public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
BasicShapeAttributes that = (BasicShapeAttributes) o;
if (drawOutline != that.drawOutline) return false;
if (drawInterior != that.drawInterior) return false;
if (enableAntialiasing != that.enableAntialiasing) return false;
if (Double.compare(that.outlineOpacity, outlineOpacity) != 0) return false;
if (Double.compare(that.interiorOpacity, interiorOpacity) != 0) return false;
if (Double.compare(that.outlineWidth, outlineWidth) != 0) return false;
if (that.outlineStippleFactor != outlineStippleFactor) return false;
if (that.outlineStipplePattern != outlineStipplePattern) return false;
if (interiorMaterial != null
? !interiorMaterial.equals(that.interiorMaterial)
: that.interiorMaterial != null) return false;
if (outlineMaterial != null
? !outlineMaterial.equals(that.outlineMaterial)
: that.outlineMaterial != null) return false;
if (interiorImageSource != null
? !interiorImageSource.equals(that.interiorImageSource)
: that.interiorImageSource != null) return false;
//noinspection RedundantIfStatement
if (Double.compare(that.interiorImageScale, interiorImageScale) != 0) return false;
return true;
}
/**
* @param m
* @param n
* @param w
* @param h
* @param pix
*/
public InteractiveRenderer(int m, int n, int w, int h) {
W = w;
H = h;
renderer = new Renderer();
pixels = renderer.init(W, H);
Geometry g = this.add();
texture = new Texture(pixels, W, H, "grid", false);
Material material = new Material();
material.setTexture(texture);
g.setMaterial(material);
g.setDoubleSided(true);
g.mesh(m, n);
g.name = "mesh";
init();
}
public int hashCode() {
int result;
long temp;
result = (drawInterior ? 1 : 0);
result = 31 * result + (drawOutline ? 1 : 0);
result = 31 * result + (enableAntialiasing ? 1 : 0);
result = 31 * result + (interiorMaterial != null ? interiorMaterial.hashCode() : 0);
result = 31 * result + (outlineMaterial != null ? outlineMaterial.hashCode() : 0);
temp = interiorOpacity != +0.0d ? Double.doubleToLongBits(interiorOpacity) : 0L;
result = 31 * result + (int) (temp ^ (temp >>> 32));
temp = outlineOpacity != +0.0d ? Double.doubleToLongBits(outlineOpacity) : 0L;
result = 31 * result + (int) (temp ^ (temp >>> 32));
temp = outlineWidth != +0.0d ? Double.doubleToLongBits(outlineWidth) : 0L;
result = 31 * result + (int) (temp ^ (temp >>> 32));
temp = outlineStippleFactor;
result = 31 * result + (int) (temp ^ (temp >>> 32));
temp = outlineStipplePattern;
result = 31 * result + (int) (temp ^ (temp >>> 32));
result = 31 * result + (interiorImageSource != null ? interiorImageSource.hashCode() : 0);
temp = Double.doubleToLongBits(interiorImageScale);
result = 31 * result + (int) (temp ^ (temp >>> 32));
return result;
}
@Override
public Material getMaterial(int x, int y, int z) {
return Material.get(getBlockType(x, y, z), getDataValue(x, y, z));
}
/**
* Builds the SRA elements that are related to this ISATAB assay. It adds runs and an experiment
* to the respective set.
*
* @return true if it could successfully build the exported items.
*/
protected boolean buildExportedAssay(
Assay assay,
SubmissionType.FILES xsubFiles,
RunSetType xrunSet,
ExperimentSetType xexperimentSet,
SampleSetType xsampleSet) {
String assayAcc = assay.getAcc();
// Now create an experiment for the input material and link it to the run
// get Material associated to the assay and get its identifier
Material material = assay.getMaterial();
String materialAcc = material.getAcc();
// create a new SRA Experiment and assign ISA Material name as SRA Experiment Title
ExperimentType xexp = ExperimentType.Factory.newInstance();
xexp.setAlias(materialAcc);
xexp.setTITLE("experiment made with the sample " + material.getName());
xexp.setCenterName(centerName);
xexp.setBrokerName(brokerName);
PlatformType xplatform = buildExportedPlatform(assay);
if (xplatform == null) {
return false;
}
xexp.setPLATFORM(xplatform);
xexp.setPROCESSING(buildExportedProcessing(assay));
STUDYREF xstudyRef = STUDYREF.Factory.newInstance();
xstudyRef.setRefname(assay.getStudy().getAcc());
xexp.setSTUDYREF(xstudyRef);
EXPERIMENTREF xexpRef = EXPERIMENTREF.Factory.newInstance();
xexpRef.setRefname(materialAcc);
DESIGN xdesign = DESIGN.Factory.newInstance();
xdesign.setDESIGNDESCRIPTION("See study and sample descriptions for details");
SAMPLEDESCRIPTOR xsampleRef = buildExportedAssaySample(assay, xsampleSet);
if (xsampleRef == null) {
return false;
}
xdesign.setSAMPLEDESCRIPTOR(xsampleRef);
LIBRARYDESCRIPTOR xlib = buildExportedLibraryDescriptor(assay);
if (xlib == null) {
return false;
}
xdesign.setLIBRARYDESCRIPTOR(xlib);
SpotDescriptorType xspotd = buildExportedSpotDescriptor(assay);
if (xspotd == null) {
return false;
}
xdesign.setSPOTDESCRIPTOR(xspotd);
xexp.setDESIGN(xdesign);
// For each file, builds one run, with one data block and one file
// TODO: We should introduce something like "Run Name", so that multiple files associated to a
// single run can be
// specified
