ProjectThing (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- ini.trakem2.persistence.DBObject
- - ini.trakem2.tree.ProjectThing

All Implemented Interfaces:: Thing, TitledThing

public final class ProjectThing
extends DBObject
implements TitledThing

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

class ProjectThing.Profile_List

Nested Classes
Modifier and Type	Class and Description
`class`	`ProjectThing.Profile_List`

Field Summary
- Fields inherited from class ini.trakem2.persistence.DBObject
  id, project

Constructor Summary

Constructors
Constructor and Description
`ProjectThing(TemplateThing template, Project project, long id, Object ob, ArrayList<ProjectThing> al_children)` Reconstruct a ProjectThing from the database, used in combination with the 'setup' method.
`ProjectThing(TemplateThing template, Project project, Object ob)` Create a new ProjectThing of the given type to contain the given Object.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`addChild(ProjectThing child, int index)` In addition, if the child contains an object of class ini.trakem2.display.Profile, reorders all children of the parent Thing by the Z of the layers of the profiles.
`boolean`	`addChild(Thing child)`
`boolean`	`canHaveAsChild(String type)`
`boolean`	`canHaveAsChild(Thing thing)`
`HashSet<ProjectThing>`	`collectSimilarThings(TemplateThing tt, HashSet<ProjectThing> hs)` Recursive into children, find those of the given type that have the same parent chain as the given TemplateThing.
`ProjectThing`	`createChild(String type)`
`ArrayList<ProjectThing>`	`createChildren(String type, int amount, boolean recursive)` Creates one instance of the given type and if recursive, also of all possible children of it, and of them, and so on.
`ProjectThing`	`createClonedChild(ProjectThing child)` At the moment only for basic types, which by definition have no children.
`void`	`debug(String indent)`
`ProjectThing`	`deepClone(Project project, boolean copy_id)` Clone this ProjectThing with its template and all its children and objects cloned, and return it.
`void`	`exportSVG(StringBuffer data, double z_scale, String indent)`
`void`	`exportXML(StringBuilder sb_body, String indent, XMLOptions options)` Expects a `HashMap<Thing,Boolean>` as `any`.
`HashSet<ProjectThing>`	`findBasicTypeChildren()` Recursive into children.
`HashSet<ProjectThing>`	`findBasicTypeChildren(HashSet<ProjectThing> hs_basic, HashSet<ProjectThing> hs_visited)` Recursive into children, and adds this instance as well if it's a basic type.
`ProjectThing`	`findChild(long id)` Recursive search for the thing of the given id.
`Thing`	`findChild(Object ob)` Recursive search for the thing that contains the given object.
`void`	`findChildren(ArrayList<ProjectThing> found, Pattern pattern, Pattern pattern_exclude, boolean shallow)` Recursive into children, searches for things whose object.toString() matches the given regex pattern, and stores the found ProjectThing in the given ArrayList.
`ArrayList<ProjectThing>`	`findChildren(String regex, String regex_exclude, boolean shallow)` Recursive into children, searches for the things whose object.toString() matches the given regex, case insensitive.
`<T> ArrayList<T>`	`findChildrenOfType(Class<T> c)` Check if this Thing directly contains any child of the given object class (including interfaces), and return them all.
`ArrayList<ProjectThing>`	`findChildrenOfType(String type)` Check if this Thing directly contains any child of the given type, and return them all.
`List<ProjectThing>`	`findChildrenOfTypeR(Class<?> c)` Finds them in order.
`HashSet<ProjectThing>`	`findChildrenOfTypeR(HashSet<ProjectThing> hs, String type)` Recursive into children.
`List<ProjectThing>`	`findChildrenOfTypeR(List<ProjectThing> list, Class<?> c)` Finds them in order.
`HashSet<ProjectThing>`	`findChildrenOfTypeR(String type)` Recursive into children.
`DBObject`	`findObject(long id)` Recursive search for the object with the given id.
`<T> List<T>`	`findObjects(Class<T> c)` Find objects of the given class, as determined by c.isInstance(this.object).
`boolean`	`fixZOrdering()` If this is of type profile_list, order all children Profile by their layer's Z coordinate, ascending.
`HashMap<String,ArrayList<ProjectThing>>`	`getByType()` Recursively browse all children to classify all nodes by type.
`ArrayList<ProjectThing>`	`getChildren()`
`TemplateThing`	`getChildTemplate(String type)`
`String`	`getInfo()` Return information on this node and its object, and also on all the children, recursively.
`String`	`getNodeInfo()` Return information on this node and its object.
`Object`	`getObject()`
`Thing`	`getParent()`
`JMenuItem[]`	`getPopupItems(ActionListener listener)`
`ProjectThing`	`getRootParent()` Crawl up until finding a parent that has no parent: the root.
`TemplateThing`	`getTemplate()`
`ArrayList<TemplateThing>`	`getTemplatePathTo(String type)` Returns a list of parent types (String), in order, for the given Thing if it exists as a child in the traversed trees.
`String`	`getTitle()` Sublcasses can override this method to provide a proper String, otherwise calls toString()
`String`	`getType()`
`boolean`	`hasChildren()`
`boolean`	`hasParent(String type)` Check if this or any of its parents are of the given type.
`boolean`	`isExpanded()`
`void`	`measure()` Measure each node, recursively into children, and at the end display all the result tables, one for each data type.
`HashMap<Class<?>,ij.measure.ResultsTable>`	`measure(HashMap<Class<?>,ij.measure.ResultsTable> ht)` Call on children things, and on itself if it contains a basic data type directly.
`boolean`	`move(int inc)` Moves this ProjectThing up and down the parent's children list.
`boolean`	`remove(boolean check)` Subclasses can override this method to perform other tasks before removing itself from the database.
`protected boolean`	`remove(boolean check, boolean remove_object)`
`boolean`	`removeChild(ProjectThing child)`
`void`	`setObject(Object object)` Used by the TMLHandler; can be used only once.
`void`	`setParent(Thing parent)`
`void`	`setTitle(String title)`
`void`	`setup()`
`void`	`setVisible(boolean b)` Switch the visibility of the Displayable objects contained here or in the children.
`Thing`	`shallowCopy()` A new copy with same template, same object and cloned table of same attributes, but no parent and no children.
`ProjectThing`	`subclone(Project pr)` Implicit id copying; assumes the ids of the object are also the same in the given project; the object, if it is a DBObject, is retrieved from the given project by matching its id.
`String`	`toString()`
`boolean`	`uniquePathExists(String type)` Check if any of the possible children of this Thing can have the given Thing as child, or any of they children can, recursing down.
`void`	`updateTitle()` Recursive into children and object (to update it's DisplayablePanel title).
`void`	`updateType(String new_type, String old_type)` Recursive into children, changes the type column in the ab_things table.

