Project (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- ini.trakem2.persistence.DBObject
- - ini.trakem2.Project

```
public class Project
extends DBObject
```
The top-level class in control.

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

Constructor Summary

Constructors
Constructor and Description

Project(long id, String title)
Constructor used by the Loader to find projects.

Constructors
Constructor and Description
`Project(long id, String title)` Constructor used by the Loader to find projects.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`addUniqueType(TemplateThing tt)` Returns false if the type exists already.
`void`	`adjustProperties()`
`Project`	`createSubproject(Rectangle roi, Layer first, Layer last, boolean ignore_hidden_patches)` Create a new subproject for the given layer range and ROI.
`void`	`decache(Object ob)`
`boolean`	`destroy()`
`void`	`exportDTD(StringBuilder sb_header, HashSet<String> hs, String indent)` Export a complete DTD listing to export the project as XML.
`void`	`exportXML(StringBuilder sb, String indent, XMLOptions options)` Subclasses can override this method to store the instance as XML.
`void`	`exportXML(Writer writer, String indent, XMLOptions options)` Export the main trakem2 tag wrapping four hierarchies (the project tag, the ProjectTree, and the Top Level LayerSet the latter including all Displayable objects) and a list of displays.
`ProjectThing`	`find(long id)` Find the ProjectThing instance with the given id.
`DBObject`	`findById(long id)`
`LayerThing`	`findLayerThing(Object ob)` Find a LayerThing that contains the given object.
`static Project`	`findProject(Loader loader)`
`ProjectThing`	`findProjectThing(Object ob)` Find a ProjectThing that contains the given object.
`boolean`	`getBooleanProperty(String key)`
`String`	`getDocType()` Returns the String to be used as Document Type of the XML file, generated from the name of the root template thing.
`int`	`getFirstMipMapLevelSaved()` Get the mipmap level at which to start saving images.
`String`	`getInfo()` Returns id and project name; this method is meant to be overriden by any of the subclasses.
`LayerTree`	`getLayerTree()`
`Loader`	`getLoader()`
`String`	`getMeaningfulTitle(Displayable d)` Searches upstream in the Project tree for things that have a user-defined name, stops at the first and returns it along with all the intermediate ones that only have a type and not a title, appended.
`String`	`getMeaningfulTitle2(Displayable d)`
`int`	`getMipMapsMode()` The mode (aka algorithmic approach) used to generate mipmaps, which defaults to `Loader.DEFAULT_MIPMAPS_MODE`.
`static String`	`getName(Class<?> c)` Returns a user-understandable name for the given class.
`String`	`getParentTitle(Displayable d)` Returns the title of the enclosing abstract node in the ProjectTree.
`TreeMap<String,TPlugIn>`	`getPlugins(String menu)`
`static Project`	`getProject(String title)`
`static ArrayList<Project>`	`getProjects()` Return a copy of the list of all open projects.
`ProjectTree`	`getProjectTree()`
`HashMap<String,String>`	`getPropertiesCopy()`
`String`	`getProperty(String key)` Returns null if not defined.
`float`	`getProperty(String key, float default_value)` Returns the default value if not defined, or if not a number or not parsable as a number.
`int`	`getProperty(String key, int default_value)`
`LayerSet`	`getRootLayerSet()`
`LayerThing`	`getRootLayerThing()`
`ProjectThing`	`getRootProjectThing()`
`TemplateThing`	`getRootTemplateThing()`
`String`	`getShortMeaningfulTitle(Displayable d)` Returns the first upstream user-defined name and type, and the id of the displayable tagged at the end.
`String`	`getShortMeaningfulTitle(ProjectThing thing, Displayable d)`
`TemplateThing`	`getTemplateThing(String type)` Returns the proper TemplateThing for the given type, complete with children and attributes if any.
`TemplateTree`	`getTemplateTree()`
`String`	`getTitle()` Sublcasses can override this method to provide a proper String, otherwise calls toString()
`static String`	`getType(Class<?> c)`
`String[]`	`getUniqueTypes()` Returns a list of existing unique types in the template tree (thus the 'project' type is not included, nor the label).
`String`	`getUNUId()` Return the Universal Near-Unique Id of this project, which may be null for non-FSLoader projects.
`static boolean`	`isBasicType(String type)` Returns true if the type is 'patch', 'layer', 'layer_set', 'profile', 'profile_list' 'pipe'.
`boolean`	`isBeingDestroyed()`
`boolean`	`isInputEnabled()`
`static boolean`	`isLayerSetType(String type)`
`static boolean`	`isLayerType(String type)`
`static boolean`	`isProjectType(String type)`
`Object`	`makeObject(TemplateThing tt)` Make an object of the type the TemplateThing can hold.
`static Project`	`newDBProject()` Create a new PostgreSQL-based TrakEM2 project.
`static Project`	`newFSProject(String arg)` Creates a new project to be based on .xml and image files, not a database.
`static Project`	`newFSProject(String arg, TemplateThing template_root)`
`static Project`	`newFSProject(String arg, TemplateThing template_root, String storage_folder)` Creates a new project to be based on .xml and image files, not a database.
`static Project`	`newFSProject(String arg, TemplateThing template_root, String storage_folder, boolean autocreate_one_layer)`
`static Project`	`openDBProject()` Open a TrakEM2 project from the database.
`static Project`	`openFSProject(String path)`
`static Project`	`openFSProject(String path, boolean open_displays)` Opens a project from an .xml file.
`void`	`parseXMLOptions(HashMap<String,String> ht_attributes)`
`void`	`remove()` Remove the project from the database and release memory.
`boolean`	`remove(boolean check)` Remove the project from the database and release memory.
`boolean`	`remove(Displayable d)` Removes an object from this Project.
`boolean`	`removeAll(Set<Displayable> col)` Calls Project.removeAll(col, null)
`boolean`	`removeAll(Set<Displayable> col, DefaultMutableTreeNode top_node)` Remove any set of Displayable objects from the Layer, LayerSet and Project Tree as necessary.
`boolean`	`removeProjectThing(Object object, boolean check)` Remove the ProjectThing that contains the given object, which will remove the object itself as well.
`boolean`	`removeProjectThing(Object object, boolean check, boolean remove_empty_parents, int levels)` Remove the ProjectThing that contains the given object, which will remove the object itself as well.
`boolean`	`removeUniqueType(String type)` Remove a unique type from the HashMap.
`void`	`resetRootLayerThing(LayerThing lt, HashMap<Thing,Boolean> ltree_exp)` For undo purposes.
`void`	`resetRootProjectThing(ProjectThing pt, HashMap<Thing,Boolean> ptree_exp)` For undo purposes.
`void`	`resetRootTemplateThing(TemplateThing tt, HashMap<Thing,Boolean> ttree_exp)` For undo purposes.
`String`	`save()` Save the project regardless of what getLoader().hasChanges() reports.
`String`	`saveAs(String xml_path, boolean overwrite)` This is not the saveAs used from the menus; this one is meant for programmatic access.
`Bureaucrat`	`saveTask(String command)`
`String`	`saveWithoutCoordinateTransforms()` Save an XML file that is stripped of coordinate transforms, and merely refers to them by the 'ct_id' attribute of each 't2_patch' element; this method will NOT overwrite the XML file but save into a new one, which is chosen from a file dialog.
`void`	`select(Displayable d)` Find the node in any tree with a Thing that contains the given Displayable, and set it selected/highlighted, deselecting everything else first.
`void`	`select(Layer layer)` Find the node in the layer tree with a Thing that contains the given object, and set it selected/highlighted, deselecting everything else first.
`int`	`setFirstMipMapLevelSaved(double level)` Returns the newly set mipmap level (an integer, made by a floor operation on `level`), or the current one if `level` is NaN or negative.
`void`	`setMipMapsMode(int mode)`
`void`	`setProperty(String key, String value)`
`void`	`setReceivesInput(boolean b)` Tells the displays concerning this Project to accept/reject input.
`void`	`setTempLoader(Loader loader)`
`void`	`setTitle(String title)`
`String`	`toString()`
`boolean`	`typeExists(String type)`
`boolean`	`updateTypeName(String old_type, String new_type)`

