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[Cdk-commits] SF.net SVN: cdk:[12709] cdk/branches/egonw-jchempaint/src/main/org/ openscience/cdk/renderer
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From: <eg...@us...> - 2008-10-15 11:56:56
|
Revision: 12709
http://cdk.svn.sourceforge.net/cdk/?rev=12709&view=rev
Author: egonw
Date: 2008-10-15 11:56:46 +0000 (Wed, 15 Oct 2008)
Log Message:
-----------
Java2DRenderer is currently the only renderer, and labeled it basic ('molecule' might be a better name
Modified Paths:
--------------
cdk/branches/egonw-jchempaint/src/main/org/openscience/cdk/renderer/ISimpleRenderer2D.java
cdk/branches/egonw-jchempaint/src/main/org/openscience/cdk/renderer/Renderer2DModel.java
Added Paths:
-----------
cdk/branches/egonw-jchempaint/src/main/org/openscience/cdk/renderer/basic/
cdk/branches/egonw-jchempaint/src/main/org/openscience/cdk/renderer/basic/Java2DRenderer.java
Removed Paths:
-------------
cdk/branches/egonw-jchempaint/src/main/org/openscience/cdk/renderer/Java2DRenderer.java
Modified: cdk/branches/egonw-jchempaint/src/main/org/openscience/cdk/renderer/ISimpleRenderer2D.java
===================================================================
--- cdk/branches/egonw-jchempaint/src/main/org/openscience/cdk/renderer/ISimpleRenderer2D.java 2008-10-15 11:56:09 UTC (rev 12708)
+++ cdk/branches/egonw-jchempaint/src/main/org/openscience/cdk/renderer/ISimpleRenderer2D.java 2008-10-15 11:56:46 UTC (rev 12709)
@@ -65,13 +65,13 @@
*
* @param model Model with rendering settings
*/
- public abstract void setRenderer2DModel(Renderer2DModel model);
+ public abstract void setRenderer2DModel(IRenderingParameters model);
/**
* The current rendering settings.
*
* @return Model with rendering settings
*/
- public abstract Renderer2DModel getRenderer2DModel();
+ public abstract IRenderingParameters getRenderer2DModel();
}
\ No newline at end of file
Deleted: cdk/branches/egonw-jchempaint/src/main/org/openscience/cdk/renderer/Java2DRenderer.java
===================================================================
--- cdk/branches/egonw-jchempaint/src/main/org/openscience/cdk/renderer/Java2DRenderer.java 2008-10-15 11:56:09 UTC (rev 12708)
+++ cdk/branches/egonw-jchempaint/src/main/org/openscience/cdk/renderer/Java2DRenderer.java 2008-10-15 11:56:46 UTC (rev 12709)
@@ -1,1226 +0,0 @@
-/* $Revision: 7636 $ $Author: nielsout $ $Date: 2007-09-02 11:46:10 +0100 (su, 02 sep 2007) $
- *
- * Copyright (C) 2007 Niels Out <nie...@us...>
- * 2008 Thorsten Meinl <Tho...@un...>
- *
- * Contact: cdk...@li...
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- * All I ask is that proper credit is given for my work, which includes
- * - but is not limited to - adding the above copyright notice to the beginning
- * of your source code files, and to any copyright notice that you may distribute
- * with programs based on this work.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
- */
-package org.openscience.cdk.renderer;
-
-import org.openscience.cdk.CDKConstants;
-import org.openscience.cdk.config.IsotopeFactory;
-import org.openscience.cdk.geometry.GeometryTools;
-import org.openscience.cdk.graph.ConnectivityChecker;
-import org.openscience.cdk.interfaces.*;
-import org.openscience.cdk.ringsearch.SSSRFinder;
-import org.openscience.cdk.tools.LoggingTool;
-import org.openscience.cdk.tools.manipulator.RingSetManipulator;
-import org.openscience.cdk.validate.ProblemMarker;
-
-import javax.vecmath.Point2d;
-import java.awt.*;
-import java.awt.font.FontRenderContext;
-import java.awt.font.TextLayout;
-import java.awt.geom.*;
-import java.util.ArrayList;
-import java.util.Iterator;
-import java.util.List;
-
-/**
- * A Java2D based 2D renderer for IChemObjects.
- *
- * @author nielsout
- * @cdk.svnrev $Revision: 9162 $
- * @cdk.module render
- */
-public class Java2DRenderer implements IJava2DRenderer {
-
- private Renderer2DModel rendererModel;
- private AffineTransform affine;
-
- protected LoggingTool logger;
- IsotopeFactory isotopeFactory;
-
- public Java2DRenderer(final Renderer2DModel model) {
- this.rendererModel = model;
- logger = new LoggingTool(this);
- }
-
- public void paintChemModel(final IChemModel model, final Graphics2D graphics) {
- // TODO Auto-generated method stub
-
- }
-
- public void paintMoleculeSet(final IMoleculeSet moleculeSet, final Graphics2D graphics) {
- // TODO Auto-generated method stub
-
- }
-
- public void paintReaction(final IReaction reaction, final Graphics2D graphics) {
- // TODO Auto-generated method stub
-
- }
-
- public void paintReactionSet(final IReactionSet reactionSet, final Graphics2D graphics) {
- // TODO Auto-generated method stub
-
- }
- /**
- * Paint the given Molecule on the graphics object at location specified by bounds.
- *
- *@param atomCon The molecule to be drawn
- *@param graphics Graphics2D to draw on
- */
- public void paintMolecule(final IAtomContainer atomCon, final Graphics2D graphics) {
-
-
- if (affine == null) {
- logger.debug("paintMolecule should be called first time with the bounds of the graphical object..");
- logger.warn("Cannot paintMolecule without transform Matrix");
- return;
- }
- graphics.transform(affine);
- logger.debug("transform matrix:" + graphics.getTransform());
-
- if (rendererModel.getUseAntiAliasing())
- {
- graphics.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
- }
- // set basic shape form for bonds
- graphics.setColor(Color.BLACK);
- graphics.setStroke(new BasicStroke(
- (float) (rendererModel.getBondWidth()/rendererModel.getBondLength()),
- BasicStroke.CAP_ROUND, BasicStroke.JOIN_ROUND)
- );
-
- IRingSet ringSet = getRingSet(atomCon);
-
- // draw bonds
- paintBonds(atomCon, ringSet, graphics);
-
- // draw atom symbols
- paintAtoms(atomCon, graphics);
- logger.debug("transform matrix:" + graphics.getTransform());
-
- }
- /**
- * Paint the given Molecule on the graphics object at location specified by bounds.
- *
- *@param atomCon The molecule to be drawn
- *@param graphics Graphics2D to draw on
- *@param bounds
- */
- public void paintMolecule(final IAtomContainer atomCon, final Graphics2D graphics,
- final Rectangle2D bounds) {
- //rendererModel.setShowAromaticity(true);
-
- // calculate the molecule boundaries via the atomContainer
- Rectangle2D molBounds = createRectangle2D(atomCon);
- if (molBounds == null || molBounds.isEmpty()) {
- logger.debug("empty atomCon? -> no molBounds -> no drawing ");
- return;
- }
- AffineTransform transformMatrix = createScaleTransform(molBounds,bounds);
- affine = transformMatrix;
-
- paintMolecule(atomCon, graphics);
- }
- protected IRingSet getRingSet(final IAtomContainer atomContainer)
- {
- IRingSet ringSet = atomContainer.getBuilder().newRingSet();
- IMoleculeSet molecules;
- try
- {
- molecules = ConnectivityChecker.partitionIntoMolecules(atomContainer);
- }
-
- catch (Exception exception)
- {
- logger.warn("Could not partition molecule: ", exception.getMessage());
- logger.debug(exception);
- return ringSet;
- }
-
- for (IAtomContainer mol : molecules.molecules()) {
- SSSRFinder sssrf = new SSSRFinder(mol);
-
- ringSet.add(sssrf.findSSSR());
- }
-
- return ringSet;
- }
- /**
- * Triggers paintAtom method for all the atoms in the given array of atoms.
