Author: paperwing
Date: 2011-07-02 07:07:24 -0700 (Sat, 02 Jul 2011)
New Revision: 26013
Modified:
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/Graphics.java
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/Vector3.java
Log:
node addition, removal added; multi-selection added, edge addition added
Modified:
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/Graphics.java
===================================================================
---
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/Graphics.java
2011-07-02 01:34:41 UTC (rev 26012)
+++
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/Graphics.java
2011-07-02 14:07:24 UTC (rev 26013)
@@ -6,8 +6,10 @@
import java.nio.ByteOrder;
import java.nio.FloatBuffer;
import java.nio.IntBuffer;
+import java.util.LinkedHashSet;
import java.util.Set;
import java.util.TreeMap;
+import java.util.TreeSet;
import javax.media.opengl.GL;
import javax.media.opengl.GL2;
@@ -20,6 +22,7 @@
import org.cytoscape.session.CyApplicationManager;
import org.cytoscape.model.CyEdge;
+import org.cytoscape.model.CyEdge.Type;
import org.cytoscape.model.CyNetworkManager;
import org.cytoscape.model.CyNode;
import org.cytoscape.view.model.CyNetworkView;
@@ -33,10 +36,12 @@
private static final float LARGE_SPHERE_RADIUS = 1.0f; // 1.5f
private static final float SMALL_SPHERE_RADIUS = 0.102f; // 0.015f
+ private static final float MINIMUM_EDGE_DRAW_DISTANCE_SQUARED =
Float.MIN_NORMAL; // 0.015f
+
private static final float EDGE_RADIUS = 0.018f;
private static final float EDGE_CURVE_DISTANCE = 0.7f;
- private static final float EDGE_CURVE_FACTOR = 0.31f;
+ private static final float EDGE_CURVE_FACTOR = 0.43f; //0.31f
private static final int EDGES_PER_RADIUS = 3;
/*
@@ -45,9 +50,9 @@
*/
private static final float DISTANCE_SCALE = 178.0f;
- private static final int NODE_SLICES_DETAIL = 24;
- private static final int NODE_STACKS_DETAIL = 24;
- private static final int EDGE_SLICES_DETAIL = 12;
+ private static final int NODE_SLICES_DETAIL = 10; // 24, 24, 12 used to
be default values for slices/stacks/slices
+ private static final int NODE_STACKS_DETAIL = 10;
+ private static final int EDGE_SLICES_DETAIL = 4;
private static final int EDGE_STACKS_DETAIL = 1;
private class DrawnNode {
@@ -74,6 +79,8 @@
private int nodeListIndex;
private int edgeListIndex;
+ private int pointerListIndex;
+
private long startTime;
private long endTime;
private int framesElapsed = 0;
@@ -82,9 +89,13 @@
private int nodeSeed = 556;
private int edgeSeed = 556;
- private int selected = -1;
- private int hovered = -1;
+ private LinkedHashSet<CyNode> selectedNodes;
+ private TreeSet<Integer> selectedNodeIndices;
+
+ private static final int NO_INDEX = -1; // Value representing that no
node index is being held
+ private int hovered = NO_INDEX;
+
private KeyboardMonitor keys;
private MouseMonitor mouse;
private SimpleCamera camera;
@@ -112,6 +123,9 @@
this.networkView = networkView;
this.visualLexicon = visualLexicon;
+
+ selectedNodes = new LinkedHashSet<CyNode>();
+ selectedNodeIndices = new TreeSet<Integer>();
}
public void trackInput(Component component) {
@@ -159,6 +173,22 @@
// normal.y(), normal.z());
// gl.glTranslated(-camera.x(), -camera.y(), -camera.z());
+ double distance = target.distance(position);
