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[Jmol-commits] CVS: Jmol/src/org/openscience/jmol/viewer/datamodel ArcTest.java,1.3,1.4 DotsRenderer.java,1.17,1.18 FrameRenderer.java,1.11,1.12 MeasurementRenderer.java,1.1,1.2 MeasurementShape.java,1.11,1.12
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From: Michael T H. <mic...@us...> - 2003-09-28 23:46:14
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Update of /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel
In directory sc8-pr-cvs1:/tmp/cvs-serv17717/src/org/openscience/jmol/viewer/datamodel
Modified Files:
ArcTest.java DotsRenderer.java FrameRenderer.java
MeasurementRenderer.java MeasurementShape.java
Log Message:
some changes to improve measurement rendering in the Graphics3D world
Index: ArcTest.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel/ArcTest.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- ArcTest.java 17 Sep 2003 20:08:41 -0000 1.3
+++ ArcTest.java 28 Sep 2003 22:41:39 -0000 1.4
@@ -114,7 +114,7 @@
pointT.set(center);
pointT.add(vector1);
matrixT.transform(pointT);
- g3d.plotPoint(viewer.transformPoint(pointT));
+ g3d.drawPixel(viewer.transformPoint(pointT));
}
}
}
Index: DotsRenderer.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel/DotsRenderer.java,v
retrieving revision 1.17
retrieving revision 1.18
diff -u -r1.17 -r1.18
--- DotsRenderer.java 25 Sep 2003 21:21:25 -0000 1.17
+++ DotsRenderer.java 28 Sep 2003 22:41:39 -0000 1.18
@@ -179,7 +179,7 @@
matrixT1.transform(torus.outerRadial, pointT1);
matrixT.transform(pointT1);
pointT1.add(pointT);
- g3d.plotPoint(viewer.transformPoint(pointT1));
+ g3d.drawPixel(viewer.transformPoint(pointT1));
}
}
}
Index: FrameRenderer.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel/FrameRenderer.java,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -r1.11 -r1.12
--- FrameRenderer.java 26 Sep 2003 08:12:58 -0000 1.11
+++ FrameRenderer.java 28 Sep 2003 22:41:39 -0000 1.12
@@ -110,7 +110,7 @@
for (int i = frame.measurementShapeCount; --i >= 0; ) {
MeasurementShape measurementShape = frame.measurementShapes[i];
- measurementShape.transform(viewer);
+ // measurementShape.transform(viewer);
measurementRenderer.render(measurementShape);
}
Index: MeasurementRenderer.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel/MeasurementRenderer.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- MeasurementRenderer.java 26 Sep 2003 08:12:58 -0000 1.1
+++ MeasurementRenderer.java 28 Sep 2003 22:41:39 -0000 1.2
@@ -77,20 +77,57 @@
default:
throw new NullPointerException();
}
- if (showMeasurementLabels)
- paintMeasurementString();
}
void renderDistance() {
+ AtomShape atomA = frame.getAtomAt(measurement.atomIndices[0]);
+ AtomShape atomB = frame.getAtomAt(measurement.atomIndices[1]);
+ int diamMax = atomA.diameter;
+ if (atomB.diameter > diamMax)
+ diamMax = atomB.diameter;
+ int zOffset = diamMax;
+ int zA = atomA.z - zOffset;
+ if (zA < 0) zA = 0;
+ int zB = atomB.z - zOffset;
+ if (zB < 0) zB = 0;
g3d.drawDottedLine(colixDistance,
- measurement.x, measurement.y, measurement.z,
- measurement.xEnd, measurement.yEnd, measurement.zEnd);
+ atomA.x, atomA.y, zA, atomB.x, atomB.y, zB);
+ paintMeasurementString((atomA.x + atomB.x) / 2,
+ (atomA.y + atomB.y) / 2,
+ (zA + zB) / 2);
}
+
void renderDihedral() {
+ AtomShape atomA = frame.getAtomAt(measurement.atomIndices[0]);
+ AtomShape atomB = frame.getAtomAt(measurement.atomIndices[1]);
+ AtomShape atomC = frame.getAtomAt(measurement.atomIndices[2]);
