Commit 62d90dfc authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 0.0+git20180523.cbaf6d1

parent ab0dd4fa

src/jloda/fx/IHasJavaFXStageAndRoot.java

+1 −1
Original line number Diff line number Diff line 
/*

 *  Copyright (C) 2015 Daniel H. Huson

 *  Copyright (C) 2018 Daniel H. Huson

 *

 *  (Some files contain contributions from other authors, who are then mentioned separately.)

 *

src/jloda/fx/JPanelWithFXStageAndRoot.java

+1 −1
Original line number Diff line number Diff line 
/*

 *  Copyright (C) 2015 Daniel H. Huson

 *  Copyright (C) 2018 Daniel H. Huson

 *

 *  (Some files contain contributions from other authors, who are then mentioned separately.)

 *

src/jloda/fx/JavaFX2PDF.java

+1 −1
Original line number Diff line number Diff line 
/*

 *  Copyright (C) 2015 Daniel H. Huson

 *  Copyright (C) 2018 Daniel H. Huson

 *

 *  (Some files contain contributions from other authors, who are then mentioned separately.)

 *

src/jloda/graph/FruchtermanReingoldLayout.java

+30 −30
Original line number Diff line number Diff line
@@ -43,9 +43,9 @@ public class FruchtermanReingoldLayout { 
    public FruchtermanReingoldLayout(Graph graph, NodeSet fixedNodes) {

        this.graph = graph;

        nodes = graph.getNodes().toArray();

        edges = new int[graph.getNumberOfEdges()][2];

        coordinates = new float[nodes.length][2];

        forceDelta = new float[nodes.length][2];

        edges = new int[2][graph.getNumberOfEdges()];

        coordinates = new float[2][nodes.length];

        forceDelta = new float[2][nodes.length];

        fixed = new BitSet();



        initialize(fixedNodes);
@@ -63,8 +63,8 @@ public class FruchtermanReingoldLayout { 
        }

        int eId = 0;

        for (Edge e = graph.getFirstEdge(); e != null; e = e.getNext()) {

            edges[eId][0] = node2id.get(e.getSource());

            edges[eId][1] = node2id.get(e.getTarget());

            edges[0][eId] = node2id.get(e.getSource());

            edges[1][eId] = node2id.get(e.getTarget());

            eId++;

        }
@@ -79,8 +79,8 @@ public class FruchtermanReingoldLayout { 
                    while (stack.size() > 0) {

                        Node w = stack.pop();

                        int id = node2id.get(w);

                        coordinates[id][0] = (float) (100 * Math.sin(2 * Math.PI * count / nodes.length));

                        coordinates[id][1] = (float) (100 * Math.cos(2 * Math.PI * count / nodes.length));

                        coordinates[0][id] = (float) (100 * Math.sin(2 * Math.PI * count / nodes.length));

                        coordinates[1][id] = (float) (100 * Math.cos(2 * Math.PI * count / nodes.length));

                        count++;

                        for (Edge e = w.getFirstAdjacentEdge(); e != null; e = w.getNextAdjacentEdge(e)) {

                            Node u = e.getOpposite(w);
@@ -114,7 +114,7 @@ public class FruchtermanReingoldLayout { 
        }



        for (int v = 0; v < nodes.length; v++) {

            result.set(nodes[v], new Point2D.Float(coordinates[v][0], coordinates[v][1]));

            result.set(nodes[v], new Point2D.Float(coordinates[0][v], coordinates[1][v]));



        }

    }
@@ -131,57 +131,57 @@ public class FruchtermanReingoldLayout { 
        for (int v1 = 0; v1 < nodes.length; v1++) {

            for (int v2 = 0; v2 < nodes.length; v2++) {

                if (v1 != v2) {

                    float xDist = coordinates[v1][0] - coordinates[v2][0];

                    float yDist = coordinates[v1][1] - coordinates[v2][1];

                    float xDist = coordinates[0][v1] - coordinates[0][v2];

                    float yDist = coordinates[1][v1] - coordinates[1][v2];

                    float dist = (float) Math.sqrt(xDist * xDist + yDist * yDist);

                    if (dist > 0) {

                        float repulsiveF = k * k / dist;

                        forceDelta[v1][0] += xDist / dist * repulsiveF;

                        forceDelta[v1][1] += yDist / dist * repulsiveF;

                        forceDelta[0][v1] += xDist / dist * repulsiveF;

                        forceDelta[1][v1] += yDist / dist * repulsiveF;

