANNOTATION=" + m.get(Arg.SSANNOTATION).getBoolean());
+ * AlignFrame if (m.get(Arg.SSANNOTATIONS) != null) {
+ * Console.debug("##### SSANNOTATIONS=" + m.get(Arg.SSANNOTATIONS).getBoolean());
* } if (m.get(Arg.NOTEMPFAC) != null) { Console.debug( "##### NOTEMPFAC=" +
* m.get(Arg.NOTEMPFAC).getBoolean()); } boolean showSecondaryStructure =
- * (m.get(Arg.SSANNOTATION) != null) ? m.get(Arg.SSANNOTATION).getBoolean() :
+ * (m.get(Arg.SSANNOTATIONS) != null) ? m.get(Arg.SSANNOTATIONS).getBoolean() :
* false; boolean showTemperatureFactor = (m.get(Arg.NOTEMPFAC) != null) ?
* !m.get(Arg.NOTEMPFAC).getBoolean() : false; Console.debug("##### tempfac=" +
* showTemperatureFactor + ", showSS=" + showSecondaryStructure);
af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol,
format);
+ boolean showAnnotations = ArgParser.getFromSubValArgOrPref(avm,
+ Arg.ANNOTATIONS, av.getSubVals(), null,
+ "SHOW_ANNOTATIONS", true);
+ af.setAnnotationsVisibility(showAnnotations, false, true);
// wrap alignment?
if (avm.getBoolean(Arg.WRAP))
if (avm.containsArg(Arg.TITLE))
af.setTitle(avm.getValue(Arg.TITLE));
- /* hacky approach to hiding the annotations */
// show secondary structure annotations?
- if (avm.getBoolean(Arg.SSANNOTATION))
+ boolean showSSAnnotations = ArgParser.getFromSubValArgOrPref(avm,
+ Arg.SSANNOTATIONS, av.getSubVals(), null,
+ "STRUCT_FROM_PDB", true);
+ if (avm.getBoolean(Arg.SSANNOTATIONS))
{
- // do this better (annotation types?)
+ af.setAnnotationsVisibility(showSSAnnotations, true, false);
+ /*
AlignmentUtils.showOrHideSequenceAnnotations(
af.getCurrentView().getAlignment(),
Collections.singleton("Secondary Structure"), null,
false, false);
+ */
}
// show temperature factor annotations?
* (showTemperatureFactor)
*/
{
+ /*
if (avm.containsArg(Arg.TEMPFAC_LABEL))
{
AlignmentAnnotation aa = AlignmentUtils
+ label);
}
}
+ */
}
// store the AlignFrame for this id
}
}
- // get TEMPFAC type from subvals or Arg.TEMPFAC
+ // showing annotations from structure file or not
+ boolean ssFromStructure = ArgParser.getFromSubValArgOrPref(avm,
+ Arg.SSANNOTATIONS, subVals, null, "STRUCT_FROM_PDB",
+ true);
+
+ // get TEMPFAC type from subvals or Arg.TEMPFAC in case user Adds
+ // reference annotations
String tftString = subVals.get("tempfac");
TFType tft = avm.getBoolean(Arg.NOTEMPFAC) ? null
: TFType.DEFAULT;
}
}
- // TODO pass PAE label
+ String sViewer = ArgParser.getFromSubValArgOrPref(avm,
+ Arg.STRUCTUREVIEWER, Position.AFTER, av, subVals,
+ "viewer", null, "jmol");
+ ViewerType viewerType = null;
+ if (!"none".equals(sViewer))
+ {
+ for (ViewerType v : EnumSet.allOf(ViewerType.class))
+ {
+ String name = v.name().toLowerCase(Locale.ROOT)
+ .replaceAll(" ", "");
+ if (sViewer.equals(name))
+ {
+ viewerType = v;
+ break;
+ }
+ }
+ }
+
+ boolean addTempFac = tft != null
+ || Cache.getDefault("ADD_TEMPFACT_ANN", false);
+
+ // TODO use ssFromStructure
StructureChooser.openStructureFileForSequence(null, null, ap, seq,
- false, structureFilepath, tft, paeFilepath, false);
+ false, structureFilepath, tft, paeFilepath, false,
+ ssFromStructure, false, viewerType);
}
}
}
+ /*
boolean doShading = avm.getBoolean(Arg.TEMPFAC_SHADING);
if (doShading)
{
Console.info("Changed colour " + acg.toString());
}
}
+ */
return theseArgsWereParsed;
}
*/
void doMain(String[] args)
{
-
if (!Platform.isJS())
{
System.setSecurityManager(null);
}
+ if (args == null)
+ args = new String[] {};
+
// Move any new getdown-launcher-new.jar into place over old
// getdown-launcher.jar
String appdirString = System.getProperty("getdownappdir");
// Leaving it in in case it gets fixed
command.add(
"-Xdock:name=" + ChannelProperties.getProperty("app_name"));
+ // this launches WITHOUT an icon in the macOS dock. Could be useful for
+ // getdown?
