List of usage examples for org.apache.commons.lang.math FloatRange getMaximumFloat
public float getMaximumFloat()
Gets the maximum number in this range as a float.
From source file:au.org.ala.delta.model.DiffUtils.java
private static boolean doCompareRealForTaxa(List<RealAttribute> attrs, boolean matchUnknowns, boolean matchInapplicables, MatchType matchType) { // sort attributes in ascending order according to range length Map<Attribute, Double> attrRangeLengths = new HashMap<Attribute, Double>(); for (RealAttribute attr : attrs) { FloatRange range = attr.getPresentRange(); attrRangeLengths.put(attr, (double) (range.getMaximumFloat() - range.getMinimumFloat())); }/* w w w . j av a2 s.co m*/ Collections.sort(attrs, new AttributeValueSizeComparator(attrRangeLengths)); if (matchType == MatchType.EXACT || matchType == MatchType.SUBSET) { boolean diff = false; for (int i = 0; i < attrs.size() - 1; i++) { RealAttribute a1 = attrs.get(i); RealAttribute a2 = attrs.get(i + 1); diff = !compareReal(a1, a2, matchUnknowns, matchInapplicables, matchType); if (diff) { break; } } return !diff; } else { // overlap - taxa must have at least one point in common // progressively calculate area of overlap int numAttrs = attrs.size(); for (int i = 0; i < numAttrs; i++) { RealAttribute a1 = attrs.get(i); FloatRange a1Range = a1.getPresentRange(); for (int j = i + 1; j < numAttrs; j++) { boolean overlap = false; RealAttribute a2 = attrs.get(j); FloatRange a2Range = a2.getPresentRange(); overlap = a2Range.overlapsRange(a1Range); if (!overlap) { return false; } } } return true; } }
From source file:au.org.ala.delta.best.Best.java
/** * Helper method for orderBest. Takes a real character's value and converts * it into a multistate value using the real character's key state * boundaries// w ww. j a va2 s . c o m * * @param realChar * The real character * @param realValue * The value for the real character * @param statePresence * This array will be filled by the method. A true value in this * array indicates that the corresponding state value is present * @return the number of key states present for the supplied real value */ public static int generateKeyStatesForRealCharacter(RealCharacter realChar, FloatRange realValue, boolean[] statePresence) { int numStatesPresent = 0; List<Float> boundariesList = realChar.getKeyStateBoundaries(); Float[] boundaries = new Float[boundariesList.size()]; boundariesList.toArray(boundaries); float rangeMin = realValue.getMinimumFloat(); float rangeMax = realValue.getMaximumFloat(); int i = 0; for (; i < boundaries.length; i++) { if (rangeMin <= boundaries[i]) { statePresence[i] = true; numStatesPresent++; break; } } for (; i < boundaries.length - 1; i++) { if (rangeMax > boundaries[i]) { statePresence[i + 1] = true; numStatesPresent++; } } return numStatesPresent; }
From source file:au.org.ala.delta.intkey.model.SortingUtils.java
/** * Helper method for orderBest. Takes a real character's value and converts * it into a multistate value using the real character's key state * boundaries/*w ww . j a va 2 s .c om*/ * * @param realChar * The real character * @param realValue * The value for the real character * @param statePresence * This array will be filled by the method. A true value in this * array indicates that the corresponding state value is present * @return the number of key states present for the supplied real value */ private static int generateKeyStatesForRealCharacter(RealCharacter realChar, FloatRange realValue, boolean[] statePresence) { int numStatesPresent = 0; List<Float> boundariesList = realChar.getKeyStateBoundaries(); Float[] boundaries = new Float[boundariesList.size()]; boundariesList.toArray(boundaries); float rangeMin = realValue.getMinimumFloat(); float rangeMax = realValue.getMaximumFloat(); int i = 0; for (; i < boundaries.length; i++) { if (rangeMin <= boundaries[i]) { statePresence[i] = true; numStatesPresent++; break; } } for (; i < boundaries.length - 1; i++) { if (rangeMax > boundaries[i]) { statePresence[i + 1] = true; numStatesPresent++; } } return numStatesPresent; }