- *
- * @param atomCon
- * @param graphics
- */
- public void paintAtoms(final IAtomContainer atomCon, final Graphics2D graphics)
- {
- for (int i = 0; i < atomCon.getAtomCount(); i++)
- {
- paintAtom(atomCon, atomCon.getAtom(i), graphics);
- }
- }
- /**
- * triggers the
- * paintColouredAtoms method if the atom has got a certain color and triggers
- * the paintAtomSymbol method if the symbol of the atom is not C
- *
- * @param container
- * @param atom
- * @param graphics
- */
- public void paintAtom(final IAtomContainer container, final IAtom atom, final Graphics2D graphics)
- {
- logger.debug("paintAtom Symbol:" + atom.getSymbol() + " atom:" + atom);
-
-
-
- boolean drawSymbol = false; //paint all Atoms for the time being
- boolean isRadical = (container.getConnectedSingleElectronsCount(atom) > 0);
- if (atom instanceof IPseudoAtom)
- {
- drawSymbol = false;
-// if (atom instanceof FragmentAtom) {
-// paintFragmentAtom((FragmentAtom)atom, atomBackColor, graphics,
-// alignment, isRadical);
-// } else {
- // paintPseudoAtomLabel((IPseudoAtom) atom, atomBackColor, graphics, alignment, isRadical);
-// }
- logger.debug("call paintPseudoAtomLabel here?");
- return;
- } else if ("H".equals(atom.getSymbol())
- && !getRenderer2DModel().getShowExplicitHydrogens()) {
- drawSymbol = false;
- } else if (!atom.getSymbol().equals("C"))
- {
- /*
- * only show element for non-carbon atoms,
- * unless (see below)...
- */
- drawSymbol = true;
- } else if (getRenderer2DModel().getKekuleStructure())
- {
- // ... unless carbon must be drawn because in Kekule mode
- drawSymbol = true;
- } else if (atom.getFormalCharge() != 0)
- {
- // ... unless carbon is charged
- drawSymbol = true;
- } else if (container.getConnectedBondsList(atom).size() < 1)
- {
- // ... unless carbon is unbonded
- drawSymbol = true;
- } else if (getRenderer2DModel().getShowEndCarbons() && (container.getConnectedBondsList(atom).size() == 1))
- {
- drawSymbol = true;
- } else if (atom.getProperty(ProblemMarker.ERROR_MARKER) != null)
- {
- // ... unless carbon is unbonded
- drawSymbol = true;
- } else if (atom.getMassNumber() != null)
- {
- try
- {
- if (atom.getMassNumber() != IsotopeFactory.getInstance(container.getBuilder()).
- getMajorIsotope(atom.getSymbol()).getMassNumber())
- {
- drawSymbol = true;
- }
- } catch (Exception exception) {
- logger.debug("Could not get an instance of IsotopeFactory");
- }
-
- } else if (isRadical) {
- drawSymbol = true;
- }
-
- if (drawSymbol == true) {
- int alignment = GeometryTools.getBestAlignmentForLabelXY(container, atom);
- //System.out.println("alignment: " + alignment);
- paintAtomSymbol(atom, graphics, alignment, isRadical);
- }
- }
- public void paintAtomSymbol(final IAtom atom, final Graphics2D graphics, final int alignment, final boolean isRadical)
- {
- Color saveColor = graphics.getColor();
- String symbol = "";
-
- if (atom.getSymbol() != null) {
- symbol = atom.getSymbol();
- }
- //symbol = "Mg"; //to test if a certain symbol is spaced out right
-
-
- Font fontAtom;
- if (rendererModel.getFont() != null) {
- fontAtom = rendererModel.getFont();
- logger.debug("the font is now: " + fontAtom);
- } else {
- fontAtom = new Font("Arial", Font.PLAIN, 12);
- }
-
- //the graphics objects has a transform which is 'reversed' to go from world coordinates
- //to screencoordinates, so transform the characters back to show them 'up-side-up'.
- double fscale = 0.055;
- double[] transmatrix = { fscale, 0, 0, -fscale};
- AffineTransform trans = new AffineTransform(transmatrix);
- fontAtom = fontAtom.deriveFont(trans);
-
- //FIXME: add this 0.4 in the RendererModel
- float sizeSmall = (float)(fontAtom.getSize2D() * 0.4);
- Font fontSmall = fontAtom.deriveFont(sizeSmall); //font for upper/lower text such as Massnumber, Charges, HydrogenCount etc..
-
- graphics.setFont(fontAtom);
-
- FontRenderContext frc = graphics.getFontRenderContext();
- TextLayout layoutAtom = new TextLayout(symbol, fontAtom, frc);
- Rectangle2D boundsAtom = layoutAtom.getBounds();
-
- //btest has to be substracted to get the text on the exact right position
- //FIXME: get right value from graphics object? (width of line? or so)
- float btest = (float) (rendererModel.getBondWidth()/rendererModel.getBondLength());
- double atomSymbolX = atom.getPoint2d().x - boundsAtom.getWidth()/2 - 0.5 * btest;
- double atomSymbolY = atom.getPoint2d().y - boundsAtom.getHeight() /2 - boundsAtom.getY();
- double atomSymbolW = boundsAtom.getWidth();
- double atomSymbolH = boundsAtom.getHeight() - boundsAtom.getY();
- double atomSymbolDNext = layoutAtom.getAdvance();//distance from X,Y to 'next' character
- double marginc = (atomSymbolDNext - atomSymbolW)/2;//margin used in calculations
- double margind = marginc * 1.4;//slightly larger margin for drawing
- double atomSymbolHOffset = boundsAtom.getY();
-
-
- // //System.out.println("the marginc is now: " + marginc + " margind: " + margind);
-
-
- //bounds around Atom Symbol
- boundsAtom.setRect(boundsAtom.getX() + atomSymbolX - margind,
- boundsAtom.getY() + atomSymbolY - margind,
- boundsAtom.getWidth() + 2 * margind,
- boundsAtom.getHeight() + 2 * margind);
-
-
- Color atomColor = rendererModel.getAtomColor(atom, Color.BLACK);
- Color otherColor = rendererModel.getForeColor();
- Color bgColor;
- if (atom == rendererModel.getHighlightedAtom()) {
- bgColor = rendererModel.getHoverOverColor();
- } else if (rendererModel.getBackColor() != null) {
- bgColor = rendererModel.getBackColor();
- } else {
- bgColor = graphics.getBackground();
- }
-
- double longestSide = Math.max(boundsAtom.getWidth(), boundsAtom.getHeight());
- longestSide *= 1.2;
- double circleX = boundsAtom.getCenterX() - longestSide / 2;
- double circleY = boundsAtom.getCenterY() - longestSide / 2;
-
- Ellipse2D.Double bgCircle = new Ellipse2D.Double(circleX, circleY,
- longestSide, longestSide);
-
- graphics.setColor(bgColor);
- graphics.fill(bgCircle);// draw atom symbol background
-
-
- double massnumberW = 0;
- //double formalChargW = 0;
- double hydroGenW = 0;
- double hydroGenCountW = 0;
- double hydroGenCountH = 0;
- double hydroGenH = 0;
-
- if (atom.getMassNumber() != null && isotopeFactory != null) {
- IIsotope majorIsotope = isotopeFactory.getMajorIsotope(atom.getSymbol());
- if (majorIsotope != null && atom.getMassNumber() != majorIsotope.getMassNumber())
- {
-
- graphics.setFont(fontSmall);
- String textMass = Integer.toString(atom.getMassNumber());
- FontRenderContext frcMass = graphics.getFontRenderContext();
- TextLayout layoutMass = new TextLayout(textMass, fontSmall, frcMass);
- Rectangle2D boundsMass = layoutMass.getBounds();
-
- massnumberW = layoutMass.getAdvance();
-
- //terrible way of getting the MassNumber on the right X location for 'every?' number
- //I would expect this to be 'screenAtomX - boundsMass.getWidth()- margin - marginSmall' but that didn't work 100% correct
- //float massNumberX = (float)(atomSymbolX - layoutMass.getAdvance() + tempWA - (float)boundsMass.getX() - marginSmall);
- double massNumberX = atomSymbolX - massnumberW;//-margin ?
