Examples with MemberPack org.ivis.layout.util.MemberPack used on opensource projects

Example 1 with MemberPack

use of org.ivis.layout.util.MemberPack in project cytoscape-impl by cytoscape.

the class SbgnPDLayout method repopulateComplexes.

/**
 * Reassigns the complex content. The outermost complex is placed first.
 */
protected void repopulateComplexes() {
    for (SbgnPDNode comp : emptiedDummyComplexMap.keySet()) {
        LGraph chGr = emptiedDummyComplexMap.get(comp);
        comp.setChild(chGr);
        this.getGraphManager().getGraphs().add(chGr);
    }
    for (int i = complexOrder.size() - 1; i >= 0; i--) {
        SbgnPDNode comp = complexOrder.get(i);
        LGraph chGr = childGraphMap.get(comp);
        // repopulate the complex
        comp.setChild(chGr);
        // if the child graph is not null, adjust the positions of members
        if (chGr != null) {
            // adjust the positions of the members
            if (compactionMethod == DefaultCompactionAlgorithm.POLYOMINO_PACKING) {
                adjustLocation(comp, chGr);
                getGraphManager().getGraphs().add(chGr);
            } else if (compactionMethod == DefaultCompactionAlgorithm.TILING) {
                getGraphManager().getGraphs().add(chGr);
                MemberPack pack = memberPackMap.get(comp);
                pack.adjustLocations(comp.getLeft(), comp.getTop());
            }
        }
    }
    for (SbgnPDNode comp : emptiedDummyComplexMap.keySet()) {
        LGraph chGr = emptiedDummyComplexMap.get(comp);
        adjustLocation(comp, chGr);
    }
    removeDummyComplexes();
    // reset
    getGraphManager().resetAllNodes();
    getGraphManager().resetAllNodesToApplyGravitation();
    getGraphManager().resetAllEdges();
    this.calculateNodesToApplyGravitationTo();
}

Example 2 with MemberPack

use of org.ivis.layout.util.MemberPack in project cytoscape-impl by cytoscape.

the class SbgnPDLayout method clearComplex.

// ********************* SECTION : TILING METHODS *********************
private void clearComplex(SbgnPDNode comp) {
    MemberPack pack = null;
    LGraph childGr = comp.getChild();
    childGraphMap.put(comp, childGr);
    if (childGr == null)
        return;
    if (compactionMethod == DefaultCompactionAlgorithm.POLYOMINO_PACKING) {
        applyPolyomino(comp);
    } else if (compactionMethod == DefaultCompactionAlgorithm.TILING) {
        pack = new MemberPack(childGr);
        memberPackMap.put(comp, pack);
    }
    if (dummyComplexList.contains(comp)) {
        for (Object o : comp.getChild().getNodes()) {
            clearDummyComplexGraphs((SbgnPDNode) o);
        }
    }
    getGraphManager().getGraphs().remove(childGr);
    comp.setChild(null);
    if (compactionMethod == DefaultCompactionAlgorithm.TILING) {
        comp.setWidth(pack.getWidth());
        comp.setHeight(pack.getHeight());
    }
    // Redirect the edges of complex members to the complex.
    if (childGr != null) {
        for (Object ch : childGr.getNodes()) {
            SbgnPDNode chNd = (SbgnPDNode) ch;
            for (Object obj : new ArrayList(chNd.getEdges())) {
                LEdge edge = (LEdge) obj;
                if (edge.getSource() == chNd) {
                    chNd.getEdges().remove(edge);
                    edge.setSource(comp);
                    comp.getEdges().add(edge);
                } else if (edge.getTarget() == chNd) {
                    chNd.getEdges().remove(edge);
                    edge.setTarget(comp);
                    comp.getEdges().add(edge);
                }
            }
        }
    }
}