From source file:au.org.ala.delta.intkey.directives.invocation.OutputDescribeDirectiveInvocation.java
private String getRealAttributeAsString(RealAttribute attr) { StringBuilder builder = new StringBuilder(); FloatRange presentRange = attr.getPresentRange(); if (presentRange != null) { builder.append(String.format("%.2f", presentRange.getMinimumFloat())); if (presentRange.getMinimumFloat() != presentRange.getMaximumFloat()) { builder.append(String.format("-%.2f", presentRange.getMaximumFloat())); }// w w w. java2s .c om if (attr.isInapplicable()) { builder.append("/-"); } } else { if (attr.isInapplicable()) { builder.append("-"); } } return builder.toString(); }
From source file:au.org.ala.delta.util.Utils.java
public static String formatFloatRangeAsString(FloatRange range) { StringBuilder builder = new StringBuilder(); float minimumValue = range.getMinimumFloat(); float maximumValue = range.getMaximumFloat(); if (minimumValue == maximumValue) { if (minimumValue == Math.round(minimumValue)) { builder.append((int) minimumValue); } else {/*from w w w. j av a2 s . com*/ builder.append(minimumValue); } } else { if (minimumValue == Math.round(minimumValue)) { builder.append((int) minimumValue); } else { builder.append(minimumValue); } builder.append("-"); if (maximumValue == Math.round(maximumValue)) { builder.append((int) maximumValue); } else { builder.append(maximumValue); } } return builder.toString(); }
From source file:au.org.ala.delta.intkey.WriteOnceIntkeyItemsFile.java
public void writeAttributeFloats(int charNumber, BitSet inapplicableBits, List<FloatRange> values, List<Float> keyStateBoundaries) { int record = updateCharacterIndex(charNumber); List<Integer> inapplicable = bitSetToInts(inapplicableBits, _header.getNItem()); record += writeToRecord(record, inapplicable); List<Float> floats = new ArrayList<Float>(); for (FloatRange range : values) { // Special cases, Float.MAX_VALUE indicates coded unknown. // -Float.MIN_VALUE indicates uncoded unknown if (range.getMinimumFloat() == Float.MAX_VALUE) { // These somewhat strange values are for CONFOR compatibility floats.add((float) CONFOR_INT_MAX); floats.add(-(float) CONFOR_INT_MAX); } else if (range.getMaximumFloat() == -Float.MAX_VALUE) { floats.add(1f);//from w w w . ja v a2 s . c om floats.add(0f); } else { floats.add(range.getMinimumFloat()); floats.add(range.getMaximumFloat()); } } writeFloatsToRecord(record, floats); int recordNum = nextAvailableRecord(); writeToRecord(recordNum, keyStateBoundaries.size()); writeFloatsToRecord(recordNum + 1, keyStateBoundaries); if (_keyStateBoundariesIndex == null) { _keyStateBoundariesIndex = new int[_header.getNChar()]; Arrays.fill(_keyStateBoundariesIndex, 0); } _keyStateBoundariesIndex[charNumber - 1] = recordNum; _header.setLSbnd(_header.getLSbnd() + keyStateBoundaries.size()); _header.setLkstat(Math.max(_header.getLkstat(), keyStateBoundaries.size())); }
From source file:au.org.ala.delta.intkey.directives.invocation.UseDirectiveInvocation.java