//
for (AssayResult ar : ProcessingUtils.findAssayResultsFromAssay(assay)) {
Data data = ar.getData();
String url = StringUtils.trimToNull(data.getUrl());
Study study = ar.getStudy();
if (url == null) {
String msg =
MessageFormat.format(
"The assay file of type {0} / {1} for study {2} has a data file node without file name, ignoring",
assay.getMeasurement().getName(),
assay.getTechnologyName(),
assay.getStudy().getAcc());
nonRepeatedMessages.add(msg + ". Data node is " + data.getName());
log.trace(msg);
return false;
}
FILE.Filetype.Enum xfileType = null;
String fileType =
StringUtils.trimToNull(data.getSingleAnnotationValue("comment:SRA File Type"));
if (fileType == null) {
// Let's try to get it from the file extension
//
fileType = StringUtils.trimToNull(FilenameUtils.getExtension(url));
if (fileType != null) {
xfileType = FILE.Filetype.Enum.forString(fileType.toLowerCase());
}
if (xfileType == null) {
String msg =
MessageFormat.format(
"The assay file of type {0} / {1} for study {2} has a data file node without the annotation "
+ "'SRA file type' and I cannot compute the file type from the file name, ignoring the assay",
assay.getMeasurement().getName(),
assay.getTechnologyName(),
assay.getStudy().getAcc());
nonRepeatedMessages.add(msg);
log.trace(msg + ". Data node is " + data.getName());
return false;
}
}
if (xfileType == null) {
// fileType is certainly non null at this point, cause it was explicitly provided and so we
// have to process it
//
xfileType = FILE.Filetype.Enum.forString(fileType.toLowerCase());
if (xfileType == null) {
String msg =
MessageFormat.format(
"The assay file of type {0} / {1} for study {2} has a bad 'SRA File Type' annotation: '"
+ fileType
+ "'"
+ ", ignoring the assy",
assay.getMeasurement().getName(),
assay.getTechnologyName(),
assay.getStudy().getAcc());
nonRepeatedMessages.add(msg);
log.trace(msg + ". Data node is " + data.getName());
return false;
}
}
RunType xrun = RunType.Factory.newInstance();
xrun.setAlias(assayAcc);
xrun.setCenterName(centerName);
xrun.setBrokerName(brokerName);
DATABLOCK dataBlock = DATABLOCK.Factory.newInstance();
FILES xfiles = FILES.Factory.newInstance();
FILE xfile = FILE.Factory.newInstance();
xfile.setFiletype(xfileType);
xfile.setFilename(url);
xfiles.addNewFILE();
xfiles.setFILEArray(0, xfile);
dataBlock.setFILES(xfiles);
xrun.addNewDATABLOCK();
xrun.setDATABLOCKArray(xrun.sizeOfDATABLOCKArray() - 1, dataBlock);
addExportedSubmissionFile(xsubFiles, url);
// TODO: remove, it's deprecated now xrun.setTotalDataBlocks ( BigInteger.ONE );
xrun.setEXPERIMENTREF(xexpRef);
xrunSet.addNewRUN();
xrunSet.setRUNArray(xrunSet.sizeOfRUNArray() - 1, xrun);
}
xexperimentSet.addNewEXPERIMENT();
xexperimentSet.setEXPERIMENTArray(xexperimentSet.sizeOfEXPERIMENTArray() - 1, xexp);
return true;
}
/** Setup the basic scene which consists of a quad and a viewpoint */
private void setupSceneGraph() {
// View group
Viewpoint vp = new Viewpoint();
Vector3f trans = new Vector3f(0, 0, 1);
Matrix4f mat = new Matrix4f();
mat.setIdentity();
mat.setTranslation(trans);
TransformGroup tx = new TransformGroup();
tx.addChild(vp);
tx.setTransform(mat);
Group scene_root = new Group();
scene_root.addChild(tx);
// Flat panel that has the viewable object as the demo
float[] coord = {0, 0, -1, 0.25f, 0, -1, 0, 0.25f, -1};
float[] normal = {0, 0, 1, 0, 0, 1, 0, 0, 1};
TriangleArray geom = new TriangleArray();
geom.setValidVertexCount(3);
geom.setVertices(TriangleArray.COORDINATE_3, coord);
geom.setNormals(normal);
Material material = new Material();
material.setDiffuseColor(new float[] {0, 0, 1});
material.setEmissiveColor(new float[] {0, 0, 1});
material.setSpecularColor(new float[] {1, 1, 1});
material.setTransparency(0.5f);
Appearance app = new Appearance();
app.setMaterial(material);
Shape3D shape = new Shape3D();
shape.setGeometry(geom);
shape.setAppearance(app);
TransformGroup tg = new TransformGroup();
Matrix4f transform = new Matrix4f();
transform.setIdentity();
transform.setTranslation(new Vector3f(0.15f, 0, -1));
tg.setTransform(transform);
Shape3D backShape = new Shape3D();
Material material2 = new Material();
material2.setDiffuseColor(new float[] {1, 0, 0});
material2.setEmissiveColor(new float[] {1, 0, 0});
material2.setSpecularColor(new float[] {1, 1, 1});
Appearance app2 = new Appearance();
app2.setMaterial(material2);
backShape.setGeometry(geom);
backShape.setAppearance(app2);
tg.addChild(backShape);
scene_root.addChild(tg);
scene_root.addChild(shape);
SimpleScene scene = new SimpleScene();
scene.setRenderedGeometry(scene_root);
scene.setActiveView(vp);
// Then the basic layer and viewport at the top:
SimpleViewport view = new SimpleViewport();
view.setDimensions(0, 0, 500, 500);
view.setScene(scene);
SimpleLayer layer = new SimpleLayer();
layer.setViewport(view);
Layer[] layers = {layer};
displayManager.setLayers(layers, 1);
}
public void setDiffuseColor(int diffuseColor) {
material.diffuseColor = diffuseColor;
}
