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Open Source Chemistry Library
/*
* Copyright (c) 1997 - 2016
* Actelion Pharmaceuticals Ltd.
* Gewerbestrasse 16
* CH-4123 Allschwil, Switzerland
*
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice, this
* list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
* 3. Neither the name of the the copyright holder nor the
* names of its contributors may be used to endorse or promote products
* derived from this software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
* ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*
*/
package com.actelion.research.gui;
import com.actelion.research.chem.*;
import com.actelion.research.chem.io.CompoundFileHelper;
import com.actelion.research.chem.io.RDFileParser;
import com.actelion.research.chem.io.RXNFileParser;
import com.actelion.research.chem.reaction.Reaction;
import com.actelion.research.gui.clipboard.ClipboardHandler;
import com.actelion.research.gui.dnd.MoleculeDropAdapter;
import com.actelion.research.gui.dnd.MoleculeTransferable;
import com.actelion.research.gui.dnd.ReactionDropAdapter;
import com.actelion.research.gui.dnd.ReactionTransferable;
import com.actelion.research.gui.hidpi.HiDPIHelper;
import com.actelion.research.util.ColorHelper;
import com.actelion.research.util.CursorHelper;
import javax.swing.*;
import java.awt.*;
import java.awt.datatransfer.Transferable;
import java.awt.dnd.*;
import java.awt.event.*;
import java.awt.geom.Rectangle2D;
import java.io.File;
import java.util.ArrayList;
public class JChemistryView extends JComponent
implements ActionListener, DragGestureListener, DragSourceListener, MouseListener, MouseMotionListener {
public static final int PASTE_AND_DROP_OPTION_ALLOW_FRAGMENT_STATE_CHANGE = 1;
public static final int PASTE_AND_DROP_OPTION_KEEP_ATOM_COLORS = 2;
public static final int PASTE_AND_DROP_OPTION_KEEP_BOND_HIGHLIGHTING = 4;
public static final int PASTE_AND_DROP_OPTION_REMOVE_CATALYSTS = 8;
public static final int PASTE_AND_DROP_OPTION_REMOVE_DRAWING_OBJECTS = 16;
public static final int PASTE_AND_DROP_OPTION_LAYOUT_REACTION = 32;
private static final String ITEM_COPY_RXN = "Copy Reaction";
private static final String ITEM_PASTE_RXN = "Paste Reaction";
private static final String ITEM_OPEN_RXN = "Open Reaction File...";
private static final String ITEM_SAVE_RXN = "Save Reaction File...";
private static final String ITEM_COPY_MOLS = "Copy Molecules";
private static final String ITEM_PASTE_MOLS = "Paste Molecules";
private static final long WARNING_MILLIS = 1200;
private static final long serialVersionUID = 20150204L;
private static final int UPDATE_REDRAW_ONLY = 0;
private static final int UPDATE_CHECK_COORDS = 1;
private static final int UPDATE_SCALE_COORDS = 2;
private static final int PASTE_AND_DROP_OPTIONS_DEFAULT = 0;
private static final int ALLOWED_DRAG_ACTIONS = DnDConstants.ACTION_COPY_OR_MOVE;
private static final int ALLOWED_DROP_ACTIONS = DnDConstants.ACTION_COPY_OR_MOVE;
private static final int DRAG_TYPE_NONE = -1;
private static final int DRAG_TYPE_REACTION = -2; // or molecule index >= 0
private ExtendedDepictor mDepictor;
private ArrayList mListener;
private Dimension mSize;
private int mChemistryType,mUpdateMode,mDisplayMode,mDragType,mCopyOrDragActions,mPasteOrDropActions,mPasteAndDropOptions;
private boolean mIsDragging,mAllowDropOrPasteWhenDisabled,mIsEditable,mShowBorder,mOpaqueBackground;
private Color mFragmentNoColor;
private MoleculeDropAdapter mMoleculeDropAdapter = null;
private ReactionDropAdapter mReactionDropAdapter = null;
private String mWarningMessage;
/**
* Creates a new JChemistryView for showing a reaction or molecules.
* A JChemistryView uses an ExtendedDepictor to handle multiple molecules or a reaction.
* For showing one molecule use a JStructureView.
* The default will support copy/paste and drag&drop from this view only,
* but dropping anything onto this view doesn't have an effect.
* Call setEditable(true) to allow changes through drag&drop and pasting.
* @param chemistryType one of ExtendedDepictor.TYPE_MOLECULES and ExtendedDepictor.TYPE_REACTION
*/
public JChemistryView(int chemistryType) {
this(chemistryType, ALLOWED_DRAG_ACTIONS, ALLOWED_DROP_ACTIONS);
}
/**
* Creates a new JChemistryView for showing a reaction or molecules.