+ // command.add("-Dapple.awt.UIElement=false");
+ // This also does not work for the dock
+ command.add("-Dcom.apple.mrj.application.apple.menu.about.name="
+ + ChannelProperties.getProperty("app_name"));
}
}
public enum Arg
{
HELP("h"), CALCULATION, MENUBAR, STATUS, SHOWOVERVIEW, ANNOTATIONS,
- COLOUR, FEATURES, GROOVY, GROUPS, HEADLESS, JABAWS, ANNOTATION,
- ANNOTATION2, DISPLAY, GUI, NEWS, SORTBYTREE, USAGESTATS, OPEN, OPENNEW,
- PROPS, QUESTIONNAIRE, SETPROP, TREE, VDOC, VSESS, OUTPUT, OUTPUTTYPE,
- SSANNOTATION, NOTEMPFAC, TEMPFAC, TEMPFAC_LABEL, TEMPFAC_DESC,
- TEMPFAC_SHADING, TITLE, PAEMATRIX, WRAP, NOSTRUCTURE, STRUCTURE, IMAGE,
+ COLOUR, FEATURES, GROOVY, GROUPS, HEADLESS, JABAWS, DISPLAY, GUI, NEWS,
+ SORTBYTREE, USAGESTATS, OPEN, OPENNEW, PROPS, QUESTIONNAIRE, SETPROP,
+ TREE, VDOC, VSESS, OUTPUT, OUTPUTTYPE, SSANNOTATIONS, NOTEMPFAC, TEMPFAC,
+ TITLE, PAEMATRIX, WRAP, NOSTRUCTURE, STRUCTURE, STRUCTUREVIEWER, IMAGE,
QUIT, CLOSE, DEBUG("d"), QUIET("q"), ARGFILE, INCREMENT, NPP("n++"),
SUBSTITUTIONS, INITSUBSTITUTIONS, NIL, SPLASH, SETARGFILE, UNSETARGFILE;
MENUBAR.setOptions(true, Opt.BOOLEAN);
STATUS.setOptions(true, Opt.BOOLEAN);
SHOWOVERVIEW.setOptions(Opt.UNARY, Opt.LINKED);
- ANNOTATIONS.setOptions(Opt.STRING, Opt.LINKED);
+ ANNOTATIONS.setOptions(Opt.BOOLEAN, Opt.LINKED);
COLOUR.setOptions(Opt.STRING, Opt.LINKED);
FEATURES.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI,
Opt.ALLOWSUBSTITUTIONS);
GROUPS.setOptions(Opt.STRING, Opt.LINKED);
HEADLESS.setOptions(Opt.UNARY, Opt.BOOTSTRAP);
JABAWS.setOptions(Opt.STRING);
- ANNOTATION.setOptions(true, Opt.BOOLEAN, Opt.LINKED);
- ANNOTATION2.setOptions(true, Opt.BOOLEAN, Opt.LINKED);
DISPLAY.setOptions(true, Opt.BOOLEAN);
GUI.setOptions(true, Opt.BOOLEAN);
NEWS.setOptions(true, Opt.BOOLEAN, Opt.BOOTSTRAP);
OUTPUT.setOptions(Opt.STRING, Opt.LINKED, Opt.ALLOWSUBSTITUTIONS);
OUTPUTTYPE.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI);
- SSANNOTATION.setOptions(Opt.BOOLEAN, Opt.LINKED);
+ SSANNOTATIONS.setOptions(Opt.BOOLEAN, Opt.LINKED);
NOTEMPFAC.setOptions(Opt.UNARY, Opt.LINKED);
TEMPFAC.setOptions(Opt.STRING, Opt.LINKED);
- TEMPFAC_LABEL.setOptions(Opt.STRING, Opt.LINKED);
- TEMPFAC_DESC.setOptions(Opt.STRING, Opt.LINKED);
- TEMPFAC_SHADING.setOptions(Opt.BOOLEAN, Opt.LINKED);
TITLE.setOptions(Opt.STRING, Opt.LINKED);
PAEMATRIX.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI,
Opt.ALLOWSUBSTITUTIONS);
NOSTRUCTURE.setOptions(Opt.UNARY, Opt.LINKED);
STRUCTURE.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI,
Opt.ALLOWSUBSTITUTIONS);
+ STRUCTUREVIEWER.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI);
WRAP.setOptions(Opt.BOOLEAN, Opt.LINKED);
IMAGE.setOptions(Opt.STRING, Opt.LINKED, Opt.ALLOWSUBSTITUTIONS);
QUIT.setOptions(Opt.UNARY);
import java.util.EnumSet;
import java.util.HashMap;
import java.util.List;
+import java.util.Locale;
import java.util.Map;
+import jalview.bin.Cache;
import jalview.bin.Console;
import jalview.bin.Jalview;
import jalview.bin.argparser.Arg.Opt;
return args;
}
+ public static enum Position
+ {
+ FIRST, BEFORE, AFTER
+ }
+
+ public static String getValueFromSubValOrArg(ArgValuesMap avm, Arg a,
+ SubVals sv)
+ {
+ return getFromSubValArgOrPref(avm, a, sv, null, null, null);
+ }
+
+ public static String getFromSubValArgOrPref(ArgValuesMap avm, Arg a,