private String formatAttributeValueForLog(Attribute attr) { if (attr instanceof TextAttribute) { return ((TextAttribute) attr).getText(); } else if (attr instanceof MultiStateAttribute) { return Utils.formatIntegersAsListOfRanges(((MultiStateAttribute) attr).getPresentStatesAsList(), "/", "-"); } else if (attr instanceof IntegerAttribute) { Set<Integer> presentValues = ((IntegerAttribute) attr).getPresentValues(); List<Integer> presentValuesList = new ArrayList<Integer>(presentValues); Collections.sort(presentValuesList); return Utils.formatIntegersAsListOfRanges(presentValuesList, "/", "-"); } else if (attr instanceof RealAttribute) { FloatRange range = ((RealAttribute) attr).getPresentRange(); StringBuilder builder = new StringBuilder(); float min = range.getMinimumFloat(); float max = range.getMaximumFloat(); if (min == max) { builder.append(min);//from w ww . j av a 2 s . c om } else { builder.append(min); builder.append("-"); builder.append(max); } return builder.toString(); } else { throw new IllegalArgumentException("Unrecognised attribute type!"); } }
From source file:au.org.ala.delta.intkey.directives.invocation.UseDirectiveInvocation.java
private Attribute promptForCharacterValue(au.org.ala.delta.model.Character ch, au.org.ala.delta.model.Character dependentChar, Set<Integer> applicableStates, DirectivePopulator populator, Specimen specimen, IntkeyContext context) { SimpleAttributeData impl = new SimpleAttributeData(false, false); if (ch instanceof MultiStateCharacter) { Set<Integer> stateValues; if (dependentChar != null) { // We are setting a value for a controlling character. Ensure // that the states that make the dependent character applicable // are pre-selected. stateValues = populator.promptForMultiStateValue((MultiStateCharacter) ch, applicableStates, dependentChar);//from ww w. ja v a 2s . c o m } else { // Get the current value of the character as set in the // specimen. If no // value is set for the character, an attribute with // unknown = true is returned. MultiStateAttribute currentAttribute = (MultiStateAttribute) specimen.getAttributeForCharacter(ch); stateValues = populator.promptForMultiStateValue((MultiStateCharacter) ch, currentAttribute.isUnknown() ? null : currentAttribute.getPresentStates(), null); } if (stateValues != null && stateValues.isEmpty() && dependentChar == null) { // User hit OK but did not select any states. Delete any value // set // for the character. if (specimen.hasValueFor(ch)) { deleteCharacter(ch, context); } return null; } else if (stateValues != null && stateValues.size() > 0) { impl.setPresentStateOrIntegerValues(stateValues); } else { return null; } } else if (ch instanceof IntegerCharacter) { // Get the current value of the character as set in the specimen. If // no // value is set for the character, an attribute with // unknown = true is returned. IntegerAttribute currentAttribute = (IntegerAttribute) specimen.getAttributeForCharacter(ch); Set<Integer> intValue = populator.promptForIntegerValue((IntegerCharacter) ch, currentAttribute.isUnknown() ? null : currentAttribute.getPresentValues()); if (intValue != null && intValue.isEmpty()) { // User hit OK but did not input any values. Delete any value // set // for the character if (specimen.hasValueFor(ch)) { deleteCharacter(ch, context); } return null; } else if (intValue != null && intValue.size() > 0) { impl.setPresentStateOrIntegerValues(intValue); } else { return null; } } else if (ch instanceof RealCharacter) { // Get the current value of the character as set in the specimen. If // no // value is set for the character, an attribute with // unknown = true is returned. RealAttribute currentAttribute = (RealAttribute) specimen.getAttributeForCharacter(ch); FloatRange floatRange = populator.promptForRealValue((RealCharacter) ch, currentAttribute.isUnknown() ? null : currentAttribute.getPresentRange()); if (floatRange != null) { // Float range with minimum and maximum value as negative // infinity indicates that the user hit OK without inputting // values. if (floatRange.getMaximumFloat() == Float.NEGATIVE_INFINITY && floatRange.getMinimumFloat() == Float.NEGATIVE_INFINITY) { // User hit OK but did not input any values. Delete any // value set // for the character if (specimen.hasValueFor(ch)) { deleteCharacter(ch, context); } return