.. java:import:: java.awt Desktop .. java:import:: java.awt Window .. java:import:: java.awt.event WindowEvent .. java:import:: java.io IOException .. java:import:: java.lang.reflect InvocationTargetException .. java:import:: java.net URI .. java:import:: java.net URISyntaxException .. java:import:: java.util ArrayList .. java:import:: java.util Collections .. java:import:: java.util HashMap .. java:import:: java.util List .. java:import:: java.util Map .. java:import:: java.util Objects .. java:import:: java.util.function Consumer .. java:import:: javax.swing JDialog .. java:import:: org.mastodon.feature FeatureSpecsService .. java:import:: org.mastodon.feature.ui FeatureColorModeConfigPage .. java:import:: org.mastodon.mamut.feature MamutFeatureProjectionsManager .. java:import:: org.mastodon.mamut.model Model .. java:import:: org.mastodon.mamut.model Spot .. java:import:: org.mastodon.mamut.plugin MamutPlugin .. java:import:: org.mastodon.mamut.plugin MamutPluginAppModel .. java:import:: org.mastodon.mamut.plugin MamutPlugins .. java:import:: org.mastodon.model.tag.ui TagSetDialog .. java:import:: org.mastodon.ui SelectionActions .. java:import:: org.mastodon.ui.coloring.feature FeatureColorModeManager .. java:import:: org.mastodon.ui.keymap CommandDescriptionProvider .. java:import:: org.mastodon.ui.keymap CommandDescriptions .. java:import:: org.mastodon.ui.keymap CommandDescriptionsBuilder .. java:import:: org.mastodon.ui.keymap KeyConfigContexts .. java:import:: org.mastodon.ui.keymap Keymap .. java:import:: org.mastodon.ui.keymap KeymapManager .. java:import:: org.mastodon.ui.keymap KeymapSettingsPage .. java:import:: org.mastodon.util RunnableActionPair .. java:import:: org.mastodon.util ToggleDialogAction .. java:import:: org.mastodon.views.bdv.overlay.ui RenderSettingsConfigPage .. java:import:: org.mastodon.views.bdv.overlay.ui RenderSettingsManager .. java:import:: org.mastodon.views.context ContextProvider .. java:import:: org.mastodon.views.grapher.display.style DataDisplayStyleManager .. java:import:: org.mastodon.views.grapher.display.style DataDisplayStyleSettingsPage .. java:import:: org.mastodon.views.trackscheme ScreenTransform .. java:import:: org.mastodon.views.trackscheme.display ColorBarOverlay.Position .. java:import:: org.mastodon.views.trackscheme.display.style TrackSchemeStyleManager .. java:import:: org.mastodon.views.trackscheme.display.style TrackSchemeStyleSettingsPage .. java:import:: org.scijava Context .. java:import:: org.scijava InstantiableException .. java:import:: org.scijava.listeners Listeners .. java:import:: org.scijava.plugin Plugin .. java:import:: org.scijava.plugin PluginInfo .. java:import:: org.scijava.plugin PluginService .. java:import:: org.scijava.ui.behaviour KeyPressedManager .. java:import:: org.scijava.ui.behaviour.util AbstractNamedAction .. java:import:: org.scijava.ui.behaviour.util Actions .. java:import:: org.scijava.ui.behaviour.util RunnableAction .. java:import:: bdv.util InvokeOnEDT .. java:import:: bdv.viewer ViewerPanel .. java:import:: net.imglib2.realtransform AffineTransform3D WindowManager ============= .. java:package:: org.mastodon.mamut :noindex: .. java:type:: public class WindowManager Main GUI class for the Mastodon Mamut application. It controls the creation of new views, and maintain a list of currently opened views. It has a \ :java:ref:`getProjectManager()`\ instance that can be used to open or create Mastodon projects. It has also the main app-model for the session. :author: Tobias Pietzsch, Jean-Yves Tinevez Methods ------- closeAllWindows ^^^^^^^^^^^^^^^ .. java:method:: public void closeAllWindows() :outertype: WindowManager Close all opened views and dialogs. computeFeatures ^^^^^^^^^^^^^^^ .. java:method:: public void