+ SubVals sv, String key, String pref, String def)
+ {
+ return getFromSubValArgOrPref(avm, a, Position.FIRST, null, sv, key,
+ pref, def);
+ }
+
+ public static String getFromSubValArgOrPref(ArgValuesMap avm, Arg a,
+ Position pos, ArgValue av, SubVals sv, String key, String pref,
+ String def)
+ {
+ if (key == null)
+ key = a.getName();
+ if (sv != null && sv.has(key) && sv.get(key) != null)
+ return sv.get(key);
+ if (avm != null && avm.containsArg(a))
+ {
+ String val = null;
+ if (pos == Position.FIRST && avm.getValue(a) != null)
+ return avm.getValue(a);
+ else if (pos == Position.BEFORE
+ && avm.getClosestPreviousArgValueOfArg(av, a) != null)
+ return avm.getClosestPreviousArgValueOfArg(av, a).getValue();
+ else if (pos == Position.AFTER
+ && avm.getClosestNextArgValueOfArg(av, a) != null)
+ return avm.getClosestNextArgValueOfArg(av, a).getValue();
+ }
+ return pref != null ? Cache.getDefault(pref, def) : def;
+ }
+
+ public static boolean getBoolFromSubValOrArg(ArgValuesMap avm, Arg a,
+ SubVals sv)
+ {
+ return getFromSubValArgOrPref(avm, a, sv, null, null, false);
+ }
+
+ public static boolean getFromSubValArgOrPref(ArgValuesMap avm, Arg a,
+ SubVals sv, String key, String pref, boolean def)
+ {
+ if (key == null)
+ key = a.getName();
+ if (sv != null && sv.has(key) && sv.get(key) != null)
+ return sv.get(key).toLowerCase(Locale.ROOT).equals("true");
+ if (avm != null && avm.containsArg(a))
+ return avm.getBoolean(a);
+ return pref != null ? Cache.getDefault(pref, def) : def;
+ }
+
}
\ No newline at end of file
{
if (m == null || !m.containsKey(a))
return false;
- return a.hasOption(Opt.STRING) ? getArgValue(a) != null
- : this.getBoolean(a);
+ return a.hasOption(Opt.STRING) ? getArgValue(a) != null : true;
}
public boolean hasValue(Arg a, String val)
@Override
public void overviewMenuItem_actionPerformed(ActionEvent e)
{
- boolean showHiddenRegions = Cache.getDefault(Preferences.SHOW_OV_HIDDEN_AT_START,
- false);
+ boolean showHiddenRegions = Cache
+ .getDefault(Preferences.SHOW_OV_HIDDEN_AT_START, false);
openOverviewPanel(showHiddenRegions);
}
return alignPanel.overviewPanel;
}
JInternalFrame frame = new JInternalFrame();
- final OverviewPanel overview = new OverviewPanel(alignPanel, frame, showHidden);
+ final OverviewPanel overview = new OverviewPanel(alignPanel, frame,
+ showHidden);
frame.setContentPane(overview);
- Desktop.addInternalFrame(frame, "", true, frame.getWidth(), frame.getHeight(),
- true, true);
+ Desktop.addInternalFrame(frame, "", true, frame.getWidth(),
+ frame.getHeight(), true, true);
frame.setFrameIcon(null);
frame.pack();
frame.setLayer(JLayeredPane.PALETTE_LAYER);
- final AlignmentPanel thePanel = this.alignPanel;
+ final AlignmentPanel thePanel = this.alignPanel;
frame.addInternalFrameListener(
new javax.swing.event.InternalFrameAdapter()
{
alignPanel.setOverviewPanel(overview);
alignPanel.setOverviewTitle(this);
-
+
return overview;
}
return showNewickTree(nf, treeTitle, null, w, h, x, y);
}
-
/**
* Add a treeviewer for the tree extracted from a Newick file object to the
* current alignment view
return tp;
}
-
public void showContactMapTree(AlignmentAnnotation aa,
PAEContactMatrix cm)
{
int x = 4, y = 5;
int w = 400, h = 500;
-
+
try
{
NewickFile fin = new NewickFile(
String title = "PAE Matrix Tree for "
