com.salsaw.msalsa.PhylogeneticTreeView.java Source code

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Here is the source code for com.salsaw.msalsa.PhylogeneticTreeView.java

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/**
 * Copyright 2015 Alessandro Daniele, Fabio Cesarato, Andrea Giraldin
 * 
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 * 
 *     http://www.apache.org/licenses/LICENSE-2.0
 * 
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
package com.salsaw.msalsa;

import java.io.File;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import java.nio.file.Files;
import java.nio.file.Paths;
import java.util.List;

import com.salsaw.msalsa.clustal.ClustalFileMapper;
import com.vaadin.navigator.View;
import com.vaadin.navigator.ViewChangeListener.ViewChangeEvent;
import com.vaadin.server.FileDownloader;
import com.vaadin.server.FileResource;
import com.vaadin.server.Resource;
import com.vaadin.shared.ui.label.ContentMode;
import com.vaadin.ui.Alignment;
import com.vaadin.ui.Button;
import com.vaadin.ui.CustomComponent;
import com.vaadin.ui.GridLayout;
import com.vaadin.ui.Label;
import com.vaadin.ui.TextArea;

/**
 * @author Alessandro Daniele, Fabio Cesarato, Andrea Giraldin
 */
public class PhylogeneticTreeView extends CustomComponent implements View {

    private GridLayout mainLayout;

    private Label title;

    private Label svgHTMLPhylogenticTree;

    private static final long serialVersionUID = 1L;

    public PhylogeneticTreeView(ClustalFileMapper clustalFileMapper) throws IOException {
        initializeUiComponents();

        // Download alignment file
        Button aligmentButton = new Button("Download alignment");
        Resource resAlignment = new FileResource(new File(clustalFileMapper.getAlignmentFilePath()));
        FileDownloader fdAln = new FileDownloader(resAlignment);
        fdAln.extend(aligmentButton);
        mainLayout.addComponent(aligmentButton);
        mainLayout.setComponentAlignment(aligmentButton, Alignment.MIDDLE_CENTER);

        // Download tree file
        Button downloadTreeButton = new Button("Download phylogentic tree");
        Resource resTree = new FileResource(new File(clustalFileMapper.getTreeFilePath()));
        FileDownloader fdTree = new FileDownloader(resTree);
        fdTree.extend(downloadTreeButton);
        mainLayout.addComponent(downloadTreeButton);
        mainLayout.setComponentAlignment(downloadTreeButton, Alignment.MIDDLE_CENTER);

        // Add and center with HTML div
        svgHTMLPhylogenticTree = new Label("<div id='svgCanvas'></div>", ContentMode.HTML);
        svgHTMLPhylogenticTree.setWidth("-1px");
        svgHTMLPhylogenticTree.setHeight("-1px");
        mainLayout.addComponent(svgHTMLPhylogenticTree);
        mainLayout.setComponentAlignment(svgHTMLPhylogenticTree, Alignment.MIDDLE_CENTER);

        // Add tab with aligment content
        String aligmentFileContent = new String(
                Files.readAllBytes(Paths.get(clustalFileMapper.getAlignmentFilePath())));
        TextArea aligmentFileTextArea = new TextArea("M-SALSA Aligment");
        aligmentFileTextArea.setWordwrap(false);
        aligmentFileTextArea.setValue(aligmentFileContent);
        aligmentFileTextArea.setWidth("100%");
        aligmentFileTextArea.setHeight("100%");
        mainLayout.addComponent(aligmentFileTextArea);
        mainLayout.setComponentAlignment(aligmentFileTextArea, Alignment.MIDDLE_CENTER);

        // Add JavaScript component to generate phylogentic tree
        JsPhyloSVG jsPhyloSVG = new JsPhyloSVG(getPhylogeneticTreeFileContent(clustalFileMapper));
        mainLayout.addComponent(jsPhyloSVG);

        setCompositionRoot(mainLayout);
    }

    private String getPhylogeneticTreeFileContent(ClustalFileMapper clustalFileMapper) throws IOException {

        List<String> lines = Files.readAllLines(Paths.get(clustalFileMapper.getPhylogeneticTreeFile()),
                StandardCharsets.UTF_8);
        StringBuilder newickTreeBuilder = new StringBuilder();
        for (String line : lines) {
            newickTreeBuilder.append(line.trim());
        }

        return newickTreeBuilder.toString();
    }

    private GridLayout initializeUiComponents() {
        mainLayout = new GridLayout();
        mainLayout.setImmediate(false);
        mainLayout.setWidth("100%");
        mainLayout.setHeight("100%");
        mainLayout.setMargin(false);

        // title
        title = new Label();
        title.setImmediate(false);
        title.setWidth("-1px");
        title.setHeight("-1px");
        title.setValue("M-SALSA");
        mainLayout.addComponent(title);
        mainLayout.setComponentAlignment(title, Alignment.MIDDLE_CENTER);

        return mainLayout;
    }

    @Override
    public void enter(ViewChangeEvent event) {
        // TODO Auto-generated method stub

    }
}