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WIP: Support for undo/redo apply colors #1242

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40b06c2
Initial merge-able undo / redo support for colors
ghutchis Jul 26, 2022
d1cf316
Merge branch 'master' into undo-colors
ghutchis Apr 11, 2023
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55 changes: 25 additions & 30 deletions avogadro/qtgui/rwmolecule.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -23,8 +23,10 @@ using Core::CrystalTools;
using Core::UnitCell;
using std::swap;

RWMolecule::RWMolecule(Molecule& mol, QObject* p) : QObject(p), m_molecule(mol), m_interactive(false)
{}
RWMolecule::RWMolecule(Molecule& mol, QObject* p)
: QObject(p), m_molecule(mol), m_interactive(false)
{
}

RWMolecule::~RWMolecule() {}

Expand All @@ -33,8 +35,7 @@ RWMolecule::AtomType RWMolecule::addAtom(unsigned char num, bool usingPositions)
auto atomId = static_cast<Index>(m_molecule.atomCount());
auto atomUid = static_cast<Index>(m_molecule.m_atomUniqueIds.size());

auto* comm =
new AddAtomCommand(*this, num, usingPositions, atomId, atomUid);
auto* comm = new AddAtomCommand(*this, num, usingPositions, atomId, atomUid);
comm->setText(tr("Add Atom"));
m_undoStack.push(comm);
return AtomType(this, atomId);
Expand Down Expand Up @@ -149,8 +150,8 @@ bool RWMolecule::setAtomicNumber(Index atomId, unsigned char num)
if (atomId >= atomCount())
return false;

auto* comm = new SetAtomicNumberCommand(
*this, atomId, m_molecule.atomicNumber(atomId), num);
auto* comm = new SetAtomicNumberCommand(*this, atomId,
m_molecule.atomicNumber(atomId), num);
comm->setText(tr("Change Element"));
m_undoStack.push(comm);
return true;
Expand All @@ -162,8 +163,7 @@ bool RWMolecule::setAtomPositions3d(const Core::Array<Vector3>& pos,
if (pos.size() != m_molecule.atomCount())
return false;

auto* comm =
new SetPositions3dCommand(*this, m_molecule.m_positions3d, pos);
auto* comm = new SetPositions3dCommand(*this, m_molecule.m_positions3d, pos);
comm->setText(undoText);
comm->setCanMerge(m_interactive);
m_undoStack.push(comm);
Expand All @@ -188,21 +188,21 @@ bool RWMolecule::setAtomPosition3d(Index atomId, const Vector3& pos,
if (m_molecule.m_positions3d.size() != m_molecule.atomCount())
m_molecule.m_positions3d.resize(m_molecule.atomCount(), Vector3::Zero());

auto* comm = new SetPosition3dCommand(
*this, atomId, m_molecule.m_positions3d[atomId], pos);
auto* comm = new SetPosition3dCommand(*this, atomId,
m_molecule.m_positions3d[atomId], pos);
comm->setText(undoText);
comm->setCanMerge(m_interactive);
m_undoStack.push(comm);
return true;
}

void RWMolecule::setAtomSelected(Index atomId, bool selected, const QString& undoText)
void RWMolecule::setAtomSelected(Index atomId, bool selected,
const QString& undoText)
{
auto* comm = new ModifySelectionCommand(*this, atomId, selected);
auto* comm = new SetSelectionCommand(*this, atomId, selected);
comm->setText(undoText);
comm->setCanMerge(true);
m_undoStack.push(comm);
// m_molecule.setAtomSelected(atomId, selected);
}

bool RWMolecule::atomSelected(Index atomId) const
Expand Down Expand Up @@ -234,14 +234,15 @@ bool RWMolecule::setFormalCharge(Index atomId, signed char charge)
return true;
}

bool RWMolecule::setColor(Index atomId, Vector3ub color)
bool RWMolecule::setColor(Index atomId, Vector3ub color,
const QString& undoText)
{
if (atomId >= atomCount())
return false;

auto* comm =
new SetAtomColorCommand(*this, atomId, m_molecule.color(atomId), color);
comm->setText(tr("Change Atom Color"));
auto* comm = new SetAtomColorCommand(*this, atomId, color);
comm->setText(undoText);
comm->setCanMerge(true);
m_undoStack.push(comm);
return true;
}
Expand Down Expand Up @@ -315,8 +316,7 @@ bool RWMolecule::setBondOrders(const Core::Array<unsigned char>& orders)
if (orders.size() != m_molecule.bondCount())
return false;

