content: /*
  * 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;
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  * 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.
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  package com.actelion.research.gui.editor;
  
  import com.actelion.research.chem.ExtendedMolecule;
  import com.actelion.research.chem.Molecule;
  import com.actelion.research.gui.generic.*;
  import com.actelion.research.gui.hidpi.HiDPIHelper;
  
  public class BondQueryFeatureDialogBuilder implements GenericEventListener<GenericActionEvent> {
  	private GenericDialog       mDialog;
      private ExtendedMolecule	mMol;
  	private int					mBond,mFirstSpanItem;
  	private GenericCheckBox     mCBSingle,mCBDouble,mCBTriple,mCBQuadruple,mCBQuintuple,mCBDelocalized,
  								mCBMetalLigand,mCBIsBridge,mCBMatchFormalOrder,mCBMatchStereo;
  	private GenericComboBox     mComboBoxRing,mComboBoxRingSize,mComboBoxMinAtoms,mComboBoxMaxAtoms;
  	private boolean             mOKSelected;
  
  	public BondQueryFeatureDialogBuilder(GenericUIHelper dialogHelper, ExtendedMolecule mol, int bond) {
  		mDialog = dialogHelper.createDialog((mol.isSelectedAtom(mol.getBondAtom(0, bond))
  				&& mol.isSelectedAtom(mol.getBondAtom(1, bond))) ?
  				"Bond Query Features (Multiple)" : "Bond Query Features", this);
  		build(mol, bond);
  		}
  
  	/**
  	 * @return true if OK was pressed and potential change was applied to molecule
  	 */
  	public boolean showDialog() {
  		mOKSelected = false;
  		mDialog.showDialog();
  		return mOKSelected;
  		}
  
  	private void build(ExtendedMolecule mol, int bond) {
  		mMol = mol;
  		mBond = bond;
  
  		int gap = HiDPIHelper.scale(8);
  		int[] hLayout = {gap, GenericDialog.FILL, GenericDialog.PREFERRED, GenericDialog.PREFERRED, gap};
          int[] vLayout = {gap, GenericDialog.PREFERRED, gap, GenericDialog.PREFERRED, GenericDialog.PREFERRED,
  					        GenericDialog.PREFERRED, GenericDialog.PREFERRED,
  		                    GenericDialog.PREFERRED, GenericDialog.PREFERRED, GenericDialog.PREFERRED, gap,
  					        GenericDialog.PREFERRED, gap, GenericDialog.PREFERRED, gap, GenericDialog.PREFERRED, gap,
  		                    GenericDialog.PREFERRED, 2*gap,
  					        GenericDialog.PREFERRED, gap/2, GenericDialog.PREFERRED, gap/2, GenericDialog.PREFERRED, 2*gap};
          mDialog.setLayout(hLayout, vLayout);
  
  		mDialog.add(mDialog.createLabel("Desired Bond type(s):"), 1, 1, 3, 1);
  
  		mCBSingle = mDialog.createCheckBox("Single");
  		mDialog.add(mCBSingle,1,3,3,3);
  
  		mCBDouble = mDialog.createCheckBox("Double");
  		mDialog.add(mCBDouble,1,4,3,4);
  
  		mCBTriple = mDialog.createCheckBox("Triple");
  		mDialog.add(mCBTriple,1,5,3,5);
  
  		mCBQuadruple = mDialog.createCheckBox("Quadruple");
  		mDialog.add(mCBQuadruple,1,6,3,6);
  
  		mCBQuintuple = mDialog.createCheckBox("Quintuple");
  		mDialog.add(mCBQuintuple,1,7,3,7);
  
  		mCBDelocalized = mDialog.createCheckBox("Delocalized");
  		mDialog.add(mCBDelocalized,1,8,3,8);
  
  		mCBMetalLigand = mDialog.createCheckBox("Coordinate (0-order)");
  		mDialog.add(mCBMetalLigand,1,9,3,9);
  
  		mComboBoxRing = mDialog.createComboBox();
  		mComboBoxRing.addItem("any ring state");
  		mComboBoxRing.addItem("is not in a ring");
  		mComboBoxRing.addItem("is any ring bond");
  		mComboBoxRing.addItem("is non-aromatic ring bond");
  		mComboBoxRing.addItem("is aromatic bond");
  		mComboBoxRing.addItem("is any non-aromatic bond");
  		mComboBoxRing.addEventConsumer(this);
  		mDialog.add(mComboBoxRing,1,11,3,11);
  
