Example usage for org.eclipse.jface.viewers IStructuredSelection toList

Introduction

In this page you can find the example usage for org.eclipse.jface.viewers IStructuredSelection toList.

Prototype

public List toList();

Source Link

Document

Returns the elements in this selection as a List.

Usage

From source file:net.bioclipse.cdk.ui.handlers.KabschAlignHandler.java

License:Open Source License

public Object execute(ExecutionEvent event) throws ExecutionException {
    ISelection sel = PlatformUI.getWorkbench().getActiveWorkbenchWindow().getSelectionService().getSelection();
    if (!sel.isEmpty() && sel instanceof IStructuredSelection) {
        IStructuredSelection ssel = (IStructuredSelection) sel;
        ICDKManager cdk = Activator.getDefault().getJavaCDKManager();
        IUIManager ui = net.bioclipse.ui.business.Activator.getDefault().getUIManager();
        List<IMolecule> molecules = new ArrayList<IMolecule>(ssel.size());
        for (Object file : ssel.toList())
            molecules.add(cdk.loadMolecule((IFile) file));
        String path = "/Virtual/aligned.sdf";
        while (ui.fileExists(path))
            path = "/Virtual/aligned" + UUID.randomUUID() + ".sdf";
        try {//from  w w  w.  j a  va  2s .  co  m
            List<ICDKMolecule> aligned = cdk.kabsch(molecules);
            List<IMolecule> alignedMols = new ArrayList<IMolecule>();
            for (IMolecule mol : aligned)
                alignedMols.add(mol);
            cdk.saveSDFile(path, alignedMols);
            ui.open(path, "net.bioclipse.jmol.editors.JmolEditor");
        } catch (BioclipseException cause) {
            throw new ExecutionException("Error while calculating RMSD matrix...", cause);
        } catch (InvocationTargetException cause) {
            throw new ExecutionException("Error while calculating RMSD matrix...", cause);
        }
    }
    return null;
}

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From source file:net.bioclipse.cdk.ui.sdfeditor.editor.MoleculesEditor.java

License:Open Source License

protected void setupDragSource() {
    int operations = DND.DROP_COPY | DND.DROP_MOVE;
    CompositeTable viewer = null;//from w  w w  .ja  v  a2s .  c  o  m
    DragSource dragSource = new DragSource(viewer, operations);
    Transfer[] transferTypes = new Transfer[] { LocalSelectionTransfer.getTransfer() };
    dragSource.setTransfer(transferTypes);

    dragSource.addDragListener(new DragSourceListener() {

        public void dragStart(DragSourceEvent event) {
            if (!getSelectedRows().isEmpty()) {
                LocalSelectionTransfer.getTransfer().setSelection(getSelectedRows());
                event.doit = true;
            } else
                event.doit = false;
        }

        public void dragSetData(DragSourceEvent event) {
            ISelection selection = LocalSelectionTransfer.getTransfer().getSelection();

            if (LocalSelectionTransfer.getTransfer().isSupportedType(event.dataType)) {

                event.data = selection;

            } else {
                IStructuredSelection selection1 = (IStructuredSelection) getSelectedRows();
                List<EditorInputData> data = new ArrayList<EditorInputData>();
                for (Object o : selection1.toList()) {
                    MoleculesIndexEditorInput input = new MoleculesIndexEditorInput((SDFElement) o);
                    data.add(EditorInputTransfer
                            .createEditorInputData("net.bioclipse.cdk.ui.editors.jchempaint", input));
                }
                event.data = data.toArray(new EditorInputData[0]);
            }

        }

        public void dragFinished(DragSourceEvent event) {
        }

    });
}

---

From source file:net.bioclipse.chemoinformatics.dialogs.PickMoleculeDialog.java

License:Open Source License

/**
 * React on treeviewer changes to be able to return the selected resources
 *///ww w  .  j a  va2 s . c  o m
public void selectionChanged(SelectionChangedEvent event) {

    IStructuredSelection selection = (IStructuredSelection) event.getSelection();
    selectedFiles = new ArrayList<IFile>();
    for (Object obj : selection.toList()) {
        if (obj instanceof IFile) {
            IFile file = (IFile) obj;
            selectedFiles.add(file);
        }
    }
}

---

From source file:net.bioclipse.core.internal.filesystem.memory.MemoryTreeSelectionDialog.java

License:Open Source License

protected void okPressed() {
    IStructuredSelection selection = (IStructuredSelection) tree.getSelection();
    setResult(selection.toList());
    super.okPressed();
}

---

From source file:net.bioclipse.ds.ui.views.DSView.java

License:Open Source License

protected void doIncludeSelectedTests() {

    IStructuredSelection sel = (IStructuredSelection) viewer.getSelection();
    for (Object obj : sel.toList()) {
        if (obj instanceof IDSTest) {
            IDSTest dstest = (IDSTest) obj;
            dstest.setExcluded(false);//from w  w  w  .  ja  v a2 s. co  m
            viewer.refresh(dstest);
        } else if (obj instanceof TestRun) {
            TestRun testrun = (TestRun) obj;
            testrun.setStatus(TestRun.NOT_STARTED);
            testrun.getTest().setExcluded(false);
            viewer.refresh(testrun);
        }
    }