Methods inherited from class ini.trakem2.persistence.DBObject
addToDatabase, getId, getProject, getShortTitle, getUniqueIdentifier, removeFromDatabase, updateInDatabase, updateInDatabase

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Constructor Detail
  - ProjectThing
```
public ProjectThing(TemplateThing template,
                    Project project,
                    Object ob)
             throws Exception
```
    Create a new ProjectThing of the given type to contain the given Object. The object cannot be null.
    
    Throws:
    
    Exception
  - ProjectThing
```
public ProjectThing(TemplateThing template,
                    Project project,
                    long id,
                    Object ob,
                    ArrayList<ProjectThing> al_children)
```
    Reconstruct a ProjectThing from the database, used in combination with the 'setup' method.
- Method Detail
  - shallowCopy
```
public Thing shallowCopy()
```
    A new copy with same template, same object and cloned table of same attributes, but no parent and no children.
    
    Specified by:
    
    shallowCopy in interface Thing
  - deepClone
```
public ProjectThing deepClone(Project project,
                              boolean copy_id)
                       throws Exception
```
    Clone this ProjectThing with its template and all its children and objects cloned, and return it. The templates are added to the project as unique types when not there yet. WARNING there isn't any conflict resolution between potentially different kinds of TemplateThing parent/child chains.
    
    Throws:
    
    Exception
  - setObject
```
public void setObject(Object object)
```
    Used by the TMLHandler; can be used only once.
  - setup
```
public void setup()
```
  - toString
```
public String toString()
```
    Specified by:
    
    toString in interface Thing
    
    Overrides:
    
    toString in class Object
  - getTitle
```
public String getTitle()
```
    Description copied from class: DBObject
    
    Sublcasses can override this method to provide a proper String, otherwise calls toString()
    
    Specified by:
    
    getTitle in interface Thing
    
    Overrides:
    
    getTitle in class DBObject
  - addChild
```
public boolean addChild(Thing child)
```
    Specified by:
    
    addChild in interface Thing
  - addChild
```
public boolean addChild(ProjectThing child,
                        int index)
```
    In addition, if the child contains an object of class ini.trakem2.display.Profile, reorders all children of the parent Thing by the Z of the layers of the profiles.
  - getChildren
```
public ArrayList<ProjectThing> getChildren()
```
    Specified by:
    
    getChildren in interface Thing
  - hasChildren
```
public boolean hasChildren()
```
    Specified by:
    
    hasChildren in interface Thing
  - removeChild
```
public boolean removeChild(ProjectThing child)
```
  - remove
```
public boolean remove(boolean check)
```
    Description copied from class: DBObject
    
    Subclasses can override this method to perform other tasks before removing itself from the database.
    
