From: <raj...@us...> - 2006-09-19 15:34:54
|
Revision: 6947 http://svn.sourceforge.net/cdk/?rev=6947&view=rev Author: rajarshi Date: 2006-09-19 08:34:40 -0700 (Tue, 19 Sep 2006) Log Message: ----------- Fixed PMD warnings Modified Paths: -------------- trunk/cdk/src/org/openscience/cdk/renderer/AlphaRenderer2D.java trunk/cdk/src/org/openscience/cdk/renderer/ArrowRenderer2D.java trunk/cdk/src/org/openscience/cdk/renderer/Renderer2D.java trunk/cdk/src/org/openscience/cdk/renderer/Renderer2DModel.java trunk/cdk/src/org/openscience/cdk/renderer/color/CDK2DAtomColors.java trunk/cdk/src/org/openscience/cdk/renderer/color/CPKAtomColors.java Modified: trunk/cdk/src/org/openscience/cdk/renderer/AlphaRenderer2D.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/renderer/AlphaRenderer2D.java 2006-09-19 15:22:26 UTC (rev 6946) +++ trunk/cdk/src/org/openscience/cdk/renderer/AlphaRenderer2D.java 2006-09-19 15:34:40 UTC (rev 6947) @@ -28,18 +28,16 @@ */ package org.openscience.cdk.renderer; -import java.awt.Color; -import java.awt.Graphics2D; -import java.awt.Shape; -import java.awt.geom.Area; -import java.awt.geom.Rectangle2D; - import org.openscience.cdk.graph.ConnectivityChecker; import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IRingSet; import org.openscience.cdk.ringsearch.SSSRFinder; import org.openscience.cdk.tools.LoggingTool; +import java.awt.*; +import java.awt.geom.Area; +import java.awt.geom.Rectangle2D; + /** * A subclass of Renderer2D that uses masks (Area Class) to make an area * erased to background. @@ -69,28 +67,23 @@ logger = new LoggingTool(this); } - public void paintEmptySpace(int x, int y, int w, int h, int border, Color backColor, Graphics2D g) + public void paintEmptySpace(int x, int y, int width, int height, int border, Color backColor, Graphics2D g) { - if ((w == 0) || (h == 0)) - { - // don't bother - we have nothing to paint - } - int[] coords = { x - border, y + border }; - double[] bounds = { getScreenSize(w + 2 * border), getScreenSize(h + 2 * border)}; + double[] bounds = { getScreenSize(width + 2 * border), getScreenSize(height + 2 * border)}; int[] screenCoords = getScreenCoordinates(coords); mask.subtract(new Area(new Rectangle2D.Double(screenCoords[0], screenCoords[1], bounds[0], bounds[1]))); } -protected IRingSet getRingSet(IAtomContainer atomCon) +protected IRingSet getRingSet(IAtomContainer atomContainer) { - IRingSet ringSet = atomCon.getBuilder().newRingSet(); + IRingSet ringSet = atomContainer.getBuilder().newRingSet(); org.openscience.cdk.interfaces.IMolecule[] molecules = null; try { - molecules = ConnectivityChecker.partitionIntoMolecules(atomCon).getMolecules(); + molecules = ConnectivityChecker.partitionIntoMolecules(atomContainer).getMolecules(); } catch (Exception exception) @@ -110,7 +103,7 @@ return ringSet; } -public void paintMolecule(IAtomContainer atomCon, Graphics2D graphics) +public void paintMolecule(IAtomContainer atomContainer, Graphics2D graphics) { // make the initial mask cover the entire dimension we are going to paint mask = @@ -121,11 +114,11 @@ paintPointerVector(graphics); } - paintAtoms(atomCon, graphics); + paintAtoms(atomContainer, graphics); Shape oldClip = graphics.getClip(); graphics.setClip(mask); - paintBonds(atomCon, getRingSet(atomCon), graphics); + paintBonds(atomContainer, getRingSet(atomContainer), graphics); graphics.setClip(oldClip); paintLassoLines(graphics); Modified: trunk/cdk/src/org/openscience/cdk/renderer/ArrowRenderer2D.