null; } impl.setRealRange(floatRange); } else { return null; } } else if (ch instanceof TextCharacter) { // Get the current value of the character as set in the specimen. If // no // value is set for the character, an attribute with // unknown = true is returned. TextAttribute currentAttribute = (TextAttribute) specimen.getAttributeForCharacter(ch); List<String> stringList = populator.promptForTextValue((TextCharacter) ch, currentAttribute.isUnknown() ? null : Arrays.asList(currentAttribute.getValueAsString().split("/"))); if (stringList != null && stringList.isEmpty()) { // User hit OK but did not input any values. Delete any // value set // for the character if (specimen.hasValueFor(ch)) { deleteCharacter(ch, context); } return null; } else if (stringList != null && stringList.size() > 0) { impl.setValueFromString(StringUtils.join(stringList, '/')); } else { return null; } } else { throw new IllegalArgumentException("Unrecognized character type"); } Attribute attr = AttributeFactory.newAttribute(ch, impl); attr.setSpecimenAttribute(true); return attr; }
From source file:au.org.ala.delta.translation.intkey.IntkeyItemsFileWriter.java
private Set<Float> writeRealAttributes(int filteredCharNumber, Character realChar, boolean wasInteger) { int unfilteredCharNumber = realChar.getCharacterId(); boolean useNormalValues = _context.getUseNormalValues(unfilteredCharNumber); List<FloatRange> values = new ArrayList<FloatRange>(); BitSet inapplicableBits = new BitSet(); Iterator<FilteredItem> items = _dataSet.filteredItems(); while (items.hasNext()) { FilteredItem item = items.next(); NumericAttribute attribute = (NumericAttribute) _dataSet.getAttribute(item.getItem().getItemNumber(), unfilteredCharNumber);//from ww w . j a va 2 s. c o m if (attribute == null || attribute.isCodedUnknown() || attribute.isInapplicable() || attribute.isVariable()) { FloatRange range = new FloatRange(Float.MAX_VALUE); values.add(range); if (isInapplicable(attribute)) { inapplicableBits.set(item.getItemNumber() - 1); } continue; } List<NumericRange> ranges = attribute.getNumericValue(); // This can happen if the attribute has a comment but no value. if (ranges.isEmpty()) { FloatRange range = new FloatRange(-Float.MAX_VALUE); values.add(range); if (isInapplicable(attribute)) { inapplicableBits.set(item.getItemNumber() - 1); } continue; } Range useRange; float min = Float.MAX_VALUE; float max = -Float.MAX_VALUE; for (NumericRange range : ranges) { if (_context.hasAbsoluteError(unfilteredCharNumber)) { range.setAbsoluteError(_context.getAbsoluteError(unfilteredCharNumber)); } else if (_context.hasPercentageError(unfilteredCharNumber)) { range.setPercentageError(_context.getPercentageError(unfilteredCharNumber)); } if (useNormalValues) { useRange = range.getNormalRange(); } else { useRange = range.getFullRange(); } min = Math.min(min, useRange.getMinimumFloat()); max = Math.max(max, useRange.getMaximumFloat()); } FloatRange floatRange = new FloatRange(min, max); values.add(floatRange); } Set<Float> floats = new HashSet<Float>(); for (FloatRange range : values) { if (range.getMinimumFloat() != Float.MAX_VALUE && range.getMinimumFloat() != -Float.MAX_VALUE) { floats.add(range.getMinimumFloat()); } else { if (range.getMinimumFloat() == -Float.MAX_VALUE && !wasInteger) { floats.add(0f); // For CONFOR compatibility, seems wrong. } } if (range.getMaximumFloat() != Float.MAX_VALUE && range.getMinimumFloat() != -Float.MAX_VALUE) { floats.add(range.getMaximumFloat()); } else { if (range.getMinimumFloat() == -Float.MAX_VALUE && !wasInteger) { floats.add(1.0f); // For CONFOR compatibility, seems wrong. } } } List<Float> boundaries = new ArrayList<Float>(floats); Collections.sort(boundaries); _itemsFile.writeAttributeFloats(filteredCharNumber, inapplicableBits, values, boundaries); return floats; }