+ AtomShape atomD = frame.getAtomAt(measurement.atomIndices[3]);
+ int diamMax = atomA.diameter;
+ if (atomB.diameter > diamMax)
+ diamMax = atomB.diameter;
+ if (atomC.diameter > diamMax)
+ diamMax = atomC.diameter;
+ if (atomD.diameter > diamMax)
+ diamMax = atomD.diameter;
+ int zOffset = diamMax;
+ int zA = atomA.z - zOffset;
+ if (zA < 0) zA = 0;
+ int zB = atomB.z - zOffset;
+ if (zB < 0) zB = 0;
+ int zC = atomC.z - zOffset;
+ if (zC < 0) zC = 0;
+ int zD = atomD.z - zOffset;
+ if (zD < 0) zD = 0;
g3d.drawDottedLine(colixDistance,
- measurement.x, measurement.y, measurement.z,
- measurement.xEnd, measurement.yEnd, measurement.zEnd);
+ atomA.x, atomA.y, zA, atomB.x, atomB.y, zB);
+ g3d.drawDottedLine(colixDistance,
+ atomB.x, atomB.y, zB, atomC.x, atomC.y, zC);
+ g3d.drawDottedLine(colixDistance,
+ atomC.x, atomC.y, zC, atomD.x, atomD.y, zD);
+ paintMeasurementString((atomA.x + atomB.x + atomC.x + atomD.x) / 4,
+ (atomA.y + atomB.y + atomC.y + atomD.y) / 4,
+ (zA + zB + zC + zD) / 4);
}
AxisAngle4f aaT = new AxisAngle4f();
@@ -99,38 +136,63 @@
void renderAngle() {
g3d.setColix(colixDistance);
+ AtomShape atomA = frame.getAtomAt(measurement.atomIndices[0]);
+ AtomShape atomB = frame.getAtomAt(measurement.atomIndices[1]);
+ AtomShape atomC = frame.getAtomAt(measurement.atomIndices[2]);
+ int diamMax = atomA.diameter;
+ if (atomB.diameter > diamMax)
+ diamMax = atomB.diameter;
+ if (atomC.diameter > diamMax)
+ diamMax = atomC.diameter;
+ int zOffset = diamMax;
+ int zA = atomA.z - zOffset;
+ if (zA < 0) zA = 0;
+ int zB = atomB.z - zOffset;
+ if (zB < 0) zB = 0;
+ int zC = atomC.z - zOffset;
+ if (zC < 0) zC = 0;
+ g3d.drawDottedLine(colixDistance,
+ atomA.x, atomA.y, zA, atomB.x, atomB.y, zB);
+ g3d.drawDottedLine(colixDistance,
+ atomB.x, atomB.y, zB, atomC.x, atomC.y, zC);
+
AxisAngle4f aa = measurement.aa;
- Vector3f vector21 = measurement.vector21;
// FIXME mth -- this really should be a function of pixelsPerAngstrom
int dotCount = (int)((aa.angle / (2 * Math.PI)) * 64);
float stepAngle = aa.angle / dotCount;
aaT.set(aa);
+ int iMid = dotCount / 2;
for (int i = dotCount; --i >= 0; ) {
aaT.angle = i * stepAngle;
matrixT.set(aaT);
- pointT.set(vector21);
- pointT.scale(0.75f);
+ pointT.set(measurement.pointArc);
matrixT.transform(pointT);
- pointT.add(measurement.center);
- g3d.plotPoint(viewer.transformPoint(pointT));
+ pointT.add(atomB.point3f);
+ Point3i screenArc = viewer.transformPoint(pointT);
+ int zArc = screenArc.z - zOffset;
+ if (zArc < 0) zArc = 0;
+ g3d.drawPixel(screenArc.x, screenArc.y, zArc);
+ if (i == iMid) {
+ pointT.set(measurement.pointArc);
+ pointT.scale(1.1f);
+ matrixT.transform(pointT);
+ pointT.add(atomB.point3f);
+ Point3i screenLabel = viewer.transformPoint(pointT);
+ int zLabel = screenLabel.z - zOffset;
+ if (zLabel < 0) zLabel = 0;
+ paintMeasurementString(screenLabel.x, screenLabel.y, zLabel);
+ }
}
- int xC, yC, zC;
- Point3i pointC = viewer.transformPoint(measurement.center);
- g3d.drawDottedLine(colixDistance,
- pointC.x, pointC.y, pointC.z, measurement.x, measurement.y, measurement.z);
- g3d.drawDottedLine(colixDistance,
- pointC.x, pointC.y, pointC.z, measurement.xEnd, measurement.yEnd, measurement.zEnd);
}
- void paintMeasurementString() {
+ void paintMeasurementString(int x, int y, int z) {
+ if (! showMeasurementLabels)
+ return;
String strMeasurement = measurement.strMeasurement;
Font font = viewer.getMeasureFont(10);
g3d.setFont(font);
FontMetrics fontMetrics = g3d.getFontMetrics(font);