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/renderer/ArrowRenderer2D.java 2006-09-19 15:22:26 UTC (rev 6946) +++ trunk/cdk/src/org/openscience/cdk/renderer/ArrowRenderer2D.java 2006-09-19 15:34:40 UTC (rev 6947) @@ -29,20 +29,17 @@ */ package org.openscience.cdk.renderer; -import java.awt.Dimension; -import java.awt.Graphics2D; -import java.awt.Polygon; -import java.awt.geom.Arc2D; -import java.awt.geom.Ellipse2D; - -import javax.vecmath.Point2d; -import javax.vecmath.Vector2d; - import org.openscience.cdk.geometry.GeometryTools; import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.tools.LoggingTool; +import javax.vecmath.Point2d; +import javax.vecmath.Vector2d; +import java.awt.*; +import java.awt.geom.Arc2D; +import java.awt.geom.Ellipse2D; + /** * A Renderer class which draws 2D representations of curly arrows as used for * representing electron movements in organic chemistry text books. @@ -62,7 +59,7 @@ double rotAngle; double offsetAngle; Point2d center; - Vector2d v3; + Vector2d vector3; //private Vector points = new Vector(16, 4); @@ -104,8 +101,8 @@ Dimension ss = r2dm.getBackgroundDimension(); Arc2D.Double arc = contructArc(arrow); graphics.draw(arc); - Polygon p = contructArrowHead(arc); - graphics.fill(p); + Polygon polygon = contructArrowHead(arc); + graphics.fill(polygon); graphics.draw(contructArrowHead(arc)); graphics.draw(new Ellipse2D.Double(center.x, ss.getHeight() - center.y, 10,10)); } @@ -116,26 +113,26 @@ IAtom start = arrow.getStart(); IAtom end = arrow.getEnd(); Arc2D.Double arc = new Arc2D.Double(); - IAtomContainer ac = start.getBuilder().newAtomContainer(); - ac.addAtom(start); - ac.addAtom(end); - center = GeometryTools.get2DCenter(ac,r2dm.getRenderingCoordinates()); - Point2d p1 = new Point2d((Point2d)r2dm.getRenderingCoordinate(start)); - Point2d p2 = new Point2d((Point2d)r2dm.getRenderingCoordinate(end)); - Vector2d v1 = new Vector2d(p1); - Vector2d v2 = new Vector2d(p2); - v2.sub(v1); + IAtomContainer atomContainer = start.getBuilder().newAtomContainer(); + atomContainer.addAtom(start); + atomContainer.addAtom(end); + center = GeometryTools.get2DCenter(atomContainer,r2dm.getRenderingCoordinates()); + Point2d point1 = new Point2d((Point2d)r2dm.getRenderingCoordinate(start)); + Point2d point2 = new Point2d((Point2d)r2dm.getRenderingCoordinate(end)); + Vector2d vector1 = new Vector2d(point1); + Vector2d vector2 = new Vector2d(point2); + vector2.sub(vector1); - rotAngle = GeometryTools.getAngle(v2.x, v2.y); + rotAngle = GeometryTools.getAngle(vector2.x, vector2.y); offsetAngle = rotAngle + (Math.PI/2); - v3 = new Vector2d(Math.cos(offsetAngle), Math.sin(offsetAngle)); - v3.normalize(); - v3.scale(20); - center.add(v3); + vector3 = new Vector2d(Math.cos(offsetAngle), Math.sin(offsetAngle)); + vector3.normalize(); + vector3.scale(20); + center.add(vector3); System.out.println("rotAngle: " + rotAngle * 360 / (Math.PI * 2)); System.out.println("offsetAngle: " + offsetAngle * 360 / (Math.PI * 2)); - arc.setArcByCenter(center.x, ss.height - center.y, p1.distance(p2)/2,(rotAngle* 360 / (Math.PI * 2)),180,Arc2D.OPEN ); + arc.setArcByCenter(center.x, ss.height - center.y, point1.distance(point2)/2,(rotAngle* 360 / (Math.PI * 2)),180,Arc2D.OPEN ); return arc; } @@ -145,20 +142,20 @@ Polygon polygon = new Polygon(); double wingOffset = (Math.PI/18); - Vector2d v2 = new Vector2d(Math.cos(offsetAngle - wingOffset ), Math.sin(offsetAngle - wingOffset)); - Vector2d v3 = new Vector2d(Math.cos(offsetAngle + wingOffset), Math.sin(offsetAngle + wingOffset )); - Point2d p2 = new Point2d(arc.getStartPoint().getX(), arc.getStartPoint().getY()); - Point2d p3 = new Point2d(arc.getStartPoint().getX(), arc.getStartPoint().getY()); - v2.normalize(); - v2.scale(10); - v3.normalize(); - v3.scale(10); + Vector2d vector2 = new Vector2d(Math.cos(offsetAngle - wingOffset ), Math.sin(offsetAngle - wingOffset)); + Vector2d vector3 = new Vector2d(Math.cos(offsetAngle + wingOffset), Math.sin(offsetAngle + wingOffset )); + Point2d point2 = new Point2d(arc.getStartPoint().getX(), arc.getStartPoint().getY()); + Point2d point3 = new Point2d(arc.getStartPoint().getX(), arc.getStartPoint().getY()); + vector2.normalize(); + vector2.scale(10); + vector3.normalize(); + vector3.scale(10); //Dimension ss = r2dm.getBackgroundDimension(); - p2.add(v2); - p3.add(v3); + point2.add(vector2); + point3.add(vector3); polygon.addPoint((int)arc.getStartPoint().getX(), (int)arc.getStartPoint().getY()); - polygon.addPoint((int)p2.x, (int)p2.y); - polygon.addPoint((int)p3.x, (int)p3.y); + polygon.addPoint((int)point2.x, (int)point2.y); + polygon.addPoint((int)point3.x, (int)point3.y); return polygon; } Modified: trunk/cdk/src/org/openscience/cdk/renderer/Renderer2D.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/renderer/Renderer2D.java 2006-09-19 15:22:26 UTC (rev 6946) +++ trunk/cdk/src/org/openscience/cdk/renderer/Renderer2D.java 2006-09-19 15:34:40 UTC (rev 6947) @@ -29,21 +29,15 @@ */ package org.openscience.cdk.renderer; -import java.awt.Graphics2D; -import java.util.Iterator; - import org.openscience.cdk.CDKConstants; 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.IChemModel; -import org.openscience.cdk.interfaces.IChemObject; -import org.openscience.cdk.interfaces.IMapping; -import org.openscience.cdk.interfaces.IMolecule; -import org.openscience.cdk.interfaces.IReaction; +import org.openscience.cdk.interfaces.*; import org.openscience.cdk.tools.manipulator.SetOfMoleculesManipulator; +import java.awt.*; +import java.util.Iterator; + /** * A Renderer class which draws 2D representations of molecules onto a given * graphics objects using information from a Renderer2DModel. <p> @@ -198,9 +192,9 @@ paintMolecule(molecules[i], graphics,false, redossr); } if(r2dm.getMerge()!=null){ - Iterator it=r2dm.getMerge().keySet().iterator(); - while(it.hasNext()){ - IAtom atom1=(IAtom)it.next(); + Iterator iterator =r2dm.getMerge().keySet().iterator(); + while(iterator.hasNext()){ + IAtom atom1=(IAtom)iterator.next(); int[] coords = { (int)atom1.getPoint2d().x,(int)atom1.getPoint2d().y}; int[] screenCoords = getScreenCoordinates(coords); graphics.setColor(r2dm.getSelectedPartColor()); Modified: trunk/cdk/src/org/openscience/cdk/renderer/Renderer2DModel.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/renderer/Renderer2DModel.java 2006-09-19 15:22:26 UTC (rev 6946) +++ trunk/cdk/src/org/openscience/cdk/renderer/Renderer2DModel.java 2006-09-19 15:34:40 UTC (rev 6947) @@ -27,18 +27,6 @@ * */ package org.openscience.cdk.renderer; -import java.awt.Color; -import java.awt.Dimension; -import java.awt.Font; -import java.awt.Point; -import java.awt.Polygon; -import java.util.EventObject; -import java.util.HashMap; -import java.util.Hashtable; -import java.util.Vector; - -import javax.vecmath.Point2d; - import org.openscience.cdk.event.ICDKChangeListener; import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IAtomContainer; @@ -46,6 +34,13 @@ import org.openscience.cdk.renderer.color.CDK2DAtomColors; import org.openscience.cdk.renderer.color.IAtomColorer; +import javax.vecmath.Point2d; +import java.awt.