Examples with SmartComparator com.github.lindenb.jvarkit.lang.SmartComparator used on opensource projects

Example 1 with SmartComparator

use of com.github.lindenb.jvarkit.lang.SmartComparator in project jvarkit by lindenb.

the class IndexCovJfx method doWork.

@Override
public int doWork(final Stage primaryStage, final List<String> args) {
    final Rectangle2D screen = Screen.getPrimary().getVisualBounds();
    final Pattern tab = Pattern.compile("[\t]");
    BufferedReader r = null;
    try {
        final File inputFile;
        if (args.isEmpty()) {
            // open gui
            final FileChooser fc = new FileChooser();
            inputFile = fc.showOpenDialog(null);
            if (inputFile == null) {
                return 0;
            }
        } else if (args.size() == 1) {
            inputFile = new File(args.get(0));
        } else {
            LOG.error("Illegal Number of arguments: " + args);
            return -1;
        }
        r = IOUtils.openFileForBufferedReading(inputFile);
        String line = r.readLine();
        if (line == null) {
            new Alert(AlertType.ERROR, "Cannot read first line of " + inputFile, ButtonType.OK).showAndWait();
            return -1;
        }
        String[] tokens = tab.split(line);
        if (tokens.length < 4 || !tokens[0].equals("#chrom") || !tokens[1].equals("start") || !tokens[2].equals("end")) {
            new Alert(AlertType.ERROR, "bad first line " + line + " in " + inputFile, ButtonType.OK).showAndWait();
            return -1;
        }
        this.sampleNames.addAll(Arrays.asList(tokens).subList(3, tokens.length).stream().map(S -> new Sample(S)).collect(Collectors.toList()));
        this.sampleListView = new ListView<>(this.sampleNames);
        final MultipleSelectionModel<Sample> sampleSelectionModel = this.sampleListView.getSelectionModel();
        sampleSelectionModel.setSelectionMode(SelectionMode.MULTIPLE);
        // this.sampleListView.setPrefWidth(200);
        final SmartComparator smartCmp = new SmartComparator();
        this.orignalndexCovRows.addAll(r.lines().filter(L -> !StringUtil.isBlank(L)).map(L -> Arrays.asList(tab.split(L))).map(T -> new IndexCovRow(T)).sorted((A, B) -> {
            int i = smartCmp.compare(A.getContig(), B.getContig());
            if (i != 0)
                return i;
            return A.getStart() - B.getStart();
        }).collect(Collectors.toList()));
        this.visibleIndexCovRows.addAll(orignalndexCovRows);
        String lastContig = null;
        for (final IndexCovRow row : this.visibleIndexCovRows) {
            if (lastContig == null || !lastContig.equals(row.getContig())) {
                this.contig2color.put(row.getContig(), this.contig2color.size() % 2 == 0 ? gray(0.96) : gray(0.98));
                lastContig = row.getContig();
            }
        }
        this.canvas = new Canvas(screen.getWidth() - 400, screen.getHeight() - 200);
        this.canvasSrollPane = new ScrollPane(canvas);
        this.canvasSrollPane.setFitToHeight(true);
        this.canvasSrollPane.setFitToWidth(true);
        this.canvasSrollPane.setHbarPolicy(ScrollBarPolicy.ALWAYS);
        this.canvasSrollPane.setHmin(0);
        // NOT HERE: see adjustScollPane();
        // this.canvasSrollPane.setHmax(this.visibleIndexCovRows.size()*CHUNK_WIDTH);
        // this.canvasSrollPane.setHvalue(0);
        this.canvasSrollPane.hvalueProperty().addListener(E -> repaintCanvas());
        final VBox root = new VBox();
        final MenuBar menuBar = new MenuBar();
        Menu menu = new Menu("Tools");
        MenuItem item = new MenuItem("Goto");
        item.setOnAction(AE -> askGoto());
        item.setAccelerator(new KeyCodeCombination(KeyCode.G, KeyCombination.CONTROL_DOWN));
        menu.getItems().add(item);
        menu.getItems().add(new SeparatorMenuItem());
        // 
        item = new MenuItem("Cleanup: remove data > DEL && data < DUP");
        item.setOnAction(AE -> askCleanup());
        menu.getItems().add(item);
        // 
        item = new MenuItem("Cleanup: remove ALL samples <= DEL or ALL samples >= DUP");
        item.setOnAction(AE -> askEveryWhere());
        menu.getItems().add(item);
        // 
        item = new MenuItem("Cleanup: keep selected samples having <= DEL or ALL samples >= DUP");
        item.setOnAction(AE -> filterForSampleSet(false));
        menu.getItems().add(item);
        // 
        item = new MenuItem("Cleanup: keep selected samples having <= DEL or ALL samples >= DUP and only those samples.");
        item.setOnAction(AE -> filterForSampleSet(true));
        menu.getItems().add(item);
        // 
        item = new MenuItem("Filter: Keep data overlapping BED file");
        item.setOnAction(AE -> filterBed(false));
