Commit de7533e7 authored by Michael Menzel's avatar Michael Menzel

added gpl notice

parent 52e44513
......@@ -381,9 +381,8 @@
<option name="skipTests" value="true" />
</component>
<component name="ProjectFrameBounds">
<option name="x" value="3840" />
<option name="width" value="1920" />
<option name="height" value="1061" />
<option name="height" value="1181" />
</component>
<component name="ProjectInspectionProfilesVisibleTreeState">
<entry key="Project Default">
......
// Copyright (C) 2018 Michael Menzel
//
// This file is part of Enhort. <https://enhort.mni.thm.de>.
//
// Enhort 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.
//
// Enhort 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 Enhort. If not, see <https://www.gnu.org/licenses/>.
package de.thm.backgroundModel;
import de.thm.genomeData.tracks.Track;
......
// Copyright (C) 2018 Michael Menzel
//
// This file is part of Enhort. <https://enhort.mni.thm.de>.
//
// Enhort 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.
//
// Enhort 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 Enhort. If not, see <https://www.gnu.org/licenses/>.
package de.thm.backgroundModel;
import de.thm.exception.CovariatesException;
......
// Copyright (C) 2018 Michael Menzel
//
// This file is part of Enhort. <https://enhort.mni.thm.de>.
//
// Enhort 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.
//
// Enhort 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 Enhort. If not, see <https://www.gnu.org/licenses/>.
package de.thm.backgroundModel;
import de.thm.calc.Distances;
......
// Copyright (C) 2018 Michael Menzel
//
// This file is part of Enhort. <https://enhort.mni.thm.de>.
//
// Enhort 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.
//
// Enhort 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 Enhort. If not, see <https://www.gnu.org/licenses/>.
package de.thm.backgroundModel;
import de.thm.genomeData.tracks.Track;
......
// Copyright (C) 2018 Michael Menzel
//
// This file is part of Enhort. <https://enhort.mni.thm.de>.
//
// Enhort 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.
//
// Enhort 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 Enhort. If not, see <https://www.gnu.org/licenses/>.
package de.thm.backgroundModel;
import de.thm.calc.Intersect;
......
// Copyright (C) 2018 Michael Menzel
//
// This file is part of Enhort. <https://enhort.mni.thm.de>.
//
// Enhort 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.
//
// Enhort 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 Enhort. If not, see <https://www.gnu.org/licenses/>.
package de.thm.backgroundModel;
import de.thm.genomeData.tracks.Track;
......
// Copyright (C) 2018 Michael Menzel
//
// This file is part of Enhort. <https://enhort.mni.thm.de>.
//
// Enhort 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.
//
// Enhort 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 Enhort. If not, see <https://www.gnu.org/licenses/>.
package de.thm.backgroundModel;
import de.thm.genomeData.tracks.ScoredTrack;
......
// Copyright (C) 2018 Michael Menzel
//
// This file is part of Enhort. <https://enhort.mni.thm.de>.
//
// Enhort 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.
//
// Enhort 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 Enhort. If not, see <https://www.gnu.org/licenses/>.
package de.thm.backgroundModel;
import java.util.Arrays;
......
// Copyright (C) 2018 Michael Menzel
//
// This file is part of Enhort. <https://enhort.mni.thm.de>.
//
// Enhort 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.
//
// Enhort 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 Enhort. If not, see <https://www.gnu.org/licenses/>.
package de.thm.backgroundModel;
import de.thm.calc.Intersect;
......
// Copyright (C) 2018 Michael Menzel
//
// This file is part of Enhort. <https://enhort.mni.thm.de>.
//
// Enhort 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.
//
// Enhort 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 Enhort. If not, see <https://www.gnu.org/licenses/>.
package de.thm.calc;
import de.thm.genomeData.tracks.DistanceTrack;
......
// Copyright (C) 2018 Michael Menzel
//
// This file is part of Enhort. <https://enhort.mni.thm.de>.
//
// Enhort 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.
//
// Enhort 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 Enhort. If not, see <https://www.gnu.org/licenses/>.
package de.thm.calc;
import de.thm.genomeData.tracks.DistanceTrack;
......
// Copyright (C) 2018 Michael Menzel
//
// This file is part of Enhort. <https://enhort.mni.thm.de>.
//
// Enhort 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.
//
// Enhort 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 Enhort. If not, see <https://www.gnu.org/licenses/>.
package de.thm.calc;
......
// Copyright (C) 2018 Michael Menzel
//
// This file is part of Enhort. <https://enhort.mni.thm.de>.
//
// Enhort 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.
//
// Enhort 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 Enhort. If not, see <https://www.gnu.org/licenses/>.
package de.thm.calc;
import de.thm.genomeData.tracks.ScoredTrack;
......
// Copyright (C) 2018 Michael Menzel
//
// This file is part of Enhort. <https://enhort.mni.thm.de>.
//
// Enhort 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.
//
// Enhort 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 Enhort. If not, see <https://www.gnu.org/licenses/>.
package de.thm.calc;
import de.thm.exception.TrackTypeNotAllowedExcpetion;
......
// Copyright (C) 2018 Michael Menzel
//
// This file is part of Enhort. <https://enhort.mni.thm.de>.
//
// Enhort 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.
//
// Enhort 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 Enhort. If not, see <https://www.gnu.org/licenses/>.
package de.thm.calc;
import de.thm.result.ResultCollector;
......
// Copyright (C) 2018 Michael Menzel
//
// This file is part of Enhort. <https://enhort.mni.thm.de>.
//
// Enhort 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.