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
  - Project
```
public Project(long id,
               String title)
```
    Constructor used by the Loader to find projects. These projects contain no loader.
- Method Detail
  - getPlugins
```
public TreeMap<String,TPlugIn> getPlugins(String menu)
```
  - getProject
```
public static Project getProject(String title)
```
  - getProjects
```
public static ArrayList<Project> getProjects()
```
    Return a copy of the list of all open projects.
  - newDBProject
```
public static Project newDBProject()
```
    Create a new PostgreSQL-based TrakEM2 project.
  - openDBProject
```
public static Project openDBProject()
```
    Open a TrakEM2 project from the database. Queries the database for existing projects and if more than one, asks which one to open.
  - newFSProject
```
public static Project newFSProject(String arg)
```
    Creates a new project to be based on .xml and image files, not a database. Images are left where they are, keeping the path to them. If the arg equals 'blank', then no template is asked for.
  - newFSProject
```
public static Project newFSProject(String arg,
                                   TemplateThing template_root)
```
  - newFSProject
```
public static Project newFSProject(String arg,
                                   TemplateThing template_root,
                                   String storage_folder)
```
    Creates a new project to be based on .xml and image files, not a database. Images are left where they are, keeping the path to them. If the arg equals 'blank', then no template is asked for; if template_root is not null that is used; else, a template file is asked for.
    