    Overrides:
    
    remove in class DBObject
  - remove
```
protected boolean remove(boolean check,
                         boolean remove_object)
```
  - setParent
```
public void setParent(Thing parent)
```
    Specified by:
    
    setParent in interface Thing
  - getParent
```
public Thing getParent()
```
    Specified by:
    
    getParent in interface Thing
  - getRootParent
```
public ProjectThing getRootParent()
```
    Crawl up until finding a parent that has no parent: the root.
  - hasParent
```
public boolean hasParent(String type)
```
    Check if this or any of its parents are of the given type.
  - setTitle
```
public void setTitle(String title)
```
    Specified by:
    
    setTitle in interface TitledThing
  - getObject
```
public Object getObject()
```
    Specified by:
    
    getObject in interface Thing
  - getChildTemplate
```
public TemplateThing getChildTemplate(String type)
```
  - canHaveAsChild
```
public boolean canHaveAsChild(Thing thing)
```
    Specified by:
    
    canHaveAsChild in interface Thing
  - uniquePathExists
```
public boolean uniquePathExists(String type)
```
    Check if any of the possible children of this Thing can have the given Thing as child, or any of they children can, recursing down. Returns true only if one possibility exists.
  - getTemplatePathTo
```
public ArrayList<TemplateThing> getTemplatePathTo(String type)
```
    Returns a list of parent types (String), in order, for the given Thing if it exists as a child in the traversed trees. This method returns the first path that it finds, avoiding a check to uniquePathExists(type).
  - getType
```
public String getType()
```
    Specified by:
    
    getType in interface Thing
  - getTemplate
```
public TemplateThing getTemplate()
```
  - getPopupItems
```
public JMenuItem[] getPopupItems(ActionListener listener)
```
  - setVisible
```
public void setVisible(boolean b)
```
    Switch the visibility of the Displayable objects contained here or in the children.
  - createChildren
```
public ArrayList<ProjectThing> createChildren(String type,
                                              int amount,
                                              boolean recursive)
```
    Creates one instance of the given type and if recursive, also of all possible children of it, and of them, and so on.
    
    Returns:
    
    all created nodes, or null if the given type cannot be contained here as a child.
  - canHaveAsChild
```
public boolean canHaveAsChild(String type)
```
  - createChild
```
public ProjectThing createChild(String type)
```
  - createClonedChild
```
public ProjectThing createClonedChild(ProjectThing child)
```
    At the moment only for basic types, which by definition have no children.
  - findChildren
```
public ArrayList<ProjectThing> findChildren(String regex,
                                            String regex_exclude,
                                            boolean shallow)
```
    Recursive into children, searches for the things whose object.toString() matches the given regex, case insensitive. If shallow, the recursive search does not look into the children of a parent that matches.
  - findChildren
```
public void findChildren(ArrayList<ProjectThing> found,
                         Pattern pattern,
                         Pattern pattern_exclude,
                         boolean shallow)
```
    Recursive into children, searches for things whose object.toString() matches the given regex pattern, and stores the found ProjectThing in the given ArrayList. If shallow, the recursive search does not look into the children of a parent that matches.
  - findChild
```
public Thing findChild(Object ob)
```
    Recursive search for the thing that contains the given object.
    
    Specified by:
    