computeFeatures() :outertype: WindowManager Displays the feature computation dialog. createBigDataViewer ^^^^^^^^^^^^^^^^^^^ .. java:method:: public MamutViewBdv createBigDataViewer() :outertype: WindowManager Creates and displays a new BDV view, with default display settings. createBigDataViewer ^^^^^^^^^^^^^^^^^^^ .. java:method:: public MamutViewBdv createBigDataViewer(Map guiState) :outertype: WindowManager Creates and displays a new BDV view, using a map to specify the display settings. The display settings are specified as a map of strings to objects. The accepted key and value types are: .. * \ ``'FramePosition'``\ → an \ ``int[]``\ array of 4 elements: x, y, width and height. * \ ``'LockGroupId'``\ → an integer that specifies the lock group id. * \ ``'SettingsPanelVisible'``\ → a boolean that specifies whether the settings panel is visible on this view. * \ ``'BdvState'``\ → a XML Element that specifies the BDV window state. See \ :java:ref:`ViewerPanel.stateToXml()`\ and \ :java:ref:`ViewerPanel.stateFromXml(org.jdom2.Element)`\ for more information. * \ ``'BdvTransform'``\ → an \ :java:ref:`AffineTransform3D`\ that specifies the view point. * \ ``'NoColoring'``\ → a boolean; if \ ``true``\ , the feature or tag coloring will be ignored. * \ ``'TagSet'``\ → a string specifying the name of the tag-set to use for coloring. If not \ ``null``\ , the coloring will be done using the tag-set. * \ ``'FeatureColorMode'``\ → a String specifying the name of the feature color mode to use for coloring. If not \ ``null``\ , the coloring will be done using the feature color mode. * \ ``'ColorbarVisible'``\ → a boolean specifying whether the colorbar is visible for tag-set and feature-based coloring. * \ ``'ColorbarPosition'``\ → a \ :java:ref:`Position`\ specifying the position of the colorbar. :param guiState: the map of settings. createBranchBigDataViewer ^^^^^^^^^^^^^^^^^^^^^^^^^ .. java:method:: public MamutBranchViewBdv createBranchBigDataViewer() :outertype: WindowManager Creates and displays a new Branch-BDV view, with default display settings. The branch version of this view displays the branch graph. createBranchBigDataViewer ^^^^^^^^^^^^^^^^^^^^^^^^^ .. java:method:: public MamutBranchViewBdv createBranchBigDataViewer(Map guiState) :outertype: WindowManager Creates and displays a new Branch-BDV view, using a map to specify the display settings. :param guiState: the settings map. **See also:** :java:ref:`.createBigDataViewer(Map)` createBranchTrackScheme ^^^^^^^^^^^^^^^^^^^^^^^ .. java:method:: public MamutBranchViewTrackScheme createBranchTrackScheme() :outertype: WindowManager Creates and displays a new Branch-TrackScheme view, with default display settings. The branch version of this view displays the branch graph. createBranchTrackScheme ^^^^^^^^^^^^^^^^^^^^^^^ .. java:method:: public MamutBranchViewTrackScheme createBranchTrackScheme(Map guiState) :outertype: WindowManager Creates and displays a new Branch-TrackScheme view, using a map to specify the display settings. :param guiState: the settings map. **See also:** :java:ref:`.createTrackScheme(Map)` createGrapher ^^^^^^^^^^^^^ .. java:method:: public MamutViewGrapher createGrapher() :outertype: WindowManager Creates and displays a new Grapher view, with default display settings. createGrapher ^^^^^^^^^^^^^ .. java:method:: public MamutViewGrapher createGrapher(Map guiState) :outertype: WindowManager Creates and displays a new Grapher view, using a map to specify the display settings. The display settings are specified as a map of strings to objects. The accepted key and value types are: .. * \ ``'FramePosition'``\ → an \ ``int[]``\ array of 4 elements: x, y, width and height. * \ ``'LockGroupId'``\ → an integer that specifies the lock group id. * \ ``'SettingsPanelVisible'``\ → a boolean that specifies whether the settings panel is visible on this view. * \ ``'NoColoring'``\ → a boolean; if \ ``true``\ , the feature or tag coloring will be ignored. * \ ``'TagSet'``\ → a string specifying the name of the tag-set to use for coloring. If not \ ``null``\ , the coloring will be done using the tag-set. * \ ``'FeatureColorMode'``\ → a @link String specifying the name of the feature color mode to use for coloring. If not \ ``null``\ , the coloring will be done using the feature color mode. * \ ``'ColorbarVisible'``\ → a boolean specifying whether the colorbar is visible for tag-set and feature-based coloring. * \ ``'ColorbarPosition'``\ → a \ :java:ref:`Position`\ specifying the position of the colorbar. * \ ``'GrapherTransform'``\ → a \ :java:ref:`org.mastodon.views.grapher.datagraph.ScreenTransform`\ specifying the region to initially zoom on the XY plot. :param guiState: the map of settings. createHierarchyTrackScheme ^^^^^^^^^^^^^^^^^^^^^^^^^^ .. java:method:: public MamutBranchViewTrackScheme createHierarchyTrackScheme() :outertype: WindowManager Creates and displays a new Hierarchy-TrackScheme view, with default display settings. createHierarchyTrackScheme ^^^^^^^^^^^^^^^^^^^^^^^^^^ .. java:method:: public MamutBranchViewTrackScheme createHierarchyTrackScheme(Map guiState) :outertype: WindowManager Creates and displays a new Hierarchy-TrackScheme view, using a map to specify the display settings. :param guiState: the settings map. **See also:** :java:ref:`.createTrackScheme(Map)` createTable ^^^^^^^^^^^ .. java:method:: public MamutViewTable createTable(Map guiState) :outertype: WindowManager Creates and displays a new Table or a Selection Table view, using a map to specify the display settings. The display settings are specified as a map of strings to objects. The accepted key and value types are: .. * \ ``'TableSelectionOnly'``\ → a boolean specifying whether the table to create will be a selection table of a full table. If \ ``true``\ , the table will only display the current content of the selection, and will listen to its changes. If \ ``false``\ , the table will display the full graph content, listen to its changes, and will be able to edit the selection. * \ ``'FramePosition'``\ → an \ ``int[]``\ array of 4 elements: x, y, width and height. * \ ``'LockGroupId'``\ → an integer that specifies the lock group id. * \ ``'SettingsPanelVisible'``\ → a boolean that specifies whether the settings panel is visible on this view. * \ ``'NoColoring'``\ → a boolean; if \ ``true``\ , the feature or tag coloring will be ignored. * \ ``'TagSet'``\ → a string specifying the name of the tag-set to use for coloring. If not \ ``null``\ , the coloring will be done using the tag-set. * \ ``'FeatureColorMode'``\ → a @link String specifying the name of the feature color mode to use for coloring. If not \ ``null``\ , the coloring will be done using the feature color mode. * \ ``'ColorbarVisible'``\ → a boolean specifying whether the colorbar is visible for tag-set and feature-based coloring. * \ ``'ColorbarPosition'``\ → a \ :java:ref:`Position`\ specifying the position of the colorbar. :param guiState: the map of settings. createTable ^^^^^^^^^^^ .. java:method:: public MamutViewTable createTable(boolean selectionOnly) :outertype: WindowManager Creates and display a new Table or Selection Table view with default settings. :param selectionOnly: if \ ``true``\ , the table will only display the current content of the selection, and will listen to its changes. If \ ``false``\ , the table will display the full graph content, listen to its changes, and will be able to edit the selection. :return: a new table view. createTrackScheme ^^^^^^^^^^^^^^^^^ .. java:method:: public MamutViewTrackScheme