+ Vector3 leftPointer =
target.add(camera.getLeft().multiply(distance / 2));
+ Vector3 rightPointer =
target.subtract(camera.getLeft().multiply(distance / 2));
+
+ gl.glPushMatrix();
+ gl.glTranslated(leftPointer.x(), leftPointer.y(),
leftPointer.z());
+ gl.glColor3f(1.0f, 0.0f, 0.0f);
+ gl.glCallList(pointerListIndex);
+ gl.glPopMatrix();
+
+ gl.glPushMatrix();
+ gl.glTranslated(rightPointer.x(), rightPointer.y(),
rightPointer.z());
+ gl.glColor3f(1.0f, 0.0f, 0.0f);
+ gl.glCallList(pointerListIndex);
+ gl.glPopMatrix();
+
float[] lightPosition = { -4.0f, 4.0f, 6.0f, 1.0f };
gl.glLightfv(GL2.GL_LIGHT0, GL2.GL_POSITION,
FloatBuffer.wrap(lightPosition));
@@ -168,7 +198,9 @@
gl.glColor3f(0.73f, 0.73f, 0.73f);
drawNodes(gl);
- gl.glColor3f(0.53f, 0.53f, 0.55f);
+ gl.glColor3f(0.51f, 0.51f, 0.53f);
+ //gl.glColor3f(0.53f, 0.53f, 0.55f);
+ //gl.glColor3f(0.73f, 0.73f, 0.73f);
drawEdges(gl);
framesElapsed++;
@@ -197,7 +229,7 @@
new Vector3(0, 1, 0), 0.04,
0.002, 0.01, 0.01, 0.4);
}
- if (pressed.contains(KeyEvent.VK_SPACE)) {
+ if (pressed.contains(KeyEvent.VK_SPACE) && false) {
System.out.println("===");
System.out.print("direction: " +
camera.getDirection());
System.out.print(", left: " + camera.getLeft());
@@ -327,9 +359,39 @@
}
if (pressed.contains(KeyEvent.VK_J)) {
- System.out.println("number of nodes: " +
networkView.getNodeViews().size());
+ CyNode hoverNode =
networkView.getModel().getNode(hovered);
+
+ if (hoverNode != null) {
+
+ for (CyNode node : selectedNodes) {
+
networkView.getModel().addEdge(node, hoverNode, false);
+
+ // TODO: Not sure if this call
is needed
+ networkView.updateView();
+ };
+ }
}
+ if (pressed.contains(KeyEvent.VK_O)) {
+ CyNode hoverNode =
networkView.getModel().getNode(hovered);
+
+ if (hoverNode != null && selectedNodes.size()
== 1) {
+ View<CyNode> hoverView =
networkView.getNodeView(hoverNode);
+ View<CyNode> selectView = hoverView;
+ for (CyNode node : selectedNodes)
{selectView = networkView.getNodeView(node);};
+
+ Vector3 hover = new
Vector3(hoverView.getVisualProperty(RichVisualLexicon.NODE_X_LOCATION),
+
hoverView.getVisualProperty(RichVisualLexicon.NODE_Y_LOCATION),
+
hoverView.getVisualProperty(RichVisualLexicon.NODE_Z_LOCATION));
+
+ Vector3 select = new
Vector3(selectView.getVisualProperty(RichVisualLexicon.NODE_X_LOCATION),
+
selectView.getVisualProperty(RichVisualLexicon.NODE_Y_LOCATION),
+
selectView.getVisualProperty(RichVisualLexicon.NODE_Z_LOCATION));
+
+ System.out.println("Distance: " +
hover.distance(select)/DISTANCE_SCALE);
+ }
+ }
+
if (held.contains(KeyEvent.VK_W)) {
camera.moveUp();
}
@@ -354,11 +416,31 @@
camera.moveForward();
}
+ if (pressed.contains(KeyEvent.VK_DELETE)) {
+ LinkedHashSet<CyEdge> edgesToBeRemoved = new
LinkedHashSet<CyEdge>();
+
+ for (CyNode node : selectedNodes) {
+ // TODO: Check if use of Type.ANY for
any edge is correct
+ // TODO: Check if this addAll method
properly skips adding edges already in the edgesToBeRemovedList
+
edgesToBeRemoved.addAll(networkView.getModel().getAdjacentEdgeList(node,
Type.ANY));
+ }
+
+ if
(!networkView.getModel().removeNodes(selectedNodes)) {
+ System.out.println("Failed to deleted
nodes: " + selectedNodes);;
+ } else {
+ // Remove edges attached to the node
+
networkView.getModel().removeEdges(edgesToBeRemoved);