}

---

From source file:net.bioclipse.ds.ui.views.DSView.java

License:Open Source License

protected void doExcludeSelectedTests() {

    IStructuredSelection sel = (IStructuredSelection) viewer.getSelection();
    for (Object obj : sel.toList()) {
        if (obj instanceof IDSTest) {
            IDSTest dstest = (IDSTest) obj;
            dstest.setExcluded(true);//from  w ww. j a  v a  2 s . c o  m
            viewer.refresh(dstest);
        } else if (obj instanceof TestRun) {
            TestRun testrun = (TestRun) obj;
            testrun.setStatus(TestRun.EXCLUDED);
            testrun.getTest().setExcluded(true);
            if (testrun.getMatches() != null)
                testrun.getMatches().clear();
            viewer.refresh(testrun);
        }
    }

}

---

From source file:net.bioclipse.jmol.cdk.views.JmolView.java

License:Open Source License

/**
 * /* w  w  w  .j a  va2s.  c  o m*/
 * @param selection
 */
private void reactOnSelection(ISelection selection) {

    if (!(selection instanceof IStructuredSelection)) {
        clearView();
        return;
    }
    IStructuredSelection eclipseSelection = (IStructuredSelection) selection;

    /*
     * Get info from selections directly or via adapter in this order:
     * 
     * 1. Collect (or generate from IMolecule) ICDKMolecules
     * 2. Collect ChemModels to visualize
     * 3. Collect atoms/bonds to highlight (IChemicalSelection)
     * 4. Collect scripts to run
     */

    //Store selected CDKMols in List
    List<ICDKMolecule> collectedCDKMols = new ArrayList<ICDKMolecule>();

    //Store chemical selections in List
    List<IChemicalSelection> chemicalSelections = new ArrayList<IChemicalSelection>();

    //Store pharmacophpreProviders in List
    List<IPharmacophoreProvider> pcoreProviders = new ArrayList<IPharmacophoreProvider>();

    //See if list is the same as previously selected
    boolean newSelection = false;
    for (Object obj : eclipseSelection.toList()) {

        if (!(lastSelected.contains(obj))) {
            newSelection = true;
        }
    }
    if (newSelection == false) {
        //            System.out.println("Omitting selection!");
        return;
    }

    //We have a new selection
    lastSelected.clear();

    //Extract molecules and chemical selection from the eclipseSelection
    //Store extracted info in lists
    extractFromSelection(eclipseSelection, collectedCDKMols, chemicalSelections, pcoreProviders);

    //Extract JmolModelSet from selection.
    //This happens when JmolEditor provides input via adapter
    JmolModelString jms = extractJmolModelsetFromSelection(eclipseSelection);
    //        System.out.println("** jms: " + jms);
    if (jms != null) {
        //            System.out.println("** jms string: " + jms.getModelString());
        //This overrides other ICDKMolecules (for now at least)
        runScript(jms.getModelString());
        return;
    }

    //TODO: continue here

    //We have now collected everything we are interested in.
    //If no fun, return
    if ((collectedCDKMols.size() <= 0) && chemicalSelections.size() <= 0) {

        return;

    }

    /*
     * If extracted molecules: Set up Chemfile and and send it to jmol
     */
    if (collectedCDKMols != null) {

        logger.debug("Extracted the following molecules from selection:");
        for (ICDKMolecule cmol : collectedCDKMols) {
            logger.debug("  * " + cmol.getName());
        }

        processMolecules(collectedCDKMols);
    }

    /*
     * Process any pharmacophoreProviders
    * This means e.g. to draw spheres and lines
    */
    if (pcoreProviders.size() > 0) {

        logger.debug("Extracted the following pcoreProviders:");
        for (IChemicalSelection csel : chemicalSelections) {
            logger.debug("  * " + csel.getSelection());
        }

        processPcoreProviders(pcoreProviders);
    }

    /*
     * Process any chemicalSelections
    * This means to show/filter/add commands to the already shown molecules
    * For example, display one or more models, highlight atoms, run scripts
    */
    if (chemicalSelections.size() > 0) {

        logger.debug("Extracted the following chemical selections:");
        for (IChemicalSelection csel : chemicalSelections) {
            logger.debug("  * " + csel.getSelection());
        }

        processChemicalSelections(chemicalSelections);
    }

}

---

From source file:net.bioclipse.jmol.cdk.views.JmolView.java

License:Open Source License

private JmolModelString extractJmolModelsetFromSelection(IStructuredSelection eclipseSelection) {

    for (Object obj : eclipseSelection.toList()) {
        if (obj instanceof JmolModelString) {
            return (JmolModelString) obj;
        }//from   w ww .  j  a v a  2  s . c  o  m

        if (obj instanceof IAdaptable) {
            IAdaptable adaptable = (IAdaptable) obj;
            JmolModelString jms = (JmolModelString) adaptable.getAdapter(JmolModelString.class);
            return jms;
        }
    }