createTrackScheme() :outertype: WindowManager Creates and displays a new TrackScheme view, with default display settings. createTrackScheme ^^^^^^^^^^^^^^^^^ .. java:method:: public MamutViewTrackScheme createTrackScheme(Map guiState) :outertype: WindowManager Creates and displays a new BDV view, using a map to specify the display settings. The display settings are specified as a map of strings to objects. The accepted key and value types are: .. * \ ``'FramePosition'``\ → an \ ``int[]``\ array of 4 elements: x, y, width and height. * \ ``'LockGroupId'``\ → an integer that specifies the lock group id. * \ ``'SettingsPanelVisible'``\ → a boolean that specifies whether the settings panel is visible on this view. * \ ``'TrackSchemeTransform'``\ → a \ :java:ref:`ScreenTransform`\ that defines the starting view zone in TrackScheme. * \ ``'NoColoring'``\ → a boolean; if \ ``true``\ , the feature or tag coloring will be ignored. * \ ``'TagSet'``\ → a string specifying the name of the tag-set to use for coloring. If not \ ``null``\ , the coloring will be done using the tag-set. * \ ``'FeatureColorMode'``\ → a @link String specifying the name of the feature color mode to use for coloring. If not \ ``null``\ , the coloring will be done using the feature color mode. * \ ``'ColorbarVisible'``\ → a boolean specifying whether the colorbar is visible for tag-set and feature-based coloring. * \ ``'ColorbarPosition'``\ → a \ :java:ref:`Position`\ specifying the position of the colorbar. :param guiState: the map of settings. editTagSets ^^^^^^^^^^^ .. java:method:: public void editTagSets() :outertype: WindowManager Displays the tag-set editor dialog. forEachBdvView ^^^^^^^^^^^^^^ .. java:method:: public void forEachBdvView(Consumer action) :outertype: WindowManager Executes the specified action for all the currently opened BDV views. :param action: the action to execute. forEachBranchTrackSchemeView ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ .. java:method:: public void forEachBranchTrackSchemeView(Consumer action) :outertype: WindowManager Executes the specified action for all the currently opened Branch-TrackScheme views. :param action: the action to execute. forEachBranchView ^^^^^^^^^^^^^^^^^ .. java:method:: public void forEachBranchView(Consumer> action) :outertype: WindowManager Executes the specified action for all the currently opened branch-graph views. :param action: the action to execute. forEachGrapherView ^^^^^^^^^^^^^^^^^^ .. java:method:: public void forEachGrapherView(Consumer action) :outertype: WindowManager Executes the specified action for all the currently opened Grapher views. :param action: the action to execute. forEachTableView ^^^^^^^^^^^^^^^^ .. java:method:: public void forEachTableView(Consumer action) :outertype: WindowManager Executes the specified action for all the currently opened Table views. :param action: the action to execute. forEachTrackSchemeView ^^^^^^^^^^^^^^^^^^^^^^ .. java:method:: public void forEachTrackSchemeView(Consumer action) :outertype: WindowManager Executes the specified action for all the currently opened TrackScheme views. :param action: the action to execute. forEachView ^^^^^^^^^^^ .. java:method:: public void forEachView(Consumer> action) :outertype: WindowManager Executes the specified action for all the currently opened views. :param action: the action to execute. getBdvWindows ^^^^^^^^^^^^^ .. java:method:: public List getBdvWindows() :outertype: WindowManager Exposes currently open BigDataViewer windows. :return: a \ :java:ref:`List`\ of \ :java:ref:`MamutViewBdv`\ . openOnlineDocumentation ^^^^^^^^^^^^^^^^^^^^^^^ .. java:method:: public void openOnlineDocumentation() :outertype: WindowManager Opens the online documentation in a browser window.