    Parameters:
    
    arg - Either "blank", "amira", "stack" or null. "blank" will generate a default template tree; "amira" will ask for importing an Amira file; "stack" will ask for importing an image stack (single multi-image file, like multi-TIFF).
    
    template_root - May be null, in which case a template DTD or XML file will be asked for, unless arg equals "blank".
    
    storage_folder - If null, a dialog asks for it.
  - newFSProject
```
public static Project newFSProject(String arg,
                                   TemplateThing template_root,
                                   String storage_folder,
                                   boolean autocreate_one_layer)
```
  - openFSProject
```
public static Project openFSProject(String path)
```
  - openFSProject
```
public static Project openFSProject(String path,
                                    boolean open_displays)
```
    Opens a project from an .xml file. If the path is null it'll be asked for. Only one project may be opened at a time.
  - setTempLoader
```
public void setTempLoader(Loader loader)
```
  - getLoader
```
public final Loader getLoader()
```
  - save
```
public String save()
```
    Save the project regardless of what getLoader().hasChanges() reports.
  - saveAs
```
public String saveAs(String xml_path,
                     boolean overwrite)
              throws IllegalArgumentException
```
    This is not the saveAs used from the menus; this one is meant for programmatic access.
    
    Throws:
    
    IllegalArgumentException
  - saveWithoutCoordinateTransforms
```
public String saveWithoutCoordinateTransforms()
```
    Save an XML file that is stripped of coordinate transforms, and merely refers to them by the 'ct_id' attribute of each 't2_patch' element; this method will NOT overwrite the XML file but save into a new one, which is chosen from a file dialog.
  - destroy
```
public boolean destroy()
```
  - isBeingDestroyed
```
public boolean isBeingDestroyed()
```
  - remove
```
public void remove()
```
    Remove the project from the database and release memory.
  - remove
```
public boolean remove(boolean check)
```
    Remove the project from the database and release memory.
    
    Overrides:
    
    remove in class DBObject
  - setTitle
```
public void setTitle(String title)
```
  - toString
```
public String toString()
```
    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()
    
    Overrides:
    