- double massNumberY = atomSymbolY + boundsAtom.getHeight() - boundsMass.getHeight() / 2;
-
- boundsMass.setRect(boundsMass.getX() + massNumberX - margind,
- boundsMass.getY() + massNumberY - margind,
- boundsMass.getWidth() + 2 * margind,
- boundsMass.getHeight() + 2 * margind);
-
- //bgColor = Color.green;
- graphics.setColor(bgColor);
-
- graphics.fill(boundsMass);// draw Mass number background
- graphics.setFont(fontSmall);
- graphics.setColor(otherColor);
- layoutMass.draw(graphics, (float)massNumberX, (float)massNumberY);// draw Mass Number
- }
- }
-
- if (atom.getHydrogenCount() != null && atom.getHydrogenCount() > 0) {
- graphics.setFont(fontAtom);
- String hChar = "H";
- FontRenderContext frcMass = graphics.getFontRenderContext();
- TextLayout layoutH = new TextLayout(hChar, fontAtom, frcMass);
- Rectangle2D boundsHydro = layoutH.getBounds();
-
- hydroGenW = layoutH.getAdvance();
-
- hydroGenH = boundsHydro.getHeight();
- graphics.setFont(fontSmall);
- String hCount = atom.getHydrogenCount().toString();
- frcMass = graphics.getFontRenderContext();
- TextLayout layoutHC = new TextLayout(hCount, fontSmall, frcMass);
- Rectangle2D boundsHydroC = layoutHC.getBounds();
-
- hydroGenCountW = layoutHC.getAdvance();
- hydroGenCountH = boundsHydroC.getHeight();
-
- double hydroGenX = atomSymbolX;
- double hydroGenY = atomSymbolY;//'H' at same height as atom Symbol
- //TODO: add margins
-
- logger.debug("test layoutAtom.getLeading(): " + layoutAtom.getLeading() + " layoutatom.getAscent(): " +
- layoutAtom.getAscent() + " layoutH.getAscent(): " + layoutH.getAscent() +
- " layoutH.getBaseline()" + layoutH.getBaseline() + " layoutAtom.getBaseline()" +
- layoutAtom.getBaseline());
-
- switch (alignment) {
- case -2: //H below atomSymbol
- hydroGenY = hydroGenY - hydroGenH + atomSymbolHOffset - 2 * marginc; break;
- case -1: //left alignment
- hydroGenX -= (hydroGenW + Math.max(hydroGenCountW, massnumberW)); break;
- case 2: //H above atomSymbol != correct
- hydroGenY += atomSymbolH + marginc + atomSymbolHOffset + 0.5 * boundsHydroC.getHeight() - boundsHydroC.getX();
- //FIXME: add height of formalCharge to this
- break;
- default: //right alignment = correct
- hydroGenX += atomSymbolDNext; break;
-
- }
-
- boundsHydro.setRect(boundsHydro.getX() + hydroGenX - margind,
- boundsHydro.getY() + hydroGenY - margind,
- boundsHydro.getWidth() + 2 * margind,
- boundsHydro.getHeight() + 2 * margind);
-
- double hydroGenCX = hydroGenX + hydroGenW;
- double hydroGenCY = hydroGenY - 0.5 * boundsHydroC.getHeight();//1,2,3,etc. 'subscript'
-
- boundsHydroC.setRect(boundsHydroC.getX() + hydroGenCX - margind,
- boundsHydroC.getY() + hydroGenCY - margind,
- boundsHydroC.getWidth() + 2 * margind,
- boundsHydroC.getHeight() + 2 * margind);
-
- graphics.setColor(bgColor);
-
- graphics.fill(boundsHydro);// draw 'H' background
- graphics.fill(boundsHydroC);// draw '1/2/3' hydrogen Count background
-
- graphics.setColor(otherColor);
-
- graphics.setFont(fontAtom);
- layoutH.draw(graphics, (float)hydroGenX, (float)hydroGenY);// draw the 'H'
- graphics.setFont(fontSmall);
- layoutHC.draw(graphics, (float)hydroGenCX, (float)hydroGenCY);// draw the hydrogen Count
-
- }
-
- if (atom.getFormalCharge() != null && atom.getFormalCharge() != 0) {
-
- graphics.setFont(fontSmall);
- String textFormal = "";
- double marginRight = 0;//margin on the right (=to hide part of bonds)
- if (atom.getFormalCharge() != 1 && atom.getFormalCharge() != -1) {
- textFormal += Integer.toString(Math.abs(atom.getFormalCharge()));
- }
-
- if (atom.getFormalCharge() > 0) {
- textFormal += "+";
- marginRight = margind;
- }
- FontRenderContext frcFormal = graphics.getFontRenderContext();
-
- double formalChargeX = atomSymbolX + atomSymbolDNext;
- double formalChargeY = atomSymbolY;
- double formalChargeH = 0;
-
- ////System.out.println("alignment: " + alignment);
-
- if (alignment == 1) {
- formalChargeX += hydroGenW + hydroGenCountW;//should hydroGenCountW be included here?
- } else if (alignment == 2) { //top alignment
- formalChargeY += hydroGenH + hydroGenCountH;
- }
- double formalChargeY2 = formalChargeY;
-
- double formalChargeW = 0;
- TextLayout layoutFormalC = layoutAtom;//have to initialize it so *something*
- if (textFormal != "") { //draw amount and optional '+'-symbol
- layoutFormalC = new TextLayout(textFormal, fontSmall, frcFormal);
- //TextLayout layoutBase = new TextLayout(baseString, fontSmall, frcFormal);
- Rectangle2D boundsFormalC = layoutFormalC.getBounds();
-
- formalChargeH = boundsFormalC.getHeight();
-
- formalChargeY += boundsAtom.getHeight() - boundsFormalC.getHeight() / 2;
-
- boundsFormalC.setRect(boundsFormalC.getX() + formalChargeX - margind,
- boundsFormalC.getY() + formalChargeY - margind,
- boundsFormalC.getWidth() + 2 * margind + marginRight,
- boundsFormalC.getHeight() + 2 * margind);
-
- graphics.setColor(bgColor);
- graphics.fill(boundsFormalC);// draw Formal Charge background
- graphics.setFont(fontSmall);
- graphics.setColor(otherColor);
- formalChargeW = layoutFormalC.getAdvance();
- }
- if (atom.getFormalCharge() < 0) { //draw the 'minus' symbol
- double formalChargeX2 = formalChargeX + formalChargeW + marginc;
- String textFormal2 = "_";
- TextLayout layoutFormal = new TextLayout(textFormal2, fontSmall, frcFormal);
- Rectangle2D boundsFormalC = layoutFormal.getBounds();
- double posiY = Math.max(boundsFormalC.getHeight(), formalChargeH) + boundsFormalC.getY();
- formalChargeY2 += boundsAtom.getHeight() + posiY / 2;//
-
- boundsFormalC.setRect(boundsFormalC.getX() + formalChargeX2 - margind,
- boundsFormalC.getY() + formalChargeY2 - 5 * margind,
- boundsFormalC.getWidth() + 2 * margind,
- boundsFormalC.getHeight() + 8 * margind);
-
- graphics.setColor(bgColor);
- graphics.fill(boundsFormalC);// draw Formal Charge background
- graphics.setFont(fontSmall);
- graphics.setColor(otherColor);
- layoutFormal.draw(graphics, (float)formalChargeX2, (float)formalChargeY2);// draw Formal Charge
- }
- if (textFormal != "") {
- layoutFormalC.draw(graphics, (float)formalChargeX, (float)formalChargeY);// draw Formal Charge
- }
- }
-
-
- graphics.setFont(fontAtom);
- graphics.setColor(atomColor);
- layoutAtom.draw(graphics, (float)atomSymbolX, (float)atomSymbolY);// draw atom symbol
-
- /* String test = "MgH";
- frc = graphics.getFontRenderContext();
- TextLayout layoutTest = new TextLayout(test, fontAtom, frc);
- double CHwidth = layoutTest.getAdvance();
- double tempv = CHwidth - atomSymbolW - hydroGenW;
-
- layoutTest.draw(graphics, (float)atomSymbolX, (float)atomSymbolY);// draw CH test
- //System.out.println("symbol width: " + atomSymbolW + " hydroGenW: " + hydroGenW +
- " total: " + (atomSymbolW + hydroGenW) + " CHwidth: " + CHwidth);
- //System.out.println("difference: " + tempv + " dif2: " + (hydroGenW - atomSymbolW) + " dif3: " + ((hydroGenW - atomSymbolW) - tempv));
- */
-
- graphics.setColor(saveColor);
- }
- /**
- * Paints a rectangle of the given color at the position of the given atom.
- * For example when the atom is highlighted.