auto* comm =
new SetBondOrdersCommand(*this, m_molecule.bondOrders(), orders);
auto* comm = new SetBondOrdersCommand(*this, m_molecule.bondOrders(), orders);
comm->setText(tr("Set Bond Orders"));
m_undoStack.push(comm);
return true;
Expand Down Expand Up @@ -350,8 +350,7 @@ bool RWMolecule::setBondPairs(const Array<std::pair<Index, Index>>& pairs)
if (p_const[i].first > p_const[i].second)
swap(p[i].first, p[i].second);

auto* comm =
new SetBondPairsCommand(*this, m_molecule.bondPairs(), p);
auto* comm = new SetBondPairsCommand(*this, m_molecule.bondPairs(), p);
comm->setText(tr("Update Bonds"));
m_undoStack.push(comm);
return true;
Expand Down Expand Up @@ -389,8 +388,7 @@ void RWMolecule::addUnitCell()
static_cast<Real>(90.0) * DEG_TO_RAD);
m_molecule.setUnitCell(cell);

auto* comm =
new AddUnitCellCommand(*this, *m_molecule.unitCell());
auto* comm = new AddUnitCellCommand(*this, *m_molecule.unitCell());
comm->setText(tr("Add Unit Cell"));
m_undoStack.push(comm);
emitChanged(Molecule::UnitCell | Molecule::Added);
Expand All @@ -402,8 +400,7 @@ void RWMolecule::removeUnitCell()
if (!m_molecule.unitCell())
return;

auto* comm =
new RemoveUnitCellCommand(*this, *m_molecule.unitCell());
auto* comm = new RemoveUnitCellCommand(*this, *m_molecule.unitCell());
comm->setText(tr("Remove Unit Cell"));
m_undoStack.push(comm);

Expand All @@ -415,8 +412,7 @@ void RWMolecule::modifyMolecule(const Molecule& newMolecule,
Molecule::MoleculeChanges changes,
const QString& undoText)
{
auto* comm =
new ModifyMoleculeCommand(*this, m_molecule, newMolecule);
auto* comm = new ModifyMoleculeCommand(*this, m_molecule, newMolecule);

comm->setText(undoText);
m_undoStack.push(comm);
Expand Down Expand Up @@ -484,8 +480,7 @@ void RWMolecule::wrapAtomsToCell()
CrystalTools::wrapAtomsToUnitCell(m_molecule);
Core::Array<Vector3> newPos = m_molecule.atomPositions3d();

auto* comm =
new SetPositions3dCommand(*this, oldPos, newPos);
auto* comm = new SetPositions3dCommand(*this, oldPos, newPos);
comm->setText(tr("Wrap Atoms to Cell"));
m_undoStack.push(comm);

Expand Down Expand Up @@ -727,4 +722,4 @@ bool RWMolecule::setForceVector(Index atomId, const Vector3& forces,
return true;
}

} // namespace Avogadro
} // namespace Avogadro::QtGui
3 changes: 2 additions & 1 deletion avogadro/qtgui/rwmolecule.h
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Original file line number Diff line number Diff line change
Expand Up @@ -293,7 +293,8 @@ class AVOGADROQTGUI_EXPORT RWMolecule : public QObject
* @param color The new color.
* @return True on success, false otherwise.
*/
bool setColor(Index atomId, Vector3ub color);
bool setColor(Index atomId, Vector3ub color,
const QString& undoText = tr("Change Atom Color"));

bool setLayer(Index atomId, size_t layer);
size_t layer(Index atomId) const;
Expand Down
87 changes: 25 additions & 62 deletions avogadro/qtgui/rwmolecule_undo.h
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Original file line number Diff line number Diff line change
Expand Up @@ -48,8 +48,8 @@ enum MergeIds
SetPosition3dMergeId,
SetForceVectorMergeId,
SetBondOrderMergeId,
ModifySelectionMergeId,
ModifyColorsMergeId
SetSelectionMergeId,
SetColorMergeId
};

