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Improved generic label formatting, superscript numbers/primes and mak…
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…e labels italic. This allows clear distinction between the substituent list 'W' and 'Tungsten'.
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@johnmay @egonw
johnmay authored and egonw committed Feb 13, 2016
1 parent 23041fc commit 177e84c
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Showing 3 changed files with 165 additions and 21 deletions.
156 changes: 136 additions & 20 deletions ...src/main/java/org/openscience/cdk/renderer/generators/standard/StandardAtomGenerator.java
View file
Expand Up @@ -45,37 +45,39 @@

/**
* Generates {@link AtomSymbol} instances with positioned adjuncts.
*
* <p/>
* <p/> Note the generator is purposefully not an {@link org.openscience.cdk.renderer.generators.IGenerator}
* and is intended as part be called from the StandardGenerator.
*
* @author John May
*/
final class StandardAtomGenerator {

/** Default options for spacing and sizing adjuncts, could be configruable parameters. */
/**
* Default options for spacing and sizing adjuncts, could be configruable parameters.
*/
private final static double DEFAULT_ADJUNCT_SPACING_RATIO = 0.15d;
private final static double DEFAULT_SUBSCRIPT_SIZE = 0.6d;

/**
* The font used in the symbol.
*/
private final Font font;
private final Font font;

/**
* Relative size of the adjunct sub/super script labels (0-1).
*/
private final double scriptSize;
private final double scriptSize;

/**
* The absolute distance to 'pad' adjunct positioning with.
*/
private final double padding;
private final double padding;

/**
* Text outline is immutable so we can create a hydrogen are reuse it.
*/
private final TextOutline defaultHydrogenLabel;
private final TextOutline defaultHydrogenLabel;

/**
* Create a standard atom generator using the specified font.
Expand Down Expand Up @@ -129,8 +131,8 @@ AtomSymbol generateSymbol(IAtomContainer container, IAtom atom, HydrogenPosition
}

return generatePeriodicSymbol(number, unboxSafely(atom.getImplicitHydrogenCount(), 0),
unboxSafely(mass, -1), unboxSafely(atom.getFormalCharge(), 0),
container.getConnectedSingleElectronsCount(atom), position);
unboxSafely(mass, -1), unboxSafely(atom.getFormalCharge(), 0),
container.getConnectedSingleElectronsCount(atom), position);
}
}

Expand All @@ -140,6 +142,118 @@ AtomSymbol generateSymbol(IAtomContainer container, IAtom atom, HydrogenPosition
* @return the atom symbol
*/
AtomSymbol generatePseudoSymbol(String label, HydrogenPosition position) {

final Font italicFont = font.deriveFont(Font.BOLD)
.deriveFont(Font.ITALIC);
List<TextOutline> outlines = new ArrayList<>(3);

int beg = 0;
int pos = 0;
int len = label.length();

// upper case followed by lower case
while (pos < len && isUpperCase(label.charAt(pos)))
pos++;
if (label.charAt(0) != 'R') // Ar is not A^r but 'Ra' is R^a etc
while (pos < len && isLowerCase(label.charAt(pos)))
pos++;

if (pos > beg) {
outlines.add(new TextOutline(label.substring(beg, pos), italicFont));
beg = pos;
// 2a etc.
while (pos < len && isDigit(label.charAt(pos)))
pos++;
while (pos < len && isLowerCase(label.charAt(pos)))
pos++;

if (pos > beg) {
TextOutline outline = new TextOutline(label.substring(beg, pos), italicFont);
outline = outline.resize(scriptSize, scriptSize);
outline = positionSuperscript(outlines.get(0), outline);
outlines.add(outline);
}

int numPrimes = 0;
PRIMES:
while (pos < len) {
switch (label.charAt(pos)) {
case '\'': numPrimes++; break;
case '`': numPrimes++; break;
case '‘': numPrimes++; break;
case '’': numPrimes++; break;
case '‛': numPrimes++; break;
case '“': numPrimes+=2; break;
case '”': numPrimes+=2; break;
case '′': numPrimes++; break;
case '″': numPrimes+=2; break;
case '‴': numPrimes+=3; break;
case '⁗': numPrimes+=4; break;
case '‵': numPrimes++; break;
case '‶': numPrimes+=2; break;
case '‷': numPrimes+=3; break;
case '´': numPrimes++; break;
case 'ˊ': numPrimes++; break;
case '́': numPrimes++; break;
case '˝': numPrimes+=2; break;
case '̋': numPrimes+=2; break;
default: break PRIMES;
}
pos++;
}

if (pos < len) {
return new AtomSymbol(new TextOutline(label, italicFont), Collections.<TextOutline>emptyList());
} else {
TextOutline outline = null;
TextOutline ref = outlines.get(outlines.size()-1);
switch (numPrimes) {
case 0: break;
case 1: outline = new TextOutline("′", font); break;
case 2: outline = new TextOutline("″", font); break;
case 3: outline = new TextOutline("‴", font); break;
default:
String lab = "";
while (numPrimes-->0)
lab += "′";
outline = new TextOutline(lab, font);
break;
}
if (outline != null) {
if (outlines.size() > 1)
outline = outline.resize(scriptSize, scriptSize);
outline = positionSuperscript(ref, outline);
outlines.add(outline);
}
}

