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EntryGroup.java 11.47 KiB
/* EntryGroup.java
*
* created: Wed Nov 11 1998
*
* This file is part of Artemis
*
* Copyright(C) 1998,1999,2000,2001,2002 Genome Research Limited
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or(at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
* $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/EntryGroup.java,v 1.1 2004-06-09 09:44:21 tjc Exp $
**/
package uk.ac.sanger.artemis;
import uk.ac.sanger.artemis.sequence.Bases;
import uk.ac.sanger.artemis.io.Range;
import uk.ac.sanger.artemis.util.ReadOnlyException;
import uk.ac.sanger.artemis.util.OutOfRangeException;
/**
* Objects that implement this interface contain a vector of Entry object,
* with additional methods for querying and changing the feature tables of
* all the entries at once.
*
* @author Kim Rutherford
* @version $Id: EntryGroup.java,v 1.1 2004-06-09 09:44:21 tjc Exp $
**/
public interface EntryGroup
extends FeatureChangeListener, EntryChangeListener
{
/**
* Return the default Entry for this EntryGroup. The "default" is the
* Entry where new features are created.
**/
Entry getDefaultEntry();
/**
* Set the default Entry. The "default" is the Entry where new features
* are created.
* @param entry The new default entry. If this Entry is not active this
* method will return immediately.
**/
void setDefaultEntry(final Entry entry);
/**
* Returns true if and only if there are any unsaved changes in any of the
* Entry objects in this EntryGroup.
**/
boolean hasUnsavedChanges();
/**
* Return the index of a feature within this object. This method treats
* all the features in all the active entries as if they were in one big
* array. The first feature of the first entry will have index 1, the
* first from the second entry will have index 1 +(the number of features
* in the first entry), etc. * @param feature The feature to find the index of.
* @return The index of the feature or -1 if the feature isn't in any of
* the entries. The first index is 0 the last is the total number of
* features in all the entries of this object minus one.
**/
int indexOf(final Feature feature);
/**
* Return the index of an Entry within this object.
* @return The index of the Entry or -1 if the Entry isn't in this Object.
**/
int indexOf(final Entry entry);
/**
* Return true if any of the active entries in the group contains the given
* feature.
**/
boolean contains(final Feature feature);
/**
* Return true if the given Entry is active(visible). The Feature objects
* in an Entry that is not active will be ignored by the methods that deal
* will features: featureAt(), indexOf(), contains(), features(), etc.
**/
boolean isActive(final Entry entry);
/**
* Set the "active" setting of the Entry at the given index. If the index
* refers to the default entry and new_active is false, the default entry
* will be set to the active entry or null if there are no active entries.
* @param index The index of the Entry to change.
* @param new_active The new active setting.
**/
void setIsActive(final int index, final boolean new_active);
/**
* Set the "active" setting of the given Entry. The Entry is the default
* entry and new_active is false, the default entry will be set to the
* active entry or null if there are no active entries.
* @param entry The Entry to activate or deactivate.
* @param new_active The new active setting.
**/
void setIsActive(final Entry entry, final boolean new_active);
/**
* Return the Entry from this EntryGroup that contains the sequence to view
* or return null if none of the entries contains a sequence.
**/
Entry getSequenceEntry();
/**
* Returns the base length of the sequence of the first Entry in this group
* or 0 if this group is empty.
**/
int getSequenceLength();
/**
* Returns the Bases object of the first Entry in this group or null if
* this group is empty.
**/
Bases getBases();
/**
* Reverse and complement the sequence and all features in every Entry in
* this EntryGroup.
**/
void reverseComplement()
throws ReadOnlyException;
/** * Return the number of entries in this EntryGroup.
**/
int size();
/**
* Return the ith Entry in this EntryGroup.
**/
Entry elementAt(final int i);
/**
* Return the Feature at the given index. This method treats all the
* features in all the entries as if they were in one big array. See
* the comment on indexOf().
* @param index The index of the required Feature.
* @return The Feature at the given index. The first index is 0 the last
* is the total number of features in all the entries of this object minus
* one. If the index is out of range then null will be returned.
**/
Feature featureAt(final int index);
/**
* Return a vector containing the references of the Feature objects within
* the given range of indices.
* @param
**/
FeatureVector getFeaturesInIndexRange(final int start_index,
final int end_index);
/**
* Return a vector containing the references of the Feature objects within
* the given range for all the active entries in the EntryGroup.
* @param range Return features that overlap this range - ie the start of
* the feature is less than or equal to the end of the range and the end
* of the feature is greater than or equal to the start of the range.