- *
- *@param atom The atom to be drawn
- *@param color The color of the atom to be drawn
- */
- public void paintColouredAtomBackground(final org.openscience.cdk.interfaces.IAtom atom, final Color color, final Graphics2D graphics)
- {
- double x = atom.getPoint2d().x;
- double y = atom.getPoint2d().y;
- logger.debug("painting paintColouredAtomBackground now at " + x + " / " + y);
- //FIXME: right size for this AtomRadius (currently estimate)
- double atomRadius = rendererModel.getHighlightRadiusModel();
-
- graphics.setColor(color);
-
- Rectangle2D shape = new Rectangle2D.Double();
- shape.setFrame(x - (atomRadius / 2), y - (atomRadius / 2), atomRadius, atomRadius);
- if(rendererModel.getIsCompact()) {
- graphics.draw(shape);
- } else {
- graphics.fill(shape);
- }
- }
- /**
- * A ring is defined aromatic if all atoms are aromatic, -or- all bonds are
- * aromatic.
- * copied from AbstractRenderer2D
- */
- public boolean ringIsAromatic(final IRing ring)
- {
- boolean isAromatic = true;
- for (int i = 0; i < ring.getAtomCount(); i++)
- {
- if (!ring.getAtom(i).getFlag(CDKConstants.ISAROMATIC))
- {
- isAromatic = false;
- }
- }
- if (!isAromatic)
- {
- isAromatic = true;
- Iterator<?> bonds = ring.bonds().iterator();
- while (bonds.hasNext()) {
- if (!((IBond)bonds.next()).getFlag(CDKConstants.ISAROMATIC)) {
- return false;
- }
- }
- }
- return isAromatic;
- }
-
- public static double distance2points(final Point2d a, final Point2d b) {
- return Math.sqrt(Math.pow(a.x - b.x, 2) + Math.pow(a.y - b.y, 2));
- }
- public static double distance2points(final double x0, final double y0, final double x1, final double y1) {
- return Math.sqrt(Math.pow(x0 - x1, 2) + Math.pow(y0 - y1, 2));
- }
- /**
- * Paints the inner bond of a double bond that is part of a ring.
- *
- *@param bond The bond to be drawn
- *@param ring The ring the bond is part of
- *@param bondColor Color of the bond
- */
- public void paintInnerBond(final org.openscience.cdk.interfaces.IBond bond, final IRing ring, final Color bondColor, final Graphics2D graphics)
- {
- Point2d center = GeometryTools.get2DCenter(ring);
- logger.debug(" paintInnerBond (=working) now at " + center);
- //next few lines draw a green and pink line just for debugging, to be removed later
- /* graphics.setColor(Color.green);
- Line2D line = new Line2D.Double(
- bond.getAtom(0).getPoint2d().x, bond.getAtom(0).getPoint2d().y,
- center.x, center.y );
- graphics.draw(line);
- Line2D line2 = new Line2D.Double(
- bond.getAtom(1).getPoint2d().x, bond.getAtom(1).getPoint2d().y,
- center.x, center.y );
- graphics.draw(line2);*/
- Point2d a = bond.getAtom(0).getPoint2d();
- Point2d b = bond.getAtom(1).getPoint2d();
-
- //TODO: put distanceconstant in the renderermodel
- double distanceconstant = 0.15; //distance between inner and outerbond (in world coordinates)
-
- double distance = distance2points(a,b);
- double u = ((center.x - a.x)*(b.x - a.x) + (center.y - a.y)*(b.y - a.y)) / (Math.pow(distance, 2));
- double px = a.x + u*(b.x - a.x);
- double py = a.y + u*(b.y - a.y);
- logger.debug("distancea and b: " + distance + " u: " + u + " px: " + px + " py " + py);
-
- Point2d z = new Point2d(px, py);
-
- /* graphics.setColor(Color.pink);
- Line2D linepink = new Line2D.Double(
- z.x,
- z.y,
- center.x,
- center.y
- );
- graphics.draw(linepink);*/
-
- double ae = distance2points(a ,z) / distance2points(center, z) * distanceconstant;
- double af = Math.sqrt(Math.pow(ae,2) + Math.pow(distanceconstant,2));
-
- double pfx = a.x + af*(center.x - a.x);
- double pfy = a.y + af*(center.y - a.y);
-
- double bh = distance2points(b, z) / distance2points(center, z) * distanceconstant;
- double bi = Math.sqrt(Math.pow(bh, 2) + Math.pow(distanceconstant,2));
-
- double pix = b.x + bi*(center.x - b.x);
- double piy = b.y + bi*(center.y - b.y);
-
- graphics.setColor(bondColor);
- Line2D linegood = new Line2D.Double(
- pfx,
- pfy,
- pix,
- piy
- );
- graphics.draw(linegood);
- }
-
- /**
- * Triggers the suitable method to paint each of the given bonds and selects
- * the right color.
- *
- *@param ringSet The set of rings the molecule contains
- */
- public void paintBonds(final IAtomContainer atomCon, final IRingSet ringSet, final Graphics2D graphics)
- {
- Color bondColor;
- IRing ring;
- ArrayList<IRing> painted_rings = new ArrayList<IRing>();
-
- logger.debug("Painting bonds...");
- for (IBond currentBond : atomCon.bonds()) {
- bondColor = rendererModel.getColorHash().get(currentBond);
- if (bondColor == null)
- {
- bondColor = rendererModel.getForeColor();
- }
- if (currentBond == rendererModel.getHighlightedBond() &&
- (rendererModel.getSelectedPart()==null || !rendererModel.getSelectedPart().contains(currentBond)))
- {
- bondColor = rendererModel.getHoverOverColor();
- for (int j = 0; j < currentBond.getAtomCount(); j++)
- {
- paintColouredAtomBackground(currentBond.getAtom(j), bondColor, graphics);
-
- }
- }
- ring = RingSetManipulator.getHeaviestRing(ringSet, currentBond);
- if (ring != null)
- {
- logger.debug("Found ring to draw");
- if (ringIsAromatic(ring) && rendererModel.getShowAromaticity())
- {
- logger.debug("Ring is aromatic");
- if (!painted_rings.contains(ring))
- {
- paintRingRing(ring, bondColor, graphics);
- painted_rings.add(ring);
- }
- paintSingleBond(currentBond, bondColor, graphics);
- } else
- {
- logger.debug("draw Ring as *not* aromatic");
- paintRingBond(currentBond, ring, bondColor, graphics);
- }
- } else
- {
- logger.debug("Drawing a non-ring bond");
- paintBond(currentBond, bondColor, graphics);
- }
- }
- }
- /**
- * Triggers the paint method suitable to the bondorder of the given bond that
- * is part of a ring with CDK's grey inner bonds.
- *
- *@param bond The Bond to be drawn.
- */
- public void paintRingBond(final org.openscience.cdk.interfaces.IBond bond, final IRing ring, final Color bondColor, final Graphics2D graphics)
- {
- Point2d center = GeometryTools.get2DCenter(ring);
- logger.debug(" painting paintRingBond now at " + center + " getOrder: " + bond.getOrder() + " bond: " + bond);
-
-
- if (bond.getOrder() == IBond.Order.SINGLE)
- {
- // Added by rstefani (in fact, code copied from paintBond)
- if (bond.getStereo() != CDKConstants.STEREO_BOND_NONE && bond.getStereo() != CDKConstants.STEREO_BOND_UNDEFINED)
- {
- // Draw stero information if available
- if (bond.getStereo() >= CDKConstants.STEREO_BOND_UP)
- {
- paintWedgeBond(bond, bondColor, graphics);
- } else
- {
- paintDashedWedgeBond(bond, bondColor, graphics);
- }
- } else
- {
- // end code by rstefani
- logger.debug(" singlebond in ring");
- paintSingleBond(bond, bondColor, graphics);
- }
- } else if (bond.getOrder() == IBond.Order.DOUBLE)
- {
-
- paintSingleBond(bond, bondColor, graphics);
- paintInnerBond(bond, ring, bondColor, graphics);
- } else if (bond.getOrder() == IBond.Order.TRIPLE)
- {
- paintTripleBond(bond, bondColor, graphics);
- } else
- {
- logger.warn("Drawing bond as single even though it has order: ", bond.getOrder());
-
- paintSingleBond(bond, bondColor, graphics);
- }
- }
- /**
- * Paints the given bond as a wedge bond.