+ cm.getReferenceSeq().getDisplayId(false);
- showColumnWiseTree(fin, aa, title, w,h, x,y);
+ showColumnWiseTree(fin, aa, title, w, h, x, y);
} catch (Throwable xx)
{
Console.error("Unexpected exception showing tree for contact matrix",
xx);
}
}
- public TreePanel showColumnWiseTree(NewickFile nf, AlignmentAnnotation aa, String treeTitle,
- int w, int h, int x, int y)
+
+ public TreePanel showColumnWiseTree(NewickFile nf, AlignmentAnnotation aa,
+ String treeTitle, int w, int h, int x, int y)
{
- try
+ try
+ {
+ nf.parse();
+ if (nf.getTree() == null)
{
- nf.parse();
- if (nf.getTree() == null)
- {
- return null;
- }
- TreePanel tp = new TreePanel(alignPanel, nf, aa, title);
-
- tp.setSize(w, h);
+ return null;
+ }
+ TreePanel tp = new TreePanel(alignPanel, nf, aa, title);
- if (x > 0 && y > 0)
- {
- tp.setLocation(x, y);
- }
+ tp.setSize(w, h);
- Desktop.addInternalFrame(tp, title, w, h);
- return tp;
- } catch (Throwable xx)
+ if (x > 0 && y > 0)
{
- Console.error("Unexpected exception showing tree for contact matrix",
- xx);
+ tp.setLocation(x, y);
}
- return null;
+
+ Desktop.addInternalFrame(tp, title, w, h);
+ return tp;
+ } catch (Throwable xx)
+ {
+ Console.error("Unexpected exception showing tree for contact matrix",
+ xx);
+ }
+ return null;
}
-
+
private boolean buildingMenu = false;
/**
* to add view name "Original" if necessary
*/
alignPanel.setOverviewTitle(this);
-
+
/*
* switch panels and set Overview title (if there is one
* because it was opened automatically)
* update non-sequence-related annotations
*/
@Override
- protected void setAnnotationsVisibility(boolean visible,
+ public void setAnnotationsVisibility(boolean visible,
boolean forSequences, boolean forAlignment)
{
AlignmentAnnotation[] anns = alignPanel.getAlignment()
import jalview.fts.core.FTSRestResponse;
import jalview.fts.service.pdb.PDBFTSRestClient;
import jalview.fts.service.threedbeacons.TDB_FTSData;
+import jalview.gui.StructureViewer.ViewerType;
import jalview.gui.structurechooser.PDBStructureChooserQuerySource;
import jalview.gui.structurechooser.StructureChooserQuerySource;
import jalview.gui.structurechooser.ThreeDBStructureChooserQuerySource;
StructureSelectionManager ssm, final PDBEntry[] pdbEntriesToView,
final AlignmentPanel alignPanel, SequenceI[] sequences)
{
+ return launchStructureViewer(ssm, pdbEntriesToView, alignPanel,
+ sequences, null);
+ }
+
+ private StructureViewer launchStructureViewer(
+ StructureSelectionManager ssm, final PDBEntry[] pdbEntriesToView,
+ final AlignmentPanel alignPanel, SequenceI[] sequences,
+ ViewerType viewerType)
+ {
long progressId = sequences.hashCode();
setProgressBar(MessageManager
.getString("status.launching_3d_structure_viewer"), progressId);
MessageManager.getString(
"status.fetching_3d_structures_for_selected_entries"),
progressId);
- theViewer.viewStructures(pdbEntriesToView, sequences, alignPanel);
+ theViewer.viewStructures(pdbEntriesToView, sequences, alignPanel,
+ viewerType);
}
else
{
"status.fetching_3d_structures_for",
pdbEntriesToView[0].getId()), progressId);
// Can we pass a pre-computeMappinged pdbFile?
- theViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
+ theViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel,
+ viewerType);
}
setProgressBar(null, progressId);
// remember the last viewer we used...