* @return The non-source key features of this feature table the are within
* the given range. The returned object is a copy - changes will not
* effect the FeatureTable object itself.
**/
FeatureVector getFeaturesInRange(final Range range)
throws OutOfRangeException;
/**
* Return a vector containing the references of the Feature objects from
* all the active entries in the EntryGroup.
* @return The non-source key features in active entries of this
* EntryGroup. The returned object is a copy - changes will not effect
* the EntryGroup object itself.
**/
FeatureVector getAllFeatures();
/**
* Return a count of the number of Feature objects from all the active
* entries in the EntryGroup.
* @return A count of the non-source key features in active entries of this
* EntryGroup.
**/
int getAllFeaturesCount();
/**
* Add an Entry to this object and then emit the appropriate EntryChange
* events.
**/
void addElement(final Entry entry);
/**
* A convenience method that does the same as addElement(Entry).
**/
void add(final Entry entry);
/** * Remove an Entry from this object and then emit the appropriate
* EntryGroupChange events. The first entry in the group can only be
* removed if it is the only Entry because the first Entry contains the
* sequence.
* @return true if the removal succeeded, false if it fails(which can
* if the given Entry isn't in this EntryGroup or if the user tries to
* remove the first Entry).
**/
boolean removeElement(final Entry entry);
/**
* A convenience method that does the same as removeElement(Entry).
**/
boolean remove(final Entry entry);
/**
* Create a new(blank) Feature in the default Entry of this EntryGroup.
* See getDefaultEntry() and Entry.createFeature().
* @return The new Feature.
**/
Feature createFeature()
throws ReadOnlyException;
/**
* Create a new(empty) Entry in this EntryGroup. See Entry.newEntry().
* @return The reference of the new Entry.
**/
Entry createEntry();
/**
* Create a new(empty) Entry in this EntryGroup. See Entry.newEntry().
* @param name The(file) name of the new Entry.
* @return The reference of the new Entry.
**/
Entry createEntry(final String name);
/**
* Returns an enumeration of the Feature objects in this EntryGroup. The
* returned FeatureEnumeration object will generate all features in this
* object in turn. The first item generated is the item at index 0, then
* the item at index 1, and so on.
**/
FeatureEnumeration features();
/**
* Adds the specified event listener to receive entry group change events
* from this object.
* @param l the event change listener.
**/
void addEntryGroupChangeListener(EntryGroupChangeListener l);
/**
* Removes the specified event listener so that it no longer receives
* entry group change events from this object.
* @param l the event change listener.
**/
void removeEntryGroupChangeListener(EntryGroupChangeListener l);
/**
* Adds the specified event listener to receive entry change events from
* this object.
* @param l the event change listener.
**/
void addEntryChangeListener(EntryChangeListener l);
/**
* Removes the specified event listener so that it no longer receives
* entry change events from this object.
* @param l the event change listener.
**/ void removeEntryChangeListener(EntryChangeListener l);
/**
* Adds the specified event listener to receive feature change events from
* this object.
* @param l the event change listener.
**/
void addFeatureChangeListener(FeatureChangeListener l);
/**
* Removes the specified event listener so that it no longer receives
* feature change events from this object.
* @param l the event change listener.
**/
void removeFeatureChangeListener(FeatureChangeListener l);
/**
* Return the reference of an EntryVector containing the active entries of
* this EntryGroup.
**/
EntryVector getActiveEntries();
/**
* This method translates the start and end of every each Range in every
* Location into another coordinate system. The Ranges will be truncated
* if necessary.
* @param constraint This contains the start and end base of the new
* coordinate system. The position given by constraint.getStart() will
* be at postion/base 1 in the new coordinate system.
* @return a copy of the EntryGroup which has been translated into the new
* coordinate system.
**/
EntryGroup truncate(final Range constraint);
/**
* Return the ActionController for this EntryGroup(for undo).
**/
ActionController getActionController();
/**
* Return true if and only if one or more of the entries or features in
* this SimpleEntryGroup are read-only.
**/
boolean isReadOnly();
/**
* Increment the reference count for this EntryGroup.
**/
void ref();
/**
* Decrement the reference count for this EntryGroup. When the reference
* count goes to zero a EntryGroupChangeEvent is sent to all
* EntryGroupChangeListeners with type EntryGroupChangeEvent.DONE_GONE.
* The listeners should then stop using the EntryGroup and release any
* associated resources.
**/
void unref();
/**
* Return the current reference count.
**/
int refCount();
}