- *
- *@param bond The singlebond to be drawn
- *@param bondColor Color of the bond
- */
- public void paintWedgeBond(final org.openscience.cdk.interfaces.IBond bond, final Color bondColor, final Graphics2D graphics)
- {
- logger.debug("painting paintWedgeBond now for: " + bond);
- double wedgeWidth = rendererModel.getBondWidth() /10;
- //perhaps introduce a new setting instead of using getBondWidth here
- logger.debug(" wedgeWidth: " + wedgeWidth);
-
- double x0, x1, y0, y1;
-
- if (bond.getStereo() == CDKConstants.STEREO_BOND_UP)
- { //FIXME: check if this is correct, I think the difference between STEREO_BOND_UP and the
- //other is which is the 'startpoint', please tell me (Nout) if this is correct.
- x0 = bond.getAtom(0).getPoint2d().x;
- x1 = bond.getAtom(1).getPoint2d().x;
- y0 = bond.getAtom(0).getPoint2d().y;
- y1 = bond.getAtom(1).getPoint2d().y;
- } else
- {
- x1 = bond.getAtom(0).getPoint2d().x;
- x0 = bond.getAtom(1).getPoint2d().x;
- y1 = bond.getAtom(0).getPoint2d().y;
- y0 = bond.getAtom(1).getPoint2d().y;
- }
- double angle;
- if ((x1 - x0) == 0) {
- angle = Math.PI / 2;
- } else {
- angle = Math.atan((y1 - y0) / (x1 - x0));
- }
- float newxup = (float)(x1 - Math.sin(angle) * wedgeWidth);
- float newyup = (float)(y1 + Math.cos(angle) * wedgeWidth);
-
- float newxdown = (float)(x1 + Math.sin(angle) * wedgeWidth);
- float newydown = (float)(y1 - Math.cos(angle) * wedgeWidth);
-
- GeneralPath p = new GeneralPath(); //create a triangle with GenaralPath
- p.moveTo((float)x0, (float)y0);
- p.lineTo(newxup, newyup);
- p.lineTo(newxdown, newydown);
- p.closePath();
-
- graphics.setColor(bondColor);
- graphics.fill(p);
- }
- /**
- * Paints the given bond as a dashed wedge bond.
- *
- *@param bond The single bond to be drawn
- *@param bondColor Color of the bond
- */
- public void paintDashedWedgeBond(final org.openscience.cdk.interfaces.IBond bond, final Color bondColor, final Graphics2D graphics)
- {
- logger.debug("painting paintDashedWedgeBond now for: " + bond);
- double wedgeWidth = rendererModel.getBondWidth() /10;
- double bondWidth = rendererModel.getBondWidth() / 40;
- double x0, x1, y0, y1;
-
- if (bond.getStereo() == CDKConstants.STEREO_BOND_DOWN)
- { //FIXME: check if this is correct, I think the difference between STEREO_BOND_UP and the
- //other is which is the 'startpoint', please tell me (Nout) if this is correct.
- x0 = bond.getAtom(0).getPoint2d().x;
- x1 = bond.getAtom(1).getPoint2d().x;
- y0 = bond.getAtom(0).getPoint2d().y;
- y1 = bond.getAtom(1).getPoint2d().y;
- } else
- {
- x1 = bond.getAtom(0).getPoint2d().x;
- x0 = bond.getAtom(1).getPoint2d().x;
- y1 = bond.getAtom(0).getPoint2d().y;
- y0 = bond.getAtom(1).getPoint2d().y;
- }
- double angle;
- if ((x1 - x0) == 0) {
- angle = Math.PI / 2;
- } else {
- angle = Math.atan((y1 - y0) / (x1 - x0));
- }
- float newxup = (float)(x1 - Math.sin(angle) * wedgeWidth);
- float newyup = (float)(y1 + Math.cos(angle) * wedgeWidth);
-
- float newxdown = (float)(x1 + Math.sin(angle) * wedgeWidth);
- float newydown = (float)(y1 - Math.cos(angle) * wedgeWidth);
-
- double bondLength = distance2points(bond.getAtom(0).getPoint2d(), bond.getAtom(1).getPoint2d());
- int numberOfLines = (int) (bondLength / bondWidth / 3);
-
- logger.debug("lines: " + numberOfLines);
-
- graphics.setColor(bondColor);
-
- double xl, xr, yl, yr;
- Line2D.Double line = new Line2D.Double();
- for (int i = 0; i < numberOfLines - 2; i++) { //do not show last line because atom symbol will be drawn on that place
- double t = (double)i / numberOfLines;
- xl = x0 + t * (newxup - x0);
- xr = x0 + t * (newxdown - x0);
- yl = y0 + t * (newyup - y0);
- yr = y0 + t * (newydown - y0);
- ////System.out.println(i + " : " + t + " from " + xl + " ; " + yl + " to: " + xr + " ; " + yr);
- line.setLine(xl, yl, xr, yr);
- graphics.draw(line);
- }
- }
-
- /**
- * Draws the ring in an aromatic ring.
- */
- public void paintRingRing(final IRing ring, final Color bondColor, final Graphics2D graphics)
- {
- Point2d center = GeometryTools.get2DCenter(ring);
- logger.debug(" painting a Ringring now at " + center);
-
- double[] minmax = GeometryTools.getMinMax(ring);
- double width = (minmax[2] - minmax[0]) * 0.7;
- double height = (minmax[3] - minmax[1]) * 0.7;
-
- //make a circle
- if (width > height) {
- width = height;
- } else if (height > width) {
- height = width;
- }
-
- double[] coords = { (center.x - (width / 2.0)), (center.y - (height / 2.0)) };
- //offset is the width of the ring
- double offset = (0.05 * Math.max(width, height));
- double offsetX2 = 2 * offset;
-
- // Fill outer oval.
- graphics.setColor(bondColor);
- Shape shape = new Ellipse2D.Double(coords[0], coords[1], width, height);
- graphics.fill(shape);
-
- // Erase inner oval.
- graphics.setColor(rendererModel.getBackColor());
- shape = new Ellipse2D.Double(coords[0] + offset, coords[1] + offset, width - offsetX2, height - offsetX2);
- graphics.fill(shape);
-
- // Reset drawing colour.
- graphics.setColor(bondColor);
- }
- /**
- * Triggers the paint method suitable to the bondorder of the given bond.
- *
- *@param bond The Bond to be drawn.
- */
- public void paintBond(final IBond bond, final Color bondColor, final Graphics2D graphics)
- {
-
- logger.debug(" paintBond, getstereo: " + bond.getStereo() + " getorder: " + bond.getOrder() + " x,y: " + bond.getAtom(0).getPoint2d().x + "," +
- bond.getAtom(0).getPoint2d().y);
-
- if (!GeometryTools.has2DCoordinates(bond)) {
- return;
- }
-
- if (!rendererModel.getShowExplicitHydrogens()) {
- if (bond.getAtom(0).getSymbol().equals("H")) {
- return;
- }
- if (bond.getAtom(1).getSymbol().equals("H")) {
- return;
- }
- }
-
- if (bond.getStereo() != CDKConstants.STEREO_BOND_NONE && bond.getStereo() != CDKConstants.STEREO_BOND_UNDEFINED)
- {
- // Draw stereo information if available
- if (bond.getStereo() >= CDKConstants.STEREO_BOND_UP)
- {
- paintWedgeBond(bond, bondColor, graphics);
- } else
- {
- paintDashedWedgeBond(bond, bondColor, graphics);
- }
- } else
- {
- // Draw bond order when no stereo info is available
- if (bond.getOrder() == CDKConstants.BONDORDER_SINGLE)
- {
- paintSingleBond(bond, bondColor, graphics);
- } else if (bond.getOrder() == CDKConstants.BONDORDER_DOUBLE)
- {
- paintDoubleBond(bond, bondColor, graphics);
- } else if (bond.getOrder() == CDKConstants.BONDORDER_TRIPLE)
- {
- paintTripleBond(bond, bondColor, graphics);
-// } else if (bond.getOrder() == 8.)
-// {
-// paintAnyBond(bond, bondColor, graphics);
- } else
- {
-
- logger.debug(" painting single bond because order = " + bond.getOrder());
- // paint all other bonds as single bonds
- paintSingleBond(bond, bondColor, graphics);
- }
- }
- }
- /**
- * Paints the given 'Any' bond.
- *
- *@param bond The given 'Any' bond to be drawn
- */
- public void paintAnyBond(final org.openscience.cdk.interfaces.IBond bond, final Color bondColor, final Graphics2D graphics)
- {
- //TODO: rewrite this old code:
-
- /*if (GeometryTools.has2DCoordinates(bond))
- {
- int[] screencoords=getScreenCoordinates(GeometryTools.getBondCoordinates(bond, r2dm.getRenderingCoordinates()));
- int dashlength=4;
- int spacelength=4;
- if ((screencoords[0] == screencoords[2]) && (screencoords[1] == screencoords[3]))
- {
- graphics.drawLine(screencoords[0], screencoords[1], screencoords[2], screencoords[3]);
- return;
- }
- double linelength = Math.sqrt((screencoords[2] - screencoords[0]) * (screencoords[2] - screencoords[0]) + (screencoords[3] - screencoords[1]) * (screencoords[3] - screencoords[1]));
- double xincdashspace = (screencoords[2] - screencoords[0]) / (linelength / (dashlength + spacelength));
- double yincdashspace = (screencoords[3] - screencoords[1]) / (linelength / (dashlength + spacelength));
- double xincdash = (screencoords[2] - screencoords[0]) / (linelength / (dashlength));
- double yincdash = (screencoords[3] - screencoords[1]) / (linelength / (dashlength));
- int counter = 0;
- for (double i = 0; i < linelength - dashlength; i += dashlength + spacelength)
- {
- graphics.drawLine((int) (screencoords[0] + xincdashspace * counter), (int) (screencoords[1] + yincdashspace * counter), (int) (screencoords[0] + xincdashspace * counter + xincdash), (int) (screencoords[1] + yincdashspace * counter + yincdash));
- counter++;
- }
- if ((dashlength + spacelength) * counter <= linelength)
- {
- graphics.drawLine((int) (screencoords[0] + xincdashspace * counter), (int) (screencoords[1] + yincdashspace * counter), screencoords[2], screencoords[3]);
- }
- }*/
- }
- /**
- * Paints the given double bond.
- *
- *@param bond The double bond to be drawn
- */
- public void paintDoubleBond(final IBond bond, final Color bondColor, final Graphics2D graphics)
- {
- if (GeometryTools.has2DCoordinates(bond))
- {
- double[] tempc = new double[] { bond.getAtom(0).getPoint2d().x, bond.getAtom(0).getPoint2d().y,
- bond.getAtom(1).getPoint2d().x, bond.getAtom(1).getPoint2d().y};
-
- double[] coords = GeometryTools.distanceCalculator(tempc, 0.1);
-
- Line2D line = new Line2D.Double(
- coords[0], coords[1], coords[6], coords[7]
- );
- paintOneBond(line, bondColor, graphics);
-
- Line2D line2 = new Line2D.Double(
- coords[2], coords[3], coords[4], coords[5]
- );
- paintOneBond(line2, bondColor, graphics);
-
- }
- }
- /**
- * Paints the given triple bond.
- *
- *@param bond The triple bond to be drawn
- */
- public void paintTripleBond(final org.openscience.cdk.interfaces.IBond bond, final Color bondColor, final Graphics2D graphics)
- {
- logger.debug("painting paintTripleBond now at " + bond.getAtom(0).getPoint2d());
-
- paintSingleBond(bond, bondColor, graphics);
- double[] tempc = new double[] { bond.getAtom(0).getPoint2d().x, bond.getAtom(0).getPoint2d().y,
- bond.getAtom(1).getPoint2d().x, bond.getAtom(1).getPoint2d().y};
-
- double[] coords = GeometryTools.distanceCalculator(tempc, 0.2);
-
- Line2D line = new Line2D.Double(
- coords[0], coords[1], coords[6], coords[7]
- );
- paintOneBond(line, bondColor, graphics);
-
- Line2D line2 = new Line2D.Double(
- coords[2], coords[3], coords[4], coords[5]
- );
- paintOneBond(line2, bondColor, graphics);
-
- //TODO: rewrite this old code:
-
- /* int[] coords = GeometryTools.distanceCalculator(GeometryTools.getBondCoordinates(bond,r2dm.getRenderingCoordinates()), (r2dm.getBondWidth() / 2 + r2dm.getBondDistance()));
-
- int[] newCoords1 = {coords[0], coords[1], coords[6], coords[7]};
- paintOneBond(newCoords1, bondColor, graphics);
-
- int[] newCoords2 = {coords[2], coords[3], coords[4], coords[5]};
- paintOneBond(newCoords2, bondColor, graphics);*/
- }
-
- public void paintSingleBond(final IBond bond, final Color bondColor, final Graphics2D graphics)
- {
- logger.debug(" painting paintSingleBond " + bond.getAtom(0).getPoint2d() + " // " + bond.getAtom(1).getPoint2d());
- if (GeometryTools.has2DCoordinates(bond))
- {
- Line2D line = new Line2D.Double(
- bond.getAtom(0).getPoint2d().x,
- bond.getAtom(0).getPoint2d().y,
- bond.getAtom(1).getPoint2d().x,
- bond.getAtom(1).getPoint2d().y
- );
- paintOneBond(line, bondColor, graphics);
- }
- }
-
- /**
- * Really paints the bond. It is triggered by all the other paintbond methods
- * to draw a polygon as wide as bond width.
- *
- * @param bondColor Color of the bond
- */
- public void paintOneBond(final Line2D line, final Color bondColor, final Graphics2D graphics)
- {
- // draw the shapes
- graphics.setColor(bondColor);
- graphics.setStroke(new BasicStroke(
- (float) (rendererModel.getBondWidth()/rendererModel.getBondLength()),
- BasicStroke.CAP_ROUND, BasicStroke.JOIN_ROUND)
- );
- graphics.setColor(bondColor);
- graphics.draw(line);
- }
-
- private AffineTransform createScaleTransform(final Rectangle2D contextBounds, final Rectangle2D rendererBounds) {
- AffineTransform affinet = new AffineTransform();
-
- //scale
- double factor = rendererModel.getZoomFactor() * (1.0 - rendererModel.getMargin() * 2.0);
- double scaleX = factor * rendererBounds.getWidth() / contextBounds.getWidth();
- double scaleY = factor * rendererBounds.getHeight() / contextBounds.getHeight();
-
- if (scaleX > scaleY) {
- ////System.out.println("Scaled by Y: " + scaleY);
- // FIXME: should be -X: to put the origin in the lower left corner
- affinet.scale(scaleY, -scaleY);
- } else {
- ////System.out.println("Scaled by X: " + scaleX);
- // FIXME: should be -X: to put the origin in the lower left corner
- affinet.scale(scaleX, -scaleX);
- }
- //translate
- double scale = affinet.getScaleX();
- ////System.out.println("scale: " + scale);
- double dx = -contextBounds.getX() * scale + 0.5 * (rendererBounds.getWidth() - contextBounds.getWidth() * scale);
- double dy = -contextBounds.getY() * scale - 0.5 * (rendererBounds.getHeight() + contextBounds.getHeight() * scale);
- //System.out.println("dx: " + dx + " dy:" +dy);
- affinet.translate(dx / scale, dy / scale);
-
- return affinet;
- }
- /**
- * Returns model coordinates from screencoordinates provided by the graphics translation.
