public Collection<GeneralMessage> check( Feature feature ) throws SanityRuleException { Collection<GeneralMessage> messages = new ArrayList<GeneralMessage>(); if ( feature.getCvFeatureType() == null ) { return messages; } String cvFeatureTypeIdentityMi = feature.getCvFeatureType().getMiIdentifier(); if ( CvFeatureType.MUTATION_DECREASING_MI_REF.equals( cvFeatureTypeIdentityMi ) || CvFeatureType.MUTATION_INCREASING_MI_REF.equals( cvFeatureTypeIdentityMi ) || CvFeatureType.MUTATION_MI_REF.equals( cvFeatureTypeIdentityMi ) || CvFeatureType.MUTATION_DISRUPTING_MI_REF.equals( cvFeatureTypeIdentityMi ) ) { Collection<Range> ranges = feature.getRanges(); for ( Range range : ranges ) { // tointervalstart - r.fromintervalend int width = range.getToIntervalStart() - range.getFromIntervalEnd(); if ( width > 2 ) { messages.add( new GeneralMessage(MessageDefinition.FEATURE_DELETION_FEATURE_TOO_LONG, feature ) ); } } } return messages; } }
if ( range.getToIntervalStart() == range.getToIntervalEnd() ) { endElement.setAttribute( "begin", "" + range.getToIntervalStart() ); endElement.setAttribute( "end", "" + range.getToIntervalEnd() );
if ( range.getToIntervalStart() == range.getToIntervalEnd() ) { endElement.setAttribute( "begin", "" + range.getToIntervalStart() ); endElement.setAttribute( "end", "" + range.getToIntervalEnd() );
if ( range.getToIntervalStart() == range.getToIntervalEnd() ) { endElement.setAttribute( "begin", "" + range.getToIntervalStart() ); endElement.setAttribute( "end", "" + range.getToIntervalEnd() );
/** * compare two ranges. * * @param range * @param location * * @return */ public static boolean areRangeEquals( Range range, LocationTag location ) { boolean equals = ( range.getFromIntervalStart() == location.getFromIntervalStart() && range.getFromIntervalEnd() == location.getFromIntervalEnd() && range.getToIntervalStart() == location.getToIntervalStart() && range.getToIntervalEnd() == location.getToIntervalEnd() ); if ( DEBUG ) { System.out.print( "RANGE from " + range.getFromIntervalStart() + ".." + range.getFromIntervalEnd() ); System.out.println( " to " + range.getToIntervalStart() + ".." + range.getToIntervalEnd() ); System.out.print( "LOCATION from " + location.getFromIntervalStart() + ".." + location.getFromIntervalEnd() ); System.out.println( " to " + location.getToIntervalStart() + ".." + location.getToIntervalEnd() ); if ( equals ) { System.out.println( "EQUALS" ); } else { System.out.println( "DIFFERENT" ); } } return equals; }
/** * compare two ranges. * * @param range * @param location * * @return */ public static boolean areRangeEquals( Range range, LocationTag location ) { boolean equals = ( range.getFromIntervalStart() == location.getFromIntervalStart() && range.getFromIntervalEnd() == location.getFromIntervalEnd() && range.getToIntervalStart() == location.getToIntervalStart() && range.getToIntervalEnd() == location.getToIntervalEnd() ); if ( DEBUG ) { System.out.print( "RANGE from " + range.getFromIntervalStart() + ".." + range.getFromIntervalEnd() ); System.out.println( " to " + range.getToIntervalStart() + ".." + range.getToIntervalEnd() ); System.out.print( "LOCATION from " + location.getFromIntervalStart() + ".." + location.getFromIntervalEnd() ); System.out.println( " to " + location.getToIntervalStart() + ".." + location.getToIntervalEnd() ); if ( equals ) { System.out.println( "EQUALS" ); } else { System.out.println( "DIFFERENT" ); } } return equals; }