+
+ // TODO: Not sure if this call is needed
+ networkView.updateView();
+ }
+ }
+
keys.update();
}
if (mouse.hasMoved() || mouse.hasNew()) {
- if (keys.getHeld().contains(KeyEvent.VK_SHIFT)) {
+ if (keys.getHeld().contains(KeyEvent.VK_ALT)) {
camera.turnRight(mouse.dX());
camera.turnDown(mouse.dY());
}
@@ -367,84 +449,124 @@
camera.zoomOut((double) mouse.dWheel());
}
- if (mouse.getPressed().contains(MouseEvent.BUTTON1) ||
true) {
- // Hnear = 2 * tan(fov / 2) * nearDist
- // in our case:
- // fov = 45 deg
- // nearDist = 0.2
-
- double fieldOfView = Math.PI / 4;
- double nearDistance = 0.2;
-
-
- double nearPlaneHeight = 2 *
Math.tan(fieldOfView / 2) * nearDistance;
- double nearPlaneWidth = nearPlaneHeight *
screenWidth / screenHeight;
-
- double percentMouseOffsetX = (double)
(mouse.x() - screenWidth) / screenWidth + 0.5;
- double percentMouseOffsetY = (double)
(mouse.y() - screenHeight) / screenHeight + 0.5;
-
- // OpenGL has up as the positive y direction,
whereas the mouse is at (0, 0) in the top left
- percentMouseOffsetY = -percentMouseOffsetY;
-
- double nearX = percentMouseOffsetX *
nearPlaneWidth;
- double nearY = percentMouseOffsetY *
nearPlaneHeight;
-
- // Obtain the near plane position vector
- Vector3 nearPosition;
- nearPosition = new
Vector3(camera.getDirection());
- nearPosition.multiplyLocal(nearDistance);
-
- nearPosition.addLocal(camera.getPosition());
-
nearPosition.addLocal(camera.getUp().multiply(nearY));
-
nearPosition.addLocal(camera.getLeft().multiply(-nearX)); // Note that nearX is
positive to the right
-
- // Obtain the projection direction vector
- Vector3 projectionDirection =
nearPosition.subtract(camera.getPosition());
- projectionDirection.normalizeLocal();
-
- double angle =
projectionDirection.angle(camera.getDirection());
- double projectionDistance =
(camera.getDistance()) / Math.cos(angle);
-
- Vector3 projection =
projectionDirection.multiply(projectionDistance);
- // projection.addLocal(camera.getPosition());
- //
projection.addLocal(camera.getPosition().subtract(eye));
- projection.addLocal(camera.getPosition());
-
- if
(mouse.getPressed().contains(MouseEvent.BUTTON1)) {
- /*
- testNode.x = (float) projection.x();
- testNode.y = (float) projection.y();
- testNode.z = (float) projection.z();
- */
- }
-
- // testNode.x = (float) nearPosition.x();
- // testNode.y = (float) nearPosition.y();
- // testNode.z = (float) nearPosition.z();
-
- // testNode.x = (float) eye.x();
- // testNode.y = (float) eye.y();
- // testNode.z = (float) eye.z();
-
- /*
- System.out.println("percentMouseOffsetX: " +
percentMouseOffsetX);
- System.out.println("percentMouseOffsetY: " +
percentMouseOffsetY);
- System.out.println("nearX: " + nearX);
- System.out.println("nearY: " + nearY);
- */
-
- // System.out.println("Mouse is at: (" +
mouse.x() + ", " + mouse.y() + ")");
-
- int result = performPick(gl, mouse.x(),
mouse.y());
+ // Perform calculations for real-time node picking:
+ //-------------------------------------------------
+
+ // Hnear = 2 * tan(fov / 2) * nearDist
+ // in our case:
+ // fov = 45 deg
+ // nearDist = 0.2
+
+ double fieldOfView = Math.PI / 4;
+ double nearDistance = 0.2;
+
+ double nearPlaneHeight = 2 * Math.tan(fieldOfView / 2)
* nearDistance;
