public void read(ByteBuffer buffer) {
next = DNATools.link(DNATools.ptr(buffer), BoidState.class); // get ptr
prev = DNATools.link(DNATools.ptr(buffer), BoidState.class); // get ptr
rules.read(buffer);
conditions.read(buffer);
actions.read(buffer);
buffer.get(name);
id = buffer.getInt();
flag = buffer.getInt();
ruleset_type = buffer.getInt();
rule_fuzziness = buffer.getFloat();
signal_id = buffer.getInt();
channels = buffer.getInt();
volume = buffer.getFloat();
falloff = buffer.getFloat();
}
public void read(ByteBuffer buffer) {
super.read(buffer);
clone.read(buffer);
curve = DNATools.link(DNATools.ptr(buffer), CurveMapping.class); // get ptr
mtex.read(buffer);
icon_imbuf = DNATools.ptr(buffer); // get ptr
preview = DNATools.link(DNATools.ptr(buffer), PreviewImage.class); // get ptr
buffer.get(icon_filepath);
normal_weight = buffer.getFloat();
blend = buffer.getShort();
ob_mode = buffer.getShort();
size = buffer.getInt();
flag = buffer.getInt();
jitter = buffer.getFloat();
spacing = buffer.getInt();
smooth_stroke_radius = buffer.getInt();
smooth_stroke_factor = buffer.getFloat();
rate = buffer.getFloat();
for (int i = 0; i < rgb.length; i++) rgb[i] = buffer.getFloat();
alpha = buffer.getFloat();
sculpt_plane = buffer.getInt();
plane_offset = buffer.getFloat();
sculpt_tool = buffer.get();
vertexpaint_tool = buffer.get();
imagepaint_tool = buffer.get();
buffer.get(pad3);
autosmooth_factor = buffer.getFloat();
crease_pinch_factor = buffer.getFloat();
plane_trim = buffer.getFloat();
height = buffer.getFloat();
texture_sample_bias = buffer.getFloat();
texture_overlay_alpha = buffer.getInt();
unprojected_radius = buffer.getFloat();
for (int i = 0; i < add_col.length; i++) add_col[i] = buffer.getFloat();
for (int i = 0; i < sub_col.length; i++) sub_col[i] = buffer.getFloat();
}
private void dnaCommand(HttpServletRequest req, DazzleResponse resp, DazzleDataSource dds)
throws IOException, DataSourceException, ServletException, DazzleException {
DazzleReferenceSource drs = (DazzleReferenceSource) dds;
List segments = DazzleTools.getSegments(dds, req, resp);
if (segments.size() == 0) {
throw new DazzleException(
DASStatus.STATUS_BAD_COMMAND_ARGUMENTS, "No segments specified for dna command");
}
// Fetch and validate the requests.
Map segmentResults = new HashMap();
for (Iterator i = segments.iterator(); i.hasNext(); ) {
Segment seg = (Segment) i.next();
try {
Sequence seq = drs.getSequence(seg.getReference());
if (seq.getAlphabet() != DNATools.getDNA()) {
throw new DazzleException(
DASStatus.STATUS_SERVER_ERROR,
"Sequence " + seg.toString() + " is not in the DNA alphabet");
}
if (seg.isBounded()) {
if (seg.getMin() < 1 || seg.getMax() > seq.length()) {
throw new DazzleException(
DASStatus.STATUS_BAD_COORDS,
"Segment " + seg.toString() + " doesn't fit sequence of length " + seq.length());
}
}
segmentResults.put(seg, seq);
} catch (NoSuchElementException ex) {
throw new DazzleException(DASStatus.STATUS_BAD_REFERENCE, ex);
} catch (DataSourceException ex) {
throw new DazzleException(DASStatus.STATUS_SERVER_ERROR, ex);
}
}
//
// Looks okay -- generate the response document
//
XMLWriter xw = resp.startDasXML("DASDNA", "dasdna.dtd");
try {
xw.openTag("DASDNA");
for (Iterator i = segmentResults.entrySet().iterator(); i.hasNext(); ) {
Map.Entry me = (Map.Entry) i.next();
Segment seg = (Segment) me.getKey();
Sequence seq = (Sequence) me.getValue();
xw.openTag("SEQUENCE");
xw.attribute("id", seg.getReference());
xw.attribute("version", drs.getLandmarkVersion(seg.getReference()));
if (seg.isBounded()) {
xw.attribute("start", "" + seg.getStart());
xw.attribute("stop", "" + seg.getStop());
} else {
xw.attribute("start", "" + 1);
xw.attribute("stop", "" + seq.length());
}
SymbolList syms = seq;
if (seg.isBounded()) {
syms = syms.subList(seg.getMin(), seg.getMax());
}
if (seg.isInverted()) {
syms = DNATools.reverseComplement(syms);
}
xw.openTag("DNA");
xw.attribute("length", "" + syms.length());
for (int pos = 1; pos <= syms.length(); pos += 60) {
int maxPos = Math.min(syms.length(), pos + 59);
xw.println(syms.subStr(pos, maxPos));
}
xw.closeTag("DNA");
xw.closeTag("SEQUENCE");
}
xw.closeTag("DASDNA");
xw.close();
} catch (Exception ex) {
throw new DazzleException(ex, "Error writing DNA document");
}
}