                    }

                }

            }

        }

        // attraction

        for (int[] edge : edges) {

            int v1 = edge[0];

            int v2 = edge[1];

            float xDist = coordinates[v1][0] - coordinates[v2][0];

            float yDist = coordinates[v1][1] - coordinates[v2][1];

        for (int i = 0; i < edges[0].length; i++) {

            int v1 = edges[0][i];

            int v2 = edges[1][i];

            float xDist = coordinates[0][v1] - coordinates[0][v2];

            float yDist = coordinates[1][v1] - coordinates[1][v2];

            float dist = (float) Math.sqrt(xDist * xDist + yDist * yDist);

            if (dist > 0) {

                float attractiveF = dist * dist / k;

                forceDelta[v1][0] -= xDist / dist * attractiveF;

                forceDelta[v1][1] -= yDist / dist * attractiveF;

                forceDelta[v2][0] += xDist / dist * attractiveF;

                forceDelta[v2][1] += yDist / dist * attractiveF;

                forceDelta[0][v1] -= xDist / dist * attractiveF;

                forceDelta[1][v1] -= yDist / dist * attractiveF;

                forceDelta[0][v2] += xDist / dist * attractiveF;

                forceDelta[1][v2] += yDist / dist * attractiveF;

            }

        }



        // gravity

        for (int v = 0; v < nodes.length; v++) {

            float distSquared = (float) Math.sqrt(coordinates[v][0] * coordinates[v][0] + coordinates[v][1] * coordinates[v][1]);

            float distSquared = (float) Math.sqrt(coordinates[0][v] * coordinates[0][v] + coordinates[1][v] * coordinates[1][v]);

            float gravityF = 0.01f * k * (float) gravity * distSquared;

            forceDelta[v][0] -= gravityF * coordinates[v][0] / distSquared;

            forceDelta[v][1] -= gravityF * coordinates[v][1] / distSquared;

            forceDelta[0][v] -= gravityF * coordinates[0][v] / distSquared;

            forceDelta[1][v] -= gravityF * coordinates[1][v] / distSquared;

        }



        // speed

        for (int v = 0; v < nodes.length; v++) {

            forceDelta[v][0] *= speed / SPEED_DIVISOR;

            forceDelta[v][1] *= speed / SPEED_DIVISOR;

            forceDelta[0][v] *= speed / SPEED_DIVISOR;

            forceDelta[1][v] *= speed / SPEED_DIVISOR;



        }



        // apply the forces:

        for (int v = 0; v < nodes.length; v++) {

            float xDist = forceDelta[v][0];

            float yDist = forceDelta[v][1];

            float xDist = forceDelta[0][v];

            float yDist = forceDelta[1][v];

            float dist = (float) Math.sqrt(xDist * xDist + yDist * yDist);

            if (dist > 0 && !fixed.get(v)) {

                float limitedDist = Math.min(maxDisplace * ((float) speed / SPEED_DIVISOR), dist);

                coordinates[v][0] += xDist / dist * limitedDist;

                coordinates[v][1] += yDist / dist * limitedDist;

                coordinates[0][v] += xDist / dist * limitedDist;

                coordinates[1][v] += yDist / dist * limitedDist;

            }

        }

    }

src/jloda/util/GFF3FileFilter.java

+20 −6
Original line number Diff line number Diff line 
/*

 *  Copyright (C) 2015 Daniel H. Huson

 *  Copyright (C) 2018 Daniel H. Huson

 *

 *  (Some files contain contributions from other authors, who are then mentioned separately.)

 *
@@ -26,8 +26,11 @@ import java.io.FilenameFilter; 
 * Daniel Huson, 12.2017

 */

public class GFF3FileFilter extends FileFilterBase implements FilenameFilter {

    public GFF3FileFilter() {

        this(true);

    private boolean lookInside = true;



    public GFF3FileFilter(boolean allowGZip, boolean lookInside, String... additionalSuffixes) {

        this(allowGZip, additionalSuffixes);

        this.lookInside = lookInside;

    }



    public GFF3FileFilter(String... additionalSuffixes) {
@@ -46,8 +49,11 @@ public class GFF3FileFilter extends FileFilterBase implements FilenameFilter { 
    public boolean accept(String fileName) {

        boolean suffixOk = super.accept(Basic.getFileNameWithoutZipOrGZipSuffix(fileName));

        if (suffixOk) {   // look inside the file

            if (lookInside) {

                final String[] lines = Basic.getFirstLinesFromFile(new File(fileName), 1);

                return lines != null && lines[0] != null && lines[0].startsWith("##gff-version 3");

            } else

                return true;

        } else

            return false;

    }
@@ -56,6 +62,14 @@ public class GFF3FileFilter extends FileFilterBase implements FilenameFilter { 
     * @return description of file matching the filter

     */

    public String getBriefDescription() {

        return "GFF Files";

        return "GFF3 Files";

    }



    public boolean isLookInside() {

        return lookInside;

    }



    public void setLookInside(boolean lookInside) {

        this.lookInside = lookInside;

    }

}