int j = fontMetrics.stringWidth(strMeasurement);
- int xT = (measurement.x + measurement.xEnd) / 2;
- int yT = (measurement.y + measurement.yEnd) / 2;
- int zT = (measurement.z + measurement.zEnd) / 2;
- g3d.drawString(strMeasurement, colixDistance, xT, yT, zT);
+ g3d.drawString(strMeasurement, colixDistance, x+2, y, z);
}
}
Index: MeasurementShape.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel/MeasurementShape.java,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -r1.11 -r1.12
--- MeasurementShape.java 26 Sep 2003 08:12:58 -0000 1.11
+++ MeasurementShape.java 28 Sep 2003 22:41:39 -0000 1.12
@@ -33,73 +33,49 @@
import javax.vecmath.Matrix3f;
import javax.vecmath.AxisAngle4f;
-public class MeasurementShape extends LineShape {
+public class MeasurementShape {
+ public int count;
public int[] atomIndices;
public String strMeasurement;
- public Point3f center, pointT;
- Vector3f vector21;
- public int count;
- AxisAngle4f aa, aaT;
- Matrix3f matrixT;
-
+ AxisAngle4f aa;
+ Point3f pointArc;
+
public MeasurementShape(JmolFrame frame, int count, int[] atomIndices) {
- Point3f point1 = frame.getAtomPoint3f(atomIndices[0]);
- Point3f point2 = frame.getAtomPoint3f(atomIndices[1]);
- Point3f point3 = null;
- Point3f point4 = null;
+ Point3f pointA = frame.getAtomPoint3f(atomIndices[0]);
+ Point3f pointB = frame.getAtomPoint3f(atomIndices[1]);
+ Point3f pointC = null;
+ Point3f pointD = null;
this.count = count;
switch (count) {
case 2:
- strMeasurement = formatDistance(point1.distance(point2));;
-
- pointOrigin = point1;
- pointEnd = point2;
+ strMeasurement = formatDistance(pointA.distance(pointB));
break;
case 3:
- point3 = frame.getAtomPoint3f(atomIndices[2]);
- vector21 = new Vector3f(point1);
- vector21.sub(point2);
- Vector3f vector23 = new Vector3f(point3);
- vector23.sub(point2);
- float angle = vector21.angle(vector23);
+ pointC = frame.getAtomPoint3f(atomIndices[2]);
+ Vector3f vectorBA = new Vector3f();
+ Vector3f vectorBC = new Vector3f();
+ vectorBA.sub(pointA, pointB);
+ vectorBC.sub(pointC, pointB);
+ float angle = vectorBA.angle(vectorBC);
float degrees = toDegrees(angle);
strMeasurement = formatAngle(degrees);
- float len21 = vector21.length();
- float len23 = vector23.length();
- if (len21 < len23)
- vector23.scale(len21/len23);
- else
- vector21.scale(len23/len21);
-
- pointOrigin = new Point3f(point2);
- pointOrigin.add(vector21);
- pointEnd = new Point3f(point2);
- pointEnd.add(vector23);
-
- center = point2;
Vector3f vectorAxis = new Vector3f();
- vectorAxis.cross(vector21, vector23);
+ vectorAxis.cross(vectorBA, vectorBC);
aa = new AxisAngle4f(vectorAxis.x, vectorAxis.y, vectorAxis.z, angle);
- pointT = new Point3f();
- aaT = new AxisAngle4f();
- matrixT = new Matrix3f();
+ vectorBA.normalize();
+ vectorBA.scale(0.5f);
+ pointArc = new Point3f(vectorBA);
+
break;
case 4:
- point3 = frame.getAtomPoint3f(atomIndices[2]);
- point4 = frame.getAtomPoint3f(atomIndices[3]);
- float dihedral = computeDihedral(point1, point2, point3, point4);
+ pointC = frame.getAtomPoint3f(atomIndices[2]);
+ pointD = frame.getAtomPoint3f(atomIndices[3]);
+ float dihedral = computeDihedral(pointA, pointB, pointC, pointD);
strMeasurement = formatAngle(dihedral);
-
- pointOrigin = new Point3f(point1);
- pointOrigin.add(point2);
- pointOrigin.scale(0.5f);
- pointEnd = new Point3f(point3);
- pointEnd.add(point4);
- pointEnd.scale(0.5f);
break;
default:
System.out.println("Invalid count to measurement shape:" + count);
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