    getTitle in class DBObject
  - getTemplateTree
```
public TemplateTree getTemplateTree()
```
  - getLayerTree
```
public LayerTree getLayerTree()
```
  - getProjectTree
```
public ProjectTree getProjectTree()
```
  - makeObject
```
public Object makeObject(TemplateThing tt)
```
    Make an object of the type the TemplateThing can hold.
  - isBasicType
```
public static boolean isBasicType(String type)
```
    Returns true if the type is 'patch', 'layer', 'layer_set', 'profile', 'profile_list' 'pipe'.
  - isProjectType
```
public static boolean isProjectType(String type)
```
  - isLayerSetType
```
public static boolean isLayerSetType(String type)
```
  - isLayerType
```
public static boolean isLayerType(String type)
```
  - removeProjectThing
```
public boolean removeProjectThing(Object object,
                                  boolean check)
```
    Remove the ProjectThing that contains the given object, which will remove the object itself as well.
  - removeProjectThing
```
public boolean removeProjectThing(Object object,
                                  boolean check,
                                  boolean remove_empty_parents,
                                  int levels)
```
    Remove the ProjectThing that contains the given object, which will remove the object itself as well.
  - select
```
public void select(Layer layer)
```
    Find the node in the layer tree with a Thing that contains the given object, and set it selected/highlighted, deselecting everything else first.
  - select
```
public void select(Displayable d)
```
    Find the node in any tree with a Thing that contains the given Displayable, and set it selected/highlighted, deselecting everything else first.
  - find
```
public ProjectThing find(long id)
```
    Find the ProjectThing instance with the given id.
  - findById
```
public DBObject findById(long id)
```
  - findLayerThing
```
public LayerThing findLayerThing(Object ob)
```
    Find a LayerThing that contains the given object.
  - findProjectThing
```
public ProjectThing findProjectThing(Object ob)
```
    Find a ProjectThing that contains the given object.
  - decache
```
public void decache(Object ob)
```
  - getRootProjectThing
```
public ProjectThing getRootProjectThing()
```
  - getRootLayerSet
```
public LayerSet getRootLayerSet()
```
  - getParentTitle
```
public String getParentTitle(Displayable d)
```
    Returns the title of the enclosing abstract node in the ProjectTree.
  - getMeaningfulTitle2
```
public String getMeaningfulTitle2(Displayable d)
```
  - getMeaningfulTitle
```
public String getMeaningfulTitle(Displayable d)
```
    Searches upstream in the Project tree for things that have a user-defined name, stops at the first and returns it along with all the intermediate ones that only have a type and not a title, appended.
  - getShortMeaningfulTitle
```
public String getShortMeaningfulTitle(Displayable d)
```
    Returns the first upstream user-defined name and type, and the id of the displayable tagged at the end. If no user-defined name is found, then the type is prepended to the id.
  - getShortMeaningfulTitle
```
public String getShortMeaningfulTitle(ProjectThing thing,
                                      Displayable d)
```
  - getType
```
public static String getType(Class<?> c)
```
  - getTemplateThing
```
public TemplateThing getTemplateThing(String type)
```
    Returns the proper TemplateThing for the given type, complete with children and attributes if any.
  - getUniqueTypes
```
public String[] getUniqueTypes()
```
    Returns a list of existing unique types in the template tree (thus the 'project' type is not included, nor the label). The basic types are guaranteed to be present even if there are no instances in the template tree. As a side effect, this method populates the HashMap of unique TemplateThing types.
  - removeUniqueType
```
public boolean removeUniqueType(String type)
```
    Remove a unique type from the HashMap. Basic types can't be removed.
  - typeExists
```
public boolean typeExists(String type)
```
  - addUniqueType
```
public boolean addUniqueType(TemplateThing tt)
```
    Returns false if the type exists already.
  - updateTypeName
```
public boolean updateTypeName(String old_type,
                              String new_type)
```
  - exportXML
```
public void exportXML(StringBuilder sb,
                      String indent,
                      XMLOptions options)
```
    Description copied from class: DBObject
    
    Subclasses can override this method to store the instance as XML.
    
    Overrides:
    
    exportXML in class DBObject
  - exportXML
```
public void exportXML(Writer writer,
                      String indent,
                      XMLOptions options)
               throws Exception
```
    Export the main trakem2 tag wrapping four hierarchies (the project tag, the ProjectTree, and the Top Level LayerSet the latter including all Displayable objects) and a list of displays.
    
    Throws:
    
    Exception
  - exportDTD
```
public void exportDTD(StringBuilder sb_header,
                      HashSet<String> hs,
                      String indent)
```
    Export a complete DTD listing to export the project as XML.
  - getDocType
```
public String getDocType()
```
    Returns the String to be used as Document Type of the XML file, generated from the name of the root template thing.
  - getName
```
public static String getName(Class<?> c)
```
    Returns a user-understandable name for the given class.
  - getInfo
```
public String getInfo()
```
    Description copied from class: DBObject
    
    Returns id and project name; this method is meant to be overriden by any of the subclasses.
    
