com.salsaw.msalsa.HomePagePresenter.java Source code

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Here is the source code for com.salsaw.msalsa.HomePagePresenter.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.file.Paths;

import org.apache.commons.io.FilenameUtils;

import com.salsaw.msalsa.algorithm.exceptions.SALSAException;
import com.salsaw.msalsa.cli.SalsaAlgorithmExecutor;
import com.salsaw.msalsa.cli.SalsaParameters;
import com.salsaw.msalsa.clustal.ClustalFileMapper;
import com.salsaw.msalsa.config.ConfigurationManager;
import com.vaadin.navigator.Navigator;

public class HomePagePresenter implements IHomePageListener {
    // CONSTANTS
    protected static final String PROCESSED = "processed";

    // FIELDS
    private final HomePageView view;
    private final Navigator navigator;
    private final SalsaParameters salsaParameters;

    public HomePagePresenter(HomePageView view, Navigator navigator, SalsaParameters salsaParameters) {
        if (view == null) {
            throw new IllegalArgumentException("view");
        }
        if (navigator == null) {
            throw new IllegalArgumentException("navigator");
        }
        if (salsaParameters == null) {
            throw new IllegalArgumentException("salsaParameters");
        }

        this.view = view;
        this.navigator = navigator;
        this.salsaParameters = salsaParameters;

        view.addListener(this);
    }

    @Override
    public void buttonClick(File file) throws SALSAException, IOException, InterruptedException {
        // Get path to correct Clustal process
        switch (salsaParameters.getClustalType()) {
        case CLUSTAL_W:
            salsaParameters.setClustalPath(
                    ConfigurationManager.getInstance().getServerConfiguration().getClustalW().getAbsolutePath());
            break;

        case CLUSTAL_O:
            salsaParameters.setClustalPath(
                    ConfigurationManager.getInstance().getServerConfiguration().getClustalO().getAbsolutePath());
            break;
        }
        salsaParameters.setClustalWPath(
                ConfigurationManager.getInstance().getServerConfiguration().getClustalW().getAbsolutePath());

        // Create M-SALSA output file name
        salsaParameters.setInputFile(file.getAbsolutePath());
        String inputFileName = FilenameUtils.getBaseName(file.getAbsolutePath());
        salsaParameters.setOutputFile(
                Paths.get(ConfigurationManager.getInstance().getServerConfiguration().getTemporaryFilePath(),
                        inputFileName + "-msalsa-aln.fasta").toString());

        SalsaAlgorithmExecutor.callClustal(salsaParameters);

        // Store path where files has been generated
        ClustalFileMapper clustalFileMapper = new ClustalFileMapper(file.getAbsolutePath());
        clustalFileMapper.setAlignmentFilePath(salsaParameters.getOutputFile());
        clustalFileMapper.setPhylogeneticTreeFile(
                Paths.get(ConfigurationManager.getInstance().getServerConfiguration().getTemporaryFilePath(),
                        inputFileName + "-msalsa-aln.ph").toString());

        // Show view with results
        final PhylogeneticTreeView testTreeView = new PhylogeneticTreeView(clustalFileMapper);
        navigator.addView(PROCESSED, testTreeView);
        navigator.navigateTo(PROCESSED);
    }
}