/** * compare two ranges. * * @param range * @param location * * @return */ public static boolean areRangeEquals( Range range, LocationTag location ) { boolean equals = ( range.getFromIntervalStart() == location.getFromIntervalStart() && range.getFromIntervalEnd() == location.getFromIntervalEnd() && range.getToIntervalStart() == location.getToIntervalStart() && range.getToIntervalEnd() == location.getToIntervalEnd() ); if ( DEBUG ) { System.out.print( "RANGE from " + range.getFromIntervalStart() + ".." + range.getFromIntervalEnd() ); System.out.println( " to " + range.getToIntervalStart() + ".." + range.getToIntervalEnd() ); System.out.print( "LOCATION from " + location.getFromIntervalStart() + ".." + location.getFromIntervalEnd() ); System.out.println( " to " + location.getToIntervalStart() + ".." + location.getToIntervalEnd() ); if ( equals ) { System.out.println( "EQUALS" ); } else { System.out.println( "DIFFERENT" ); } } return equals; }
protected UniquenessStringBuilder createUniquenessString(Range range) { if (keyExists(range)) { UniquenessStringBuilder builder = getKey(range); if (builder != null){ return builder; } else{ identityToCrc.remove(System.identityHashCode(range)); } } UniquenessStringBuilder sb = new UniquenessStringBuilder(); putKey(range, sb); if (range == null) return sb; // type from sb.append(createUniquenessString(range.getFromCvFuzzyType())); // interval from sb.append(range.getFromIntervalStart() + "-" + range.getFromIntervalEnd()); // type to sb.append(createUniquenessString(range.getToCvFuzzyType())); // interval end sb.append(range.getToIntervalStart() + "-" + range.getToIntervalEnd()); return sb; }
protected UniquenessStringBuilder createUniquenessString(Range range) { if (keyExists(range)) { UniquenessStringBuilder builder = getKey(range); if (builder != null){ return builder; } else{ identityToCrc.remove(System.identityHashCode(range)); } } UniquenessStringBuilder sb = new UniquenessStringBuilder(); putKey(range, sb); if (range == null) return sb; // type from sb.append(createUniquenessString(range.getFromCvFuzzyType())); // interval from sb.append(range.getFromIntervalStart() + "-" + range.getFromIntervalEnd()); // type to sb.append(createUniquenessString(range.getToCvFuzzyType())); // interval end sb.append(range.getToIntervalStart() + "-" + range.getToIntervalEnd()); return sb; }
if ( range.getToIntervalStart() == range.getToIntervalEnd() ) { endElement.setAttribute( "begin", "" + range.getToIntervalStart() ); endElement.setAttribute( "end", "" + range.getToIntervalEnd() );
/** * @param range : the range to convert * @return the range as a String * If the range is invalid, will return fromIntervalStart-toIntervalEnd */ public static String convertRangeIntoString(Range range) { if (range == null) { throw new IllegalArgumentException("The range cannot be null."); } if (isABadRange(range, null)) { return range.getFromIntervalStart() + RANGE_SEPARATOR + range.getToIntervalEnd(); //throw new IllegalRangeException(getBadRangeInfo(range, null)); } String startPosition = positionToString(range.getFromCvFuzzyType(), range.getFromIntervalStart(), range.getFromIntervalEnd()); String endPosition = positionToString(range.getToCvFuzzyType(), range.getToIntervalStart(), range.getToIntervalEnd()); return startPosition + RANGE_SEPARATOR + endPosition; }
/** * @param range : the range to convert * @return the range as a String * If the range is invalid, will return fromIntervalStart-toIntervalEnd */ public static String convertRangeIntoString(Range range) { if (range == null) { throw new IllegalArgumentException("The range cannot be null."); } if (isABadRange(range, null)) { return range.getFromIntervalStart() + RANGE_SEPARATOR + range.getToIntervalEnd(); //throw new IllegalRangeException(getBadRangeInfo(range, null)); } String startPosition = positionToString(range.getFromCvFuzzyType(), range.getFromIntervalStart(), range.getFromIntervalEnd()); String endPosition = positionToString(range.getToCvFuzzyType(), range.getToIntervalStart(), range.getToIntervalEnd()); return startPosition + RANGE_SEPARATOR + endPosition; }