    findChild in interface Thing
  - findChild
```
public ProjectThing findChild(long id)
```
    Recursive search for the thing of the given id.
  - findObject
```
public DBObject findObject(long id)
```
    Recursive search for the object with the given id.
  - measure
```
public HashMap<Class<?>,ij.measure.ResultsTable> measure(HashMap<Class<?>,ij.measure.ResultsTable> ht)
```
    Call on children things, and on itself if it contains a basic data type directly. All children of the same type report to the same table. Result tables are returned without ever displaying them.
  - measure
```
public void measure()
```
    Measure each node, recursively into children, and at the end display all the result tables, one for each data type.
  - exportSVG
```
public void exportSVG(StringBuffer data,
                      double z_scale,
                      String indent)
```
  - findChildrenOfType
```
public ArrayList<ProjectThing> findChildrenOfType(String type)
```
    Check if this Thing directly contains any child of the given type, and return them all.
  - findChildrenOfType
```
public <T> ArrayList<T> findChildrenOfType(Class<T> c)
```
    Check if this Thing directly contains any child of the given object class (including interfaces), and return them all. This method looks at the object wrapped by the ProjectThing, and returns a list of objects whose class or superclass or interface matches c.
  - findChildrenOfTypeR
```
public HashSet<ProjectThing> findChildrenOfTypeR(String type)
```
    Recursive into children.
  - findChildrenOfTypeR
```
public HashSet<ProjectThing> findChildrenOfTypeR(HashSet<ProjectThing> hs,
                                                 String type)
```
    Recursive into children.
  - findChildrenOfTypeR
```
public List<ProjectThing> findChildrenOfTypeR(Class<?> c)
```
    Finds them in order. Recursive into children.
  - findChildrenOfTypeR
```
public List<ProjectThing> findChildrenOfTypeR(List<ProjectThing> list,
                                              Class<?> c)
```
    Finds them in order. Recursive into children.
  - findObjects
```
public <T> List<T> findObjects(Class<T> c)
```
    Find objects of the given class, as determined by c.isInstance(this.object).
  - findBasicTypeChildren
```
public HashSet<ProjectThing> findBasicTypeChildren()
```
    Recursive into children.
  - findBasicTypeChildren
```
public HashSet<ProjectThing> findBasicTypeChildren(HashSet<ProjectThing> hs_basic,
                                                   HashSet<ProjectThing> hs_visited)
```
    Recursive into children, and adds this instance as well if it's a basic type.
  - updateTitle
```
public void updateTitle()
```
    Recursive into children and object (to update it's DisplayablePanel title). Does not affect the database.
  - updateType
```
public void updateType(String new_type,
                       String old_type)
```
    Recursive into children, changes the type column in the ab_things table. Only if the given 'type' is equal to this instance's template type, the type will be updated in the database and the title will be updated wherever it shows.
  - collectSimilarThings
```
public HashSet<ProjectThing> collectSimilarThings(TemplateThing tt,
                                                  HashSet<ProjectThing> hs)
```
    Recursive into children, find those of the given type that have the same parent chain as the given TemplateThing.
  - exportXML
```
public void exportXML(StringBuilder sb_body,
                      String indent,
                      XMLOptions options)
```
    Expects a HashMap<Thing,Boolean> as any.
    
    Overrides:
    
    exportXML in class DBObject
  - debug
```
public void debug(String indent)
```
    Specified by:
    
    debug in interface Thing
  - fixZOrdering
```
public boolean fixZOrdering()
```
    If this is of type profile_list, order all children Profile by their layer's Z coordinate, ascending.
  - isExpanded
```
public boolean isExpanded()
```
    Specified by:
    
    isExpanded in interface Thing
  - getNodeInfo
```
public String getNodeInfo()
```
    Return information on this node and its object.
  - getInfo
```
public String getInfo()
```
    Return information on this node and its object, and also on all the children, recursively.
    
    Specified by:
    
    getInfo in interface Thing
    
    Overrides:
    
    getInfo in class DBObject
  - subclone
```
public ProjectThing subclone(Project pr)
```
    Implicit id copying; assumes the ids of the object are also the same in the given project; the object, if it is a DBObject, is retrieved from the given project by matching its id.
  - move
```
public boolean move(int inc)
```
    Moves this ProjectThing up and down the parent's children list. Returns false if no movement was done.
  - getByType
```
public HashMap<String,ArrayList<ProjectThing>> getByType()
```
    Recursively browse all children to classify all nodes by type. Returns a table of String types and ArrayList ProjectThing.

Class ProjectThing

Nested Class Summary

Field Summary

Fields inherited from class ini.trakem2.persistence.DBObject

Constructor Summary

Method Summary

Methods inherited from class ini.trakem2.persistence.DBObject

Methods inherited from class java.lang.Object

Constructor Detail

ProjectThing

ProjectThing

Method Detail

shallowCopy

deepClone

setObject

setup

toString

getTitle

addChild

addChild

getChildren

hasChildren

removeChild

remove

remove

setParent

getParent

getRootParent

hasParent

setTitle

getObject

getChildTemplate

canHaveAsChild

uniquePathExists

getTemplatePathTo

getType

getTemplate

getPopupItems

setVisible

createChildren

canHaveAsChild

createChild

createClonedChild

findChildren

findChildren

findChild

findChild

findObject

measure

measure

exportSVG

findChildrenOfType

findChildrenOfType

findChildrenOfTypeR

findChildrenOfTypeR

findChildrenOfTypeR

findChildrenOfTypeR

findObjects

findBasicTypeChildren

findBasicTypeChildren

updateTitle

updateType

collectSimilarThings

exportXML

debug

fixZOrdering

isExpanded

getNodeInfo

getInfo

subclone

move

getByType