  		mComboBoxRingSize = mDialog.createComboBox();
  		mComboBoxRingSize.addItem("any ring size");
  		mComboBoxRingSize.addItem("is in 3-membered ring");
  		mComboBoxRingSize.addItem("is in 4-membered ring");
  		mComboBoxRingSize.addItem("is in 5-membered ring");
  		mComboBoxRingSize.addItem("is in 6-membered ring");
  		mComboBoxRingSize.addItem("is in 7-membered ring");
  		mComboBoxRingSize.addItem("smallest ring 8 to 11");
  		mComboBoxRingSize.addItem("smallest ring >= 12");
  		mDialog.add(mComboBoxRingSize, 1,13,3,13);
  
  		mCBMatchFormalOrder = mDialog.createCheckBox("Match formal bond order");
  		mCBMatchFormalOrder.setSelected((mol.getBondQueryFeatures(bond) & Molecule.cBondQFMatchFormalOrder) != 0);
  		mCBMatchFormalOrder.addEventConsumer(this);
  		mDialog.add(mCBMatchFormalOrder, 1,15,3,15);
  
  		mCBMatchStereo = mDialog.createCheckBox("Match Stereo Configuration");
  		mCBMatchStereo.setSelected((mol.getBondQueryFeatures(bond) & Molecule.cBondQFMatchStereo) != 0);
  		mCBMatchStereo.addEventConsumer(this);
  		mDialog.add(mCBMatchStereo, 1,17,3,17);
  
  		mCBIsBridge = mDialog.createCheckBox("Is atom bridge between");
          mCBIsBridge.addEventConsumer(this);
  		mDialog.add(mCBIsBridge,1,19,3,19);
  
          mComboBoxMinAtoms = mDialog.createComboBox();
          int itemCount = (1 << Molecule.cBondQFBridgeMinBits);
          for (int i=0; i<itemCount; i++)
              mComboBoxMinAtoms.addItem(""+i);
  		mDialog.add(mComboBoxMinAtoms,2,21);
  		mDialog.add(mDialog.createLabel(" and"),3,21);
          mComboBoxMinAtoms.addEventConsumer(this);
  
          mComboBoxMaxAtoms = mDialog.createComboBox();
          populateComboBoxMaxAtoms(0);
  		mDialog.add(mComboBoxMaxAtoms,2,23);
  		mDialog.add(mDialog.createLabel(" atoms"),3,23);
  
          mMol.ensureHelperArrays(Molecule.cHelperRings);
          setInitialStates();
  		}
  
  	@Override
  	public void eventHappened(GenericActionEvent e) {
  		if (e.getWhat() == GenericActionEvent.WHAT_CANCEL) {
  			mDialog.disposeDialog();
  			}
  		else if (e.getWhat() == GenericActionEvent.WHAT_OK) {
  			setQueryFeatures();
  			mOKSelected = true;
  			mDialog.disposeDialog();
  			}
          else if (e.getSource() == mCBIsBridge || e.getSource() == mComboBoxRing) {
              enableItems();
              }
          else if (e.getSource() == mComboBoxMinAtoms) {
              int minAtoms = mComboBoxMinAtoms.getSelectedIndex();
              if (mFirstSpanItem != minAtoms)  {
                  int maxAtoms = mFirstSpanItem + mComboBoxMaxAtoms.getSelectedIndex();
                  int itemCount = populateComboBoxMaxAtoms(minAtoms);
                  if (maxAtoms < minAtoms)
                      mComboBoxMaxAtoms.setSelectedIndex(0);
                  else if (maxAtoms < minAtoms+itemCount)
                      mComboBoxMaxAtoms.setSelectedIndex(maxAtoms-minAtoms);
                  else
                      mComboBoxMaxAtoms.setSelectedIndex(itemCount-1);
  
                  mFirstSpanItem = minAtoms;
                  }
              }
  		}
  
  
  	private void setInitialStates() {
  		int queryFeatures = mMol.getBondQueryFeatures(mBond);
  		int bondOrder = (mMol.getBondType(mBond) == Molecule.cBondTypeDelocalized
  					  || mMol.isDelocalizedBond(mBond)) ?
  						6 : mMol.getBondOrder(mBond);
  
