use of org.cytoscape.view.presentation.property.values.Handle in project cytoscape-impl by cytoscape.
the class BendImpl method parseSerializableString.
public static Bend parseSerializableString(String strRepresentation) {
final Bend bend = new BendImpl();
// Validate
if (strRepresentation == null)
return bend;
final String[] parts = strRepresentation.split("\\|");
for (int i = 0; i < parts.length; i++) {
final String str = parts[i];
final Handle handle = HandleImpl.parseSerializableString(str);
if (handle != null)
bend.insertHandleAt(i, handle);
}
return bend;
}
use of org.cytoscape.view.presentation.property.values.Handle in project cytoscape-impl by cytoscape.
the class DEdgeView method addHandlePoint.
/**
* Add a new handle and returns its index.
*
* @param pt location of handle
* @return new handle index.
*/
protected int addHandlePoint(final Point2D pt) {
synchronized (graphView.m_lock) {
// Obtain existing Bend object
final Bend bend = graphView.m_edgeDetails.getBend(model, true);
if (bend.getAllHandles().size() == 0) {
// anchors object is empty. Add first handle.
addHandleInternal(0, pt);
// Index of this handle, which is first (0)
return 0;
}
final Point2D sourcePt = graphView.getDNodeView(getCyEdge().getSource()).getOffset();
final Point2D targetPt = graphView.getDNodeView(getCyEdge().getTarget()).getOffset();
final Handle firstHandle = bend.getAllHandles().get(0);
final Point2D point = firstHandle.calculateHandleLocation(graphView.getViewModel(), this);
double bestDist = (pt.distance(sourcePt) + pt.distance(point)) - sourcePt.distance(point);
int bestInx = 0;
for (int i = 1; i < bend.getAllHandles().size(); i++) {
final Handle handle1 = bend.getAllHandles().get(i);
final Handle handle2 = bend.getAllHandles().get(i - 1);
final Point2D point1 = handle1.calculateHandleLocation(graphView.getViewModel(), this);
final Point2D point2 = handle2.calculateHandleLocation(graphView.getViewModel(), this);
final double distCand = (pt.distance(point2) + pt.distance(point1)) - point1.distance(point2);
if (distCand < bestDist) {
bestDist = distCand;
bestInx = i;
}
}
final int lastIndex = bend.getAllHandles().size() - 1;
final Handle lastHandle = bend.getAllHandles().get(lastIndex);
final Point2D lastPoint = lastHandle.calculateHandleLocation(graphView.getViewModel(), this);
final double lastCand = (pt.distance(targetPt) + pt.distance(lastPoint)) - targetPt.distance(lastPoint);
if (lastCand < bestDist) {
bestDist = lastCand;
bestInx = bend.getAllHandles().size();
}
addHandleInternal(bestInx, pt);
return bestInx;
}
}
use of org.cytoscape.view.presentation.property.values.Handle in project cytoscape-impl by cytoscape.
the class LayerOrderNode method layout.
public void layout() {
taskMonitor.setProgress(0.0);
taskMonitor.setStatusMessage("Capturing snapshot of network and selected nodes");
if (cancelled)
return;
/* construct node list with selected nodes first */
int numLayoutNodes = nodesToLayOut.size();
if (numLayoutNodes == 1) {
// We were asked to do a hierchical layout of a single node -- done!
return;
}
HashMap<Long, Integer> suid2Index = new HashMap<Long, Integer>(numLayoutNodes);
List<View<CyNode>> nodeViews = new ArrayList<View<CyNode>>(nodesToLayOut);
int index = 0;
for (View<CyNode> view : nodeViews) {
CyNode node = view.getModel();
Long suid = node.getSUID();
suid2Index.put(suid, index);
index++;
}
if (cancelled)
return;
/* create edge list from edges between selected nodes */
LinkedList<Edge> edges = new LinkedList();
for (View<CyEdge> ev : networkView.getEdgeViews()) {
// FIXME: much better would be to query adjacent edges of selected nodes...