+ double nearPlaneWidth = nearPlaneHeight * screenWidth /
screenHeight;
+
+ double percentMouseOffsetX = (double) (mouse.x() -
screenWidth) / screenWidth + 0.5;
+ double percentMouseOffsetY = (double) (mouse.y() -
screenHeight) / screenHeight + 0.5;
+
+ // OpenGL has up as the positive y direction, whereas
the mouse is at (0, 0) in the top left
+ percentMouseOffsetY = -percentMouseOffsetY;
+
+ double nearX = percentMouseOffsetX * nearPlaneWidth;
+ double nearY = percentMouseOffsetY * nearPlaneHeight;
+
+ // Obtain the near plane position vector
+ Vector3 nearPosition;
+ nearPosition = new Vector3(camera.getDirection());
+ nearPosition.multiplyLocal(nearDistance);
+
+ nearPosition.addLocal(camera.getPosition());
+ nearPosition.addLocal(camera.getUp().multiply(nearY));
+
nearPosition.addLocal(camera.getLeft().multiply(-nearX)); // Note that nearX is
positive to the right
+
+ // Obtain the projection direction vector
+ Vector3 projectionDirection =
nearPosition.subtract(camera.getPosition());
+ projectionDirection.normalizeLocal();
+
+ double angle =
projectionDirection.angle(camera.getDirection());
+ double projectionDistance = (camera.getDistance()) /
Math.cos(angle);
+
+ Vector3 projection =
projectionDirection.multiply(projectionDistance);
+ // projection.addLocal(camera.getPosition());
+ //
projection.addLocal(camera.getPosition().subtract(eye));
+ projection.addLocal(camera.getPosition());
+
+ // Code for testing functionality of converting mouse
coordinates to 3D coordinates
+ /*
+ testNode.x = (float) projection.x();
+ testNode.y = (float) projection.y();
+ testNode.z = (float) projection.z();
+ */
+
+ // testNode.x = (float) nearPosition.x();
+ // testNode.y = (float) nearPosition.y();
+ // testNode.z = (float) nearPosition.z();
+
+ // testNode.x = (float) eye.x();
+ // testNode.y = (float) eye.y();
+ // testNode.z = (float) eye.z();
+
+ /*
+ System.out.println("percentMouseOffsetX: " +
percentMouseOffsetX);
+ System.out.println("percentMouseOffsetY: " +
percentMouseOffsetY);
+ System.out.println("nearX: " + nearX);
+ System.out.println("nearY: " + nearY);
+ */
+
+ // System.out.println("Mouse is at: (" + mouse.x() + ",
" + mouse.y() + ")");
+
+ int result = performPick(gl, mouse.x(), mouse.y());
- hovered = result;
+ hovered = result;
+
+ if (mouse.getPressed().contains(MouseEvent.BUTTON1)) {
- if
(mouse.getPressed().contains(MouseEvent.BUTTON1)) {
- selected = result;
+ // If control was pressed, prepare to add a node
+ if
(keys.getHeld().contains(KeyEvent.VK_CONTROL)) {
- System.out.println("Selected: " +
selected);
+ CyNode added =
networkView.getModel().addNode();
+ networkView.updateView();
+
+ View<CyNode> viewAdded =
networkView.getNodeView(added);
+
+ // TODO: Maybe throw an exception if
viewAdded is null
+ if (viewAdded != null) {
+
viewAdded.setVisualProperty(RichVisualLexicon.NODE_X_LOCATION, projection.x() *
DISTANCE_SCALE);
+
viewAdded.setVisualProperty(RichVisualLexicon.NODE_Y_LOCATION, projection.y() *
DISTANCE_SCALE);
+
viewAdded.setVisualProperty(RichVisualLexicon.NODE_Z_LOCATION, projection.z() *
DISTANCE_SCALE);
+
+ // Update the hovered node
+ // TODO: This might not be
needed if the node were added through some way other than the mouse
+ hovered = added.getIndex();
+ }
+ // Otherwise, prepare to select the node