  		if ((queryFeatures & Molecule.cBondTypeSingle) != 0 || bondOrder == 1)
  			mCBSingle.setSelected(true);
  		if ((queryFeatures & Molecule.cBondTypeDouble) != 0 || bondOrder == 2)
  			mCBDouble.setSelected(true);
  		if ((queryFeatures & Molecule.cBondTypeTriple) != 0 || bondOrder == 3)
  			mCBTriple.setSelected(true);
  		if ((queryFeatures & Molecule.cBondTypeQuadruple) != 0 || bondOrder == 4)
  			mCBQuadruple.setSelected(true);
  		if ((queryFeatures & Molecule.cBondTypeQuintuple) != 0 || bondOrder == 5)
  			mCBQuintuple.setSelected(true);
  		if ((queryFeatures & Molecule.cBondTypeDelocalized) != 0 || bondOrder == 6)
  			mCBDelocalized.setSelected(true);
  		if ((queryFeatures & Molecule.cBondTypeMetalLigand) != 0 || bondOrder == 0)
  			mCBMetalLigand.setSelected(true);
  		if ((queryFeatures & Molecule.cBondQFMatchFormalOrder) != 0)
  			mCBMatchFormalOrder.setSelected(true);
  		if ((queryFeatures & Molecule.cBondQFMatchStereo) != 0)
  			mCBMatchStereo.setSelected(true);
  
  		int ringState = queryFeatures & Molecule.cBondQFRingState;
  		int aromState = queryFeatures & Molecule.cBondQFAromState;
  		if (ringState == Molecule.cBondQFNotRing)
  			mComboBoxRing.setSelectedIndex(1);
  		else if (aromState == Molecule.cBondQFAromatic)
  			mComboBoxRing.setSelectedIndex(4);
  		else if (ringState == Molecule.cBondQFRing)
  			mComboBoxRing.setSelectedIndex(aromState == 0 ? 2 : 3);
  		else
  			mComboBoxRing.setSelectedIndex(aromState == 0 ? 0 : 5);
  
  		int ringSize = (queryFeatures & Molecule.cBondQFRingSize) >> Molecule.cBondQFRingSizeShift;
  		mComboBoxRingSize.setSelectedIndex((ringSize == 0) ? 0 : (ringSize <= 2) ? ringSize+5 : ringSize-2);
  
          if ((queryFeatures & Molecule.cBondQFBridge) != 0) {
              mCBIsBridge.setSelected(true);
              int minAtoms = (queryFeatures & Molecule.cBondQFBridgeMin) >> Molecule.cBondQFBridgeMinShift;
              int atomSpan = (queryFeatures & Molecule.cBondQFBridgeSpan) >> Molecule.cBondQFBridgeSpanShift;
              mComboBoxMinAtoms.setSelectedIndex(minAtoms);
              populateComboBoxMaxAtoms(minAtoms);
              mComboBoxMaxAtoms.setSelectedIndex(atomSpan);
              }
          else
  	        mComboBoxMaxAtoms.setSelectedIndex(0);
  
          enableItems();
          }
  
  
      private int populateComboBoxMaxAtoms(int minAtoms) {
          mComboBoxMaxAtoms.removeAllItems();
          int itemCount = (1 << Molecule.cBondQFBridgeSpanBits);
          for (int i=0; i<itemCount; i++)
              mComboBoxMaxAtoms.addItem(""+(minAtoms+i));
          return itemCount;
          }
  
      private void enableItems() {
          boolean bridgeIsSelected = mCBIsBridge.isSelected();
          mCBSingle.setEnabled(!bridgeIsSelected);
          mCBDouble.setEnabled(!bridgeIsSelected);
          mCBTriple.setEnabled(!bridgeIsSelected);
  	    mCBQuadruple.setEnabled(!bridgeIsSelected);
  	    mCBQuintuple.setEnabled(!bridgeIsSelected);
          mCBDelocalized.setEnabled(!bridgeIsSelected);
  		mCBMetalLigand.setEnabled(!bridgeIsSelected);
          mCBMatchStereo.setEnabled(!bridgeIsSelected
          						&& mMol.getBondOrder(mBond) == 2	// exclude BINAP-type stereo bonds for now
          						&& mMol.getBondParity(mBond) != Molecule.cBondParityNone
          						&& mMol.getBondParity(mBond) != Molecule.cBondParityUnknown);
          mComboBoxRing.setEnabled(!bridgeIsSelected);
          mComboBoxRingSize.setEnabled(!bridgeIsSelected && mComboBoxRing.getSelectedIndex() != 1);
          mComboBoxMinAtoms.setEnabled(bridgeIsSelected);
          mComboBoxMaxAtoms.setEnabled(bridgeIsSelected);
          }
  