* A JChemistryView uses an ExtendedDepictor to handle multiple molecules or a reaction.
* For showing one molecule use a JStructureView.
* The default will support copy/paste and drag&drop from this view only,
* but dropping anything onto this view doesn't have an effect.
* Call setEditable(true) to allow changes through drag&drop and pasting.
* @param chemistryType one of the ExtendedDepictor.TYPE_... options
* @param allowedCopyOrDragActions DnDConstants.ACTION_xxx
* @param allowedPasteOrDropActions DnDConstants.ACTION_xxx
*/
public JChemistryView(int chemistryType, int allowedCopyOrDragActions, int allowedPasteOrDropActions) {
mChemistryType = chemistryType;
mCopyOrDragActions = allowedCopyOrDragActions;
mPasteOrDropActions = allowedPasteOrDropActions;
mPasteAndDropOptions = PASTE_AND_DROP_OPTIONS_DEFAULT;
initializeDragAndDrop();
addMouseListener(this);
addMouseMotionListener(this);
mDragType = DRAG_TYPE_NONE;
mIsEditable = false;
}
public int getChemistryType() {
return mChemistryType;
}
public void setContent(StereoMolecule mol) {
setContent(mol, null);
}
public void setContent(StereoMolecule mol[]) {
setContent(mol, null);
}
public void setContent(Reaction rxn) {
setContent(rxn, null);
}
public void setContent(StereoMolecule mol, DrawingObjectList drawingObjectList) {
mDepictor = new ExtendedDepictor(mol, drawingObjectList, true);
mDepictor.setDisplayMode(mDisplayMode);
mDepictor.setFragmentNoColor(mFragmentNoColor);
mUpdateMode = UPDATE_SCALE_COORDS;
mDragType = DRAG_TYPE_NONE;
repaint();
}
public void setContent(StereoMolecule[] mol, DrawingObjectList drawingObjectList) {
mDepictor = new ExtendedDepictor(mol, drawingObjectList, true);
mDepictor.setDisplayMode(mDisplayMode);
mDepictor.setFragmentNoColor(mFragmentNoColor);
mUpdateMode = UPDATE_SCALE_COORDS;
mDragType = DRAG_TYPE_NONE;
repaint();
}
public void setContent(Reaction rxn, DrawingObjectList drawingObjectList) {
mDepictor = new ExtendedDepictor(rxn, drawingObjectList, rxn == null ? false : rxn.isReactionLayoutRequired(), true);
mDepictor.setDisplayMode(mDisplayMode);
mDepictor.setFragmentNoColor(mFragmentNoColor);
mUpdateMode = UPDATE_SCALE_COORDS;
mDragType = DRAG_TYPE_NONE;
repaint();
}
public void setOpaqueBackground(boolean b) {
mOpaqueBackground = b;
}
/**
* fragment status change on drop is allowed then dropping a fragment (molecule)
* on a molecule (fragment) inverts the status of the view's chemical object.
* As default status changes are prohibited.
* @param options flag list of PASTE_AND_DROP_OPTION...
*/
public void setPasteAndDropOptions(int options) {
mPasteAndDropOptions = options;
}
public void setAllowDropOrPasteWhenDisabled(boolean b) {
mAllowDropOrPasteWhenDisabled = b;
}
@Override
public void setEnabled(boolean enable) {
boolean changed = (enable != isEnabled());
super.setEnabled(enable);
if (changed) {
if (mMoleculeDropAdapter != null)
mMoleculeDropAdapter.setActive(enable);
if (mReactionDropAdapter != null)
mReactionDropAdapter.setActive(enable);
if (enable)
mDepictor.setOverruleColor(null, null);
else
mDepictor.setOverruleColor(ColorHelper.getContrastColor(Color.GRAY, getBackground()), getBackground());
repaint();
}
}
public boolean isEditable() {
return mIsEditable;
}
public void setEditable(boolean b) {
if (mIsEditable != b)
mIsEditable = b;
}
public void setFragmentNoColor(Color c) {
// use setFragmentNoColor(null) if you don't want fragment numbers to be shown