currently under the mouse cursor
+ } else {
+ CyNode picked =
networkView.getModel().getNode(result);
+
+ // TODO: Perhaps throw exception if the
node was found to be null, ie. invalid index
+ // Note though the above case could
also be caused by picked == NO_INDEX
+ if (picked != null) {
+
+ // If the user did not hold
down shift, unselect other nodes
+ if
(!keys.getHeld().contains(KeyEvent.VK_SHIFT)) {
+
+ selectedNodes.clear();
+
selectedNodeIndices.clear();
+ }
+
+ if
(selectedNodes.contains(picked)) {
+
selectedNodes.remove(picked);
+
selectedNodeIndices.remove(picked.getIndex());
+ } else {
+
selectedNodes.add(picked);
+
selectedNodeIndices.add(picked.getIndex());
+ }
+
+ System.out.println("Selected
node index: " + picked.getIndex());
+ }
}
-
}
mouse.update();
@@ -492,7 +614,7 @@
glu.gluLookAt(position.x(), position.y(), position.z(),
target.x(),
target.y(), target.z(), up.x(), up.y(), up.z());
- gl.glPushName(-1);
+ gl.glPushName(NO_INDEX);
drawNodes(gl);
//drawEdges(gl);
@@ -526,7 +648,7 @@
}
}
} else {
- selected = -1;
+ selected = NO_INDEX;
}
return selected;
@@ -548,7 +670,7 @@
gl.glTranslatef(x, y, z);
- if (index == selected) {
+ if (selectedNodeIndices.contains(index)) {
gl.glColor3f(0.52f, 0.70f, 0.52f);
gl.glScalef(1.1f, 1.1f, 1.1f);
gl.glCallList(nodeListIndex);
@@ -639,16 +761,23 @@
direction = p2.subtract(p0);
p1Offset = direction.cross(0, 1, 0);
p1Offset.normalizeLocal();
- p1Offset.multiplyLocal(EDGE_CURVE_FACTOR *
Math.sqrt(direction.magnitude()));
+ // Shift the square root graph one to the left and one
down to get smoother curves
+ p1Offset.multiplyLocal(EDGE_CURVE_FACTOR *
(Math.sqrt(direction.magnitude() + 1) - 1));
+
p1.addLocal(p1Offset);
p1.rotate(direction, 2 * Math.PI *
(pairs.get(pairIdentifier) - 1) / EDGES_PER_RADIUS);
-
- drawQuadraticEdge(gl, p0, p1, p2, 5);
+
+ drawQuadraticEdge(gl, p0, p1, p2, 4);
}
}
private void drawQuadraticEdge(GL2 gl, Vector3 p0, Vector3 p1, Vector3
p2, int numSegments) {
+ // TODO: Allow the minimum distance to be changed
+ if (p0.distanceSquared(p2) <
MINIMUM_EDGE_DRAW_DISTANCE_SQUARED) {
+ return;
+ }
+
// Equation for Quadratic Bezier curve:
// B(t) = (1 - t)^2P0 + 2(1 - t)tP1 + t^2P2, t in [0, 1]
@@ -700,21 +829,19 @@
// Extend by c * tan(theta/2)
extend2 = EDGE_RADIUS * Math.tan(currentAngle / 2);
-
direction = points[i + 1].subtract(points[i]);
direction.normalizeLocal();
- if (framesElapsed == 2) {
- System.out.println("Segment: " + i);
- System.out.println("Current segment angle: " +
currentAngle);
- System.out.println("Current extend1: " +
extend1);
- System.out.println("Current extend2: " +
extend2);
- System.out.println("Current p0: " + p0);
- System.out.println("Current p1: " + p1);
- System.out.println("Current p2: " + p2);
- System.out.println("Current direction: " +
direction);
-
- }
+// if (framesElapsed == 2) {
+// System.out.println("Segment: " + i);
+// System.out.println("Current segment angle: " +
currentAngle);
+// System.out.println("Current extend1: " +
extend1);
+// System.out.println("Current extend2: " +
extend2);
+// System.out.println("Current p0: " + p0);
+// System.out.println("Current p1: " + p1);
+// System.out.println("Current p2: " + p2);
+// System.out.println("Current direction: " +
direction);
+// }