// Base class for undo commands that can be merged together, overriding the
Expand Down Expand Up @@ -348,25 +348,6 @@ class SetAtomFormalChargeCommand : public RWMolecule::UndoCommand
} // namespace

namespace {
class SetAtomColorCommand : public RWMolecule::UndoCommand
{
Index m_atomId;
Vector3ub m_oldColor;
Vector3ub m_newColor;

public:
SetAtomColorCommand(RWMolecule& m, Index atomId, Vector3ub oldColor,
Vector3ub newColor)
: UndoCommand(m), m_atomId(atomId), m_oldColor(oldColor),
m_newColor(newColor)
{
}

void redo() override { m_molecule.setColor(m_atomId, m_newColor); }

void undo() override { m_molecule.setColor(m_atomId, m_oldColor); }
};

class SetLayerCommand : public RWMolecule::UndoCommand
{
Index m_atomId;
Expand Down Expand Up @@ -687,14 +668,14 @@ class ModifyLabelCommand : public RWMolecule::UndoCommand
} // namespace

namespace {
class ModifySelectionCommand : public MergeUndoCommand<ModifySelectionMergeId>
class SetSelectionCommand : public MergeUndoCommand<SetSelectionMergeId>
{
std::vector<bool> m_newSelectedAtoms;
std::vector<bool> m_oldSelectedAtoms;

public:
ModifySelectionCommand(RWMolecule& m, Index atomId, bool selected)
: MergeUndoCommand<ModifySelectionMergeId>(m)
SetSelectionCommand(RWMolecule& m, Index atomId, bool selected)
: MergeUndoCommand<SetSelectionMergeId>(m)
{
Index atomCount = m_mol.molecule().atomCount();
m_oldSelectedAtoms.resize(atomCount);
Expand Down Expand Up @@ -724,8 +705,8 @@ class ModifySelectionCommand : public MergeUndoCommand<ModifySelectionMergeId>

bool mergeWith(const QUndoCommand* other) override
{
const ModifySelectionCommand* o =
dynamic_cast<const ModifySelectionCommand*>(other);
const SetSelectionCommand* o =
dynamic_cast<const SetSelectionCommand*>(other);
if (!o)
return false;

Expand All @@ -743,66 +724,48 @@ class ModifySelectionCommand : public MergeUndoCommand<ModifySelectionMergeId>
};
} // namespace

/*
namespace {
class ModifyColorCommand : public MergeUndoCommand<ModifyColorMergeId>
class SetAtomColorCommand : public MergeUndoCommand<SetColorMergeId>
{
Array<Vector3ub> m_newSelectedAtoms;
Array<Vector3ub> m_oldSelectedAtoms;
Array<Vector3ub> m_oldColors;
Array<Vector3ub> m_newColors;

public:
ModifySelectionCommand(RWMolecule& m, Index atomId, bool selected)
: MergeUndoCommand<ModifySelectionMergeId>(m)
SetAtomColorCommand(RWMolecule& m, Index atomId, Vector3ub newColor)
: MergeUndoCommand<SetColorMergeId>(m)
{
Index atomCount = m_mol.molecule().atomCount();
m_oldSelectedAtoms.reserve(atomCount);
m_newSelectedAtoms.reserve(atomCount);
m_oldColors.resize(m_molecule.atomCount());
m_newColors.resize(m_molecule.atomCount());

for (Index i = 0; i < atomCount; ++i) {
m_oldSelectedAtoms[i] = m_molecule.atomSelected(i);
m_newSelectedAtoms[i] = m_molecule.atomSelected(i);
}
m_oldColors = m_mol.molecule().colors();

m_newSelectedAtoms[atomId] = selected;
m_newColors = m_mol.molecule().colors();
m_newColors[atomId] = newColor;
}

void redo() override
{
Index atomCount = m_mol.molecule().atomCount();
for (Index i = 0; i < atomCount; ++i)
m_mol.molecule().setAtomSelected(i, m_newSelectedAtoms[i]);
}
void redo() override { m_mol.molecule().setColors(m_newColors); }

void undo() override
{
Index atomCount = m_mol.molecule().atomCount();
for (Index i = 0; i < atomCount; ++i)
m_mol.molecule().setAtomSelected(i, m_oldSelectedAtoms[i]);
}
void undo() override { m_mol.molecule().setColors(m_oldColors); }

bool mergeWith(const QUndoCommand* other) override
{
const ModifySelectionCommand* o =
dynamic_cast<const ModifySelectionCommand*>(other);
const SetAtomColorCommand* o =
dynamic_cast<const SetAtomColorCommand*>(other);
if (o) {
// check if the atom count matches
Index numAtoms = m_oldSelectedAtoms.size();
if (numAtoms != o->m_oldSelectedAtoms.size() ||
numAtoms != o->m_newSelectedAtoms.size()) {
Index numAtoms = m_oldColors.size();
if (numAtoms != o->m_oldColors.size() ||
numAtoms != o->m_newColors.size()) {
return false;
}

