void RefinementState::calcEnergy ()
{
int i, j;
float r;
Vec2f d;
energy = 0;
for (i = _graph.vertexBegin(); i < _graph.vertexEnd(); i = _graph.vertexNext(i))
for (j = _graph.vertexBegin(); j < _graph.vertexEnd(); j = _graph.vertexNext(j))
{
if (i == j)
continue;
d.diff(layout[i], layout[j]);
r = d.lengthSqr();
if (r < 0.0001f)
r = 5000000.f;
else
r = 1 / r;
energy += r;
}
energy /= 2;
}
// Translate branch on 0.1 of vector [v1,v2]
void RefinementState::stretchBranch (const Filter &branch, const RefinementState &state, int v1_idx, int v2_idx, int val)
{
int i;
float r, sh = 0.1f * val;
const Vec2f &v1 = state.layout[v1_idx];
const Vec2f &v2 = state.layout[v2_idx];
Vec2f d;
d.diff(v2, v1);
r = d.length();
if (r < EPSILON)
throw Error("too small edge");
d.scale(sh / r);
if (branch.valid(v1_idx))
d.negate();
layout.clear_resize(state.layout.size());
for (i = _graph.vertexBegin(); i < _graph.vertexEnd(); i = _graph.vertexNext(i))
{
if (!branch.valid(i))
layout[i].sum(state.layout[i], d);
else
layout[i] = state.layout[i];
}
}
// Rotate branch around vertex v1
void RefinementState::rotateBranch (const Filter &branch, const RefinementState &state, int v_idx, float angle)
{
int i;
float co, si;
const Vec2f &v = state.layout[v_idx];
Vec2f d;
angle = DEG2RAD(angle);
co = cos(angle);
si = sin(angle);
layout.clear_resize(state.layout.size());
for (i = _graph.vertexBegin(); i < _graph.vertexEnd(); i = _graph.vertexNext(i))
{
if (!branch.valid(i))
{
d.diff(state.layout[i], v);
d.rotate(si, co);
layout[i].sum(d, v);
} else
layout[i] = state.layout[i];
}
}
// Flip all verices from branch around (v1,v2)
void RefinementState::flipBranch (const Filter &branch, const RefinementState &state, int v1_idx, int v2_idx)
{
int i;
float r, t;
const Vec2f &v1 = state.layout[v1_idx];
const Vec2f &v2 = state.layout[v2_idx];
Vec2f d;
d.diff(v2, v1);
r = d.lengthSqr();
if (r < 0.000000001f)
throw Error("too small edge");
layout.clear_resize(state.layout.size());
for (i = _graph.vertexBegin(); i < _graph.vertexEnd(); i = _graph.vertexNext(i))
{
if (!branch.valid(i))
{
const Vec2f &vi = state.layout[i];
t = ((vi.x - v1.x) * d.x + (vi.y - v1.y) * d.y) / r;
layout[i].set(2 * d.x * t + 2 * v1.x - vi.x, 2 * d.y * t + 2 * v1.y - vi.y);
} else
layout[i] = state.layout[i];
}
}
void Vec2f::rotateAroundSegmentEnd (const Vec2f &a, const Vec2f &b, float angle)
{
Vec2f c;
c.diff(a, b);
c.rotate(angle);
sum(b, c);
}
// Calculate position by adding one unit with given angle to the segment
void MoleculeLayoutGraph::_calculatePos (float phi, const Vec2f &v1, const Vec2f &v2, Vec2f &v)
{
float alpha;
Vec2f dir;
dir.diff(v2, v1);
alpha = dir.tiltAngle();
alpha += phi;
v.set(v1.x + cos(alpha), v1.y + sin(alpha));
}
RefinementState::RefinementState (MoleculeLayoutGraph &graph) :
dist(0.f),
energy(0),
height(0.f),
CP_INIT,
TL_CP_GET(layout),
_graph(graph)
{
}
void RefinementState::calcDistance (int v1, int v2)
