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/** |
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$Id $ |
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Copyright (C) 2015 Nicklas Nordborg |
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This file is part of BASE - BioArray Software Environment. |
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Available at http://base.thep.lu.se/ |
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BASE is free software; you can redistribute it and/or |
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modify it under the terms of the GNU General Public License |
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as published by the Free Software Foundation; either version 3 |
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of the License, or (at your option) any later version. |
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BASE is distributed in the hope that it will be useful, |
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but WITHOUT ANY WARRANTY; without even the implied warranty of |
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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GNU General Public License for more details. |
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You should have received a copy of the GNU General Public License |
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along with BASE. If not, see <http://www.gnu.org/licenses/>. |
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*/ |
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package net.sf.basedb.util.annotations; |
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import net.sf.basedb.core.Annotatable; |
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import net.sf.basedb.core.AnnotationType; |
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import net.sf.basedb.core.BioPlate; |
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import net.sf.basedb.core.BioPlateType; |
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import net.sf.basedb.core.ItemSubtype; |
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import net.sf.basedb.core.Subtypable; |
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import net.sf.basedb.core.snapshot.AnnotationSnapshot; |
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import net.sf.basedb.util.filter.Filter; |
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/** |
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Class for holding rules for how annotations should be inherited from |
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parent items. If {@link #getRemove()} is set, it override all other |
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settings and all inherited annotation for the specified annotation type |
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are removed. |
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|
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@author nicklas |
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@since 3.5 |
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*/ |
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public class InheritSpecification |
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implements Filter<AnnotationSnapshot> |
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{ |
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|
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private final int annotationTypeId; |
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private final AnnotationType annotationType; |
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|
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private boolean remove; |
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private boolean clone; |
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private boolean resync; |
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private ItemSubtype subtype; |
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private boolean noDuplicates = true; |
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private boolean replaceExisting = false; |
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|
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/** |
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Creates a new specification for the given annotation type. |
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*/ |
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public InheritSpecification(AnnotationType annotationType) |
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{ |
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this.annotationTypeId = annotationType.getId(); |
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this.annotationType = annotationType; |
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} |
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public AnnotationType getAnnotationType() |
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{ |
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return annotationType; |
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} |
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|
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/** |
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Set a flag to remove all inherited annotations of the specified annotation type. |
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Note that if this setting is enabled, it override all other settings. |
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*/ |
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public void setRemove(boolean remove) |
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{ |
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this.remove = remove; |
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} |
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|
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public boolean getRemove() |
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{ |
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return remove; |
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} |
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|
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/** |
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Set a flag to inherit annotations by cloning the original values. Use this |
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if you do not want changes to the original annotation to be reflected in |
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the inherited (=cloned) annotations. |
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@since 3.6 |
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*/ |
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public void setClone(boolean clone) |
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{ |
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this.clone = clone; |
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} |
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|
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public boolean getClone() |
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{ |
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return clone; |
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} |
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public void setResyncCloned(boolean resync) |
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{ |
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this.resync = resync; |
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} |
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|
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public boolean getResync() |
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{ |
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return resync; |
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} |
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|
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/** |
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Set the subtype a parent item must have if annotations should be |
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inherited from it. Set to null to inherit from any parent. |
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*/ |
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public void setItemSubtype(ItemSubtype subtype) |
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{ |
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this.subtype = subtype; |
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} |
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|
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public ItemSubtype getItemSubtype() |
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{ |
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return subtype; |
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} |
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|
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/** |
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If this flag is set (default=true), only one annotation of the specified |
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annotation type can be inherited. |
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*/ |
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public void setNoDuplicates(boolean noDuplicates) |
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{ |
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this.noDuplicates = noDuplicates; |
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} |
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|
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public boolean getNoDuplicates() |
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{ |
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return noDuplicates; |
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} |
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|
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/** |
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If this flag is set (default=false), existing inherited annotations |
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of the specified annotation type are removed before inheriting new |
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ones. Note that existing annotations are only replaced if a new annotation |
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is found. |
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*/ |
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public void setReplaceExisting(boolean replaceExisting) |
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{ |
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this.replaceExisting = replaceExisting; |
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} |
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|
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public boolean getReplaceExisting() |
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{ |
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return replaceExisting; |
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} |
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|
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/** |
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Checks if the parent item has a subtype matching the subtype (if any) |
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in this specification. If the parent item is a {@link BioPlate} we |
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check the subtype of bioplate type ({@link BioPlateType#getItemSubtype()}) |
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@return TRUE if the subtype matches or if this specification doesn't set any subtype |
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*/ |
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boolean isAcceptableParent(Annotatable parent) |
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{ |
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if (subtype == null) return true; |
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ItemSubtype subtypeToCheck = null; |
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if (parent instanceof Subtypable) |
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{ |
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subtypeToCheck = ((Subtypable)parent).getItemSubtype(); |
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} |
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else if (parent instanceof BioPlate) |
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{ |
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BioPlateType plateType = ((BioPlate)parent).getBioPlateType(); |
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subtypeToCheck = plateType != null ? plateType.getItemSubtype() : null; |
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} |
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return subtype.equals(subtypeToCheck); |
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} |
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|
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@Override |
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public boolean evaluate(AnnotationSnapshot snapshot) |
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{ |
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return snapshot.getAnnotationTypeId() == annotationTypeId; |
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} |
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|
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} |