Examples with UtilitiesUserParameters com.compomics.util.parameters.UtilitiesUserParameters used on opensource projects

Example 1 with UtilitiesUserParameters

use of com.compomics.util.parameters.UtilitiesUserParameters in project peptide-shaker by compomics.

the class PrideSearchParametersDialog method okButtonActionPerformed.

// GEN-LAST:event_cancelButtonActionPerformed
/**
 * Open SearchGUI with the given search parameters.
 *
 * @param evt
 */
private void okButtonActionPerformed(java.awt.event.ActionEvent evt) {
    // GEN-FIRST:event_okButtonActionPerformed
    prideReShakeGUI.setVisible(false);
    this.setVisible(false);
    boolean openSearchGUI = true;
    // check if we have a valid SearchGUI location.
    try {
        UtilitiesUserParameters utilitiesUserPreferences = UtilitiesUserParameters.loadUserParameters();
        if (utilitiesUserPreferences.getSearchGuiPath() == null || !(new File(utilitiesUserPreferences.getSearchGuiPath()).exists())) {
            SearchGuiSetupDialog searchGuiSetupDialog = new SearchGuiSetupDialog(prideReShakeGUI, true);
            openSearchGUI = !searchGuiSetupDialog.isDialogCanceled();
        }
    } catch (Exception e) {
        prideReShakeGUI.getPeptideShakerGUI().catchException(e);
    }
    if (openSearchGUI) {
        new Thread(new Runnable() {

            public void run() {
                try {
                    File outputFolder = null;
                    if (!mgfFiles.isEmpty() || !rawFiles.isEmpty()) {
                        if (!mgfFiles.isEmpty()) {
                            outputFolder = new File(mgfFiles.get(0).getParentFile(), "search_results");
                        } else {
                            outputFolder = new File(rawFiles.get(0).getParentFile(), "search_results");
                        }
                        if (!outputFolder.exists()) {
                            boolean success = outputFolder.mkdir();
                            if (!success) {
                                outputFolder = null;
                            }
                        }
                    }
                    ToolFactory.startSearchGUI(prideReShakeGUI, mgfFiles, rawFiles, fastaFile, prideSearchParametersFile, outputFolder, species, speciesType, psProjectName);
                    prideReShakeGUI.getPeptideShakerGUI().close();
                } catch (Exception e) {
                    prideReShakeGUI.getPeptideShakerGUI().catchException(e);
                }
            }
        }, "StartSearchGUI").start();
    }
}

Example 2 with UtilitiesUserParameters

use of com.compomics.util.parameters.UtilitiesUserParameters in project peptide-shaker by compomics.

the class WelcomeDialog method downloadSearchGUI.

/**
 * Download SearchGUI.
 *
 * @return true if not canceled
 */
public boolean downloadSearchGUI() {
    boolean firstTimeInstall = true;
    String installPath = null;
    UtilitiesUserParameters utilitiesUserPreferences = peptideShakerGUI.getUtilitiesUserParameters();
    if (utilitiesUserPreferences.getSearchGuiPath() != null) {
        if (new File(utilitiesUserPreferences.getSearchGuiPath()).getParentFile() != null && new File(utilitiesUserPreferences.getSearchGuiPath()).getParentFile().getParentFile() != null) {
            installPath = new File(utilitiesUserPreferences.getSearchGuiPath()).getParentFile().getParent();
        }
    }
    final File downloadFolder;
    if (installPath == null) {
        installPath = "user.home";
        downloadFolder = FileChooserUtil.getUserSelectedFolder(this, "Select SearchGUI Folder", installPath, "SearchGUI Folder", "Select", false);
    } else {
        firstTimeInstall = false;
        downloadFolder = new File(installPath);
    }
    final boolean finalFirstTimeInstall = firstTimeInstall;
    if (downloadFolder != null) {
        progressDialog = new ProgressDialogX(DUMMY_PARENT_FRAME, Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/peptide-shaker.gif")), Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/peptide-shaker-orange.gif")), true);
        progressDialog.setPrimaryProgressCounterIndeterminate(true);
        progressDialog.setTitle("Downloading SearchGUI. Please Wait...");
        new Thread(new Runnable() {

            public void run() {
                try {
                    progressDialog.setVisible(true);
                } catch (IndexOutOfBoundsException e) {
                // ignore
                }
            }
        }, "ProgressDialog").start();
        Thread thread = new Thread("DownloadThread") {

