Package org.broad.igv.batch

Examples of org.broad.igv.batch.CommandExecutor$SortAlignmentsHandler

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        tstSearchEGFR(tracks);
    }

    @Test
    public void testBatchCommand_Error() throws Exception{
        CommandExecutor cmdexec = new CommandExecutor();
        String cmd = "org.broad.igv.tools.motiffinder.MotifFinderPlugin blarg " + EGFR_begseq;
        String resp = cmdexec.execute(cmd);
        assertTrue("Expected ERROR, was " + resp, resp.contains("ERROR"));

        assertEquals(2, IGV.getInstance().getVisibleTrackCount());
    }
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        assertEquals(2, IGV.getInstance().getVisibleTrackCount());
    }

    @Test
    public void testBatchCommand() throws Exception{
        CommandExecutor cmdexec = new CommandExecutor();
        String cmd = "org.broad.igv.tools.motiffinder.MotifFinderPlugin find " + EGFR_begseq;
        String resp = cmdexec.execute(cmd);
        assertTrue("Expected OK, was " + resp, resp.contains("OK"));

        List<Track> finderTracks = new ArrayList<Track>(2);
        //Slight weakness here, we require that the tracks be in order positive/negative,
        //but don't check that
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Related Classes of org.broad.igv.batch.CommandExecutor$SortAlignmentsHandler

  • com.google.common.eventbus.EventBus
  • org.broad.igv.dev.api.batch.Command
  • org.broad.igv.feature.Locus
  • org.broad.igv.feature.RegionOfInterest
  • org.broad.igv.renderer.DataRange
  • org.broad.igv.sam.AlignmentTrack
  • org.broad.igv.tools.motiffinder.MotifFinderPluginHeadedTest
  • org.broad.igv.track.RegionScoreType
  • java.net.URI
  • java.util.concurrent.Future
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