// drawSingleEdge(gl,
//
points[i].subtract(direction.multiply(extend1)),
@@ -723,6 +850,24 @@
drawSingleEdge(gl,
points[i],
points[i + 1]);
+
+// if (framesElapsed == 3) {
+// if
(points[i].subtract(direction.multiply(extend1)).magnitude() > 100) {
+// System.out.println("points[i]: " +
points[i].subtract(direction.multiply(extend1)));
+// }
+//
+// if (points[i +
1].add(direction.multiply(extend2)).magnitude() > 100) {
+// System.out.println("points[i + 1]: " +
points[i + 1].add(direction.multiply(extend2)));
+// System.out.println("extend2 info,
Segment: " + i);
+// System.out.println("Current segment
angle: " + currentAngle);
+// System.out.println("Current extend1: "
+ extend1);
+// System.out.println("Current extend2: "
+ extend2);
+// System.out.println("Current p0: " + p0);
+// System.out.println("Current p1: " + p1);
+// System.out.println("Current p2: " + p2);
+// System.out.println("Current direction:
" + direction);
+// }
+// }
extend1 = extend2;
}
@@ -832,6 +977,7 @@
private void createDisplayLists(GL2 gl) {
nodeListIndex = gl.glGenLists(1);
edgeListIndex = gl.glGenLists(1);
+ pointerListIndex = gl.glGenLists(1);
GLUT glut = new GLUT();
GLU glu = new GLU();
@@ -847,10 +993,23 @@
// NODE_STACKS_DETAIL);
gl.glEndList();
+ GLUquadric quadric2 = glu.gluNewQuadric();
+ glu.gluQuadricDrawStyle(quadric2, GLU.GLU_FILL);
+ glu.gluQuadricNormals(quadric2, GLU.GLU_SMOOTH); // TODO:
Experiment with GLU_FLAT for efficiency
+
gl.glNewList(edgeListIndex, GL2.GL_COMPILE);
- glu.gluCylinder(quadric, EDGE_RADIUS, EDGE_RADIUS, 1.0,
+ glu.gluCylinder(quadric2, EDGE_RADIUS, EDGE_RADIUS, 1.0,
EDGE_SLICES_DETAIL, EDGE_STACKS_DETAIL);
gl.glEndList();
+
+ GLUquadric pointerQuadric = glu.gluNewQuadric();
+ glu.gluQuadricDrawStyle(pointerQuadric, GLU.GLU_LINE);
+ glu.gluQuadricNormals(pointerQuadric, GLU.GLU_NONE);
+
+ gl.glNewList(pointerListIndex, GL2.GL_COMPILE);
+ glu.gluSphere(pointerQuadric, SMALL_SPHERE_RADIUS / 4, 4,
+ 4);
+ gl.glEndList();
}
private void initLighting(GLAutoDrawable drawable) {
Modified:
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/Vector3.java
===================================================================
---
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/Vector3.java
2011-07-02 01:34:41 UTC (rev 26012)
+++
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/Vector3.java
2011-07-02 14:07:24 UTC (rev 26013)
@@ -74,6 +74,9 @@
double cosArgument = (x * other.x + y * other.y + z *
other.z)/Math.sqrt(lengthSquare * otherLengthSquare);
if (Double.isNaN(cosArgument)) {
+ System.out.println("cosArgument NaN");
+ System.out.println("lengthSquare: " + lengthSquare);
+ System.out.println("otherLengthSquare: " +
otherLengthSquare);
return 0;
} else if (cosArgument >= 1) {
return 0;
@@ -147,6 +150,10 @@
return Math.sqrt(Math.pow(x - other.x, 2) + Math.pow(y -
other.y, 2) + Math.pow(z - other.z, 2));
}
+ public double distanceSquared(Vector3 other) {
+ return Math.pow(x - other.x, 2) + Math.pow(y - other.y, 2) +
Math.pow(z - other.z, 2);
+ }
+
// Project the vector onto the plane passing through the origin,
perpendicular to the given normal
public Vector3 projectNormal(Vector3 normal) {
return subtract(normal.multiply(this.dot(normal)));
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