    Overrides:
    
    getInfo in class DBObject
  - findProject
```
public static Project findProject(Loader loader)
```
  - setReceivesInput
```
public void setReceivesInput(boolean b)
```
    Tells the displays concerning this Project to accept/reject input.
  - isInputEnabled
```
public boolean isInputEnabled()
```
  - createSubproject
```
public Project createSubproject(Rectangle roi,
                                Layer first,
                                Layer last,
                                boolean ignore_hidden_patches)
```
    Create a new subproject for the given layer range and ROI. Create a new Project using the given project as template. This means the DTD of the given project is copied, as well as the storage and mipmaps folders; everything else is empty in the new project.
  - parseXMLOptions
```
public void parseXMLOptions(HashMap<String,String> ht_attributes)
```
  - getPropertiesCopy
```
public HashMap<String,String> getPropertiesCopy()
```
  - getProperty
```
public String getProperty(String key)
```
    Returns null if not defined.
  - getProperty
```
public float getProperty(String key,
                         float default_value)
```
    Returns the default value if not defined, or if not a number or not parsable as a number.
  - getProperty
```
public int getProperty(String key,
                       int default_value)
```
  - getBooleanProperty
```
public boolean getBooleanProperty(String key)
```
  - setProperty
```
public void setProperty(String key,
                        String value)
```
  - setFirstMipMapLevelSaved
```
public final int setFirstMipMapLevelSaved(double level)
```
    Returns the newly set mipmap level (an integer, made by a floor operation on level), or the current one if level is NaN or negative.
  - getFirstMipMapLevelSaved
```
public final int getFirstMipMapLevelSaved()
```
    Get the mipmap level at which to start saving images. E.g. if level is 2, then mipmaps for levels 0 and 1 are not saved, and 2, 3, 4 ... are saved.
  - adjustProperties
```
public void adjustProperties()
```
  - getUNUId
```
public String getUNUId()
```
    Return the Universal Near-Unique Id of this project, which may be null for non-FSLoader projects.
  - remove
```
public final boolean remove(Displayable d)
```
    Removes an object from this Project.
  - removeAll
```
public final boolean removeAll(Set<Displayable> col)
```
    Calls Project.removeAll(col, null)
  - removeAll
```
public final boolean removeAll(Set<Displayable> col,
                               DefaultMutableTreeNode top_node)
```
    Remove any set of Displayable objects from the Layer, LayerSet and Project Tree as necessary. ASSUMES there aren't any nested LayerSet objects in col.
  - resetRootProjectThing
```
public void resetRootProjectThing(ProjectThing pt,
                                  HashMap<Thing,Boolean> ptree_exp)
```
    For undo purposes.
  - resetRootTemplateThing
```
public void resetRootTemplateThing(TemplateThing tt,
                                   HashMap<Thing,Boolean> ttree_exp)
```
    For undo purposes.
  - resetRootLayerThing
```
public void resetRootLayerThing(LayerThing lt,
                                HashMap<Thing,Boolean> ltree_exp)
```
    For undo purposes.
  - getRootTemplateThing
```
public TemplateThing getRootTemplateThing()
```
  - getRootLayerThing
```
public LayerThing getRootLayerThing()
```
  - saveTask
```
public Bureaucrat saveTask(String command)
```
  - getMipMapsMode
```
public int getMipMapsMode()
```
    The mode (aka algorithmic approach) used to generate mipmaps, which defaults to Loader.DEFAULT_MIPMAPS_MODE.
  - setMipMapsMode
```
public void setMipMapsMode(int mode)
```
    See Also:
    
    getMipMapsMode()

Class Project

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

Project

Method Detail

getPlugins

getProject

getProjects

newDBProject

openDBProject

newFSProject

newFSProject

newFSProject

newFSProject

openFSProject

openFSProject

setTempLoader

getLoader

save

saveAs

saveWithoutCoordinateTransforms

destroy

isBeingDestroyed

remove

remove

setTitle

toString

getTitle

getTemplateTree

getLayerTree

getProjectTree

makeObject

isBasicType

isProjectType

isLayerSetType

isLayerType

removeProjectThing

removeProjectThing

select

select

find

findById

findLayerThing

findProjectThing

decache

getRootProjectThing

getRootLayerSet

getParentTitle

getMeaningfulTitle2

getMeaningfulTitle

getShortMeaningfulTitle

getShortMeaningfulTitle

getType

getTemplateThing

getUniqueTypes

removeUniqueType

typeExists

addUniqueType

updateTypeName

exportXML

exportXML

exportDTD

getDocType

getName

getInfo

findProject

setReceivesInput

isInputEnabled

createSubproject

parseXMLOptions

getPropertiesCopy

getProperty

getProperty

getProperty

getBooleanProperty