            @Override
            public void run() {
                try {
                    URL jarRepository = new URL("http", "genesis.ugent.be", "/maven2/");
                    if (finalFirstTimeInstall) {
                        downloadLatestZipFromRepo(downloadFolder, "SearchGUI", "eu.isas.searchgui", "SearchGUI", "searchgui.ico", null, jarRepository, false, true, new GUIFileDAO(), progressDialog);
                    } else {
                        downloadLatestZipFromRepo(new File(peptideShakerGUI.getUtilitiesUserParameters().getSearchGuiPath()).toURI().toURL(), "SearchGUI", false, "searchgui.ico", null, jarRepository, false, true, new GUIFileDAO(), progressDialog);
                    }
                } catch (IOException e) {
                    e.printStackTrace();
                } catch (URISyntaxException e) {
                    e.printStackTrace();
                } catch (XMLStreamException e) {
                    e.printStackTrace();
                }
            }
        };
        thread.start();
        try {
            thread.join();
        } catch (InterruptedException e) {
            e.printStackTrace();
        }
        if (progressDialog.isRunCanceled()) {
            progressDialog.setRunFinished();
            return false;
        } else if (!progressDialog.isRunFinished()) {
            progressDialog.setRunFinished();
        }
        return true;
    }
    return false;
}

Example 3 with UtilitiesUserParameters

use of com.compomics.util.parameters.UtilitiesUserParameters in project peptide-shaker by compomics.

the class DatabaseHelpDialog method browseDatabaseSettingsActionPerformed.

// </editor-fold>//GEN-END:initComponents
/**
 * Opens a file chooser where the user can select the database file.
 *
 * @param evt
 */
private void browseDatabaseSettingsActionPerformed(java.awt.event.ActionEvent evt) {
    // GEN-FIRST:event_browseDatabaseSettingsActionPerformed
    File startLocation = null;
    File utilitiesDbFolder = utilitiesUserParameters.getDbFolder();
    if (utilitiesDbFolder != null && utilitiesDbFolder.exists()) {
        startLocation = utilitiesDbFolder;
    }
    if (startLocation == null) {
        startLocation = new File(getLastSelectedFolder(lastSelectedFolder));
    }
    UtilitiesUserParameters utilitiesUserPreferences = UtilitiesUserParameters.loadUserParameters();
    if (utilitiesUserPreferences.getDbFolder() != null && utilitiesUserPreferences.getDbFolder().exists()) {
        startLocation = utilitiesUserPreferences.getDbFolder();
    }
    if (selectedFastaFile != null) {
        File fastaFile = new File(selectedFastaFile);
        if (fastaFile.exists()) {
            startLocation = fastaFile.getParentFile();
        }
    }
    JFileChooser fc = new JFileChooser(startLocation);
    FileFilter filter = new FileFilter() {

        @Override
        public boolean accept(File myFile) {
            return myFile.getName().toLowerCase().endsWith("fasta") || myFile.isDirectory();
        }

        @Override
        public String getDescription() {
            return "Supported formats: FASTA (.fasta)";
        }
    };
    fc.setFileFilter(filter);
    int result = fc.showOpenDialog(this);
    if (result == JFileChooser.APPROVE_OPTION) {
        File selectedFile = fc.getSelectedFile();
        selectedFastaFile = selectedFile.getAbsolutePath();
        if (selectedFile.getName().contains(" ")) {
            renameFastaFileName();
        } else {
            databaseSettingsTxt.setText(selectedFastaFile);
        }
        lastSelectedFolder.setLastSelectedFolder(SequenceDbDetailsDialog.lastFolderKey, selectedFastaFile);
        targetDecoySettingsButton.setEnabled(true);
        // check if the database contains decoys
        if (!selectedFastaFile.endsWith(fastaParameters.getTargetDecoyFileNameSuffix() + ".fasta")) {
            int value = JOptionPane.showConfirmDialog(this, "The selected FASTA file does not seem to contain decoy sequences.\n" + "Decoys are required by PeptideShaker. Add decoys?", "Add Decoy Sequences?", JOptionPane.YES_NO_OPTION);
            if (value == JOptionPane.YES_OPTION) {
                targetDecoySettingsButtonActionPerformed(null);
            }
        }
        validateParametersInput(false);
    }
}