* Copyright (c) 2007-2012 The Broad Institute, Inc.

* SOFTWARE COPYRIGHT NOTICE

* This software and its documentation are the copyright of the Broad Institute, Inc. All rights are reserved.

*

* This software is supplied without any warranty or guaranteed support whatsoever. The Broad Institute is not responsible for its use, misuse, or functionality.

*

* This software is licensed under the terms of the GNU Lesser General Public License (LGPL),

* Version 2.1 which is available at http://www.opensource.org/licenses/lgpl-2.1.php.

*/

* User: jacob

* Date: 2013-Feb-15

*/

    @BeforeClass

    public static void setUpClass() throws Exception {

        pluginPath = "resources/cufflinks_plugin.xml";

        AbstractPluginTest.setUpClass();

    }

    /**

     * Load some alignment data and run cufflinks on it.

     *

     * @param chr

     * @param start

     * @param end

     * @param inFile

     * @return The transcripts.gtf file cufflinks calculated

     */

    private List<Object> basicRunCufflinks(String chr, int start, int end, File inFile) throws Exception{

        //Load some alignment data

        ResourceLocator locator = new ResourceLocator(inFile.getAbsolutePath());

        AlignmentDataManager dataManager = new AlignmentDataManager(locator, genome);

        AlignmentTrack alignmentTrack = new AlignmentTrack(locator, dataManager, genome);

        dataManager.loadAlignments(chr, start, end, null, null);

        PluginSpecReader.Command command = tool.commandList.get(0);

        List<Argument> argumentList = command.argumentList;

        LinkedHashMap<Argument, Object> arguments = new LinkedHashMap<Argument, Object>(argumentList.size());

        //Fill in the input arguments

        for(int argNum = 0; argNum < argumentList.size(); argNum++) {

            Argument argument = argumentList.get(argNum);

            String argName = argument.getName();

            Object value = argument.getDefaultValue();

            if(argName.equalsIgnoreCase("Output Dir")){

                value = TestUtils.TMP_OUTPUT_DIR;

            }else if(argName.equalsIgnoreCase("Track")){

                value = alignmentTrack;

            }

            if(argument.getType() == Argument.InputType.BOOL){

                value = Boolean.parseBoolean((String) value);

            }

            arguments.put(argument, value);

        }

        List<String> commands = Arrays.asList(toolPath);

        PluginFeatureSource featureSource = new PluginFeatureSource(commands, arguments, command.outputList.get(0), pluginPath);

        PluginDataSource geneTrackingSource = new PluginDataSource(genome, commands, arguments, command.outputList.get(1), pluginPath);

        return Arrays.asList(featureSource, geneTrackingSource);

    }

    @Test

    public void testBasic() throws Exception{

        String chr = "chr1";

        int start = 151666493 - 1;

        int end = start + 10000;

        File inFile = new File(TestUtils.LARGE_DATA_DIR, "HG00171.hg18.bam");

        List sources = basicRunCufflinks(chr, start, end, inFile);

        PluginFeatureSource featureSource = (PluginFeatureSource) sources.get(0);

        PluginDataSource geneTrackingSource = (PluginDataSource) sources.get(1);

        Iterator<Feature> features = featureSource.getFeatures(chr, start, end);

        int count = countNonNullFeatures(features);

        assertTrue("No features read" , count > 0);

        assertTrue("No longest feature", geneTrackingSource.getLongestFeature(chr) > 0);

        DataTile dataTile = geneTrackingSource.getRawData(chr, start, end);

        assertNotNull("No fpkm data returned", dataTile);

        assertFalse(dataTile.isEmpty());

    }

    private int countNonNullFeatures(Iterator<Feature> featureIterator){

        int count = 0;

        while(featureIterator.hasNext()){

            Feature feat = featureIterator.next();

            assertNotNull(feat);

            count++;

        }

        return count;

    }

    @Test

    public void testCufflinksExample_test_data() throws Exception{

        String chr = "test_chromosome";

        int start = 0;

        int end = start + 400;

        File inFile = new File(TestUtils.DATA_DIR + "sam", "cufflinks_test_data.sam");

        TestUtils.createIndex(inFile.getAbsolutePath());

        Iterator<Feature> features = ((PluginFeatureSource) basicRunCufflinks(chr, start, end, inFile).get(0)).getFeatures(chr, start, end);

        List<Feature> combinedFeatures = new GFFFeatureSource.GFFCombiner().addFeatures(features).combineFeatures();

        assertEquals("Wrong number of transcripts", 1, combinedFeatures.size());

        BasicFeature transcript = (BasicFeature) combinedFeatures.get(0);

        assertEquals(53 - 1, transcript.getStart());

        assertEquals(550, transcript.getEnd());

        assertEquals(3, transcript.getExonCount());

        String transFPKM = transcript.getAttributes().get("FPKM");

        assertTrue("Transcript FPKM invalid: " + transFPKM, transFPKM.startsWith("105"));

        int[] exonStarts = new int[]{53,351,501};

        int[] exonEnds = new int[]{250,400,550};

        for(int ii= 0; ii < 3; ii++){

            Exon exon = transcript.getExons().get(ii);

            assertEquals(exonStarts[ii] - 1, exon.getStart());

            assertEquals(exonEnds[ii], exon.getEnd());

            String exonFPKM = transcript.getAttributes().get("FPKM");

            assertTrue("Exon FPKM invalid: " + exonFPKM, exonFPKM.startsWith("105"));

            assertTrue(exonFPKM.startsWith("105"));

        }

    }

}