//
// Enhort 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 Enhort. If not, see <https://www.gnu.org/licenses/>.
package de.thm.calc;
import de.thm.genomeData.tracks.InOutTrack;
......
// Copyright (C) 2018 Michael Menzel
//
// This file is part of Enhort. <https://enhort.mni.thm.de>.
//
// Enhort 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.
//
// Enhort 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 Enhort. If not, see <https://www.gnu.org/licenses/>.
package de.thm.calc;
import de.thm.genomeData.tracks.Track;
......
// Copyright (C) 2018 Michael Menzel
//
// This file is part of Enhort. <https://enhort.mni.thm.de>.
//
// Enhort 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.
//
// Enhort 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 Enhort. If not, see <https://www.gnu.org/licenses/>.
package de.thm.genomeData.sql;
import de.thm.genomeData.tracks.TrackEntry;
......
// Copyright (C) 2018 Michael Menzel
//
// This file is part of Enhort. <https://enhort.mni.thm.de>.
//
// Enhort 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.
//
// Enhort 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 Enhort. If not, see <https://www.gnu.org/licenses/>.
package de.thm.genomeData.tracks;
import de.thm.genomeData.sql.DBConnector;
......
// Copyright (C) 2018 Michael Menzel
//
// This file is part of Enhort. <https://enhort.mni.thm.de>.
//
// Enhort 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.
//
// Enhort 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 Enhort. If not, see <https://www.gnu.org/licenses/>.
package de.thm.genomeData.tracks;
import de.thm.misc.ChromosomSizes;
......
// Copyright (C) 2018 Michael Menzel
//
// This file is part of Enhort. <https://enhort.mni.thm.de>.
//
// Enhort 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.
//
// Enhort 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 Enhort. If not, see <https://www.gnu.org/licenses/>.
package de.thm.genomeData.tracks;
import de.thm.exception.NoTracksLeftException;
......
// Copyright (C) 2018 Michael Menzel
//
// This file is part of Enhort. <https://enhort.mni.thm.de>.
//
// Enhort 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.
//
// Enhort 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 Enhort. If not, see <https://www.gnu.org/licenses/>.
package de.thm.genomeData.tracks;
import de.thm.misc.ChromosomSizes;
......
// Copyright (C) 2018 Michael Menzel
//
// This file is part of Enhort. <https://enhort.mni.thm.de>.
//
// Enhort 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.
//
// Enhort 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 Enhort. If not, see <https://www.gnu.org/licenses/>.
package de.thm.logo;
import de.thm.positionData.Sites;
......
// Copyright (C) 2018 Michael Menzel
//
// This file is part of Enhort. <https://enhort.mni.thm.de>.
//
// Enhort 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.
//
// Enhort 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 Enhort. If not, see <https://www.gnu.org/licenses/>.
package de.thm.logo;
import de.thm.misc.ChromosomSizes;
......
// Copyright (C) 2018 Michael Menzel
//
// This file is part of Enhort. <https://enhort.mni.thm.de>.
//
// Enhort 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.
//
// Enhort 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 Enhort. If not, see <https://www.gnu.org/licenses/>.
package de.thm.logo;
import de.thm.positionData.Sites;
......
// Copyright (C) 2018 Michael Menzel
//
// This file is part of Enhort. <https://enhort.mni.thm.de>.
//
// Enhort 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.
//
// Enhort 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 Enhort. If not, see <https://www.gnu.org/licenses/>.
package de.thm.misc;
import de.thm.genomeData.tracks.NamedTrack;
......
// Copyright (C) 2018 Michael Menzel
//
// This file is part of Enhort. <https://enhort.mni.thm.de>.
//
// Enhort 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.
//
// Enhort 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 Enhort. If not, see <https://www.gnu.org/licenses/>.
package de.thm.misc;
import de.thm.exception.TrackTypeNotAllowedExcpetion;
......
// Copyright (C) 2018 Michael Menzel
//
// This file is part of Enhort. <https://enhort.mni.thm.de>.
//
// Enhort 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.
//
// Enhort 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 Enhort. If not, see <https://www.gnu.org/licenses/>.
package de.thm.precalc;
import de.thm.genomeData.tracks.Track;
......
// Copyright (C) 2018 Michael Menzel
//
// This file is part of Enhort. <https://enhort.mni.thm.de>.
//
// Enhort 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.
//
// Enhort 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 Enhort. If not, see <https://www.gnu.org/licenses/>.
package de.thm.precalc;
import de.thm.backgroundModel.BackgroundModelFactory;
......
// Copyright (C) 2018 Michael Menzel
//
// This file is part of Enhort. <https://enhort.mni.thm.de>.
//
// Enhort 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.
//
// Enhort 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 Enhort. If not, see <https://www.gnu.org/licenses/>.
package de.thm.precalc;
import de.thm.backgroundModel.BackgroundModel;
......
// Copyright (C) 2018 Michael Menzel
//
// This file is part of Enhort. <https://enhort.mni.thm.de>.
//
// Enhort 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.
//
// Enhort 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 Enhort. If not, see <https://www.gnu.org/licenses/>.
package de.thm.precalc;
import de.thm.misc.Genome;
......
// Copyright (C) 2018 Michael Menzel
//
// This file is part of Enhort. <https://enhort.mni.thm.de>.
//
// Enhort 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.
//
// Enhort 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 Enhort. If not, see <https://www.gnu.org/licenses/>.
package de.thm.run;
import de.thm.backgroundModel.BackgroundModelFactory;
......
// Copyright (C) 2018 Michael Menzel
//
// This file is part of Enhort. <https://enhort.mni.thm.de>.
//