{
Vec2f d;
d.diff(layout[v1], layout[v2]);
dist = d.lengthSqr();
}
void MoleculeLayout::_updateDataSGroups ()
{
// Move Data-SGroups with absolute coordinates according to new position
QS_DEF(Array<int>, layout_graph_mapping);
layout_graph_mapping.resize(_molecule.vertexEnd());
layout_graph_mapping.fffill();
for (int i = _layout_graph->vertexBegin(); i < _layout_graph->vertexEnd(); i = _layout_graph->vertexNext(i))
{
int vi = _layout_graph->getVertexExtIdx(i);
layout_graph_mapping[vi] = i;
}
for (int i = _molecule.sgroups.begin(); i != _molecule.sgroups.end(); i = _molecule.sgroups.next(i))
{
SGroup &sg = _molecule.sgroups.getSGroup(i);
if (sg.sgroup_type == SGroup::SG_TYPE_DAT)
{
DataSGroup &group = (DataSGroup &)sg;
if (!group.relative)
{
Vec2f before;
_molecule.getSGroupAtomsCenterPoint(group, before);
Vec2f after;
for (int j = 0; j < group.atoms.size(); j++)
{
int ai = group.atoms[j];
const LayoutVertex &vert = _layout_graph->getLayoutVertex(layout_graph_mapping[ai]);
after.x += vert.pos.x;
after.y += vert.pos.y;
}
if (group.atoms.size() != 0)
after.scale(1.0f / group.atoms.size());
Vec2f delta;
delta.diff(after, before);
group.display_pos.add(delta);
}
}
}
}
void RenderGrid::draw ()
{
_width = _cnvOpt.width;
_height = _cnvOpt.height;
_rc.fontsClear();
bool enableRefAtoms = refAtoms.size() > 0 && _factory.isItemMolecule(objs[0]);
if (enableRefAtoms && refAtoms.size() != objs.size())
throw Error("Number of reference atoms should be same as the number of objects");
bool enableTitles = titles.size() > 0;
if (enableTitles && titles.size() != objs.size())
throw Error("Number of titles should be same as the number of objects");
nRows = (objs.size() + nColumns - 1) / nColumns;
commentSize.set(0,0);
commentOffset = 0;
if (comment >= 0) {
_factory.getItem(comment).init();
_factory.getItem(comment).estimateSize();
commentSize.copy(_factory.getItem(comment).size);
commentOffset = _cnvOpt.commentOffset;
}
maxsz.set(0,0);
Vec2f refSizeLT, refSizeRB;
Array<float> columnExtentLeft, columnExtentRight, rowExtentTop, rowExtentBottom;
columnExtentLeft.clear_resize(nColumns);
columnExtentRight.clear_resize(nColumns);
columnExtentLeft.fill(0);
columnExtentRight.fill(0);
rowExtentTop.clear_resize(nRows);
rowExtentBottom.clear_resize(nRows);
rowExtentTop.fill(0);
rowExtentBottom.fill(0);
for (int i = 0; i < objs.size(); ++i) {
if (enableRefAtoms)
_factory.getItemMolecule(objs[i]).refAtom = refAtoms[i];
_factory.getItem(objs[i]).init();
_factory.getItem(objs[i]).setObjScale(_getObjScale(objs[i]));
_factory.getItem(objs[i]).estimateSize();
if (enableRefAtoms) {
const Vec2f& r = _factory.getItemMolecule(objs[i]).refAtomPos;
Vec2f d;
d.diff(_factory.getItemMolecule(objs[i]).size, r);
refSizeLT.max(r);
int col = i % nColumns;
int row = i / nColumns;
columnExtentLeft[col] = __max(columnExtentLeft[col], r.x);
columnExtentRight[col] = __max(columnExtentRight[col], d.x);