  
      private void setQueryFeatures() {
          if (isSelectedBond(mBond)) {
              for (int bond=0; bond<mMol.getAllBonds(); bond++)
                  if (isSelectedBond(bond))
                      setQueryFeatures(bond);
              }
          else {
              setQueryFeatures(mBond);
              }
  
  	    mMol.validateBondQueryFeatures();
          }
  
  
      private void setQueryFeatures(int bond) {
  		int queryFeatures = 0;
  
          if (mCBIsBridge.isSelected()) {
              int minAtoms = mComboBoxMinAtoms.getSelectedIndex();
              int atomSpan = mComboBoxMaxAtoms.getSelectedIndex();
              queryFeatures |= (minAtoms << Molecule.cBondQFBridgeMinShift);
              queryFeatures |= (atomSpan << Molecule.cBondQFBridgeSpanShift);
              queryFeatures &= ~Molecule.cBondQFAllBondTypes;
  			mMol.setBondType(bond, Molecule.cBondTypeSingle);
              }
          else {
  			if (mCBSingle.isSelected())
  				queryFeatures |= Molecule.cBondTypeSingle;
  			if (mCBDouble.isSelected())
  				queryFeatures |= Molecule.cBondTypeDouble;
  			if (mCBTriple.isSelected())
  				queryFeatures |= Molecule.cBondTypeTriple;
  			if (mCBQuadruple.isSelected())
  				queryFeatures |= Molecule.cBondTypeQuadruple;
  			if (mCBQuintuple.isSelected())
  				queryFeatures |= Molecule.cBondTypeQuintuple;
  			if (mCBDelocalized.isSelected())
  				queryFeatures |= Molecule.cBondTypeDelocalized;
  			if (mCBMetalLigand.isSelected())
  				queryFeatures |= Molecule.cBondTypeMetalLigand;
  
  			if (mComboBoxRing.getSelectedIndex() != 0) {
  				if (mComboBoxRing.getSelectedIndex() == 1) {
  					if (!mMol.isRingBond(bond))
  						queryFeatures |= Molecule.cBondQFNotRing;
  					}
  				else if (mComboBoxRing.getSelectedIndex() == 2) {
  					if (!mMol.isRingBond(bond))
  						queryFeatures |= Molecule.cBondQFRing;
  					}
  				else if (mComboBoxRing.getSelectedIndex() == 3) {
  					if (!mMol.isAromaticBond(bond))
  						queryFeatures |= Molecule.cBondQFNotAromatic | Molecule.cBondQFRing;
  					}
  				else if (mComboBoxRing.getSelectedIndex() == 4) {
  					if (!mMol.isAromaticBond(bond))
  						queryFeatures |= Molecule.cBondQFAromatic;
  					}
  				else if (mComboBoxRing.getSelectedIndex() == 5) {
  					if (!mMol.isAromaticBond(bond))
  						queryFeatures |= Molecule.cBondQFNotAromatic;
  					}
      			}
  
  			if (mComboBoxRingSize.getSelectedIndex() != 0) {
  				int ringSize = mComboBoxRingSize.getSelectedIndex() + 2;
  				if (ringSize > 7)	// ringsize 8-11 is encoded as 1; ringsize >12 is encoded as 2
  					ringSize -= 7;
  				int implicitSize = mMol.getBondRingSize(bond);
  				if (ringSize <= 2 || ringSize != implicitSize) {	// options 1 and 2 cover spans and cannot be implicit
  					queryFeatures |= (ringSize << Molecule.cBondQFRingSizeShift);
  					}
  				}
  
  			if (mCBMatchFormalOrder.isSelected())
  				queryFeatures |= Molecule.cBondQFMatchFormalOrder;
  			if (mCBMatchStereo.isSelected())
  				queryFeatures |= Molecule.cBondQFMatchStereo;
              }
  
  		mMol.setBondQueryFeature(bond, Molecule.cBondQFAllFeatures, false);
  		mMol.setBondQueryFeature(bond, queryFeatures, true);
  		mMol.adaptBondTypeToQueryFeatures(bond);
  		}
  
      private boolean isSelectedBond(int bond) {
          return mMol.isSelectedAtom(mMol.getBondAtom(0, bond))
              && mMol.isSelectedAtom(mMol.getBondAtom(1, bond));
          }
  	}
  