boolean doXferSettings)
{
openStructureFileForSequence(ssm, sc, ap, seq, prompt, sFilename, tft,
- paeFilename, false, true, doXferSettings);
+ paeFilename, false, true, doXferSettings, null);
}
public static void openStructureFileForSequence(
StructureSelectionManager ssm, StructureChooser sc,
AlignmentPanel ap, SequenceI seq, boolean prompt,
String sFilename, TFType tft, String paeFilename,
- boolean forceHeadless, boolean showAnnotations,
- boolean doXferSettings)
+ boolean forceHeadless, boolean showRefAnnotations,
+ boolean doXferSettings, ViewerType viewerType)
{
boolean headless = forceHeadless;
if (sc == null)
{
- headless = true;
+ // headless = true;
prompt = false;
sc = new StructureChooser(new SequenceI[] { seq }, seq, ap, false);
}
// if headless, "false" in the sc constructor above will avoid GUI behaviour
// in sc.launchStructureViewer()
- sc.launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap,
- new SequenceI[]
- { seq });
+ if (!headless && !(viewerType == null))
+ sc.launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap,
+ new SequenceI[]
+ { seq }, viewerType);
if (headless)
sc.mainFrame.dispose();
- if (showAnnotations)
+ if (showRefAnnotations)
showReferenceAnnotationsForSequence(ap.alignFrame, seq);
}
public JalviewStructureDisplayI viewStructures(PDBEntry[] pdbs,
SequenceI[] seqs, AlignmentPanel ap)
{
+ return viewStructures(pdbs, seqs, ap, null);
+ }
+
+ public JalviewStructureDisplayI viewStructures(PDBEntry[] pdbs,
+ SequenceI[] seqs, AlignmentPanel ap, ViewerType viewerType)
+ {
JalviewStructureDisplayI viewer = onlyOnePdb(pdbs, seqs, ap);
if (viewer != null)
{
return viewer;
}
- ViewerType viewerType = getViewerType();
+ if (viewerType == null)
+ viewerType = getViewerType();
Map<PDBEntry, SequenceI[]> seqsForPdbs = getSequencesForPdbs(pdbs,
seqs);
public JalviewStructureDisplayI viewStructures(PDBEntry pdb,
SequenceI[] seqsForPdb, AlignmentPanel ap)
{
+ return viewStructures(pdb, seqsForPdb, ap, null);
+ }
+
+ public JalviewStructureDisplayI viewStructures(PDBEntry pdb,
+ SequenceI[] seqsForPdb, AlignmentPanel ap, ViewerType viewerType)
+ {
if (sview != null)
{
sview.setAlignAddedStructures(superposeAdded);
sview.raiseViewer();
return sview;
}
- ViewerType viewerType = getViewerType();
+ if (viewerType == null)
+ viewerType = getViewerType();
if (viewerType.equals(ViewerType.JMOL))
{
sview = new AppJmol(pdb, seqsForPdb, null, ap);
* @param forAlignment
* update non-sequence-related annotations
*/
- protected void setAnnotationsVisibility(boolean visible,
+ public void setAnnotationsVisibility(boolean visible,
boolean forSequences, boolean forAlignment)
{
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.util.Arrays;
+import java.util.EnumSet;
import java.util.List;
import javax.swing.AbstractCellEditor;
*/
structViewer.setFont(LABEL_FONT);
structViewer.setBounds(new Rectangle(190, ypos, 120, height));
+ for (ViewerType v : EnumSet.allOf(ViewerType.class))
+ {
+ structViewer.addItem(v.name());
+ }
+ /*
structViewer.addItem(ViewerType.JMOL.name());
structViewer.addItem(ViewerType.CHIMERA.name());
structViewer.addItem(ViewerType.CHIMERAX.name());
structViewer.addItem(ViewerType.PYMOL.name());
+ */
structViewer.addActionListener(new ActionListener()
{
@Override
--- /dev/null
+package jalview.bin;
+
+import java.util.Date;
+import java.util.List;
+
+import org.testng.Assert;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import jalview.api.AlignViewportI;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
+import jalview.gui.StructureViewerBase;
+
+@Test
+public class CommandsTest2
+{
+ @BeforeClass(alwaysRun = true)
+ public static void setUpBeforeClass() throws Exception
+ {
+ Cache.loadProperties("test/jalview/testProps.jvprops");
+ Date oneHourFromNow = new Date(
+ System.currentTimeMillis() + 3600 * 1000);
+ Cache.setDateProperty("JALVIEW_NEWS_RSS_LASTMODIFIED", oneHourFromNow);
+ if (Desktop.instance != null)
+ Desktop.instance.closeAll_actionPerformed(null);
+
+ }
+
+ @AfterClass(alwaysRun = true)
+ public static void resetProps()
+ {
+ Cache.loadProperties("test/jalview/testProps.jvprops");
+ }
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ @AfterMethod(alwaysRun = true)
+ public void tearDown()
+ {
+ if (Desktop.instance != null)
+ Desktop.instance.closeAll_actionPerformed(null);
+ }