public Collection<Field> fieldsForAnnotation( Range range ) { Collection<Field> fields = new ArrayList<Field>(); addField( "Undetermined", ( range.isUndetermined() ? "Yes" : "No" ), fields ); String from = "[" + range.getFromIntervalStart() + ".." + range.getFromIntervalEnd() + "]"; addField( "From", from, fields ); String fromFuzzy = null; if ( range.getFromCvFuzzyType() != null ) { fromFuzzy = range.getFromCvFuzzyType().getShortLabel(); } addField( "From type", fromFuzzy, fields ); String to = "[" + range.getToIntervalStart() + ".." + range.getToIntervalEnd() + "]"; addField( "To", to, fields ); String toFuzzy = null; if ( range.getToCvFuzzyType() != null ) { toFuzzy = range.getToCvFuzzyType().getShortLabel(); } addField( "To type", toFuzzy, fields ); return fields; }
else if (startStatus.isGreaterThan() && !endStatus.isGreaterThan() && range.getFromIntervalStart() == range.getToIntervalStart()) { return true; return arePositionsOverlapping(range.getFromIntervalStart(), range.getFromIntervalEnd(), range.getToIntervalStart(), range.getToIntervalEnd());
else if (startStatus.isGreaterThan() && !endStatus.isGreaterThan() && range.getFromIntervalStart() == range.getToIntervalStart()) { return true; return arePositionsOverlapping(range.getFromIntervalStart(), range.getFromIntervalEnd(), range.getToIntervalStart(), range.getToIntervalEnd());
final boolean hasTo = ( range.getToIntervalStart() != 0 && range.getToIntervalEnd() != 0 );
protected Range cloneRange(Range range) throws IntactClonerException { if (range == null) { throw new IllegalArgumentException("You must give a non null range"); } Range clone = new Range(); clonerManager.addClone(range, clone); clone.setFromIntervalStart(range.getFromIntervalStart()); clone.setFromIntervalEnd(range.getFromIntervalEnd()); clone.setToIntervalStart(range.getToIntervalStart()); clone.setToIntervalEnd(range.getToIntervalEnd()); clone.setSequence(range.getSequence()); clone.setFullSequence(range.getFullSequence()); clone.setUpStreamSequence(range.getUpStreamSequence()); clone.setDownStreamSequence(range.getDownStreamSequence()); clone.setFromCvFuzzyType(clone(range.getFromCvFuzzyType())); clone.setToCvFuzzyType(clone(range.getToCvFuzzyType())); clone.setFeature(clone(range.getFeature())); return clone; }
protected Range cloneRange(Range range) throws IntactClonerException { if (range == null) { throw new IllegalArgumentException("You must give a non null range"); } Range clone = new Range(); clonerManager.addClone(range, clone); clone.setFromIntervalStart(range.getFromIntervalStart()); clone.setFromIntervalEnd(range.getFromIntervalEnd()); clone.setToIntervalStart(range.getToIntervalStart()); clone.setToIntervalEnd(range.getToIntervalEnd()); clone.setSequence(range.getSequence()); clone.setFullSequence(range.getFullSequence()); clone.setUpStreamSequence(range.getUpStreamSequence()); clone.setDownStreamSequence(range.getDownStreamSequence()); clone.setFromCvFuzzyType(clone(range.getFromCvFuzzyType())); clone.setToCvFuzzyType(clone(range.getToCvFuzzyType())); clone.setFeature(clone(range.getFeature())); return clone; }
final int toIntervalStart = range.getToIntervalStart(); final int toIntervalEnd = range.getToIntervalEnd();
final int toIntervalStart = range.getToIntervalStart(); final int toIntervalEnd = range.getToIntervalEnd();