        menu.getItems().add(item);
        // 
        item = new MenuItem("Filter: Keep data NOT overlapping BED file");
        item.setOnAction(AE -> filterBed(true));
        menu.getItems().add(item);
        // 
        item = new MenuItem("Revert: Restore original data");
        item.setOnAction(AE -> doRestoreOriginalData());
        item.setAccelerator(new KeyCodeCombination(KeyCode.R, KeyCombination.CONTROL_DOWN));
        menu.getItems().add(item);
        menu.getItems().add(new SeparatorMenuItem());
        item = new MenuItem("Next Interesting");
        item.setOnAction(AE -> goToNextInteresting(1));
        item.setAccelerator(new KeyCodeCombination(KeyCode.N, KeyCombination.CONTROL_DOWN));
        menu.getItems().add(item);
        item = new MenuItem("Previous Interesting");
        item.setOnAction(AE -> goToNextInteresting(-1));
        item.setAccelerator(new KeyCodeCombination(KeyCode.P, KeyCombination.CONTROL_DOWN));
        menu.getItems().add(item);
        menu.getItems().add(new SeparatorMenuItem());
        item = new MenuItem("Quit");
        menu.getItems().add(item);
        item.setOnAction(AE -> {
            Platform.exit();
        });
        menuBar.getMenus().add(menu);
        root.getChildren().add(menuBar);
        final HBox toolboxPane = new HBox();
        Label label = new Label("DEL when \u2264 :");
        toolboxPane.getChildren().add(label);
        this.deletionSpinner = new Spinner<>(0.0, 0.9, DEFAULT_deletionTreshold, 0.05);
        label.setLabelFor(this.deletionSpinner);
        this.deletionSpinner.valueProperty().addListener((a, b, c) -> repaintCanvas());
        toolboxPane.getChildren().add(this.deletionSpinner);
        label = new Label("DUP when \u2265 :");
        toolboxPane.getChildren().add(label);
        this.duplicationSpinner = new Spinner<>(1.1, 10.0, DEFAULT_duplicationTreshold, 0.05);
        this.duplicationSpinner.valueProperty().addListener((a, b, c) -> repaintCanvas());
        label.setLabelFor(this.duplicationSpinner);
        toolboxPane.getChildren().add(this.duplicationSpinner);
        label = new Label(" Jump to :");
        toolboxPane.getChildren().add(label);
        final TextField jumpToTextField = new TextField();
        jumpToTextField.setPromptText("chrom:pos");
        jumpToTextField.setPrefColumnCount(15);
        toolboxPane.getChildren().add(jumpToTextField);
        label.setLabelFor(jumpToTextField);
        jumpToTextField.setOnAction(AE -> askGoto(jumpToTextField.getText()));
        final Button goButton = new Button("Go");
        toolboxPane.getChildren().add(goButton);
        goButton.setOnAction(AE -> askGoto(jumpToTextField.getText()));
        root.getChildren().add(toolboxPane);
        // HBox hbox = new HBox(sampleListView,this.canvasSrollPane);
        final GridPane grid = new GridPane();
        grid.setHgap(10);
        grid.setVgap(10);
        grid.setPadding(new Insets(5, 5, 5, 5));
        grid.add(this.sampleListView, 0, 0, 1, 1);
        grid.add(this.canvasSrollPane, 1, 0, 9, 1);
        // final StackPane root = new StackPane();
        root.getChildren().add(grid);
        final Scene scene = new Scene(root);
        primaryStage.setTitle(IndexCovJfx.class.getSimpleName() + " " + this.sampleNames.size() + " Sample(s) " + this.visibleIndexCovRows.size() + " Point(s).");
        primaryStage.setOnShown(E -> {
            adjustScollPane();
            this.canvasSrollPane.requestFocus();
            repaintCanvas();
            if (this.isUnitText()) {
                Platform.exit();
            }
        });
        this.canvasSrollPane.setOnKeyPressed(e -> {
            if (e.getCode() == KeyCode.LEFT) {
                canvasSrollPane.setHvalue(Math.max(canvasSrollPane.getHmin(), canvasSrollPane.getHvalue() - CHUNK_WIDTH));
            }
            if (e.getCode() == KeyCode.RIGHT) {
                canvasSrollPane.setHvalue(Math.min(canvasSrollPane.getHmax(), canvasSrollPane.getHvalue() + CHUNK_WIDTH));
            }
        });
        primaryStage.setScene(scene);
        primaryStage.show();
        /*sampleSelectionModel.selectedItemProperty().addListener(E->{
	        	repaintCanvas();
				});
	        sampleSelectionModel.selectedItemProperty().addListener(E->repaintCanvas());*/
        sampleSelectionModel.getSelectedIndices().addListener(new ListChangeListener<Integer>() {

            @Override
            public void onChanged(Change<? extends Integer> c) {
                repaintCanvas();
            }
        });
    } catch (final Exception err) {
        LOG.error(err);
        new Alert(AlertType.ERROR, "Error " + err, ButtonType.OK).showAndWait();
        return -1;
    } finally {
        CloserUtil.close(r);
    }
    return 0;
}