+
+ @Test(
+ groups =
+ { "Functional" },
+ dataProvider = "structureOpeningArgsParams")
+ public void structureOpeningArgsTest(String cmdLine, int seqNum,
+ int annNum, int viewerNum)
+ {
+ String[] args = cmdLine.split("\\s+");
+
+ Jalview.main(args);
+ AlignFrame[] afs = Desktop.getAlignFrames();
+ Assert.assertNotNull(afs);
+ Assert.assertTrue(afs.length > 0);
+
+ AlignFrame af = afs[0];
+ Assert.assertNotNull(af);
+
+ AlignmentPanel ap = af.alignPanel;
+ Assert.assertNotNull(ap);
+
+ AlignmentI al = ap.getAlignment();
+ Assert.assertNotNull(al);
+
+ List<SequenceI> seqs = al.getSequences();
+ Assert.assertNotNull(seqs);
+
+ Assert.assertEquals(seqs.size(), seqNum, "Wrong number of sequences");
+
+ AlignViewportI av = ap.getAlignViewport();
+ Assert.assertNotNull(av);
+
+ AlignmentAnnotation[] aas = al.getAlignmentAnnotation();
+ int visibleAnn = 0;
+ for (AlignmentAnnotation aa : aas)
+ {
+ if (aa.visible)
+ visibleAnn++;
+ }
+
+ Assert.assertEquals(visibleAnn, annNum,
+ "Wrong number of visible annotations");
+
+ if (viewerNum > -1)
+ {
+ try
+ {
+ Thread.sleep(100);
+ } catch (InterruptedException e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ List<StructureViewerBase> openViewers = Desktop.instance
+ .getStructureViewers(ap, null);
+ Assert.assertNotNull(openViewers);
+ Assert.assertEquals(openViewers.size(), viewerNum,
+ "Wrong number of structure viewers opened");
+ }
+ }
+
+ @DataProvider(name = "structureOpeningArgsParams")
+ public Object[][] structureOpeningArgsParams()
+ {
+ /*
+ String cmdLine,
+ int seqNum,
+ int annNum,
+ int viewerNum,
+ String propsFile
+ */
+ return new Object[][] { { "--nonews --nosplash --debug "
+ + "--open=examples/uniref50.fa " + "--colour=gecos:flower "
+ + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
+ + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
+ + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
+ 15, 7, 1 },
+ { "--nonews --nosplash --debug " + "--open=examples/uniref50.fa "
+ + "--colour=gecos:flower "
+ + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
+ + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
+ + "--props=test/jalview/bin/commandsTest2.jvprops2 ",
+ 15, 4, 1 },
+ { "--nonews --nosplash --debug " + "--open=examples/uniref50.fa "
+ + "--colour=gecos:flower "
+ + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
+ + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
+ + "--nossannotations "
+ + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
+ 15, 4, 1 },
+ { "--nonews --nosplash --debug " + "--open=examples/uniref50.fa "
+ + "--colour=gecos:flower "
+ + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
+ + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
+ + "--noannotations "
+ + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
+ 15, 3, 1 },
+ { "--nonews --nosplash --debug " + "--open=examples/uniref50.fa "
+ + "--colour=gecos:flower "
+ + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
+ + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
+ + "--noannotations " + "--nossannotations "
+ + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
+ 15, 0, 1 },
+ { "--nonews --nosplash --debug " + "--open=examples/uniref50.fa "
+ + "--colour=gecos:flower "
+ + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
+ + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
+ + "--noannotations " + "--nossannotations "
+ + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
+ 15, 0, 1 },
+ { "--argfile=test/jalview/bin/commandsTest2.argfile1 ", 16, 19, 3 },
+ { "--argfile=test/jalview/bin/commandsTest2.argfile2 ", 16, 0, 2 },
+ //
+ };
+ }
+}
--- /dev/null
+--debug
+--nonews
+--nosplash
+--substitutions
+--open=examples/test_fab41.result/sample.a2m
+--annotations
+--ssannotations
+--colour=gecos:flower
+--structure=[viewer=jmol;tempfac=plddt;paematrix={dirname}/test_fab41_unrelaxed_rank_1_model_3_scores.json]{dirname}/test_fab41_unrelaxed_rank_1_model_3.pdb
+--structure={dirname}/test_fab41_unrelaxed_rank_2_model_4.pdb
+--structureviewer=jmol
+--paematrix={dirname}/test_fab41_unrelaxed_rank_2_model_4_scores.json
+--tempfac=plddt
+--structure={dirname}/test_fab41_unrelaxed_rank_3_model_2.pdb
+--structureviewer=jmol
+--paematrix={dirname}/test_fab41_unrelaxed_rank_3_model_2_scores.json
+--tempfac=plddt