// line up text
for (int i = 1; i < outlines.size(); i++) {
TextOutline ref = outlines.get(i - 1);
TextOutline curr = outlines.get(i);
outlines.set(i, positionAfter(ref, curr));
}

return new AtomSymbol(outlines.get(0),
outlines.subList(1, outlines.size()));
} else {
return new AtomSymbol(new TextOutline(label, italicFont), Collections.<TextOutline>emptyList());
}
}

private boolean isUpperCase(char c) {
return c >= 'A' && c <= 'Z';
}

private boolean isLowerCase(char c) {
return c >= 'a' && c <= 'z';
}

private boolean isDigit(char c) {
return c >= '0' && c <= '9';
}

AtomSymbol generateAbbreviatedSymbol(String label, HydrogenPosition position) {
List<String> tokens = new ArrayList<>();
if (AbbreviationLabel.parse(label, tokens)) {
return generateAbbreviationSymbol(tokens, position);
Expand All @@ -151,7 +265,7 @@ AtomSymbol generatePseudoSymbol(String label, HydrogenPosition position) {
/**
* Generate a formatted abbreviation AtomSymbol for the given Hydrogen position.
*
* @param tokens the parsed tokens
* @param tokens the parsed tokens
* @param position hydrogen position - determines if we reverse the label
* @return the generated symbol
*/
Expand Down Expand Up @@ -187,11 +301,11 @@ AtomSymbol generateAbbreviationSymbol(List<String> tokens, HydrogenPosition posi

// position the outlines relative to each other
for (int i = 1; i < outlines.size(); i++) {
TextOutline ref = outlines.get(i - 1);
TextOutline ref = outlines.get(i - 1);
TextOutline curr = outlines.get(i);
// charge aligns to symbol not a subscript part
if (fTexts.get(i).style == AbbreviationLabel.STYLE_SUPSCRIPT &&
fTexts.get(i-1).style == AbbreviationLabel.STYLE_SUBSCRIPT && i > 1) {
fTexts.get(i - 1).style == AbbreviationLabel.STYLE_SUBSCRIPT && i > 1) {
ref = outlines.get(i - 2);
}
outlines.set(i, positionAfter(ref, curr));
Expand Down Expand Up @@ -225,15 +339,15 @@ AtomSymbol generateAbbreviationSymbol(List<String> tokens, HydrogenPosition posi
* @return laid out atom symbol
*/
AtomSymbol generatePeriodicSymbol(final int number, final int hydrogens, final int mass, final int charge,
final int unpaired, HydrogenPosition position) {
final int unpaired, HydrogenPosition position) {

TextOutline element = new TextOutline(Elements.ofNumber(number).symbol(), font);
TextOutline hydrogenAdjunct = defaultHydrogenLabel;

// the hydrogen count, charge, and mass adjuncts are script size
TextOutline hydrogenCount = new TextOutline(Integer.toString(hydrogens), font).resize(scriptSize, scriptSize);
TextOutline chargeAdjunct = new TextOutline(chargeAdjunctText(charge, unpaired), font).resize(scriptSize,
scriptSize);
scriptSize);
TextOutline massAdjunct = new TextOutline(Integer.toString(mass), font).resize(scriptSize, scriptSize);

// position each adjunct relative to the element label and each other
Expand Down Expand Up @@ -296,7 +410,7 @@ TextOutline positionSubscript(TextOutline label, TextOutline subscript) {
final Rectangle2D hydrogenBounds = label.getBounds();
final Rectangle2D hydrogenCountBounds = subscript.getBounds();
subscript = subscript.translate((hydrogenBounds.getMaxX() + padding) - hydrogenCountBounds.getMinX(),
(hydrogenBounds.getMaxY() + (hydrogenCountBounds.getHeight() / 2)) - hydrogenCountBounds.getMaxY());
(hydrogenBounds.getMaxY() + (hydrogenCountBounds.getHeight() / 2)) - hydrogenCountBounds.getMaxY());
return subscript;
}

Expand Down Expand Up @@ -329,7 +443,7 @@ TextOutline positionAfter(TextOutline before, TextOutline after) {
* @return positioned charge label
*/
TextOutline positionChargeLabel(int hydrogens, HydrogenPosition position, TextOutline charge, TextOutline element,
TextOutline hydrogen) {
TextOutline hydrogen) {

final Rectangle2D chargeBounds = charge.getBounds();