mFragmentNoColor = c;
if (mDepictor != null)
mDepictor.setFragmentNoColor(c);
}
public void setDisplayMode(int displayMode) {
mDisplayMode = displayMode;
if (mDepictor != null)
mDepictor.setDisplayMode(displayMode);
}
public void paintComponent(Graphics g) {
super.paintComponent(g);
if (mDepictor == null)
return;
Dimension theSize = getSize();
if (theSize.width == 0 || theSize.height == 0)
return;
Insets insets = getInsets();
theSize.width -= insets.left + insets.right;
theSize.height -= insets.top + insets.bottom;
if (mSize == null
|| mSize.width != theSize.width
|| mSize.height != theSize.height
|| mUpdateMode == UPDATE_SCALE_COORDS) {
mDepictor.validateView(g, new Rectangle2D.Double(insets.left, insets.top, theSize.width, theSize.height),
AbstractDepictor.cModeInflateToMaxAVBL);
}
else if (mUpdateMode == UPDATE_CHECK_COORDS) {
mDepictor.validateView(g, new Rectangle2D.Double(insets.left, insets.top, theSize.width, theSize.height), 0);
}
mSize = theSize;
Graphics2D g2 = (Graphics2D)g;
g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
g2.setRenderingHint(RenderingHints.KEY_STROKE_CONTROL, RenderingHints.VALUE_STROKE_PURE);
g2.setRenderingHint(RenderingHints.KEY_FRACTIONALMETRICS, RenderingHints.VALUE_FRACTIONALMETRICS_ON);
Color fg = g2.getColor();
g2.setColor(UIManager.getColor(isEditable() && isEnabled() ? "TextField.background" : "TextField.inactiveBackground"));
g2.fill(new Rectangle(insets.left, insets.top, theSize.width, theSize.height));
g2.setColor(fg);
mDepictor.setForegroundColor(getForeground(), getBackground());
if (mShowBorder && mDragType != DRAG_TYPE_NONE) {
Color bg = getBackground();
Color color = ColorHelper.perceivedBrightness(bg) < 0.5f ? bg.brighter() : bg.darker();
g.setColor(color);
Rectangle2D.Double rect = (mDragType == DRAG_TYPE_REACTION) ? getChemistryBounds() : getMoleculeBounds(mDragType);
Stroke oldStroke = ((Graphics2D)g).getStroke();
((Graphics2D)g).setStroke(new BasicStroke(HiDPIHelper.scale(2), BasicStroke.CAP_ROUND, BasicStroke.JOIN_ROUND));
int arc = (int)Math.min(rect.height/4, Math.min(rect.width/4, HiDPIHelper.scale(10)));
g.drawRoundRect((int)rect.x, (int)rect.y, (int)rect.width, (int)rect.height, arc, arc);
((Graphics2D)g).setStroke(oldStroke);
if (mDragType == DRAG_TYPE_REACTION) {
final String msg = "";
int fontSize = HiDPIHelper.scale(7);
g.setFont(getFont().deriveFont((float)fontSize));
int msgWidth = g.getFontMetrics().stringWidth(msg);
int x = (int)(rect.x+(rect.width-msgWidth)/2);
int y = (int)(rect.y+rect.height-fontSize/2);
g.drawString(msg, x, y);
}
}
mDepictor.paint(g);
if (mWarningMessage != null) {
int fontSize = HiDPIHelper.scale(12);
g.setFont(getFont().deriveFont(Font.BOLD, (float)fontSize));
Color original = g.getColor();
g.setColor(Color.RED);
FontMetrics metrics = g.getFontMetrics();
Rectangle2D bounds = metrics.getStringBounds(mWarningMessage, g);
g.drawString(mWarningMessage, insets.left+(int)(theSize.width-bounds.getWidth())/2,
insets.top+metrics.getHeight());
g.setColor(original);
}
mUpdateMode = UPDATE_REDRAW_ONLY;
}
/**
* Returns the bounding rectangle of the indicated molecule,
* if multiple molecules are shown, e.g. of a reaction.
* @param i
* @return bounds or null, if i is out of range
*/
public Rectangle2D.Double getMoleculeBounds(int i) {
return mDepictor == null || i >= mDepictor.getMoleculeCount() ?