+--structure=[viewer=none]{dirname}/test_fab41_unrelaxed_rank_4_model_5.pdb
+--paematrix={dirname}/test_fab41_unrelaxed_rank_4_model_5_scores.json
+--tempfac=plddt
+--structure={dirname}/test_fab41_unrelaxed_rank_5_model_1.pdb
+--structureviewer=none
+--tempfac=plddt
+--paematrix={dirname}/test_fab41_unrelaxed_rank_5_model_1_scores.json
+#--headless
--- /dev/null
+--debug
+--nonews
+--nosplash
+--substitutions
+--open=examples/test_fab41.result/sample.a2m
+--noannotations
+--nossannotations
+--colour=gecos:flower
+--structure=[tempfac=plddt;paematrix={dirname}/test_fab41_unrelaxed_rank_1_model_3_scores.json]{dirname}/test_fab41_unrelaxed_rank_1_model_3.pdb
+--structureviewer=none
+--structure={dirname}/test_fab41_unrelaxed_rank_2_model_4.pdb
+--structureviewer=jmol
+--paematrix={dirname}/test_fab41_unrelaxed_rank_2_model_4_scores.json
+--tempfac=plddt
+--structure={dirname}/test_fab41_unrelaxed_rank_3_model_2.pdb
+--structureviewer=jmol
+--paematrix={dirname}/test_fab41_unrelaxed_rank_3_model_2_scores.json
+--tempfac=plddt
+--structure=[viewer=none]{dirname}/test_fab41_unrelaxed_rank_4_model_5.pdb
+--paematrix={dirname}/test_fab41_unrelaxed_rank_4_model_5_scores.json
+--tempfac=plddt
+--structure={dirname}/test_fab41_unrelaxed_rank_5_model_1.pdb
+--structureviewer=none
+--tempfac=plddt
+--paematrix={dirname}/test_fab41_unrelaxed_rank_5_model_1_scores.json
+#--headless
--- /dev/null
+SHOW_STARTUP_FILE=false
+SPLASH=false
+STRUCT_FROM_PDB=true
+ADD_TEMPFACT_ANN=true
--- /dev/null
+SHOW_STARTUP_FILE=false
+SPLASH=false
+STRUCT_FROM_PDB=false
+ADD_TEMPFACT_ANN=true
import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertTrue;
+import java.io.File;
import java.util.Collection;
+import java.util.List;
import java.util.Vector;
import org.junit.Assert;
import org.testng.annotations.AfterMethod;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
+import jalview.api.AlignViewportI;
+import jalview.bin.Cache;
+import jalview.bin.Jalview;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
import jalview.fts.service.pdb.PDBFTSRestClientTest;
import jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient;
import jalview.fts.threedbeacons.TDBeaconsFTSRestClientTest;
+import jalview.gui.StructureViewer.ViewerType;
import jalview.gui.structurechooser.PDBStructureChooserQuerySource;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormatException;
+import jalview.io.FileFormatI;
+import jalview.io.FileLoader;
+import jalview.io.IdentifyFile;
import jalview.jbgui.FilterOption;
+import jalview.structure.StructureImportSettings.TFType;
import junit.extensions.PA;
@Test(singleThreaded = true)
assertEquals("abcde12345afg",
PDBStructureChooserQuerySource.sanitizeSeqName(name));
}
+
+ @Test(groups = { "Functional" }, dataProvider = "openStructureFileParams")
+ public void openStructureFileForSequenceTest(String alfile, String seqid,
+ String sFilename, TFType tft, String paeFilename,
+ boolean showRefAnnotations, boolean doXferSettings,
+ ViewerType viewerType, int seqNum, int annNum, int viewerNum,
+ String propsFile)
+ {
+ Cache.loadProperties(
+ propsFile == null ? "test/jalview/io/testProps.jvprops"
+ : propsFile);
+
+ Jalview.main(
+ propsFile == null ? null : new String[]
+ { "--props", propsFile });
+ if (Desktop.instance != null)
+ Desktop.instance.closeAll_actionPerformed(null);
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.OK_OPTION);
+
+ FileLoader fileLoader = new FileLoader(true);
+ FileFormatI format = null;
+ File alFile = new File(alfile);
+ try
+ {
+ format = new IdentifyFile().identify(alFile, DataSourceType.FILE);
+ } catch (FileFormatException e1)
+ {
+ Assert.fail(
+ "Unknown file format for '" + alFile.getAbsolutePath() + "'");
+ }
+
+ AlignFrame af = fileLoader.LoadFileWaitTillLoaded(alFile,
+ DataSourceType.FILE, format);
+ AlignmentPanel ap = af.alignPanel;
+ Assert.assertNotNull("No alignPanel", ap);
+
+ AlignmentI al = ap.getAlignment();
+ Assert.assertNotNull(al);
+
+ SequenceI seq = al.findName(seqid);
+ Assert.assertNotNull("Sequence '" + seqid + "' not found in alignment",
+ seq);
+
+ StructureChooser.openStructureFileForSequence(null, null, ap, seq,
+ false, sFilename, tft, paeFilename, false, showRefAnnotations,
+ doXferSettings, viewerType);
+
+ List<SequenceI> seqs = al.getSequences();
+ Assert.assertNotNull(seqs);
+