*; +import java.util.EventObject; +import java.util.HashMap; +import java.util.Hashtable; +import java.util.Vector; + /** * Model for Renderer2D that contains settings for drawing objects. * @@ -79,7 +74,7 @@ private double highlightRadius = 10.0; - private boolean drawNumbers = false; + private boolean willDrawNumbers = false; private boolean showAtomAtomMapping = true; @@ -427,7 +422,7 @@ */ public boolean drawNumbers() { - return this.drawNumbers; + return this.willDrawNumbers; } public boolean getKekuleStructure() { @@ -491,7 +486,7 @@ */ public void setDrawNumbers(boolean drawNumbers) { - this.drawNumbers = drawNumbers; + this.willDrawNumbers = drawNumbers; fireChange(); } @@ -499,7 +494,7 @@ * Returns true if atom numbers are drawn. */ public boolean getDrawNumbers() { - return drawNumbers; + return willDrawNumbers; } @@ -582,14 +577,11 @@ */ public void setHighlightedAtom(IAtom highlightedAtom) { - if ((this.highlightedAtom == null) && - (highlightedAtom == null)) { - // do not do anything, nothing has changed - } else { + if ((this.highlightedAtom != null) || (highlightedAtom != null)) { this.highlightedAtom = highlightedAtom; fireChange(); } - } + } @@ -611,14 +603,11 @@ */ public void setHighlightedBond(IBond highlightedBond) { - if ((this.highlightedBond == null) && - (highlightedBond == null)) { - // do not do anything, nothing has changed - } else { + if ((this.highlightedBond != null) || (highlightedBond != null)) { this.highlightedBond = highlightedBond; fireChange(); } - } + } @@ -683,11 +672,11 @@ /** * Sets the atom colorer. * - * @param ac the new colorer. + * @param atomColorer the new colorer. */ - public void setAtomColorer(final IAtomColorer ac) + public void setAtomColorer(final IAtomColorer atomColorer) { - colorer = ac; + colorer = atomColorer; } /** @@ -901,29 +890,29 @@ /** - * Gets the toolTipText for a certain atom. + * Gets the toolTipText for atom certain atom. * - * @param a The atom. + * @param atom The atom. * @return The toolTipText value. */ - public String getToolTipText(IAtom a) { - if (toolTipTextMap.get(a) != null) { - return ((String) toolTipTextMap.get(a)); - } else { - return (null); - } + public String getToolTipText(IAtom atom) { + if (toolTipTextMap.get(atom) != null) { + return ((String) toolTipTextMap.get(atom)); + } else { + return null; + } } - - - /** + + + /** * Sets the showTooltip attribute. * - * @param b The new value. + * @param showToolTip The new value. */ - public void setShowTooltip(boolean b){ - showTooltip=b; + public void setShowTooltip(boolean showToolTip) { + this.showTooltip = showToolTip; fireChange(); - } + } /** Modified: trunk/cdk/src/org/openscience/cdk/renderer/color/CDK2DAtomColors.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/renderer/color/CDK2DAtomColors.java 2006-09-19 15:22:26 UTC (rev 6946) +++ trunk/cdk/src/org/openscience/cdk/renderer/color/CDK2DAtomColors.java 2006-09-19 15:34:40 UTC (rev 6947) @@ -24,10 +24,10 @@ */ package org.openscience.cdk.renderer.color; -import java.awt.Color; - import org.openscience.cdk.interfaces.IAtom; +import java.awt.