null : mDepictor.getMoleculeDepictor(i).getBoundingRect();
}
public Rectangle2D.Double getChemistryBounds() {
if (mDepictor == null || mDepictor.getMoleculeCount() == 0)
return null;
Rectangle2D.Double rect = null;
for (int i=0; i();
mListener.add(l);
}
public void removeStructureListener(StructureListener l) {
if(mListener != null)
mListener.remove(l);
}
public void informListeners() {
if (mListener != null)
for (StructureListener l:mListener)
l.structureChanged(null);
}
public boolean canDrop() {
return isEditable() && (isEnabled() || mAllowDropOrPasteWhenDisabled) && !mIsDragging;
}
private void initializeDragAndDrop() {
if (mCopyOrDragActions != DnDConstants.ACTION_NONE)
DragSource.getDefaultDragSource().createDefaultDragGestureRecognizer(this, mCopyOrDragActions, this);
if(mPasteOrDropActions != DnDConstants.ACTION_NONE) {
if (mChemistryType == ExtendedDepictor.TYPE_MOLECULES) {
mMoleculeDropAdapter = new MoleculeDropAdapter() {
public void onDropMolecule(StereoMolecule m,Point pt) {
if (m != null && canDrop()) {
pasteOrDropMolecule(m);
onDrop();
}
updateBorder(false);
}
public void dragEnter(DropTargetDragEvent e) {
boolean drop = canDrop() && isDropOK(e) ;
if (!drop)
e.rejectDrag();
// updateBorder(drop);
}
public void dragExit(DropTargetEvent e) {
// updateBorder(false);
}
};
new DropTarget(this, mPasteOrDropActions, mMoleculeDropAdapter, true);
// new DropTarget(this,mAllowedDropAction,mDropAdapter,true, getSystemFlavorMap());
}
if (mChemistryType == ExtendedDepictor.TYPE_REACTION) {
mReactionDropAdapter = new ReactionDropAdapter() {
public void onDropReaction(Reaction r, Point pt) {
if (r != null && canDrop()) {
pasteOrDropReaction(r);
onDrop();
}
updateBorder(false);
}
public void dragEnter(DropTargetDragEvent e) {
boolean drop = canDrop() && isDropOK(e) ;
if (!drop)
e.rejectDrag();
// updateBorder(drop);
}
public void dragExit(DropTargetEvent e) {
// updateBorder(false);
}
};
new DropTarget(this, mPasteOrDropActions, mReactionDropAdapter, true);
// new DropTarget(this,mAllowedDropAction,mDropAdapter,true, getSystemFlavorMap());
}
}
}
private void pasteOrDropMolecule(StereoMolecule m) {
StereoMolecule mol = new StereoMolecule(m);
if ((mPasteAndDropOptions & PASTE_AND_DROP_OPTION_KEEP_ATOM_COLORS) == 0)
mol.removeAtomColors();
if ((mPasteAndDropOptions & PASTE_AND_DROP_OPTION_KEEP_BOND_HIGHLIGHTING) == 0)
mol.removeBondHiliting();
if ((mPasteAndDropOptions & PASTE_AND_DROP_OPTION_ALLOW_FRAGMENT_STATE_CHANGE) == 0 && mDepictor != null)
mol.setFragment(mDepictor.isFragment());
setContent(mol);
repaint();
informListeners();
}
private void pasteOrDropReaction(Reaction r) {
Reaction rxn = new Reaction(r);
if ((mPasteAndDropOptions & PASTE_AND_DROP_OPTION_KEEP_ATOM_COLORS) == 0)
for (int m=0; m {
try { Thread.sleep(WARNING_MILLIS); } catch (InterruptedException ie) {}
mWarningMessage = null;
repaint();
} ).start();
}
public Transferable getMoleculeTransferable() {
StereoMolecule mol = (mDragType < 0) ? null : mDepictor.getMolecule(mDragType).getCompactCopy();
return new MoleculeTransferable(mol);
}
public Transferable getReactionTransferable() {
return new ReactionTransferable(mDepictor.getReaction());
}
public void dragEnter(DragSourceDragEvent e) {
DragSourceContext context = e.getDragSourceContext();
int dropAction = e.getDropAction();
if ((dropAction & ALLOWED_DRAG_ACTIONS) != 0) {
context.setCursor(DragSource.DefaultCopyDrop);
}
else {
context.setCursor(DragSource.DefaultCopyNoDrop);
}
}
public void dragOver(DragSourceDragEvent e) {}
public void dragExit(DragSourceEvent e) {}
public void dragDropEnd(DragSourceDropEvent e) {
System.out.println("dragDropEnd()");
mIsDragging = false;
mDragType = DRAG_TYPE_NONE;
repaint();
}
public void dropActionChanged(DragSourceDragEvent e) {
DragSourceContext context = e.getDragSourceContext();
int dropAction = e.getDropAction();
if ((dropAction & ALLOWED_DRAG_ACTIONS) != 0) {
context.setCursor(DragSource.DefaultCopyDrop);
}
else {
context.setCursor(DragSource.DefaultCopyNoDrop);
}
}
public void dragGestureRecognized(DragGestureEvent e) {
if((e.getDragAction() & ALLOWED_DRAG_ACTIONS) != 0 && mDragType != DRAG_TYPE_NONE) {
Transferable transferable = (mDragType == DRAG_TYPE_REACTION) ?
getReactionTransferable() : getMoleculeTransferable();
if (transferable != null) {
try {
e.startDrag(CursorHelper.getCursor(CursorHelper.cFistCursor), transferable, this);
mIsDragging = true;
// e.startDrag(DragSource.DefaultCopyNoDrop, transferable, this);
}
catch (InvalidDnDOperationException idoe) {
System.err.println(idoe);
}
}
}
}
// Drag notifications if needed by subclasses
protected void onDragEnter() {}
protected void onDragExit() {}
protected void onDragOver() {}
protected void onDrop() {}
}
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