- *
- * @return Point2D in real world coordinates
- */
- public Point2d getCoorFromScreen(final int screenX, final int screenY) {
- Point2D ptSrc = new Point2D.Double(screenX, screenY);
- Point2D ptDst = new Point2D.Double();
- try {
- affine.inverseTransform(ptSrc, ptDst);
- }
- catch (Exception exception) {
- //System.out.println("Unable to reverse affine transformation");
- System.exit(0);
- }
- return new Point2d(ptDst.getX(), ptDst.getY());
- }
- /**
- * @param ptSrc in real world coordinates (ie not screencoordinates)
- */
- public static void showClosestAtomOrBond(final IAtomContainer container, final Point2d ptSrc) {
- IAtom atom = GeometryTools.getClosestAtom( ptSrc.x, ptSrc.y, container);
- double Atomdist = atom.getPoint2d().distance(ptSrc);
- //System.out.println("closest Atom distance: " + Atomdist + " Atom:" + atom);
-
- IBond bond = GeometryTools.getClosestBond( ptSrc.x, ptSrc.y, container);
- Point2d bondCenter = GeometryTools.get2DCenter(bond.atoms());
- double Bonddist = bondCenter.distance(ptSrc);
- //System.out.println("closest Bond distance: " + Bonddist + " Bond: " + bond);
- }
-
- public Rectangle2D createRectangle2D(final IAtomContainer atomCon) {
- if (atomCon == null || atomCon.getAtomCount() == 0) {
- return null;
- }
-
- float xmin, xmax = (float)atomCon.getAtom(0).getPoint2d().x;
- xmin = xmax;
- float ymin, ymax = (float)atomCon.getAtom(0).getPoint2d().y;
- ymin = ymax;
- float y,x;
- for (int i = 1; i < atomCon.getAtomCount(); i++) {
- y = (float)atomCon.getAtom(i).getPoint2d().y;
- x = (float)atomCon.getAtom(i).getPoint2d().x;
- if (x < xmin) {
- xmin = x;
- } else if (x > xmax) {
- xmax = x;
- }
- if (y < ymin) {
- ymin = y;
- } else if (y > ymax) {
- ymax = y;
- }
- }
- float margin = 1; //1 is ~enough margin to make symbols + text appear on screen
- Rectangle2D result = new Rectangle2D.Float();
- result.setRect(xmin - margin, ymin - margin, (xmax - xmin) + 2 * margin, (ymax - ymin) + 2 * margin);
- return result;
- }
- private Rectangle2D createRectangle2D(final List<?> shapes) {
- Iterator<?> it = shapes.iterator();
-
- if (it.hasNext()) {
- Rectangle2D result = ((Shape) it.next()).getBounds2D();
-
- while (it.hasNext()) {
- Rectangle2D.union(result, ((Shape) it.next()).getBounds2D(), result);
- }
-
- // FIXME: make a decent estimate for the margin
- double margin = result.getHeight() / 20; //5% margin
- if (margin < 1) {
- margin = 1; //1 is ~enough to make symbols + text appear on screen
- }
- result.setRect(result.getMinX() - margin, result.getMinY() - margin, result.getWidth() + 2 * margin, result.getHeight() + 2 * margin);
-
- return result;
- } else {
- return null;
- }
- }
-
- public Renderer2DModel getRenderer2DModel() {
- return this.rendererModel;
- }
-
- public void setRenderer2DModel(final Renderer2DModel model) {
- this.rendererModel = model;
- }
-}
Modified: cdk/branches/egonw-jchempaint/src/main/org/openscience/cdk/renderer/Renderer2DModel.java
===================================================================
--- cdk/branches/egonw-jchempaint/src/main/org/openscience/cdk/renderer/Renderer2DModel.java 2008-10-15 11:56:09 UTC (rev 12708)
+++ cdk/branches/egonw-jchempaint/src/main/org/openscience/cdk/renderer/Renderer2DModel.java 2008-10-15 11:56:46 UTC (rev 12709)
@@ -1,4 +1,4 @@
-/* $Revision$ $Author$ $Date$
+/* $Revision: 12144 $ $Author: egonw $ $Date: 2008-09-02 22:53:30 +0200 (Tue, 02 Sep 2008) $
*
* Copyright (C) 1997-2007 The Chemistry Development Kit (CDK) project
*
@@ -51,9 +51,9 @@
* Model for {@link Renderer2DModel} that contains settings for drawing objects.
*
* @cdk.module render
- * @cdk.svnrev $Revision$
+ * @cdk.svnrev $Revision: 12144 $
*/
-public class Renderer2DModel implements java.io.Serializable, Cloneable {
+public class Renderer2DModel implements IRenderingParameters, java.io.Serializable, Cloneable {
private static final long serialVersionUID = -4420308906715213445L;
@@ -77,8 +77,7 @@
private Color externalHighlightColor = Color.orange;
/**
- * @deprecated old way of storing highlightRadius based on screensize,
- * new one: {@link #highlightRadiusModel}
+ * @deprecated old way of storing highlightRadius based on screensize, new one: {@link #highlightRadiusModel()}
*/
@Deprecated private double highlightRadius = 10.0;
private double highlightRadiusModel = 0.7;
@@ -543,8 +542,7 @@
* marked highlighted if a pointer device is placed within this radius.
*
* @param highlightRadius the highlight radius of all atoms (in screensize)
- * @deprecated old way of getting highlightRadius,
- * new one: {@link #setHighlightRadiusModel(double)}
+ * @deprecated old way of getting highlightRadius, new one: {@link #setHighlightRadiusModel()}
*/
@Deprecated public void setHighlightRadius(double highlightRadius)
{
Copied: cdk/branches/egonw-jchempaint/src/main/org/openscience/cdk/renderer/basic/Java2DRenderer.java (from rev 12708, cdk/branches/egonw-jchempaint/src/main/org/openscience/cdk/renderer/Java2DRenderer.java)
===================================================================
--- cdk/branches/egonw-jchempaint/src/main/org/openscience/cdk/renderer/basic/Java2DRenderer.java (rev 0)
+++ cdk/branches/egonw-jchempaint/src/main/org/openscience/cdk/renderer/basic/Java2DRenderer.java 2008-10-15 11:56:46 UTC (rev 12709)
@@ -0,0 +1,1256 @@
+/* $Revision: 7636 $ $Author: nielsout $ $Date: 2007-09-02 11:46:10 +0100 (su, 02 sep 2007) $
+ *
+ * Copyright (C) 2007 Niels Out <nie...@us...>
+ * 2008 Thorsten Meinl <Tho...@un...>
+ *
+ * Contact: cdk...@li...
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ * All I ask is that proper credit is given for my work, which includes
+ * - but is not limited to - adding the above copyright notice to the beginning
+ * of your source code files, and to any copyright notice that you may distribute
+ * with programs based on this work.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ */
+package org.openscience.cdk.renderer.basic;
+
+import java.awt.BasicStroke;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.Graphics2D;
+import java.awt.RenderingHints;
+import java.awt.Shape;
+import java.awt.font.FontRenderContext;
+import java.awt.font.TextLayout;
+import java.awt.geom.AffineTransform;
+import java.awt.geom.Ellipse2D;
+import java.awt.geom.GeneralPath;
+import java.awt.geom.Line2D;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+
+import javax.vecmath.Point2d;
+
+import org.openscience.cdk.CDKConstants;
+import org.openscience.cdk.config.IsotopeFactory;
+import org.openscience.cdk.geometry.GeometryTools;
+import org.openscience.cdk.graph.ConnectivityChecker;
+import org.openscience.cdk.interfaces.IAtom;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.IBond;
+import org.openscience.cdk.interfaces.IChemModel;
+import org.openscience.cdk.interfaces.IIsotope;
+import org.openscience.cdk.interfaces.IMoleculeSet;
+import org.openscience.cdk.interfaces.IPseudoAtom;
+import org.openscience.cdk.interfaces.IReaction;
+import org.openscience.cdk.interfaces.IReactionSet;
+import org.openscience.cdk.interfaces.IRing;
+import org.openscience.cdk.interfaces.IRingSet;
+import org.openscience.cdk.renderer.IJava2DRenderer;
+import org.openscience.cdk.renderer.IRenderingParameters;
+import org.openscience.cdk.renderer.Renderer2DModel;
+import org.openscience.cdk.ringsearch.SSSRFinder;
+import org.openscience.cdk.tools.LoggingTool;
+import org.openscience.cdk.tools.manipulator.RingSetManipulator;
+import org.openscience.cdk.validate.ProblemMarker;
+
+/**
+ * A Java2D based 2D renderer for IChemObjects.
+ *
+ * @author nielsout
+ * @cdk.svnrev $Revision: 9162 $
+ * @cdk.module render
+ */
+public class Java2DRenderer implements IJava2DRenderer {
+
+ private Renderer2DModel rendererModel;
+ private AffineTransform affine;
+
+ protected LoggingTool logger;
+ IsotopeFactory isotopeFactory;
+
+ public Java2DRenderer(final Renderer2DModel model) {
+ this.rendererModel = model;
+ logger = new LoggingTool(this);
+ }
+
+ public void paintChemModel(final IChemModel model, final Graphics2D graphics) {
+ // TODO Auto-generated method stub
+
+ }
+
+ public void paintMoleculeSet(final IMoleculeSet moleculeSet, final Graphics2D graphics) {
+ // TODO Auto-generated method stub
+
+ }
+
+ public void paintReaction(final IReaction reaction, final Graphics2D graphics) {
+ // TODO Auto-generated method stub
+
+ }
+
+ public void paintReactionSet(final IReactionSet reactionSet, final Graphics2D graphics) {
+ // TODO Auto-generated method stub
+
+ }
+ /**
+ * Paint the given Molecule on the graphics object at location specified by bounds.
