com.ggvaidya.scinames.summary.DatasetSimilarityView.java Source code

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Here is the source code for com.ggvaidya.scinames.summary.DatasetSimilarityView.java

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/*
 *
 *  NameClustersView
 *  Copyright (C) 2017 Gaurav Vaidya
 *
 *  This file is part of SciNames.
 *
 *  SciNames is free software: you can redistribute it and/or modify
 *  it under the terms of the GNU General Public License as published by
 *  the Free Software Foundation, either version 3 of the License, or
 *  (at your option) any later version.
 *
 *  SciNames is distributed in the hope that it will be useful,
 *  but WITHOUT ANY WARRANTY; without even the implied warranty of
 *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *  GNU General Public License for more details.
 *
 *  You should have received a copy of the GNU General Public License
 *  along with SciNames.  If not, see <http://www.gnu.org/licenses/>.
 *
 */

package com.ggvaidya.scinames.summary;

import java.math.BigDecimal;
import java.math.RoundingMode;
import java.util.List;
import java.util.Set;
import java.util.logging.Logger;
import java.util.stream.Collectors;

import com.ggvaidya.scinames.model.Dataset;
import com.ggvaidya.scinames.model.NameCluster;
import com.ggvaidya.scinames.model.NameClusterManager;
import com.ggvaidya.scinames.tabulardata.TabularDataViewController;
import com.ggvaidya.scinames.ui.ProjectView;
import com.google.common.collect.HashBasedTable;
import com.google.common.collect.Sets;
import com.google.common.collect.Table;

import javafx.beans.property.ReadOnlyStringWrapper;
import javafx.collections.FXCollections;
import javafx.collections.ObservableList;
import javafx.scene.Scene;
import javafx.scene.control.TableColumn;
import javafx.scene.control.cell.PropertyValueFactory;
import javafx.stage.Stage;

/**
 * A DatasetSimilarityView displays similarity between timepoints.
 * It uses the TabularDataView to do this.
 * 
 * @author Gaurav Vaidya <gaurav@ggvaidya.com>
 */
public final class DatasetSimilarityView {
    private Logger LOGGER = Logger.getLogger(DatasetSimilarityView.class.getSimpleName());

    private Stage stage;
    private Scene scene;
    private ProjectView projectView;
    private TabularDataViewController controller;

    public Stage getStage() {
        return stage;
    }

    public DatasetSimilarityView(ProjectView pv) {
        projectView = pv;
        stage = new Stage();

        controller = TabularDataViewController.createTabularDataView();
        scene = controller.getScene();
        init();

        // Go go stagey scene.
        stage.setScene(scene);
    }

    public void init() {
        // Setup stage.
        stage.setTitle("Timepoint similarity");

        // Setup table.
        controller.getTableEditableProperty().set(false);
        //controller.setTableColumnResizeProperty(TableView.CONSTRAINED_RESIZE_POLICY);
        ObservableList<TableColumn> cols = controller.getTableColumnsProperty();
        cols.clear();

        // Set up columns.
        TableColumn<Dataset, String> colTimepointName = new TableColumn<>("Timepoint");
        colTimepointName.setCellValueFactory(new PropertyValueFactory<>("name"));
        colTimepointName.setPrefWidth(100.0);
        cols.add(colTimepointName);

        // Precalculating.
        double lowest = 100.0;
        Dataset tpLowest1 = null;
        Dataset tpLowest2 = null;

        LOGGER.info("Starting precalculating.");

        Table<Dataset, Dataset, String> data = HashBasedTable.create();
        for (Dataset tp : projectView.getProject().getDatasets()) {
            for (Dataset colTP : projectView.getProject().getDatasets()) {
                if (data.contains(tp, colTP))
                    continue;

                NameClusterManager manager = projectView.getProject().getNameClusterManager();
                Set<NameCluster> leftTP = tp.getRecognizedNames(projectView.getProject())
                        .map(n -> manager.getCluster(n).get()).collect(Collectors.toSet());
                Set<NameCluster> rightTP = colTP.getRecognizedNames(projectView.getProject())
                        .map(n -> manager.getCluster(n).get()).collect(Collectors.toSet());

                // Overlapping name concepts.
                Sets.SetView<NameCluster> union = Sets.union(leftTP, rightTP);
                Sets.SetView<NameCluster> intersection = Sets.intersection(leftTP, rightTP);

                double res = (((double) intersection.size()) / union.size() * 100);

                if (lowest > res) {
                    lowest = res;
                    tpLowest1 = tp;
                    tpLowest2 = colTP;
                }

                String result = new BigDecimal(res).setScale(2, RoundingMode.DOWN).toPlainString() + "% ("
                        + intersection.size() + " identical out of " + union.size() + ")";

                data.put(tp, colTP, result);
                data.put(colTP, tp, result);
            }
        }

        LOGGER.info("Precalculating done.");

        // Setup headertext.
        String str_lowest = "";
        if (tpLowest1 != null && tpLowest2 != null) {
            str_lowest = " (lowest: " + new BigDecimal(lowest).setScale(2, RoundingMode.DOWN).toPlainString()
                    + "% between " + tpLowest1.getName() + " and " + tpLowest2.getName() + ")";
        }
        controller.getHeaderTextProperty().set("How similar is each timepoint to every other?" + str_lowest);
        controller.getHeaderTextEditableProperty().set(false);

        // Create a column for every timepoint here.
        projectView.getProject().getDatasets().forEach((Dataset colTP) -> {
            TableColumn<Dataset, String> colTimepoint = new TableColumn<>(colTP.getName());
            colTimepoint.setCellValueFactory((TableColumn.CellDataFeatures<Dataset, String> features) -> {
                Dataset tp = features.getValue();

                return new ReadOnlyStringWrapper(data.get(tp, colTP));
            });
            colTimepoint.setPrefWidth(100.0);
            cols.add(colTimepoint);
        });

        // Set table items.
        List<Dataset> timepoints = projectView.getProject().getDatasets();
        controller.getTableItemsProperty().set(FXCollections.observableList(timepoints));
    }
}