// merge these, by grabbing the new selected atoms
for (Index i = 0; i < numAtoms; ++i)
m_newSelectedAtoms[i] = o->m_newSelectedAtoms[i];

m_newColors = o->m_newColors;
return true;
}
return false;
}
};
} // namespace
*/

} // namespace QtGui
} // namespace Avogadro
Expand Down
20 changes: 12 additions & 8 deletions avogadro/qtplugins/applycolors/applycolors.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,7 @@
#include <avogadro/core/residue.h>
#include <avogadro/core/residuecolors.h>
#include <avogadro/qtgui/molecule.h>
#include <avogadro/qtgui/rwmolecule.h>

#include <QtCore/QDebug>
#include <QtCore/QStringList>
Expand Down Expand Up @@ -229,7 +230,8 @@ void ApplyColors::applyIndexColors()

float indexFraction = float(i) / float(numAtoms);

m_molecule->atom(i).setColor(rainbowGradient(indexFraction, type));
m_molecule->undoMolecule()->setColor(
i, rainbowGradient(indexFraction, type), tr("Index Color"));
}

m_molecule->emitChanged(QtGui::Molecule::Atoms);
Expand All @@ -250,14 +252,14 @@ void ApplyColors::applyChargeColors()

// populate the dialog to choose the model and colormap
ChargeColorDialog dialog;
for (const auto &model : identifiers) {
for (const auto& model : identifiers) {
auto name = Calc::ChargeManager::instance().nameForModel(model);
dialog.modelCombo->addItem(name.c_str(), model.c_str());
}
dialog.exec();
if (dialog.result() != QDialog::Accepted)
return;

// get the model and colormap
const auto model = dialog.modelCombo->currentData().toString().toStdString();
const auto colormapName = dialog.colorMapCombo->currentText();
Expand All @@ -282,7 +284,8 @@ void ApplyColors::applyChargeColors()
if (isSelection && !m_molecule->atomSelected(i))
continue;

m_molecule->atom(i).setColor(chargeGradient(charges(i, 0), clamp, type));
m_molecule->undoMolecule()->setColor(
i, chargeGradient(charges(i, 0), clamp, type), tr("Charge Color"));
}

m_molecule->emitChanged(QtGui::Molecule::Atoms);
Expand Down Expand Up @@ -325,7 +328,8 @@ void ApplyColors::applyDistanceColors()
Real distance = diff.norm();
Real distanceFraction = distance / size;

m_molecule->atom(i).setColor(rainbowGradient(distanceFraction, type));
m_molecule->undoMolecule()->setColor(
i, rainbowGradient(distanceFraction, type), tr("Distance Color"));
}

m_molecule->emitChanged(QtGui::Molecule::Atoms);
Expand All @@ -344,7 +348,7 @@ void ApplyColors::resetColors()
continue;

Vector3ub color(Core::Elements::color(m_molecule->atomicNumber(i)));
m_molecule->atom(i).setColor(color);
m_molecule->undoMolecule()->setColor(i, color, tr("Reset Color"));
}

m_molecule->emitChanged(QtGui::Molecule::Atoms);
Expand All @@ -367,7 +371,7 @@ void ApplyColors::applyCustomColor(const QColor& new_color)
if (isSelection && !m_molecule->atomSelected(i))
continue;

m_molecule->atom(i).setColor(color);
m_molecule->undoMolecule()->setColor(i, color, tr("Custom Color"));
}

m_molecule->emitChanged(QtGui::Molecule::Atoms);
Expand Down Expand Up @@ -570,4 +574,4 @@ void ApplyColors::applyShapelyColors()
m_molecule->emitChanged(QtGui::Molecule::Atoms);
}

} // namespace Avogadro
} // namespace Avogadro::QtPlugins