+ *
+ *@param atomCon The molecule to be drawn
+ *@param graphics Graphics2D to draw on
+ */
+ public void paintMolecule(final IAtomContainer atomCon, final Graphics2D graphics) {
+
+
+ if (affine == null) {
+ logger.debug("paintMolecule should be called first time with the bounds of the graphical object..");
+ logger.warn("Cannot paintMolecule without transform Matrix");
+ return;
+ }
+ graphics.transform(affine);
+ logger.debug("transform matrix:" + graphics.getTransform());
+
+ if (rendererModel.getUseAntiAliasing())
+ {
+ graphics.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
+ }
+ // set basic shape form for bonds
+ graphics.setColor(Color.BLACK);
+ graphics.setStroke(new BasicStroke(
+ (float) (rendererModel.getBondWidth()/rendererModel.getBondLength()),
+ BasicStroke.CAP_ROUND, BasicStroke.JOIN_ROUND)
+ );
+
+ IRingSet ringSet = getRingSet(atomCon);
+
+ // draw bonds
+ paintBonds(atomCon, ringSet, graphics);
+
+ // draw atom symbols
+ paintAtoms(atomCon, graphics);
+ logger.debug("transform matrix:" + graphics.getTransform());
+
+ }
+ /**
+ * Paint the given Molecule on the graphics object at location specified by bounds.
+ *
+ *@param atomCon The molecule to be drawn
+ *@param graphics Graphics2D to draw on
+ *@param bounds
+ */
+ public void paintMolecule(final IAtomContainer atomCon, final Graphics2D graphics,
+ final Rectangle2D bounds) {
+ //rendererModel.setShowAromaticity(true);
+
+ // calculate the molecule boundaries via the atomContainer
+ Rectangle2D molBounds = createRectangle2D(atomCon);
+ if (molBounds == null || molBounds.isEmpty()) {
+ logger.debug("empty atomCon? -> no molBounds -> no drawing ");
+ return;
+ }
+ AffineTransform transformMatrix = createScaleTransform(molBounds,bounds);
+ affine = transformMatrix;
+
+ paintMolecule(atomCon, graphics);
+ }
+ protected IRingSet getRingSet(final IAtomContainer atomContainer)
+ {
+ IRingSet ringSet = atomContainer.getBuilder().newRingSet();
+ IMoleculeSet molecules;
+ try
+ {
+ molecules = ConnectivityChecker.partitionIntoMolecules(atomContainer);
+ }
+
+ catch (Exception exception)
+ {
+ logger.warn("Could not partition molecule: ", exception.getMessage());
+ logger.debug(exception);
+ return ringSet;
+ }
+
+ for (IAtomContainer mol : molecules.molecules()) {
+ SSSRFinder sssrf = new SSSRFinder(mol);
+
+ ringSet.add(sssrf.findSSSR());
+ }
+
+ return ringSet;
+ }
+ /**
+ * Triggers paintAtom method for all the atoms in the given array of atoms.
+ *
+ * @param atomCon
+ * @param graphics
+ */
+ public void paintAtoms(final IAtomContainer atomCon, final Graphics2D graphics)
+ {
+ for (int i = 0; i < atomCon.getAtomCount(); i++)
+ {
+ paintAtom(atomCon, atomCon.getAtom(i), graphics);
+ }
+ }
+ /**
+ * triggers the
+ * paintColouredAtoms method if the atom has got a certain color and triggers
+ * the paintAtomSymbol method if the symbol of the atom is not C
+ *
+ * @param container
+ * @param atom
+ * @param graphics
+ */
+ public void paintAtom(final IAtomContainer container, final IAtom atom, final Graphics2D graphics)
+ {
+ logger.debug("paintAtom Symbol:" + atom.getSymbol() + " atom:" + atom);
+
+
+
+ boolean drawSymbol = false; //paint all Atoms for the time being
+ boolean isRadical = (container.getConnectedSingleElectronsCount(atom) > 0);
+ if (atom instanceof IPseudoAtom)
+ {
+ drawSymbol = false;
+// if (atom instanceof FragmentAtom) {
+// paintFragmentAtom((FragmentAtom)atom, atomBackColor, graphics,
+// alignment, isRadical);
+// } else {
+ // paintPseudoAtomLabel((IPseudoAtom) atom, atomBackColor, graphics, alignment, isRadical);
+// }
+ logger.debug("call paintPseudoAtomLabel here?");
+ return;
+ } else if ("H".equals(atom.getSymbol())
+ && !getRenderer2DModel().getShowExplicitHydrogens()) {
+ drawSymbol = false;
+ } else if (!atom.getSymbol().equals("C"))
+ {
+ /*
+ * only show element for non-carbon atoms,
+ * unless (see below)...
+ */
+ drawSymbol = true;
+ } else if (getRenderer2DModel().getKekuleStructure())
+ {
+ // ... unless carbon must be drawn because in Kekule mode
+ drawSymbol = true;
+ } else if (atom.getFormalCharge() != 0)
+ {
+ // ... unless carbon is charged
+ drawSymbol = true;
+ } else if (container.getConnectedBondsList(atom).size() < 1)
+ {
+ // ... unless carbon is unbonded
+ drawSymbol = true;
+ } else if (getRenderer2DModel().getShowEndCarbons() && (container.getConnectedBondsList(atom).size() == 1))
+ {
+ drawSymbol = true;
+ } else if (atom.getProperty(ProblemMarker.ERROR_MARKER) != null)
+ {
+ // ... unless carbon is unbonded
+ drawSymbol = true;
+ } else if (atom.getMassNumber() != null)
+ {
+ try
+ {
+ if (atom.getMassNumber() != IsotopeFactory.getInstance(container.getBuilder()).
+ getMajorIsotope(atom.getSymbol()).getMassNumber())
+ {
+ drawSymbol = true;
+ }
+ } catch (Exception exception) {
+ logger.debug("Could not get an instance of IsotopeFactory");
+ }
+
+ } else if (isRadical) {
+ drawSymbol = true;
+ }
+
+ if (drawSymbol == true) {
+ int alignment = GeometryTools.getBestAlignmentForLabelXY(container, atom);
+ //System.out.println("alignment: " + alignment);
+ paintAtomSymbol(atom, graphics, alignment, isRadical);
+ }
+ }
+ public void paintAtomSymbol(final IAtom atom, final Graphics2D graphics, final int alignment, final boolean isRadical)
+ {
+ Color saveColor = graphics.getColor();
+ String symbol = "";
+
+ if (atom.getSymbol() != null) {
+ symbol = atom.getSymbol();
+ }
+ //symbol = "Mg"; //to test if a certain symbol is spaced out right
+
+
+ Font fontAtom;
+ if (rendererModel.getFont() != null) {
+ fontAtom = rendererModel.getFont();
+ logger.debug("the font is now: " + fontAtom);
+ } else {
+ fontAtom = new Font("Arial", Font.PLAIN, 12);
+ }
+
+ //the graphics objects has a transform which is 'reversed' to go from world coordinates
+ //to screencoordinates, so transform the characters back to show them 'up-side-up'.
+ double fscale = 0.055;
+ double[] transmatrix = { fscale, 0, 0, -fscale};
+ AffineTransform trans = new AffineTransform(transmatrix);
+ fontAtom = fontAtom.deriveFont(trans);
+
+ //FIXME: add this 0.4 in the RendererModel
+ float sizeSmall = (float)(fontAtom.getSize2D() * 0.4);
+ Font fontSmall = fontAtom.deriveFont(sizeSmall); //font for upper/lower text such as Massnumber, Charges, HydrogenCount etc..
+
+ graphics.setFont(fontAtom);
+
+ FontRenderContext frc = graphics.getFontRenderContext();
+ TextLayout layoutAtom = new TextLayout(symbol, fontAtom, frc);
+ Rectang...
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