Expand All @@ -343,7 +457,7 @@ TextOutline positionChargeLabel(int hydrogens, HydrogenPosition position, TextOu
else if (hydrogens > 1 && position == Above) referenceBounds = hydrogen.getBounds();

return charge.translate((referenceBounds.getMaxX() + padding) - chargeBounds.getMinX(),
(referenceBounds.getMinY() - (chargeBounds.getHeight() / 2)) - chargeBounds.getMinY());
(referenceBounds.getMinY() - (chargeBounds.getHeight() / 2)) - chargeBounds.getMinY());
}

/**
Expand All @@ -358,7 +472,7 @@ TextOutline positionMassLabel(TextOutline massLabel, TextOutline elementLabel) {
final Rectangle2D elementBounds = elementLabel.getBounds();
final Rectangle2D massBounds = massLabel.getBounds();
return massLabel.translate((elementBounds.getMinX() - padding) - massBounds.getMaxX(),
(elementBounds.getMinY() - (massBounds.getHeight() / 2)) - massBounds.getMinY());
(elementBounds.getMinY() - (massBounds.getHeight() / 2)) - massBounds.getMinY());
}

/**
Expand All @@ -376,7 +490,7 @@ TextOutline positionMassLabel(TextOutline massLabel, TextOutline elementLabel) {
* @return required adjustment to x-axis
*/
private double hydrogenXDodge(int hydrogens, int mass, TextOutline elementLabel, TextOutline hydrogenLabel,
TextOutline hydrogenCount, TextOutline massLabel) {
TextOutline hydrogenCount, TextOutline massLabel) {
if (mass < 0 && hydrogens > 1) {
return (elementLabel.getBounds().getMinX() - padding) - hydrogenCount.getBounds().getMaxX();
} else if (mass >= 0) {
Expand Down Expand Up @@ -417,9 +531,11 @@ private static int unboxSafely(Integer value, int defaultValue) {
return value != null ? value : defaultValue;
}

/** Characters used in the charge label. */
/**
* Characters used in the charge label.
*/
private static final char BULLET = '•', // '\u2022'
PLUS = '+', MINUS = '−'; // '\u2212' and not a hyphen
PLUS = '+', MINUS = '−'; // '\u2212' and not a hyphen

/**
* Create the charge adjunct text for the specified charge and number of unpaired electrons.
Expand Down
2 changes: 1 addition & 1 deletion ...sic/src/main/java/org/openscience/cdk/renderer/generators/standard/StandardGenerator.java
View file
Expand Up @@ -341,7 +341,7 @@ private AtomSymbol[] generateAtomSymbols(IAtomContainer container,
auxVectors.add(hPosition.vector());

if (remapped) {
symbols[i] = atomGenerator.generatePseudoSymbol(symbolRemap.get(atom), hPosition);
symbols[i] = atomGenerator.generateAbbreviatedSymbol(symbolRemap.get(atom), hPosition);
} else {
symbols[i] = atomGenerator.generateSymbol(container, atom, hPosition);
}
Expand Down
28 changes: 28 additions & 0 deletions ...test/java/org/openscience/cdk/renderer/generators/standard/StandardAtomGeneratorTest.java
View file
Expand Up @@ -359,6 +359,34 @@ public void numberedRgroupSymbol() {
assertThat(shapes.size(), is(2));
}

@Test
public void RgroupSymbol2A() {
AtomSymbol atomSymbol = atomGenerator.generatePseudoSymbol("R2a", HydrogenPosition.Right);
List<Shape> shapes = atomSymbol.getOutlines();
assertThat(shapes.size(), is(2));
}

@Test
public void RgroupSymbolY() {
AtomSymbol atomSymbol = atomGenerator.generatePseudoSymbol("Y1a2", HydrogenPosition.Right);
List<Shape> shapes = atomSymbol.getOutlines();
assertThat(shapes.size(), is(1));
}

@Test
public void RgroupSymbolPrime() {
AtomSymbol atomSymbol = atomGenerator.generatePseudoSymbol("R'", HydrogenPosition.Right);
List<Shape> shapes = atomSymbol.getOutlines();
assertThat(shapes.size(), is(2));
}

@Test
public void RgroupSymbolNumberedPrime() {
AtomSymbol atomSymbol = atomGenerator.generatePseudoSymbol("R2'", HydrogenPosition.Right);
List<Shape> shapes = atomSymbol.getOutlines();
assertThat(shapes.size(), is(3));
}

@Test
public void pseudoSymbol() {
AtomSymbol atomSymbol = atomGenerator.generatePseudoSymbol("Protein", HydrogenPosition.Right);
Expand Down

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