Integer edgeFrom = suid2Index.get(ev.getModel().getSource().getSUID());
Integer edgeTo = suid2Index.get(ev.getModel().getTarget().getSUID());
if ((edgeFrom == null) || (edgeTo == null)) {
// Must be from an unselected node
continue;
}
if (cancelled)
return;
if ((numLayoutNodes <= 1) || ((edgeFrom < numLayoutNodes) && (edgeTo < numLayoutNodes))) {
/* add edge to graph */
Edge theEdge = new Edge(edgeFrom, edgeTo);
edges.add(theEdge);
}
}
/* find horizontal and vertical coordinates of each node */
Edge[] edge = new Edge[edges.size()];
edges.toArray(edge);
Graph graph = new Graph(numLayoutNodes, edge);
/*
int edgeIndex;
for (edgeIndex = 0; edgeIndex<edge.length; edgeIndex++) {
System.out.println("Edge: " + edge[edgeIndex].getFrom() + " - " + edge[edgeIndex].getTo());
}
*/
int[] cI = graph.componentIndex();
int x;
/*
System.out.println("Node index:\n");
for (x=0; x<graph.getNodecount(); x++) {
System.out.println(cI[x]);
}
System.out.println("Partitioning into components:\n");
*/
taskMonitor.setProgress(0.1);
taskMonitor.setStatusMessage("Finding connected components");
if (cancelled)
return;
int[] renumber = new int[cI.length];
Graph[] component = graph.partition(cI, renumber);
final int numComponents = component.length;
int[][] layer = new int[numComponents][];
int[][] horizontalPosition = new int[numComponents][];
Graph[] reduced = new Graph[component.length];
Graph[] reducedTmp = new Graph[component.length];
HashMap<Integer, Edge>[] dummy2Edge = new HashMap[component.length];
int[] dummyStartForComp = new int[component.length];
HashMap<Edge, View<CyEdge>>[] myEdges2EdgeViews = new HashMap[component.length];
for (x = 0; x < component.length; x++) {
/*
System.out.println("plain component:\n");
System.out.println(component[x]);
System.out.println("filtered component:\n");
System.out.println(component[x].getGraphWithoutOneOrTwoCycles());
System.out.println("nonmulti component:\n");
System.out.println(component[x].getGraphWithoutMultipleEdges());
int cycleEliminationPriority[] = component[x].getCycleEliminationVertexPriority();
System.out.println("acyclic component:\n");
System.out.println(component[x].getGraphWithoutCycles(cycleEliminationPriority));
System.out.println("reduced component:\n");
System.out.println(component[x].getReducedGraph());
System.out.println("layer assignment:\n");
*/
taskMonitor.setProgress((20 + ((40 * (x * 3)) / numComponents / 3)) / 100.0);
taskMonitor.setStatusMessage("making acyclic transitive reduction");
Thread.yield();
if (cancelled)
return;
reducedTmp[x] = component[x].getReducedGraph();
taskMonitor.setProgress((20 + ((40 * ((x * 3) + 1)) / numComponents / 3)) / 100.0);
taskMonitor.setStatusMessage("layering nodes vertically");
Thread.yield();
if (cancelled)
return;
layer[x] = reducedTmp[x].getVertexLayers();
LinkedList<Integer> layerWithDummy = new LinkedList<Integer>();
for (int i = 0; i < layer[x].length; i++) layerWithDummy.add(Integer.valueOf(layer[x][i]));
/*
int y;
for (y=0;y<layer[x].length;y++) {
System.out.println("" + y + " : " + layer[x][y]);
}
System.out.println("horizontal position:\n");
*/
/* Insertion of the dummy nodes in the graph */
Edge[] allEdges = component[x].GetEdges();
LinkedList<Edge> edgesWithAdd = new LinkedList<Edge>();
int dummyStart = component[x].getNodecount();
dummyStartForComp[x] = dummyStart;
dummy2Edge[x] = new HashMap<Integer, Edge>();
for (int i = 0; i < allEdges.length; i++) {
int from = allEdges[i].getFrom();
int to = allEdges[i].getTo();
if (layer[x][from] == (layer[x][to] + 1)) {
edgesWithAdd.add(allEdges[i]);
} else {
if (layer[x][from] < layer[x][to]) {
int tmp = from;
from = to;
to = tmp;
}
layerWithDummy.add(Integer.valueOf(layer[x][to] + 1));
dummy2Edge[x].put(Integer.valueOf(layerWithDummy.size() - 1), allEdges[i]);
edgesWithAdd.add(new Edge(layerWithDummy.size() - 1, to));
for (int j = layer[x][to] + 2; j < layer[x][from]; j++) {
layerWithDummy.add(Integer.valueOf(j));
dummy2Edge[x].put(Integer.valueOf(layerWithDummy.size() - 1), allEdges[i]);
edgesWithAdd.add(new Edge(layerWithDummy.size() - 1, layerWithDummy.size() - 2));
}
edgesWithAdd.add(new Edge(from, layerWithDummy.size() - 1));
}
}
allEdges = new Edge[edgesWithAdd.size()];
edgesWithAdd.toArray(allEdges);
reduced[x] = new Graph(layerWithDummy.size(), allEdges);
reduced[x].setDummyNodesStart(dummyStart);
reduced[x].setReduced(true);
int[] layerNew = new int[layerWithDummy.size()];
Iterator<Integer> iter = layerWithDummy.iterator();
for (int i = 0; i < layerNew.length; i++) layerNew[i] = iter.next();
layer[x] = layerNew;
taskMonitor.setProgress((20 + ((40 * ((x * 3) + 2)) / numComponents / 3)) / 100.0);
taskMonitor.setStatusMessage("positioning nodes within layer");
Thread.yield();
if (cancelled)
return;
horizontalPosition[x] = reduced[x].getHorizontalPositionReverse(layer[x]);
/*
for (y=0;y<horizontalPosition[x].length;y++) {
System.out.println("" + y + " : " + horizontalPosition[x][y]);
}
*/
}
int resize = renumber.length;
for (int i = 0; i < component.length; i++) resize += (layer[i].length - dummyStartForComp[i]);
int[] newRenumber = new int[resize];
int[] newcI = new int[resize];
for (int i = 0; i < renumber.length; i++) {
newRenumber[i] = renumber[i];
newcI[i] = cI[i];
}
int t = renumber.length;
for (int i = 0; i < reduced.length; i++) {
for (int j = reduced[i].getDummyNodesStart(); j < reduced[i].getNodecount(); j++) {
newRenumber[t] = j;
newcI[t] = i;
t++;
}
}
renumber = newRenumber;
cI = newcI;
edges = new LinkedList<Edge>();
for (int i = 0; i < reduced.length; i++) {
edge = reduced[i].GetEdges();
for (int j = 0; j < edge.length; j++) {
// uzasna budzevina!!!!!! // FIXME: what does this mean?
int from = -1;
int to = -1;
for (int k = 0; k < cI.length; k++) {
if ((cI[k] == i) && (renumber[k] == edge[j].getFrom()))
from = k;
if ((cI[k] == i) && (renumber[k] == edge[j].getTo()))
to = k;
if ((from != -1) && (to != -1))
break;
}
// edges.add(new Edge(to, from));
edges.add(new Edge(from, to));
}
}
edge = new Edge[edges.size()];
edges.toArray(edge);
graph = new Graph(resize, edge);
taskMonitor.setProgress(0.6);
taskMonitor.setStatusMessage("Repositioning nodes in view");
Thread.yield();
if (cancelled)
return;
/* order nodeviews by layout order */
HierarchyFlowLayoutOrderNode[] flowLayoutOrder = new HierarchyFlowLayoutOrderNode[resize];
for (x = 0; x < resize; x++) {
if (x < numLayoutNodes)
flowLayoutOrder[x] = new HierarchyFlowLayoutOrderNode(nodeViews.get(x), cI[x], reduced[cI[x]].getNodecount(), layer[cI[x]][renumber[x]], horizontalPosition[cI[x]][renumber[x]], x);
else
flowLayoutOrder[x] = new HierarchyFlowLayoutOrderNode(null, cI[x], reduced[cI[x]].getNodecount(), layer[cI[x]][renumber[x]], horizontalPosition[cI[x]][renumber[x]], x);
nodes2HFLON.put(x, flowLayoutOrder[x]);
}
Arrays.sort(flowLayoutOrder);
int lastComponent = -1;
int lastLayer = -1;
int startBandY = context.topEdge;
int cleanBandY = context.topEdge;
int startComponentX = context.leftEdge;
int cleanComponentX = context.leftEdge;
int startLayerY = context.topEdge;
int cleanLayerY = context.topEdge;
int cleanLayerX = context.leftEdge;
int[] layerStart = new int[numLayoutNodes + 1];
/* layout nodes which are selected */
int nodeIndex;
/* layout nodes which are selected */
int lastComponentEnd = -1;
for (nodeIndex = 0; nodeIndex < resize; nodeIndex++) {
HierarchyFlowLayoutOrderNode node = flowLayoutOrder[nodeIndex];
int currentComponent = node.componentNumber;
int currentLayer = node.layer;
View<CyNode> currentView = node.nodeView;
taskMonitor.setProgress((60 + ((40 * (nodeIndex + 1)) / resize)) / 100.0);
taskMonitor.setStatusMessage("layering nodes vertically");
Thread.yield();
if (cancelled)
return;
if (lastComponent == -1) {
/* this is the first component */
lastComponent = currentComponent;
lastLayer = currentLayer;
layerStart[currentLayer] = -1;
}
if (lastComponent != currentComponent) {
/* new component */
// first call function for Horizontal Positioning of nodes in lastComponent
int[] minXArray = new int[1];
int maxX = HorizontalNodePositioning(nodeIndex - flowLayoutOrder[nodeIndex - 1].componentSize, nodeIndex - 1, flowLayoutOrder, graph, renumber, cI, dummyStartForComp, minXArray);
int minX = minXArray[0];
lastComponentEnd = nodeIndex - 1;
for (int i = nodeIndex - flowLayoutOrder[nodeIndex - 1].componentSize; i <= (nodeIndex - 1); i++) flowLayoutOrder[i].xPos -= (minX - startComponentX);
maxX -= (minX - startComponentX);
layerStart[lastLayer] = startComponentX;
/* initialize for new component */
startComponentX = cleanComponentX + context.componentSpacing;
if (maxX > startComponentX)
startComponentX = maxX + context.componentSpacing;
if (startComponentX > context.rightMargin) {
/* new band */
startBandY = cleanBandY + context.bandGap;
cleanBandY = startBandY;
startComponentX = context.leftEdge;
cleanComponentX = context.leftEdge;
}
startLayerY = startBandY;
cleanLayerY = startLayerY;
cleanLayerX = startComponentX;
layerStart[currentLayer] = -1;
} else if (lastLayer != currentLayer) {
/* new layer */
layerStart[lastLayer] = startComponentX;
startLayerY = cleanLayerY + context.nodeVerticalSpacing;
cleanLayerY = startLayerY;
cleanLayerX = startComponentX;
layerStart[currentLayer] = -1;
}
node.setXPos(cleanLayerX);
node.setYPos(startLayerY);
cleanLayerX += context.nodeHorizontalSpacing;
int currentBottom;
int currentRight;
if (currentView != null) {
currentBottom = startLayerY + currentView.getVisualProperty(BasicVisualLexicon.NODE_HEIGHT).intValue();
currentRight = cleanLayerX + currentView.getVisualProperty(BasicVisualLexicon.NODE_WIDTH).intValue();
} else {
currentBottom = startLayerY;
currentRight = cleanLayerX;
}
if (currentBottom > cleanBandY)
cleanBandY = currentBottom;
if (currentRight > cleanComponentX)
cleanComponentX = currentRight;
if (currentBottom > cleanLayerY)
cleanLayerY = currentBottom;
if (currentRight > cleanLayerX)
cleanLayerX = currentRight;
lastComponent = currentComponent;
lastLayer = currentLayer;
}
if (cancelled)
return;
/* Set horizontal positions of last component */
int[] minXArray = new int[1];
HorizontalNodePositioning(lastComponentEnd + 1, resize - 1, flowLayoutOrder, graph, renumber, cI, dummyStartForComp, minXArray);
int minX = minXArray[0];
for (int i = lastComponentEnd + 1; i < resize; i++) flowLayoutOrder[i].xPos -= (minX - startComponentX);
/* Map edges to edge views in order to map dummy nodes to edge bends properly */
for (View<CyEdge> ev : networkView.getEdgeViews()) {
Integer edgeFrom = suid2Index.get(ev.getModel().getSource().getSUID());
Integer edgeTo = suid2Index.get(ev.getModel().getTarget().getSUID());
if ((edgeFrom == null) || (edgeTo == null)) {
// Must be from an unselected node
continue;
}
if ((numLayoutNodes <= 1) || ((edgeFrom < numLayoutNodes) && (edgeTo < numLayoutNodes))) {
/* add edge to graph */
Edge theEdge = component[cI[edgeFrom]].GetTheEdge(renumber[edgeFrom], renumber[edgeTo]);
if (myEdges2EdgeViews[cI[edgeFrom]] == null)
myEdges2EdgeViews[cI[edgeFrom]] = new HashMap<Edge, View<CyEdge>>();
myEdges2EdgeViews[cI[edgeFrom]].put(theEdge, ev);
}
}
for (nodeIndex = 0; nodeIndex < resize; nodeIndex++) {
HierarchyFlowLayoutOrderNode node = flowLayoutOrder[nodeIndex];
if (node.nodeView != null) {
View<CyNode> currentView = node.nodeView;
currentView.setVisualProperty(BasicVisualLexicon.NODE_X_LOCATION, Double.valueOf((double) node.getXPos()));
currentView.setVisualProperty(BasicVisualLexicon.NODE_Y_LOCATION, Double.valueOf((double) node.getYPos()));
}
}
final HandleFactory handleFactory = serviceRegistrar.getService(HandleFactory.class);
final BendFactory bendFactory = serviceRegistrar.getService(BendFactory.class);
for (nodeIndex = 0; nodeIndex < resize; nodeIndex++) {
HierarchyFlowLayoutOrderNode node = flowLayoutOrder[nodeIndex];
if (node.nodeView == null) {
Edge theEdge = (Edge) dummy2Edge[cI[node.graphIndex]].get(Integer.valueOf(renumber[node.graphIndex]));
View<CyEdge> ev = myEdges2EdgeViews[cI[node.graphIndex]].get(theEdge);
if (ev != null) {
View<CyNode> source = networkView.getNodeView(ev.getModel().getSource());
View<CyNode> target = networkView.getNodeView(ev.getModel().getTarget());
double k = (getYPositionOf(target) - getYPositionOf(source)) / (getXPositionOf(target) - getXPositionOf(source));
double xPos = getXPositionOf(source);
if (k != 0)
xPos += ((node.yPos - getYPositionOf(source)) / k);
Bend b = bendFactory.createBend();
Handle h = handleFactory.createHandle(networkView, ev, xPos, node.yPos);
b.insertHandleAt(0, h);
ev.setVisualProperty(BasicVisualLexicon.EDGE_BEND, b);
}
}
}
for (nodeIndex = 0; nodeIndex < resize; nodeIndex++) {
HierarchyFlowLayoutOrderNode node = flowLayoutOrder[nodeIndex];
if (node.nodeView == null) {
Edge theEdge = dummy2Edge[cI[node.graphIndex]].get(Integer.valueOf(renumber[node.graphIndex]));
View<CyEdge> ev = myEdges2EdgeViews[cI[node.graphIndex]].get(theEdge);
if (ev != null) {
List<Handle> handles = ev.getVisualProperty(BasicVisualLexicon.EDGE_BEND).getAllHandles();
for (Handle h : handles) {
Point2D handelPt = h.calculateHandleLocation(networkView, ev);
if (handelPt.getY() == node.yPos) {
h.defineHandle(networkView, ev, (double) (node.xPos), (double) (node.yPos));
break;
}
}
}
}
}
taskMonitor.setProgress(1.0);
taskMonitor.setStatusMessage("hierarchical layout complete");
}
use of org.cytoscape.view.presentation.property.values.Handle in project cytoscape-impl by cytoscape.
the class InnerCanvas method handleArrowKeys.
/**
* Arrow key handler.
* They are used to pan and mode nodes/edge bend handles.
* @param k key event
*/
private void handleArrowKeys(KeyEvent k) {
final int code = k.getKeyCode();
double move = 1.0;
// Adjust increment if Shift key is pressed
if (k.isShiftDown())
move = 15.0;
// Pan if CTR is pressed.
if (isControlOrMetaDown(k)) {
// Pan
if (code == KeyEvent.VK_UP) {
pan(0, move);
} else if (code == KeyEvent.VK_DOWN) {
pan(0, -move);
} else if (code == KeyEvent.VK_LEFT) {
pan(-move, 0);
} else if (code == KeyEvent.VK_RIGHT) {
pan(move, 0);
}
return;
}
if (m_view.m_nodeSelection) {
// move nodes
final long[] selectedNodes = m_view.getSelectedNodeIndices();
for (int i = 0; i < selectedNodes.length; i++) {
DNodeView nv = ((DNodeView) m_view.getDNodeView(selectedNodes[i]));
double xPos = nv.getXPosition();
double yPos = nv.getYPosition();
if (code == KeyEvent.VK_UP) {
yPos -= move;
} else if (code == KeyEvent.VK_DOWN) {
yPos += move;
} else if (code == KeyEvent.VK_LEFT) {
xPos -= move;
} else if (code == KeyEvent.VK_RIGHT) {
xPos += move;
}
nv.setOffset(xPos, yPos);
}
// move edge anchors
LongEnumerator anchorsToMove = m_view.m_selectedAnchors.searchRange(Integer.MIN_VALUE, Integer.MAX_VALUE, false);
while (anchorsToMove.numRemaining() > 0) {
final long edgeAndAnchor = anchorsToMove.nextLong();
final long edge = edgeAndAnchor >>> 6;
final int anchorInx = (int) (edgeAndAnchor & 0x000000000000003f);
final DEdgeView ev = (DEdgeView) m_view.getDEdgeView(edge);
if (!ev.isValueLocked(BasicVisualLexicon.EDGE_BEND)) {
Bend defaultBend = ev.getDefaultValue(BasicVisualLexicon.EDGE_BEND);
if (ev.getVisualProperty(BasicVisualLexicon.EDGE_BEND) == defaultBend) {
ev.setLockedValue(BasicVisualLexicon.EDGE_BEND, new BendImpl((BendImpl) defaultBend));
} else {
ev.setLockedValue(BasicVisualLexicon.EDGE_BEND, new BendImpl((BendImpl) ev.getBend()));
}
}
final Bend bend = ev.getVisualProperty(BasicVisualLexicon.EDGE_BEND);
final Handle handle = bend.getAllHandles().get(anchorInx);
final Point2D newPoint = handle.calculateHandleLocation(m_view.getViewModel(), ev);
m_floatBuff1[0] = (float) newPoint.getX();
m_floatBuff1[1] = (float) newPoint.getY();
if (code == KeyEvent.VK_UP) {
ev.moveHandleInternal(anchorInx, m_floatBuff1[0], m_floatBuff1[1] - move);
} else if (code == KeyEvent.VK_DOWN) {
ev.moveHandleInternal(anchorInx, m_floatBuff1[0], m_floatBuff1[1] + move);
} else if (code == KeyEvent.VK_LEFT) {
ev.moveHandleInternal(anchorInx, m_floatBuff1[0] - move, m_floatBuff1[1]);
} else if (code == KeyEvent.VK_RIGHT) {
ev.moveHandleInternal(anchorInx, m_floatBuff1[0] + move, m_floatBuff1[1]);
}
}
repaint();
}
}
use of org.cytoscape.view.presentation.property.values.Handle in project cytoscape-impl by cytoscape.
the class BendImpl method getSerializableString.
@Override
public String getSerializableString() {
final StringBuilder builder = new StringBuilder();
for (Handle handle : handles) builder.append(handle.getSerializableString() + DELIMITER);
final String serialized = builder.toString();
if (serialized.length() == 0)
return "";
return serialized.substring(0, serialized.length() - 1);
}
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