    //Default is null
    return null;
}

---

From source file:net.bioclipse.jmol.cdk.views.JmolView.java

License:Open Source License

private void extractFromSelection(IStructuredSelection ssel, List<ICDKMolecule> collectedCDKMols,
        List<IChemicalSelection> chemicalSelections, List<IPharmacophoreProvider> pcoreProviders) {

    //Loop all selections; if they can provide AC: add to moleculeSet
    for (Object obj : ssel.toList()) {

        boolean storeSelection = false;

        //If we have an ICDKMolecule, just get the AC directly
        if (obj instanceof ICDKMolecule) {
            ICDKMolecule cdkmol = (ICDKMolecule) obj;
            collectedCDKMols.add(cdkmol);
            storeSelection = true;/*from  ww  w  .j  a  v a  2 s.  c  o  m*/

            //                if (cdkmol.getAtomContainer()==null){
            //                    logger.debug("CDKMolecule but can't get AtomContainer.");
            //                }
            //                //Only add if have 3D coords
            //                IAtomContainer ac=cdkmol.getAtomContainer();
            //                if (GeometryTools.has3DCoordinates(ac)){
            //                    addAtomContainer( displayedModels, ac );
            //                }
        }

        //Else try to get the different adapters
        else if (obj instanceof IAdaptable) {
            IAdaptable ada = (IAdaptable) obj;

            //Handle case where Iadaptable can return a molecule
            Object molobj = ada.getAdapter(net.bioclipse.core.domain.IMolecule.class);
            if (molobj != null) {
                //If adaptable returns a cdkmolecule, add it directly 
                if (molobj instanceof ICDKMolecule) {
                    ICDKMolecule cdkmol = (ICDKMolecule) molobj;
                    collectedCDKMols.add(cdkmol);
                }

                //If adaptable at least returns an IMolecule
                //we can create CDKMolecule from it (this is costly though)
                else if (molobj instanceof net.bioclipse.core.domain.IMolecule) {
                    net.bioclipse.core.domain.IMolecule bcmol = (net.bioclipse.core.domain.IMolecule) molobj;
                    try {
                        //Lengthy operation, as via CML or SMILES
                        ICDKMolecule cdkmol = cdk.asCDKMolecule(bcmol);
                        collectedCDKMols.add(cdkmol);
                    } catch (BioclipseException e) {
                        e.printStackTrace();
                    }
                }
                storeSelection = true;
            }

            //Handle case where Iadaptable can return atoms to be highlighted
            Object chemSelectionObj = ada.getAdapter(IChemicalSelection.class);
            if (chemSelectionObj != null) {
                chemicalSelections.add((IChemicalSelection) chemSelectionObj);
                storeSelection = true;
            }

            //Handle case where Iadaptable can return models to be shown
            Object chemModelSel = ada.getAdapter(ModelSelection.class);
            if (chemModelSel != null) {
                chemicalSelections.add((IChemicalSelection) chemModelSel);
                storeSelection = true;
            }

            //Handle case where Iadaptable can return a script
            Object scriptSelection = ada.getAdapter(ScriptSelection.class);
            if (scriptSelection != null) {
                chemicalSelections.add((ScriptSelection) scriptSelection);
                storeSelection = true;
            }

            //Handle case where Iadaptable can return a pharmacophoreProvider
            Object pcoreProvider = ada.getAdapter(IPharmacophoreProvider.class);
            if (pcoreProvider != null) {
                pcoreProviders.add((IPharmacophoreProvider) pcoreProvider);
                storeSelection = true;
            }

        } //End of adaptable collection

        if (storeSelection == true) {
            System.out.println("Storing selection in jmol");
            lastSelected.add(obj);
        }

    } //End of loop over selections
}

---

From source file:net.bioclipse.metaprint2d.ui.actions.MetaPrint2DBatchHandler.java

License:Open Source License

public Object execute(ExecutionEvent event) throws ExecutionException {

    ISelection selection = PlatformUI.getWorkbench().getActiveWorkbenchWindow().getSelectionService()
            .getSelection();//w  w w  .ja v  a 2 s  . c o  m
    if (selection == null) {
        showError("Selection is empty");
        return null;
    }

    if (!(selection instanceof IStructuredSelection)) {
        showError("Selection does not contain an SDF or CML file.");
        return null;
    }

    IStructuredSelection ssel = (IStructuredSelection) selection;

    IMetaPrint2DManager m2d = Activator.getDefault().getMetaPrint2DManager();

    List<String> errors = new ArrayList<String>();

    for (Object obj : ssel.toList()) {
        if (obj instanceof IFile) {
            IFile file = (IFile) obj;
            try {
                m2d.calculate(file, true);
            } catch (Exception e) {
                e.printStackTrace();
                errors.add(" Error calculating file: '" + file + "': " + e.getMessage());
            }
        }
    }

    if (errors.size() > 0) {
        String emsg = "Metaprint2D calculation experienced the following errors:\n";
        for (String er : errors) {
            emsg = emsg + "\n - " + er;
        }
        showError(emsg);
    }

    return null;

}

---

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