+ Assert.assertEquals("Wrong number of sequences", seqNum, seqs.size());
+
+ AlignViewportI av = ap.getAlignViewport();
+ Assert.assertNotNull(av);
+
+ AlignmentAnnotation[] aas = al.getAlignmentAnnotation();
+ int visibleAnn = 0;
+ for (AlignmentAnnotation aa : aas)
+ {
+ if (aa.visible)
+ visibleAnn++;
+ }
+ Assert.assertEquals("Wrong number of viewed annotations", annNum,
+ visibleAnn);
+
+ if (viewerNum > -1)
+ {
+ try
+ {
+ Thread.sleep(100);
+ } catch (InterruptedException e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ List<StructureViewerBase> openViewers = Desktop.instance
+ .getStructureViewers(ap, null);
+ Assert.assertNotNull(openViewers);
+ Assert.assertEquals("Wrong number of structure viewers opened",
+ viewerNum, openViewers.size());
+ }
+
+ if (af != null)
+ {
+ af.setVisible(false);
+ af.dispose();
+ }
+ }
+
+ @DataProvider(name = "openStructureFileParams")
+ public Object[][] openStructureFileParams()
+ {
+ /*
+ String alFile,
+ String seqid,
+ String structureFilename,
+ TFType tft,
+ String paeFilename,
+ boolean showRefAnnotations,
+ boolean doXferSettings, // false for Commands
+ ViewerType viewerType,
+ int seqNum,
+ int annNum,
+ int viewerNum,
+ String propsFile
+ */
+ return new Object[][] {
+ /*
+ */
+ { "examples/uniref50.fa", "FER1_SPIOL",
+ "examples/AlphaFold/AF-P00221-F1-model_v4.cif", TFType.DEFAULT,
+ "examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json",
+ true, false, null, 15, 7, 0, null },
+ { "examples/uniref50.fa", "FER1_SPIOL",
+ "examples/AlphaFold/AF-P00221-F1-model_v4.cif", TFType.PLDDT,
+ "examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json",
+ true, false, null, 15, 7, 0, null },
+ { "examples/uniref50.fa", "FER1_SPIOL",
+ "examples/AlphaFold/AF-P00221-F1-model_v4.cif", TFType.PLDDT,
+ "examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json",
+ false, false, null, 15, 4, 0, null },
+ { "examples/uniref50.fa", "FER1_SPIOL",
+ "examples/AlphaFold/AF-P00221-F1-model_v4.cif", TFType.DEFAULT,
+ "examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json",
+ true, false, ViewerType.JMOL, 15, 7, 1, null },
+ { "examples/uniref50.fa", "FER1_SPIOL",
+ "examples/AlphaFold/AF-P00221-F1-model_v4.cif", TFType.PLDDT,
+ "examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json",
+ true, false, ViewerType.JMOL, 15, 7, 1, null },
+ { "examples/uniref50.fa", "FER1_SPIOL",
+ "examples/AlphaFold/AF-P00221-F1-model_v4.cif", TFType.PLDDT,
+ "examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json",
+ false, false, ViewerType.JMOL, 15, 4, 1, null }, };
+ }
+
}
WRAP_ALIGNMENT=false
#DAS_REGISTRY_URL=http\://www.dasregistry.org/das/ # retired 01/05/2015
DAS_REGISTRY_URL=http\://www.ebi.ac.uk/das-srv/registry/das/
+SPLASH=false
package jalview.ws.dbsources;
+import java.io.File;
import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import org.json.simple.parser.ParseException;
import org.junit.Assert;
+import org.testng.FileAssert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import jalview.datamodel.Sequence;
+import jalview.gui.Desktop;
import jalview.gui.JvOptionPane;
+import jalview.structure.StructureMapping;
+import jalview.structure.StructureSelectionManager;
import jalview.ws.datamodel.alphafold.PAEContactMatrix;
public class EBIAlphaFoldTest
new FileInputStream(paeFile)));
Assert.assertNotEquals("No data from " + paeFile, cm.getMax(), 0);
}
+
+ @Test(groups = { "Functional" }, dataProvider = "getPDBandPAEfiles")
+ public void checkImportPAEToStructure(String pdbFile, String paeFile)
+ {
+ FileInputStream paeInput = null;
+ try
+ {
+ paeInput = new FileInputStream(paeFile);
+ } catch (FileNotFoundException e)
+ {
+ e.printStackTrace();
+ FileAssert.assertFile(new File(paeFile),
+ "Test file '" + paeFile + "' doesn't seem to exist");
+ }
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+
+ StructureMapping[] smArray = ssm.getMapping(pdbFile);
+
+ try
+ {
+ boolean done = EBIAlfaFold.importPaeJSONAsContactMatrixToStructure(
+ smArray, paeInput, "label");
+ Assert.assertTrue(
+ "Import of '" + paeFile + "' didn't complete successfully",
+ done);
+ } catch (IOException | ParseException e)
+ {
+ e.printStackTrace();
+ }
+
+ }
}
--- /dev/null
+#!/usr/bin/env sh
+
+java -cp "./bin/main:./j11lib/*:./resources:./help" jalview.bin.Launcher "${@}"
git://source.jalview.org / jalview.git / commitdiff