rowExtentTop[row] = __max(rowExtentTop[row], r.y);
rowExtentBottom[row] = __max(rowExtentBottom[row], d.y);
refSizeRB.max(d);
} else {
maxsz.max(_factory.getItem(objs[i]).size);
}
}
if (enableRefAtoms)
maxsz.sum(refSizeLT, refSizeRB);
maxTitleSize.set(0,0);
titleOffset = 0;
if (enableTitles) {
titleOffset = _cnvOpt.titleOffset;
for (int i = 0; i < titles.size(); ++i) {
_factory.getItem(titles[i]).init();
_factory.getItem(titles[i]).estimateSize();
maxTitleSize.max(_factory.getItem(titles[i]).size);
}
}
outerMargin.x = (float)(minMarg + _cnvOpt.marginX);
outerMargin.y = (float)(minMarg + _cnvOpt.marginY);
_width = __min(_width, _getMaxWidth());
_height = __min(_height, _getMaxHeight());
scale = _getScale(_width, _height);
if (_width < 1)
_width = _getDefaultWidth(scale);
if (_height < 1)
_height = _getDefaultHeight(scale);
_rc.initContext(_width, _height);
cellsz.set(__max(maxsz.x * scale, maxTitleSize.x),
maxsz.y * scale + maxTitleSize.y + titleOffset);
clientArea.set(cellsz.x * nColumns + _cnvOpt.gridMarginX * (nColumns - 1),
cellsz.y * nRows + _cnvOpt.gridMarginY * (nRows - 1));
_rc.init();
if (_cnvOpt.xOffset > 0 || _cnvOpt.yOffset > 0)
_rc.translate((float)_cnvOpt.xOffset, (float)_cnvOpt.yOffset);
_rc.translate(outerMargin.x, outerMargin.y);
if (_cnvOpt.commentPos == COMMENT_POS_TOP) {
_drawComment();
_rc.translate(0, (float)commentOffset);
}
_rc.storeTransform();
{
_rc.translate((_width - clientArea.x) / 2 - outerMargin.x, (_height - commentSize.y - commentOffset - clientArea.y) / 2 - outerMargin.y);
for (int i = 0; i < objs.size(); ++i) {
_rc.storeTransform();
{
int y = i / nColumns;
int x = i % nColumns;
Vec2f size(_factory.getItem(objs[i]).size);
_rc.translate(x * (cellsz.x + _cnvOpt.gridMarginX), y * (cellsz.y + _cnvOpt.gridMarginY));
_rc.storeTransform();
{
if (enableRefAtoms) {
_rc.translate(0.5f * (cellsz.x - (columnExtentRight[x] + columnExtentLeft[x]) * scale), 0.5f * (maxsz.y - (rowExtentBottom[y]+ rowExtentTop[y])) * scale);
const Vec2f r = _factory.getItemMolecule(objs[i]).refAtomPos;
_rc.translate((columnExtentLeft[x] - r.x) * scale, (rowExtentTop[y] - r.y) * scale);
} else {
_rc.translate(0.5f * (cellsz.x - size.x * scale), 0.5f * (maxsz.y - size.y) * scale);
}
_rc.scale(scale);
_factory.getItem(objs[i]).render();
}
_rc.restoreTransform();
_rc.removeStoredTransform();
_rc.translate(0, maxsz.y * scale + titleOffset);
if (enableTitles) {
Vec2f titleSize(_factory.getItem(titles[i]).size);
_rc.translate(_cnvOpt.titleAlign.getBboxRelativeOffset() * (cellsz.x - titleSize.x), 0.5f * (maxTitleSize.y - titleSize.y));
_factory.getItem(titles[i]).render();
}
}
_rc.restoreTransform();
_rc.removeStoredTransform();
}
}
_rc.restoreTransform();
_rc.removeStoredTransform();
if (_cnvOpt.commentPos == COMMENT_POS_BOTTOM) {
_rc.translate(0, _height - commentOffset - commentSize.y - 2*outerMargin.y);
_drawComment();
}
}