*; + /** * Gives a short table of atom colors for 2D display. * @@ -50,33 +50,33 @@ return getAtomColor(a, DEFAULT); } - public Color getAtomColor(IAtom a, Color defaultColor) { - Color c = defaultColor; - int atomnumber = a.getAtomicNumber(); + public Color getAtomColor(IAtom atom, Color defaultColor) { + Color color = defaultColor; + int atomnumber = atom.getAtomicNumber(); if (atomnumber != 0) { switch (atomnumber) { - case 1: c = CDK2DAtomColors.HYDROGEN; break; - case 6: c = CDK2DAtomColors.CARBON; break; - case 7: c = CDK2DAtomColors.NITROGEN; break; - case 8: c = CDK2DAtomColors.OXYGEN; break; - case 15: c = CDK2DAtomColors.PHOSPHORUS; break; - case 16: c = CDK2DAtomColors.SULPHUR; break; + case 1: color = CDK2DAtomColors.HYDROGEN; break; + case 6: color = CDK2DAtomColors.CARBON; break; + case 7: color = CDK2DAtomColors.NITROGEN; break; + case 8: color = CDK2DAtomColors.OXYGEN; break; + case 15: color = CDK2DAtomColors.PHOSPHORUS; break; + case 16: color = CDK2DAtomColors.SULPHUR; break; } } else { - String symbol = a.getSymbol(); + String symbol = atom.getSymbol(); if (symbol.equals("N")) { - c = CDK2DAtomColors.NITROGEN; + color = CDK2DAtomColors.NITROGEN; } if (symbol.equals("O")) { - c = CDK2DAtomColors.OXYGEN; + color = CDK2DAtomColors.OXYGEN; } if (symbol.equals("P")) { - c = CDK2DAtomColors.PHOSPHORUS; + color = CDK2DAtomColors.PHOSPHORUS; } if (symbol.equals("S")) { - c = CDK2DAtomColors.SULPHUR; + color = CDK2DAtomColors.SULPHUR; } } - return c; + return color; } } Modified: trunk/cdk/src/org/openscience/cdk/renderer/color/CPKAtomColors.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/renderer/color/CPKAtomColors.java 2006-09-19 15:22:26 UTC (rev 6946) +++ trunk/cdk/src/org/openscience/cdk/renderer/color/CPKAtomColors.java 2006-09-19 15:34:40 UTC (rev 6947) @@ -24,11 +24,11 @@ */ package org.openscience.cdk.renderer.color; -import java.awt.Color; +import org.openscience.cdk.interfaces.IAtom; + +import java.awt.*; import java.util.HashMap; -import org.openscience.cdk.interfaces.IAtom; - /** * Colors atoms using CPK color scheme {@cdk.cite BER2001}. * @@ -133,38 +133,38 @@ ////////// /** - * Returns the font color for a given atom. + * Returns the font color for atom given atom. * - * @param a the atom. + * @param atom the atom. * @return A color for the atom. */ - public Color getAtomColor(IAtom a) + public Color getAtomColor(IAtom atom) { - return getAtomColor(a, DEEP_PINK); + return getAtomColor(atom, DEEP_PINK); } /** - * Returns the font color for a given atom. + * Returns the font color for atom given atom. * - * @param a the atom. - * @param defaultColor a default color. + * @param atom the atom. + * @param defaultColor atom default color. * @return A color for the atom. The default colour is used if none is * found for the atom. */ - public Color getAtomColor(IAtom a, Color defaultColor) + public Color getAtomColor(IAtom atom, Color defaultColor) { - Color c = defaultColor; - Integer number = new Integer(a.getAtomicNumber()); - String symbol = a.getSymbol().toUpperCase(); + Color color = defaultColor; + Integer number = new Integer(atom.getAtomicNumber()); + String symbol = atom.getSymbol().toUpperCase(); if (ATOM_COLORS.containsKey(number)) { - c = (Color) ATOM_COLORS.get(number); // lookup by atomic number. + color = (Color) ATOM_COLORS.get(number); // lookup by atomic number. } else if (ATOM_COLORS.containsKey(symbol)) { - c = (Color) ATOM_COLORS.get(symbol); // lookup by atomic symbol. + color = (Color) ATOM_COLORS.get(symbol); // lookup by atomic symbol. } - return new Color(c.getRed(), c.getGreen(), c.getBlue()); // return a copy. + return new Color(color.getRed(), color.getGreen(), color.getBlue()); // return atom copy. } } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |