--- /dev/null
--- /dev/null
++/target/
--- /dev/null
-#Properties file for taxeditor-editor\r
-Bundle-Vendor.0 = EDIT\r
-Bundle-Name.0 = EDIT Taxonomic Editor - Editor Bundle\r
-command.name.17 = Set Basionym\r
-command.name.18 = Remove Basionym\r
-editor.name = Multipage Taxon Editor\r
-editor.name.0 = Taxon Name Editor\r
-editor.name.1 = Key\r
-editor.name.2 = Polytomous Key Graph Editor\r
-editor.name.3 = Polytomous Key List Editor\r
-editor.name.4 = Cdm Authority Editor\r
-editor.name.5 = Derivative View\r
-view.name = Factual Data\r
-view.name.0 = Uses\r
-view.name.1 = Media\r
-view.name.2 = Concept Relations\r
-view.name.3 = Concept Graph\r
-category.name = Taxonomic Editor\r
-command.label = Reference\r
-command.label.0 = Name\r
-command.label.1 = Team\r
-command.label.2 = Person\r
-command.label.3 = Specimen\r
-command.label.4 = Factual Data\r
-command.label.5 = Media\r
-command.label.6 = Concept\r
-command.label.7 = Concept Graph\r
-command.label.8 = Open Parent\r
-menu.label = New\r
-command.label.9 = Heterotypic Synonym\r
-command.label.10 = Homotypic Synonym\r
-command.label.11 = Synonym In Homotypical Group\r
-menu.label.0 = Change To\r
-command.label.12 = Accepted Taxon\r
-command.label.13 = Synonym\r
-command.label.14 = Misapplication\r
-command.label.15 = Delete\r
-command.label.16 = Delete All Empty Names\r
-command.label.17 = Swap Synonym With Accepted\r
-command.label.18 = Show Details\r
-command.label.19 = Save\r
-command.label.20 = New Node\r
-command.label.21 = Delete\r
-command.label.22 = Apply Layout\r
-command.label.23 = New Key Number\r
-command.label.24 = New Alternative\r
-command.label.25 = Refresh Nodes\r
-command.label.26 = Delete\r
-command.label.27 = New Factual Data\r
-menu.label.1 = New\r
-command.label.28 = Move Description to Taxon\r
-command.label.29 = Move Elements to Taxon\r
-command.label.30 = Delete\r
-command.label.31 = Save\r
-menu.label.2 = New Derivative\r
-command.label.32 = New Use\r
-command.label.33 = New Use Summary\r
-command.label.34 = New Use Record\r
-command.label.35 = Delete\r
-command.label.36 = Save\r
-command.label.37 = New Image Gallery\r
-command.label.38 = New Image\r
-command.label.39 = Move Image Up In List\r
-command.label.40 = Move Image Down In List\r
-command.label.41 = Delete\r
-command.label.42 = Save\r
-menu.label.3 = New\r
-command.label.43 = Open Related Concept\r
-command.label.44 = Delete\r
-command.label.45 = Edit Authorities\r
-extension.name = Name Commands\r
-category.name.0 = -- Name Editor\r
-command.name = Open Parent\r
-command.name.0 = Create Homotypic Synonym\r
-command.name.1 = Create Heterotypic Synonym\r
-command.name.2 = Create Synonym In Homotypical Group\r
-command.name.3 = Change To Synonym\r
-command.name.4 = Change To Accepted Taxon\r
-command.name.5 = Change To Misapplication\r
-command.name.6 = Swap Synonym With Accepted\r
-\r
-command.name.7 = Set Basionym / Original Combination\r
-command.name.8 = Remove Basionym / Original Combination\r
-command.name.9 = Delete All Empty Names\r
-category.name.1 = -- Factual\r
-command.name.10 = Create Description Element\r
-command.name.11 = New Description\r
-command.name.12 = Move Description Elements to Taxon\r
-command.name.13 = Move Description to Taxon\r
-category.name.2 = -- New Uses\r
-command.name.14 = New Use\r
-command.name.15 = New Use Summary\r
-command.name.16 = New Use Record\r
-category.name.3 = -- Media\r
-command.name.19 = Move Image Down In List\r
-command.name.20 = New Image Gallery\r
-command.name.21 = New Image\r
-command.name.22 = Move Image Up In List\r
-category.name.4 = -- New Entity\r
-command.name.23 = New Reference\r
-command.name.24 = New Name\r
-command.name.25 = New Team\r
-command.name.26 = New Person\r
-command.name.27 = New Specimen\r
-category.name.5 = -- Polytomous Keys\r
-command.name.28 = New Child Node\r
-command.name.29 = New Sibling Node\r
-command.name.30 = Refresh Node Numbering\r
-command.name.31 = Apply Layout\r
-category.name.6 = -- Concept Relations\r
-command.name.32 = Create Concept Relation\r
-command.name.33 = Open Related Concept\r
-category.name.7 = -- Group\r
-command.name.34 = Edit CDM Authorities\r
-command.name.35 = Open Derivative View\r
-scheme.description = The default key binding scheme for the Taxonomic Editor\r
-scheme.name = Taxonomic Editor Default Key Bindings\r
-editor.name.6 = Specimen Import Editor\r
-editor.name.7 = Gbif Import Editor\r
-editor.name.8 = Checklist Editor\r
-view.name.4 = Specimen Import\r
-view.name.5 = GBIF Specimen Import\r
-command.label.46 = Name\r
-command.label.47 = Reference\r
-command.label.48 = Datasource\r
-command.label.49 = Misapplication\r
-command.label.50 = Use Existing Image\r
-command.name.36 = Create Misapplication\r
-command.name.37 = Use Existing Image\r
-command.name.38 = Open Checklist Editor\r
-command.name.39 = New Datasource\r
-wizard.name = Specimen Search/Import\r
-wizard.description = Queries data provider for specimens with specified parameters.\nNote: Query results are currently limited to 100.\r
-command.name.40 = Validation\r
-view.name.6 = Validation\r
-marker.field.0 = Object Type\r
-marker.field.1 = Object\r
-marker.field.2 = Attribute\r
-marker.field.3 = Problematic Value\r
-marker.field.4 = Problem description\r
-marker.field.5 = Validator\r
-marker.field.6 = Entity Class\r
-marker.field.7 = Entity Id\r
-extension.name.0 = Validation Error\r
-command.label.51 = Open in Specimen Editor\r
-command.label.52 = Delete\r
-command.label.53 = Create Field Unit\r
-command.label.54 = Delete (with children)\r
-command.tooltip = Show Only Individuals Associations\r
-command.label.55 = Open Associated Specimens\r
-command.name.41 = Show Only Individual Associations\r
-command.name.42 = Open Taxon Editor\r
-command.name.43 = Create Field Unit\r
-command.name.44 = Deep Delete\r
-command.name.46 = Move Synonym (Homotypical Group) to another Accepted Taxon\r
-command.label.56 = Move Synonym (Homotypical Group) to another Accepted Taxon\r
-markerContentGenerator.name = Validation Problems Marker Generator\r
-command.name.45 = Delete\r
-command.name.47 = Delete\r
-commandParameter.name = taxonUUID\r
-Bundle-Name = Editor Bundle\r
-command.name.48 = delete\r
-command.name.49 = delete\r
++#Properties file for taxeditor-editor
++Bundle-Vendor.0 = EDIT
++Bundle-Name.0 = EDIT Taxonomic Editor - Editor Bundle
++command.name.17 = Set Basionym
++command.name.18 = Remove Basionym
++editor.name = Multipage Taxon Editor
++editor.name.0 = Taxon Name Editor
++editor.name.1 = Key
++editor.name.2 = Polytomous Key Graph Editor
++editor.name.3 = Polytomous Key List Editor
++editor.name.4 = Cdm Authority Editor
++editor.name.5 = Derivative View
++view.name = Factual Data
++view.name.0 = Uses
++view.name.1 = Media
++view.name.2 = Concept Relations
++view.name.3 = Concept Graph
++category.name = Taxonomic Editor
++command.label = Reference
++command.label.0 = Name
++command.label.1 = Team
++command.label.2 = Person
++command.label.3 = Specimen
++command.label.4 = Factual Data
++command.label.5 = Media
++command.label.6 = Concept
++command.label.7 = Concept Graph
++command.label.8 = Open Parent
++menu.label = New
++command.label.9 = Heterotypic Synonym
++command.label.10 = Homotypic Synonym
++command.label.11 = Synonym In Homotypical Group
++menu.label.0 = Change To
++command.label.12 = Accepted Taxon
++command.label.13 = Synonym
++command.label.14 = Misapplication
++command.label.15 = Delete
++command.label.16 = Delete All Empty Names
++command.label.17 = Swap Synonym With Accepted
++command.label.18 = Show Details
++command.label.19 = Save
++command.label.20 = New Node
++command.label.21 = Delete
++command.label.22 = Apply Layout
++command.label.23 = New Key Number
++command.label.24 = New Alternative
++command.label.25 = Refresh Nodes
++command.label.26 = Delete
++command.label.27 = New Factual Data
++menu.label.1 = New
++command.label.28 = Move Description to Taxon
++command.label.29 = Move Elements to Taxon
++command.label.30 = Delete
++command.label.31 = Save
++menu.label.2 = New Derivative
++command.label.32 = New Use
++command.label.33 = New Use Summary
++command.label.34 = New Use Record
++command.label.35 = Delete
++command.label.36 = Save
++command.label.37 = New Image Gallery
++command.label.38 = New Image
++command.label.39 = Move Image Up In List
++command.label.40 = Move Image Down In List
++command.label.41 = Delete
++command.label.42 = Save
++menu.label.3 = New
++command.label.43 = Open Related Concept
++command.label.44 = Delete
++command.label.45 = Edit Authorities
++extension.name = Name Commands
++category.name.0 = -- Name Editor
++command.name = Open Parent
++command.name.0 = Create Homotypic Synonym
++command.name.1 = Create Heterotypic Synonym
++command.name.2 = Create Synonym In Homotypical Group
++command.name.3 = Change To Synonym
++command.name.4 = Change To Accepted Taxon
++command.name.5 = Change To Misapplication
++command.name.6 = Swap Synonym With Accepted
++
++command.name.7 = Set Basionym / Original Combination
++command.name.8 = Remove Basionym / Original Combination
++command.name.9 = Delete All Empty Names
++category.name.1 = -- Factual
++command.name.10 = Create Description Element
++command.name.11 = New Description
++command.name.12 = Move Description Elements to Taxon
++command.name.13 = Move Description to Taxon
++category.name.2 = -- New Uses
++command.name.14 = New Use
++command.name.15 = New Use Summary
++command.name.16 = New Use Record
++category.name.3 = -- Media
++command.name.19 = Move Image Down In List
++command.name.20 = New Image Gallery
++command.name.21 = New Image
++command.name.22 = Move Image Up In List
++category.name.4 = -- New Entity
++command.name.23 = New Reference
++command.name.24 = New Name
++command.name.25 = New Team
++command.name.26 = New Person
++command.name.27 = New Specimen
++category.name.5 = -- Polytomous Keys
++command.name.28 = New Child Node
++command.name.29 = New Sibling Node
++command.name.30 = Refresh Node Numbering
++command.name.31 = Apply Layout
++category.name.6 = -- Concept Relations
++command.name.32 = Create Concept Relation
++command.name.33 = Open Related Concept
++category.name.7 = -- Group
++command.name.34 = Edit CDM Authorities
++command.name.35 = Open Derivative View
++scheme.description = The default key binding scheme for the Taxonomic Editor
++scheme.name = Taxonomic Editor Default Key Bindings
++editor.name.6 = Specimen Import Editor
++editor.name.7 = Gbif Import Editor
++editor.name.8 = Checklist Editor
++view.name.4 = Specimen Import
++view.name.5 = GBIF Specimen Import
++command.label.46 = Name
++command.label.47 = Reference
++command.label.48 = Datasource
++command.label.49 = Misapplication
++command.label.50 = Use Existing Image
++command.name.36 = Create Misapplication
++command.name.37 = Use Existing Image
++command.name.38 = Open Checklist Editor
++command.name.39 = New Datasource
++wizard.name = Specimen Search/Import
++wizard.description = Queries data provider for specimens with specified parameters.\nNote: Query results are currently limited to 100.
++command.name.40 = Validation
++view.name.6 = Validation
++marker.field.0 = Object Type
++marker.field.1 = Object
++marker.field.2 = Attribute
++marker.field.3 = Problematic Value
++marker.field.4 = Problem description
++marker.field.5 = Validator
++marker.field.6 = Entity Class
++marker.field.7 = Entity Id
++extension.name.0 = Validation Error
++command.label.51 = Open in Specimen Editor
++command.label.52 = Delete
++command.label.53 = Create Field Unit
++command.label.54 = Delete (with children)
++command.tooltip = Show Only Individuals Associations
++command.label.55 = Open Associated Specimens
++command.name.41 = Show Only Individual Associations
++command.name.42 = Open Taxon Editor
++command.name.43 = Create Field Unit
++command.name.44 = Deep Delete
++command.name.46 = Move Synonym (Homotypical Group) to another Accepted Taxon
++command.label.56 = Move Synonym (Homotypical Group) to another Accepted Taxon
++markerContentGenerator.name = Validation Problems Marker Generator
++command.name.45 = Delete
++command.name.47 = Delete
++commandParameter.name = taxonUUID
++Bundle-Name = Editor Bundle
++command.name.48 = delete
++command.name.49 = delete
+ command.name.50 = delete
--- /dev/null
-#Properties file for taxeditor-editor\r
-Bundle-Vendor.0 = EDIT\r
-Bundle-Name.0 = EDIT Taxonomic Editor - Editor Bundle\r
-command.name.17 = Set Basionym\r
-command.name.18 = Remove Basionym\r
-editor.name = Multipage Taxon Editor\r
-editor.name.0 = Taxon Name Editor\r
-editor.name.1 = Key\r
-editor.name.2 = Polytomous Key Graph Editor\r
-editor.name.3 = Polytomous Key List Editor\r
-editor.name.4 = Cdm Authority Editor\r
-editor.name.5 = Derivate View\r
-view.name = Factual Data\r
-view.name.0 = Uses\r
-view.name.1 = Media\r
-view.name.2 = Concept Relations\r
-view.name.3 = Concept Graph\r
-category.name = Taxonomic Editor\r
-command.label = Reference\r
-command.label.0 = Name\r
-command.label.1 = Team\r
-command.label.2 = Person\r
-command.label.3 = Specimen\r
-command.label.4 = Factual Data\r
-command.label.5 = Media\r
-command.label.6 = Concept\r
-command.label.7 = Concept Graph\r
-command.label.8 = Open Parent\r
-menu.label = New\r
-command.label.9 = Heterotypic Synonym\r
-command.label.10 = Homotypic Synonym\r
-command.label.11 = Synonym In Homotypical Group\r
-menu.label.0 = Change To\r
-command.label.12 = Accepted Taxon\r
-command.label.13 = Synonym\r
-command.label.14 = Misapplication\r
-command.label.15 = Delete\r
-command.label.16 = Delete All Empty Names\r
-command.label.17 = Swap Synonym With Accepted\r
-command.label.18 = Show Details\r
-command.label.19 = Save\r
-command.label.20 = New Node\r
-command.label.21 = Delete\r
-command.label.22 = Apply Layout\r
-command.label.23 = New Key Number\r
-command.label.24 = New Alternative\r
-command.label.25 = Refresh Nodes\r
-command.label.26 = Delete\r
-command.label.27 = New Factual Data\r
-menu.label.1 = New\r
-command.label.28 = Move Description to Taxon\r
-command.label.29 = Move Elements to Taxon\r
-command.label.30 = Delete\r
-command.label.31 = Save\r
-menu.label.2 = New Derivate\r
-command.label.32 = New Use\r
-command.label.33 = New Use Summary\r
-command.label.34 = New Use Record\r
-command.label.35 = Delete\r
-command.label.36 = Save\r
-command.label.37 = New Image Gallery\r
-command.label.38 = New Image\r
-command.label.39 = Move Image Up In List\r
-command.label.40 = Move Image Down In List\r
-command.label.41 = Delete\r
-command.label.42 = Save\r
-menu.label.3 = New\r
-command.label.43 = Open Related Concept\r
-command.label.44 = Delete\r
-command.label.45 = Edit Authorities\r
-extension.name = Name Commands\r
-category.name.0 = -- Name Editor\r
-command.name = Open Parent\r
-command.name.0 = Create Homotypic Synonym\r
-command.name.1 = Create Heterotypic Synonym\r
-command.name.2 = Create Synonym In Homotypical Group\r
-command.name.3 = Change To Synonym\r
-command.name.4 = Change To Accepted Taxon\r
-command.name.5 = Change To Misapplication\r
-command.name.6 = Swap Synonym With Accepted\r
-command.name.7 = Set Basionym / Original Combination\r
-command.name.8 = Remove Basionym / Original Combination\r
-command.name.9 = Delete All Empty Names\r
-category.name.1 = -- Factual\r
-command.name.10 = Create Description Element\r
-command.name.11 = New Description\r
-command.name.12 = Move Description Elements to Taxon\r
-command.name.13 = Move Description to Taxon\r
-category.name.2 = -- New Uses\r
-command.name.14 = New Use\r
-command.name.15 = New Use Summary\r
-command.name.16 = New Use Record\r
-category.name.3 = -- Media\r
-command.name.19 = Move Image Down In List\r
-command.name.20 = New Image Gallery\r
-command.name.21 = New Image\r
-command.name.22 = Move Image Up In List\r
-category.name.4 = -- New Entity\r
-command.name.23 = New Reference\r
-command.name.24 = New Name\r
-command.name.25 = New Team\r
-command.name.26 = New Person\r
-command.name.27 = New Specimen\r
-category.name.5 = -- Polytomous Keys\r
-command.name.28 = New Child Node\r
-command.name.29 = New Sibling Node\r
-command.name.30 = Refresh Node Numbering\r
-command.name.31 = Apply Layout\r
-category.name.6 = -- Concept Relations\r
-command.name.32 = Create Concept Relation\r
-command.name.33 = Open Related Concept\r
-category.name.7 = -- Group\r
-command.name.34 = Edit CDM Authorities\r
-command.name.35 = Open Derivate View\r
-scheme.description = The default key binding scheme for the Taxonomic Editor\r
-scheme.name = Taxonomic Editor Default Key Bindingseditor.name.6 = Specimen Import Editor\r
-editor.name.7 = Gbif Import Editor\r
-editor.name.8 = Checklist Editor\r
-view.name.4 = Specimen Import\r
-view.name.5 = GBIF Specimen Import\r
-command.label.46 = Name\r
-command.label.47 = Reference\r
-command.label.48 = Datasource\r
-command.label.49 = Misapplication\r
-command.label.50 = Use Existing Image\r
-command.name.36 = Create Misapplication\r
-command.name.37 = Use Existing Image\r
-command.name.38 = Open Checklist Editor\r
-command.name.39 = New Datasource\r
-wizard.name = Specimen Search/Import\r
-wizard.description = Queries data provider for specimens with specified parameters.\nNote: Query results are currently limited to 100.\r
-command.name.40 = Validation\r
-view.name.6 = Validation\r
-marker.field.0 = Object Type\r
-marker.field.1 = Object\r
-marker.field.2 = Attribute\r
-marker.field.3 = Problematic Value\r
-marker.field.4 = Problem description\r
-marker.field.5 = Validator\r
-marker.field.6 = Entity Class\r
++#Properties file for taxeditor-editor
++Bundle-Vendor.0 = EDIT
++Bundle-Name.0 = EDIT Taxonomic Editor - Editor Bundle
++command.name.17 = Set Basionym
++command.name.18 = Remove Basionym
++editor.name = Multipage Taxon Editor
++editor.name.0 = Taxon Name Editor
++editor.name.1 = Key
++editor.name.2 = Polytomous Key Graph Editor
++editor.name.3 = Polytomous Key List Editor
++editor.name.4 = Cdm Authority Editor
++editor.name.5 = Derivate View
++view.name = Factual Data
++view.name.0 = Uses
++view.name.1 = Media
++view.name.2 = Concept Relations
++view.name.3 = Concept Graph
++category.name = Taxonomic Editor
++command.label = Reference
++command.label.0 = Name
++command.label.1 = Team
++command.label.2 = Person
++command.label.3 = Specimen
++command.label.4 = Factual Data
++command.label.5 = Media
++command.label.6 = Concept
++command.label.7 = Concept Graph
++command.label.8 = Open Parent
++menu.label = New
++command.label.9 = Heterotypic Synonym
++command.label.10 = Homotypic Synonym
++command.label.11 = Synonym In Homotypical Group
++menu.label.0 = Change To
++command.label.12 = Accepted Taxon
++command.label.13 = Synonym
++command.label.14 = Misapplication
++command.label.15 = Delete
++command.label.16 = Delete All Empty Names
++command.label.17 = Swap Synonym With Accepted
++command.label.18 = Show Details
++command.label.19 = Save
++command.label.20 = New Node
++command.label.21 = Delete
++command.label.22 = Apply Layout
++command.label.23 = New Key Number
++command.label.24 = New Alternative
++command.label.25 = Refresh Nodes
++command.label.26 = Delete
++command.label.27 = New Factual Data
++menu.label.1 = New
++command.label.28 = Move Description to Taxon
++command.label.29 = Move Elements to Taxon
++command.label.30 = Delete
++command.label.31 = Save
++menu.label.2 = New Derivate
++command.label.32 = New Use
++command.label.33 = New Use Summary
++command.label.34 = New Use Record
++command.label.35 = Delete
++command.label.36 = Save
++command.label.37 = New Image Gallery
++command.label.38 = New Image
++command.label.39 = Move Image Up In List
++command.label.40 = Move Image Down In List
++command.label.41 = Delete
++command.label.42 = Save
++menu.label.3 = New
++command.label.43 = Open Related Concept
++command.label.44 = Delete
++command.label.45 = Edit Authorities
++extension.name = Name Commands
++category.name.0 = -- Name Editor
++command.name = Open Parent
++command.name.0 = Create Homotypic Synonym
++command.name.1 = Create Heterotypic Synonym
++command.name.2 = Create Synonym In Homotypical Group
++command.name.3 = Change To Synonym
++command.name.4 = Change To Accepted Taxon
++command.name.5 = Change To Misapplication
++command.name.6 = Swap Synonym With Accepted
++command.name.7 = Set Basionym / Original Combination
++command.name.8 = Remove Basionym / Original Combination
++command.name.9 = Delete All Empty Names
++category.name.1 = -- Factual
++command.name.10 = Create Description Element
++command.name.11 = New Description
++command.name.12 = Move Description Elements to Taxon
++command.name.13 = Move Description to Taxon
++category.name.2 = -- New Uses
++command.name.14 = New Use
++command.name.15 = New Use Summary
++command.name.16 = New Use Record
++category.name.3 = -- Media
++command.name.19 = Move Image Down In List
++command.name.20 = New Image Gallery
++command.name.21 = New Image
++command.name.22 = Move Image Up In List
++category.name.4 = -- New Entity
++command.name.23 = New Reference
++command.name.24 = New Name
++command.name.25 = New Team
++command.name.26 = New Person
++command.name.27 = New Specimen
++category.name.5 = -- Polytomous Keys
++command.name.28 = New Child Node
++command.name.29 = New Sibling Node
++command.name.30 = Refresh Node Numbering
++command.name.31 = Apply Layout
++category.name.6 = -- Concept Relations
++command.name.32 = Create Concept Relation
++command.name.33 = Open Related Concept
++category.name.7 = -- Group
++command.name.34 = Edit CDM Authorities
++command.name.35 = Open Derivate View
++scheme.description = The default key binding scheme for the Taxonomic Editor
++scheme.name = Taxonomic Editor Default Key Bindingseditor.name.6 = Specimen Import Editor
++editor.name.7 = Gbif Import Editor
++editor.name.8 = Checklist Editor
++view.name.4 = Specimen Import
++view.name.5 = GBIF Specimen Import
++command.label.46 = Name
++command.label.47 = Reference
++command.label.48 = Datasource
++command.label.49 = Misapplication
++command.label.50 = Use Existing Image
++command.name.36 = Create Misapplication
++command.name.37 = Use Existing Image
++command.name.38 = Open Checklist Editor
++command.name.39 = New Datasource
++wizard.name = Specimen Search/Import
++wizard.description = Queries data provider for specimens with specified parameters.\nNote: Query results are currently limited to 100.
++command.name.40 = Validation
++view.name.6 = Validation
++marker.field.0 = Object Type
++marker.field.1 = Object
++marker.field.2 = Attribute
++marker.field.3 = Problematic Value
++marker.field.4 = Problem description
++marker.field.5 = Validator
++marker.field.6 = Entity Class
+ marker.field.7 = Entity Id
--- /dev/null
--- /dev/null
++/*.jar
--- /dev/null
-/**\r
-* Copyright (C) 2007 EDIT\r
-* European Distributed Institute of Taxonomy\r
-* http://www.e-taxonomy.eu\r
-*\r
-* The contents of this file are subject to the Mozilla Public License Version 1.1\r
-* See LICENSE.TXT at the top of this package for the full license terms.\r
-*/\r
-package eu.etaxonomy.taxeditor.molecular.editor;\r
-\r
-\r
-import info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramArea;\r
-import info.bioinfweb.tic.input.TICMouseAdapter;\r
-import info.bioinfweb.tic.input.TICMouseEvent;\r
-\r
-import org.eclipse.ui.PartInitException;\r
-\r
-import eu.etaxonomy.taxeditor.model.MessagingUtils;\r
-import eu.etaxonomy.taxeditor.molecular.TaxeditorMolecularPlugin;\r
-import eu.etaxonomy.taxeditor.molecular.handler.ShowPherogramHandler;\r
-\r
-\r
-\r
-/**\r
- * Listens to mouse events on data areas displaying a pherogram in {@link AlignmentEditor}.\r
- *\r
- * @author Ben Stöver\r
- * @date 25.11.2014\r
- */\r
-public class PherogramMouseListener extends TICMouseAdapter {\r
- private final PherogramArea area;\r
-\r
-\r
- public PherogramMouseListener(PherogramArea area) {\r
- super();\r
- this.area = area;\r
- }\r
-\r
-\r
- @Override\r
- public boolean mousePressed(TICMouseEvent event) {\r
- if (event.getClickCount() == 2) { // Double click\r
- try {\r
- ShowPherogramHandler.showPherogram(area.getModel());\r
- }\r
- catch (PartInitException e) {\r
- MessagingUtils.errorDialog("Unable to create pherogram view", null, e.getLocalizedMessage(),\r
- TaxeditorMolecularPlugin.PLUGIN_ID, e, false); //TODO set pluginID\r
- }\r
- return true;\r
- }\r
- else {\r
- return false;\r
- }\r
- }\r
-}\r
++/**
++* Copyright (C) 2007 EDIT
++* European Distributed Institute of Taxonomy
++* http://www.e-taxonomy.eu
++*
++* The contents of this file are subject to the Mozilla Public License Version 1.1
++* See LICENSE.TXT at the top of this package for the full license terms.
++*/
++package eu.etaxonomy.taxeditor.molecular.editor;
++
++
++import info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramArea;
++import info.bioinfweb.tic.input.TICMouseAdapter;
++import info.bioinfweb.tic.input.TICMouseEvent;
++
++import org.eclipse.ui.PartInitException;
++
++import eu.etaxonomy.taxeditor.model.MessagingUtils;
++import eu.etaxonomy.taxeditor.molecular.TaxeditorMolecularPlugin;
++import eu.etaxonomy.taxeditor.molecular.handler.ShowPherogramHandler;
++
++
++
++/**
++ * Listens to mouse events on data areas displaying a pherogram in {@link AlignmentEditor}.
++ *
++ * @author Ben Stöver
++ * @date 25.11.2014
++ */
++public class PherogramMouseListener extends TICMouseAdapter {
++ private final PherogramArea area;
++
++
++ public PherogramMouseListener(PherogramArea area) {
++ super();
++ this.area = area;
++ }
++
++
++ @Override
++ public boolean mousePressed(TICMouseEvent event) {
++ if (event.getClickCount() == 2) { // Double click
++ try {
++ ShowPherogramHandler.showPherogram(area.getModel());
++ }
++ catch (PartInitException e) {
++ MessagingUtils.errorDialog("Unable to create pherogram view", null, e.getLocalizedMessage(),
++ TaxeditorMolecularPlugin.PLUGIN_ID, e, false); //TODO set pluginID
++ }
++ return true;
++ }
++ else {
++ return false;
++ }
++ }
++}
--- /dev/null
-/**\r
-* Copyright (C) 2007 EDIT\r
-* European Distributed Institute of Taxonomy\r
-* http://www.e-taxonomy.eu\r
-*\r
-* The contents of this file are subject to the Mozilla Public License Version 1.1\r
-* See LICENSE.TXT at the top of this package for the full license terms.\r
-*/\r
-package eu.etaxonomy.taxeditor.molecular.editor;\r
-\r
-\r
-import info.bioinfweb.libralign.pherogram.PherogramFormats.QualityOutputType;\r
-import info.bioinfweb.libralign.pherogram.model.PherogramComponentModel;\r
-import info.bioinfweb.libralign.pherogram.view.PherogramView;\r
-import info.bioinfweb.tic.SWTComponentFactory;\r
-\r
-import org.eclipse.swt.SWT;\r
-import org.eclipse.swt.widgets.Composite;\r
-import org.eclipse.ui.PartInitException;\r
-import org.eclipse.ui.PlatformUI;\r
-import org.eclipse.ui.part.ViewPart;\r
-\r
-\r
-\r
-/**\r
- * Component that allows to view a pherogram without the distortion due to aligning it to a sequence as in\r
- * {@link AlignmentEditor}.\r
- *\r
- * @author Ben Stöver\r
- * @date Nov 20, 2014\r
- */\r
-public class PherogramViewPart extends ViewPart {\r
- public static final String ID = "eu.etaxonomy.taxeditor.molecular.PherogramView";\r
-\r
- private PherogramView pherogramView = null;\r
-\r
-\r
- public static PherogramViewPart createView(PherogramComponentModel model) throws PartInitException {\r
- PherogramViewPart view = (PherogramViewPart)PlatformUI.getWorkbench().getActiveWorkbenchWindow().getActivePage().showView(ID);\r
- view.getPherogramView().getTraceCurveView().setModel(model);\r
- view.getPherogramView().assignSize();\r
- return view;\r
- }\r
-\r
-\r
- public PherogramView getPherogramView() {\r
- if (pherogramView == null) {\r
- pherogramView = new PherogramView();\r
- pherogramView.getTraceCurveView().getFormats().setShowProbabilityValues(true);\r
- pherogramView.getTraceCurveView().setHorizontalScale(1);\r
- pherogramView.getTraceCurveView().setVerticalScale(100);\r
- pherogramView.getTraceCurveView().getFormats().setQualityOutputType(QualityOutputType.NONE); //TODO Make this user defined\r
- pherogramView.getTraceCurveView().getFormats().setShowProbabilityValues(false);\r
- }\r
- return pherogramView;\r
- }\r
-\r
-\r
- @Override\r
- public void createPartControl(Composite parent) {\r
- SWTComponentFactory.getInstance().getSWTComponent(getPherogramView(), parent, SWT.NONE);\r
- getPherogramView().assignSize();\r
- }\r
-\r
-\r
- @Override\r
- public void setFocus() {} // nothing to do\r
-}\r
++/**
++* Copyright (C) 2007 EDIT
++* European Distributed Institute of Taxonomy
++* http://www.e-taxonomy.eu
++*
++* The contents of this file are subject to the Mozilla Public License Version 1.1
++* See LICENSE.TXT at the top of this package for the full license terms.
++*/
++package eu.etaxonomy.taxeditor.molecular.editor;
++
++
++import info.bioinfweb.libralign.pherogram.PherogramFormats.QualityOutputType;
++import info.bioinfweb.libralign.pherogram.model.PherogramComponentModel;
++import info.bioinfweb.libralign.pherogram.view.PherogramView;
++import info.bioinfweb.tic.SWTComponentFactory;
++
++import org.eclipse.swt.SWT;
++import org.eclipse.swt.widgets.Composite;
++import org.eclipse.ui.PartInitException;
++import org.eclipse.ui.PlatformUI;
++import org.eclipse.ui.part.ViewPart;
++
++
++
++/**
++ * Component that allows to view a pherogram without the distortion due to aligning it to a sequence as in
++ * {@link AlignmentEditor}.
++ *
++ * @author Ben Stöver
++ * @date Nov 20, 2014
++ */
++public class PherogramViewPart extends ViewPart {
++ public static final String ID = "eu.etaxonomy.taxeditor.molecular.PherogramView";
++
++ private PherogramView pherogramView = null;
++
++
++ public static PherogramViewPart createView(PherogramComponentModel model) throws PartInitException {
++ PherogramViewPart view = (PherogramViewPart)PlatformUI.getWorkbench().getActiveWorkbenchWindow().getActivePage().showView(ID);
++ view.getPherogramView().getTraceCurveView().setModel(model);
++ view.getPherogramView().assignSize();
++ return view;
++ }
++
++
++ public PherogramView getPherogramView() {
++ if (pherogramView == null) {
++ pherogramView = new PherogramView();
++ pherogramView.getTraceCurveView().getFormats().setShowProbabilityValues(true);
++ pherogramView.getTraceCurveView().setHorizontalScale(1);
++ pherogramView.getTraceCurveView().setVerticalScale(100);
++ pherogramView.getTraceCurveView().getFormats().setQualityOutputType(QualityOutputType.NONE); //TODO Make this user defined
++ pherogramView.getTraceCurveView().getFormats().setShowProbabilityValues(false);
++ }
++ return pherogramView;
++ }
++
++
++ @Override
++ public void createPartControl(Composite parent) {
++ SWTComponentFactory.getInstance().getSWTComponent(getPherogramView(), parent, SWT.NONE);
++ getPherogramView().assignSize();
++ }
++
++
++ @Override
++ public void setFocus() {} // nothing to do
++}
--- /dev/null
-// $Id$\r
-/**\r
-* Copyright (C) 2015 EDIT\r
-* European Distributed Institute of Taxonomy\r
-* http://www.e-taxonomy.eu\r
-*\r
-* The contents of this file are subject to the Mozilla Public License Version 1.1\r
-* See LICENSE.TXT at the top of this package for the full license terms.\r
-*/\r
-package eu.etaxonomy.taxeditor.molecular.handler;\r
-\r
-\r
-import org.eclipse.core.commands.AbstractHandler;\r
-import org.eclipse.core.commands.ExecutionEvent;\r
-import org.eclipse.core.commands.ExecutionException;\r
-import org.eclipse.ui.IEditorPart;\r
-\r
-import eu.etaxonomy.taxeditor.model.AbstractUtility;\r
-import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;\r
-\r
-\r
-\r
-\r
-/**\r
- * Abstract implementation for all handlers triggering actions in an active instance of\r
- * {@link AlignmentEditor}.\r
- *\r
- * @author Ben Stöver\r
- * @date 19.06.2015\r
- */\r
-public abstract class AbstractAlignmentEditorHandler extends AbstractHandler {\r
- @Override\r
- public Object execute(ExecutionEvent event) throws ExecutionException {\r
- IEditorPart activeEditor = AbstractUtility.getActiveEditor();\r
- if (activeEditor instanceof AlignmentEditor) {\r
- doExecute(event, (AlignmentEditor)activeEditor);\r
- }\r
- return null;\r
- }\r
-\r
-\r
- public abstract void doExecute(ExecutionEvent event, AlignmentEditor editor) throws ExecutionException;\r
-}\r
++// $Id$
++/**
++* Copyright (C) 2015 EDIT
++* European Distributed Institute of Taxonomy
++* http://www.e-taxonomy.eu
++*
++* The contents of this file are subject to the Mozilla Public License Version 1.1
++* See LICENSE.TXT at the top of this package for the full license terms.
++*/
++package eu.etaxonomy.taxeditor.molecular.handler;
++
++
++import org.eclipse.core.commands.AbstractHandler;
++import org.eclipse.core.commands.ExecutionEvent;
++import org.eclipse.core.commands.ExecutionException;
++import org.eclipse.ui.IEditorPart;
++
++import eu.etaxonomy.taxeditor.model.AbstractUtility;
++import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;
++
++
++
++
++/**
++ * Abstract implementation for all handlers triggering actions in an active instance of
++ * {@link AlignmentEditor}.
++ *
++ * @author Ben Stöver
++ * @date 19.06.2015
++ */
++public abstract class AbstractAlignmentEditorHandler extends AbstractHandler {
++ @Override
++ public Object execute(ExecutionEvent event) throws ExecutionException {
++ IEditorPart activeEditor = AbstractUtility.getActiveEditor();
++ if (activeEditor instanceof AlignmentEditor) {
++ doExecute(event, (AlignmentEditor)activeEditor);
++ }
++ return null;
++ }
++
++
++ public abstract void doExecute(ExecutionEvent event, AlignmentEditor editor) throws ExecutionException;
++}
--- /dev/null
-// $Id$\r
-/**\r
-* Copyright (C) 2015 EDIT\r
-* European Distributed Institute of Taxonomy\r
-* http://www.e-taxonomy.eu\r
-*\r
-* The contents of this file are subject to the Mozilla Public License Version 1.1\r
-* See LICENSE.TXT at the top of this package for the full license terms.\r
-*/\r
-package eu.etaxonomy.taxeditor.molecular.handler;\r
-\r
-\r
-import info.bioinfweb.libralign.alignmentarea.AlignmentArea;\r
-import info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramArea;\r
-import info.bioinfweb.libralign.pherogram.PherogramComponent;\r
-\r
-import java.util.Iterator;\r
-\r
-import org.eclipse.core.commands.AbstractHandler;\r
-import org.eclipse.core.commands.ExecutionEvent;\r
-import org.eclipse.core.commands.ExecutionException;\r
-import org.eclipse.ui.IWorkbenchPart;\r
-\r
-import eu.etaxonomy.taxeditor.model.AbstractUtility;\r
-import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;\r
-import eu.etaxonomy.taxeditor.molecular.editor.PherogramViewPart;\r
-\r
-\r
-\r
-/**\r
- * Abstract handler implementation allows to performs the concrete operation either on an instance of\r
- * {@link PherogramViewPart} or all {@link AlignmentArea}s inside an instance of {@link AlignmentEditor}.\r
- *\r
- * @author Ben Stöver\r
- * @date 23.06.2015\r
- */\r
-public abstract class AbstractPherogramComponentHandler extends AbstractHandler {\r
- @Override\r
- public Object execute(ExecutionEvent event) throws ExecutionException {\r
- IWorkbenchPart activePart = AbstractUtility.getActivePart();\r
-\r
- if (activePart instanceof AlignmentEditor) {\r
- AlignmentEditor editor = (AlignmentEditor)activePart;\r
- Iterator<Integer> idIterator = editor.getReadsArea().getAlignmentModel().sequenceIDIterator();\r
- while (idIterator.hasNext()) {\r
- PherogramArea area = editor.getPherogramArea(idIterator.next());\r
- if (area != null) {\r
- doExecute(event, area);\r
- }\r
- }\r
- }\r
- else if (activePart instanceof PherogramViewPart) {\r
- doExecute(event, ((PherogramViewPart)activePart).getPherogramView().getTraceCurveView());\r
- }\r
- return null;\r
- }\r
-\r
-\r
- public abstract void doExecute(ExecutionEvent event, PherogramComponent component) throws ExecutionException;\r
-}\r
++// $Id$
++/**
++* Copyright (C) 2015 EDIT
++* European Distributed Institute of Taxonomy
++* http://www.e-taxonomy.eu
++*
++* The contents of this file are subject to the Mozilla Public License Version 1.1
++* See LICENSE.TXT at the top of this package for the full license terms.
++*/
++package eu.etaxonomy.taxeditor.molecular.handler;
++
++
++import info.bioinfweb.libralign.alignmentarea.AlignmentArea;
++import info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramArea;
++import info.bioinfweb.libralign.pherogram.PherogramComponent;
++
++import java.util.Iterator;
++
++import org.eclipse.core.commands.AbstractHandler;
++import org.eclipse.core.commands.ExecutionEvent;
++import org.eclipse.core.commands.ExecutionException;
++import org.eclipse.ui.IWorkbenchPart;
++
++import eu.etaxonomy.taxeditor.model.AbstractUtility;
++import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;
++import eu.etaxonomy.taxeditor.molecular.editor.PherogramViewPart;
++
++
++
++/**
++ * Abstract handler implementation allows to performs the concrete operation either on an instance of
++ * {@link PherogramViewPart} or all {@link AlignmentArea}s inside an instance of {@link AlignmentEditor}.
++ *
++ * @author Ben Stöver
++ * @date 23.06.2015
++ */
++public abstract class AbstractPherogramComponentHandler extends AbstractHandler {
++ @Override
++ public Object execute(ExecutionEvent event) throws ExecutionException {
++ IWorkbenchPart activePart = AbstractUtility.getActivePart();
++
++ if (activePart instanceof AlignmentEditor) {
++ AlignmentEditor editor = (AlignmentEditor)activePart;
++ Iterator<Integer> idIterator = editor.getReadsArea().getAlignmentModel().sequenceIDIterator();
++ while (idIterator.hasNext()) {
++ PherogramArea area = editor.getPherogramArea(idIterator.next());
++ if (area != null) {
++ doExecute(event, area);
++ }
++ }
++ }
++ else if (activePart instanceof PherogramViewPart) {
++ doExecute(event, ((PherogramViewPart)activePart).getPherogramView().getTraceCurveView());
++ }
++ return null;
++ }
++
++
++ public abstract void doExecute(ExecutionEvent event, PherogramComponent component) throws ExecutionException;
++}
--- /dev/null
-// $Id$\r
-/**\r
-* Copyright (C) 2015 EDIT\r
-* European Distributed Institute of Taxonomy\r
-* http://www.e-taxonomy.eu\r
-*\r
-* The contents of this file are subject to the Mozilla Public License Version 1.1\r
-* See LICENSE.TXT at the top of this package for the full license terms.\r
-*/\r
-package eu.etaxonomy.taxeditor.molecular.handler;\r
-\r
-\r
-import info.bioinfweb.libralign.pherogram.PherogramComponent;\r
-\r
-import org.eclipse.core.commands.ExecutionEvent;\r
-import org.eclipse.core.commands.ExecutionException;\r
-\r
-\r
-\r
-/**\r
- * Switches between the quality output types available for components displaying pherograms.\r
- *\r
- * @author Ben Stöver\r
- * @date 19.06.2015\r
- */\r
-public class ChangePherogramQualityOutputType extends AbstractPherogramComponentHandler {\r
- @Override\r
- public void doExecute(ExecutionEvent event, PherogramComponent component) throws ExecutionException {\r
- component.getFormats().changeQualityOutputType();\r
- }\r
-}\r
++// $Id$
++/**
++* Copyright (C) 2015 EDIT
++* European Distributed Institute of Taxonomy
++* http://www.e-taxonomy.eu
++*
++* The contents of this file are subject to the Mozilla Public License Version 1.1
++* See LICENSE.TXT at the top of this package for the full license terms.
++*/
++package eu.etaxonomy.taxeditor.molecular.handler;
++
++
++import info.bioinfweb.libralign.pherogram.PherogramComponent;
++
++import org.eclipse.core.commands.ExecutionEvent;
++import org.eclipse.core.commands.ExecutionException;
++
++
++
++/**
++ * Switches between the quality output types available for components displaying pherograms.
++ *
++ * @author Ben Stöver
++ * @date 19.06.2015
++ */
++public class ChangePherogramQualityOutputType extends AbstractPherogramComponentHandler {
++ @Override
++ public void doExecute(ExecutionEvent event, PherogramComponent component) throws ExecutionException {
++ component.getFormats().changeQualityOutputType();
++ }
++}
--- /dev/null
-/**\r
-* Copyright (C) 2007 EDIT\r
-* European Distributed Institute of Taxonomy\r
-* http://www.e-taxonomy.eu\r
-*\r
-* The contents of this file are subject to the Mozilla Public License Version 1.1\r
-* See LICENSE.TXT at the top of this package for the full license terms.\r
-*/\r
-package eu.etaxonomy.taxeditor.molecular.handler;\r
-\r
-\r
-import org.eclipse.core.commands.ExecutionEvent;\r
-import org.eclipse.core.commands.ExecutionException;\r
-\r
-import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;\r
-\r
-\r
-\r
-\r
-/**\r
- * Handler that creates the consensus sequence from all single read sequences in the active instance\r
- * of {@link AlignmentEditor}. A previously present consensus sequence will be overwritten.\r
- *\r
- * @author Ben Stöver\r
- * @date 19.06.2015\r
- * @see UpdateConsensusSequenceHandler\r
- * @see AlignmentEditor#createConsensusSequence()\r
- */\r
-public class CreateConsensusSequenceHandler extends AbstractAlignmentEditorHandler {\r
- @Override\r
- public void doExecute(ExecutionEvent event, AlignmentEditor editor) throws ExecutionException {\r
- editor.createConsensusSequence();\r
- }\r
-}\r
++/**
++* Copyright (C) 2007 EDIT
++* European Distributed Institute of Taxonomy
++* http://www.e-taxonomy.eu
++*
++* The contents of this file are subject to the Mozilla Public License Version 1.1
++* See LICENSE.TXT at the top of this package for the full license terms.
++*/
++package eu.etaxonomy.taxeditor.molecular.handler;
++
++
++import org.eclipse.core.commands.ExecutionEvent;
++import org.eclipse.core.commands.ExecutionException;
++
++import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;
++
++
++
++
++/**
++ * Handler that creates the consensus sequence from all single read sequences in the active instance
++ * of {@link AlignmentEditor}. A previously present consensus sequence will be overwritten.
++ *
++ * @author Ben Stöver
++ * @date 19.06.2015
++ * @see UpdateConsensusSequenceHandler
++ * @see AlignmentEditor#createConsensusSequence()
++ */
++public class CreateConsensusSequenceHandler extends AbstractAlignmentEditorHandler {
++ @Override
++ public void doExecute(ExecutionEvent event, AlignmentEditor editor) throws ExecutionException {
++ editor.createConsensusSequence();
++ }
++}
--- /dev/null
-// $Id$\r
-/**\r
-* Copyright (C) 2015 EDIT\r
-* European Distributed Institute of Taxonomy\r
-* http://www.e-taxonomy.eu\r
-*\r
-* The contents of this file are subject to the Mozilla Public License Version 1.1\r
-* See LICENSE.TXT at the top of this package for the full license terms.\r
-*/\r
-package eu.etaxonomy.taxeditor.molecular.handler;\r
-\r
-\r
-import org.eclipse.core.commands.ExecutionEvent;\r
-import org.eclipse.core.commands.ExecutionException;\r
-\r
-import eu.etaxonomy.taxeditor.model.MessagingUtils;\r
-import eu.etaxonomy.taxeditor.molecular.TaxeditorMolecularPlugin;\r
-import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;\r
-\r
-\r
-\r
-/**\r
- * Handler that cuts the base call sequence of a pherogram attached to the current sequence on the left\r
- * of the current selection or cursor position.\r
- *\r
- * @author Ben Stöver\r
- * @date 15.06.2015\r
- */\r
-public class CutPherogramLeftHandler extends AbstractAlignmentEditorHandler {\r
- @Override\r
- public void doExecute(ExecutionEvent event, AlignmentEditor editor) throws ExecutionException {\r
- String errorMessage = editor.cutPherogramLeft();\r
- if (errorMessage != null) {\r
- MessagingUtils.errorDialog("Unable to cut base call sequence", this, errorMessage, TaxeditorMolecularPlugin.PLUGIN_ID, null, false);\r
- }\r
- }\r
-}\r
++// $Id$
++/**
++* Copyright (C) 2015 EDIT
++* European Distributed Institute of Taxonomy
++* http://www.e-taxonomy.eu
++*
++* The contents of this file are subject to the Mozilla Public License Version 1.1
++* See LICENSE.TXT at the top of this package for the full license terms.
++*/
++package eu.etaxonomy.taxeditor.molecular.handler;
++
++
++import org.eclipse.core.commands.ExecutionEvent;
++import org.eclipse.core.commands.ExecutionException;
++
++import eu.etaxonomy.taxeditor.model.MessagingUtils;
++import eu.etaxonomy.taxeditor.molecular.TaxeditorMolecularPlugin;
++import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;
++
++
++
++/**
++ * Handler that cuts the base call sequence of a pherogram attached to the current sequence on the left
++ * of the current selection or cursor position.
++ *
++ * @author Ben Stöver
++ * @date 15.06.2015
++ */
++public class CutPherogramLeftHandler extends AbstractAlignmentEditorHandler {
++ @Override
++ public void doExecute(ExecutionEvent event, AlignmentEditor editor) throws ExecutionException {
++ String errorMessage = editor.cutPherogramLeft();
++ if (errorMessage != null) {
++ MessagingUtils.errorDialog("Unable to cut base call sequence", this, errorMessage, TaxeditorMolecularPlugin.PLUGIN_ID, null, false);
++ }
++ }
++}
--- /dev/null
-// $Id$\r
-/**\r
-* Copyright (C) 2015 EDIT\r
-* European Distributed Institute of Taxonomy\r
-* http://www.e-taxonomy.eu\r
-*\r
-* The contents of this file are subject to the Mozilla Public License Version 1.1\r
-* See LICENSE.TXT at the top of this package for the full license terms.\r
-*/\r
-package eu.etaxonomy.taxeditor.molecular.handler;\r
-\r
-\r
-import org.eclipse.core.commands.ExecutionEvent;\r
-import org.eclipse.core.commands.ExecutionException;\r
-\r
-import eu.etaxonomy.taxeditor.model.MessagingUtils;\r
-import eu.etaxonomy.taxeditor.molecular.TaxeditorMolecularPlugin;\r
-import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;\r
-\r
-\r
-\r
-/**\r
- * Handler that cuts the base call sequence of a pherogram attached to the current sequence on the right\r
- * of the current selection or cursor position.\r
- *\r
- * @author BenStoever\r
- * @date 15.06.2015\r
- */\r
-public class CutPherogramRightHandler extends AbstractAlignmentEditorHandler {\r
- @Override\r
- public void doExecute(ExecutionEvent event, AlignmentEditor editor) throws ExecutionException {\r
- String errorMessage = editor.cutPherogramRight();\r
- if (errorMessage != null) {\r
- MessagingUtils.errorDialog("Unable to cut base call sequence", this, errorMessage, TaxeditorMolecularPlugin.PLUGIN_ID, null, false);\r
- }\r
- }\r
-}\r
++// $Id$
++/**
++* Copyright (C) 2015 EDIT
++* European Distributed Institute of Taxonomy
++* http://www.e-taxonomy.eu
++*
++* The contents of this file are subject to the Mozilla Public License Version 1.1
++* See LICENSE.TXT at the top of this package for the full license terms.
++*/
++package eu.etaxonomy.taxeditor.molecular.handler;
++
++
++import org.eclipse.core.commands.ExecutionEvent;
++import org.eclipse.core.commands.ExecutionException;
++
++import eu.etaxonomy.taxeditor.model.MessagingUtils;
++import eu.etaxonomy.taxeditor.molecular.TaxeditorMolecularPlugin;
++import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;
++
++
++
++/**
++ * Handler that cuts the base call sequence of a pherogram attached to the current sequence on the right
++ * of the current selection or cursor position.
++ *
++ * @author BenStoever
++ * @date 15.06.2015
++ */
++public class CutPherogramRightHandler extends AbstractAlignmentEditorHandler {
++ @Override
++ public void doExecute(ExecutionEvent event, AlignmentEditor editor) throws ExecutionException {
++ String errorMessage = editor.cutPherogramRight();
++ if (errorMessage != null) {
++ MessagingUtils.errorDialog("Unable to cut base call sequence", this, errorMessage, TaxeditorMolecularPlugin.PLUGIN_ID, null, false);
++ }
++ }
++}
--- /dev/null
-// $Id$\r
-/**\r
-* Copyright (C) 2015 EDIT\r
-* European Distributed Institute of Taxonomy\r
-* http://www.e-taxonomy.eu\r
-*\r
-* The contents of this file are subject to the Mozilla Public License Version 1.1\r
-* See LICENSE.TXT at the top of this package for the full license terms.\r
-*/\r
-package eu.etaxonomy.taxeditor.molecular.handler;\r
-\r
-\r
-import java.net.URL;\r
-\r
-import org.eclipse.core.runtime.FileLocator;\r
-import org.eclipse.core.runtime.Path;\r
-import org.eclipse.jface.resource.ImageDescriptor;\r
-\r
-import eu.etaxonomy.taxeditor.molecular.TaxeditorMolecularPlugin;\r
-\r
-\r
-\r
-/**\r
- * Implements shared functionality for handler implementations using tool bar icons.\r
- *\r
- * @author Ben Stöver\r
- * @date 15.06.2015\r
- */\r
-public class HandlerTools { //TODO Move this class or method somewhere else?\r
- public static ImageDescriptor createImageDescriptor(String iconName) {\r
- URL url = FileLocator.find(TaxeditorMolecularPlugin.getDefault().getBundle(),\r
- new Path("icons/" + iconName), null);\r
- if (url != null) {\r
- return ImageDescriptor.createFromURL(url);\r
- }\r
- else {\r
- throw new InternalError("Icon \"" + iconName + "\" could not be loaded."); //TODO Throw other type of exception?\r
- }\r
- }\r
-}\r
++// $Id$
++/**
++* Copyright (C) 2015 EDIT
++* European Distributed Institute of Taxonomy
++* http://www.e-taxonomy.eu
++*
++* The contents of this file are subject to the Mozilla Public License Version 1.1
++* See LICENSE.TXT at the top of this package for the full license terms.
++*/
++package eu.etaxonomy.taxeditor.molecular.handler;
++
++
++import java.net.URL;
++
++import org.eclipse.core.runtime.FileLocator;
++import org.eclipse.core.runtime.Path;
++import org.eclipse.jface.resource.ImageDescriptor;
++
++import eu.etaxonomy.taxeditor.molecular.TaxeditorMolecularPlugin;
++
++
++
++/**
++ * Implements shared functionality for handler implementations using tool bar icons.
++ *
++ * @author Ben Stöver
++ * @date 15.06.2015
++ */
++public class HandlerTools { //TODO Move this class or method somewhere else?
++ public static ImageDescriptor createImageDescriptor(String iconName) {
++ URL url = FileLocator.find(TaxeditorMolecularPlugin.getDefault().getBundle(),
++ new Path("icons/" + iconName), null);
++ if (url != null) {
++ return ImageDescriptor.createFromURL(url);
++ }
++ else {
++ throw new InternalError("Icon \"" + iconName + "\" could not be loaded."); //TODO Throw other type of exception?
++ }
++ }
++}
--- /dev/null
-/**\r
-* Copyright (C) 2007 EDIT\r
-* European Distributed Institute of Taxonomy\r
-* http://www.e-taxonomy.eu\r
-*\r
-* The contents of this file are subject to the Mozilla Public License Version 1.1\r
-* See LICENSE.TXT at the top of this package for the full license terms.\r
-*/\r
-package eu.etaxonomy.taxeditor.molecular.handler;\r
-\r
-\r
-import org.eclipse.core.commands.ExecutionEvent;\r
-import org.eclipse.core.commands.ExecutionException;\r
-\r
-import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;\r
-\r
-\r
-\r
-\r
-/**\r
- * Reverse complements the single read sequence in an active {@link AlignmentEditor}, where the alignment cursor\r
- * is currently located.\r
- *\r
- * @author Ben Stöver\r
- */\r
-public class ReverseComplementHandler extends AbstractAlignmentEditorHandler {\r
- @Override\r
- public void doExecute(ExecutionEvent event, AlignmentEditor editor) throws ExecutionException {\r
- editor.reverseComplementSelectedSequences();\r
- }\r
-}\r
++/**
++* Copyright (C) 2007 EDIT
++* European Distributed Institute of Taxonomy
++* http://www.e-taxonomy.eu
++*
++* The contents of this file are subject to the Mozilla Public License Version 1.1
++* See LICENSE.TXT at the top of this package for the full license terms.
++*/
++package eu.etaxonomy.taxeditor.molecular.handler;
++
++
++import org.eclipse.core.commands.ExecutionEvent;
++import org.eclipse.core.commands.ExecutionException;
++
++import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;
++
++
++
++
++/**
++ * Reverse complements the single read sequence in an active {@link AlignmentEditor}, where the alignment cursor
++ * is currently located.
++ *
++ * @author Ben Stöver
++ */
++public class ReverseComplementHandler extends AbstractAlignmentEditorHandler {
++ @Override
++ public void doExecute(ExecutionEvent event, AlignmentEditor editor) throws ExecutionException {
++ editor.reverseComplementSelectedSequences();
++ }
++}
--- /dev/null
-package eu.etaxonomy.taxeditor.molecular.handler;\r
-\r
-\r
-import info.bioinfweb.libralign.pherogram.model.PherogramComponentModel;\r
-\r
-import java.net.URI;\r
-\r
-import org.eclipse.core.commands.AbstractHandler;\r
-import org.eclipse.core.commands.ExecutionEvent;\r
-import org.eclipse.core.commands.ExecutionException;\r
-import org.eclipse.jface.viewers.ISelection;\r
-import org.eclipse.jface.viewers.TreeNode;\r
-import org.eclipse.ui.PartInitException;\r
-import org.eclipse.ui.handlers.HandlerUtil;\r
-\r
-import eu.etaxonomy.cdm.model.media.MediaUtils;\r
-import eu.etaxonomy.cdm.model.molecular.SingleRead;\r
-import eu.etaxonomy.taxeditor.editor.EditorUtil;\r
-import eu.etaxonomy.taxeditor.model.MessagingUtils;\r
-import eu.etaxonomy.taxeditor.molecular.TaxeditorMolecularPlugin;\r
-import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;\r
-import eu.etaxonomy.taxeditor.molecular.editor.PherogramViewPart;\r
-\r
-\r
-\r
-/**\r
- * Displays an undistorted pherogram with {@link PherogramViewPart}.\r
- *\r
- * @author Ben Stöver\r
- *\r
- */\r
-public class ShowPherogramHandler extends AbstractHandler {\r
- public static void showPherogram(PherogramComponentModel model) throws PartInitException {\r
- PherogramViewPart.createView(model);\r
- }\r
-\r
-\r
- @Override\r
- public Object execute(ExecutionEvent event) throws ExecutionException {\r
- ISelection currentSelection = HandlerUtil.getCurrentSelection(event);\r
- TreeNode treeNodeOfSelection = EditorUtil.getTreeNodeOfSelection(currentSelection);\r
- if (treeNodeOfSelection != null && treeNodeOfSelection.getValue() instanceof SingleRead) {\r
- //TODO Can the parent node (containing the cut positions) be extracted from SingleRead?\r
- try {\r
- SingleRead singleRead = (SingleRead)treeNodeOfSelection.getValue();\r
- URI uri = null;\r
- if (singleRead.getPherogram() != null) { // Pherogram objects without URI are possible.\r
- uri = MediaUtils.getFirstMediaRepresentationPart(singleRead.getPherogram()).getUri();\r
- }\r
-\r
- if (uri == null) {\r
- MessagingUtils.messageDialog("No pherogram available", this,\r
- "The selected read does not have an associated pherogram.");\r
- }\r
- else {\r
- showPherogram(new PherogramComponentModel(AlignmentEditor.readPherogram(uri)));\r
- }\r
- }\r
- catch (Exception e) {\r
- MessagingUtils.errorDialog("Error", null, e.getLocalizedMessage(), TaxeditorMolecularPlugin.PLUGIN_ID,\r
- e, false);\r
- }\r
- }\r
- return null;\r
- }\r
-}\r
++package eu.etaxonomy.taxeditor.molecular.handler;
++
++
++import info.bioinfweb.libralign.pherogram.model.PherogramComponentModel;
++
++import java.net.URI;
++
++import org.eclipse.core.commands.AbstractHandler;
++import org.eclipse.core.commands.ExecutionEvent;
++import org.eclipse.core.commands.ExecutionException;
++import org.eclipse.jface.viewers.ISelection;
++import org.eclipse.jface.viewers.TreeNode;
++import org.eclipse.ui.PartInitException;
++import org.eclipse.ui.handlers.HandlerUtil;
++
++import eu.etaxonomy.cdm.model.media.MediaUtils;
++import eu.etaxonomy.cdm.model.molecular.SingleRead;
++import eu.etaxonomy.taxeditor.editor.EditorUtil;
++import eu.etaxonomy.taxeditor.model.MessagingUtils;
++import eu.etaxonomy.taxeditor.molecular.TaxeditorMolecularPlugin;
++import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;
++import eu.etaxonomy.taxeditor.molecular.editor.PherogramViewPart;
++
++
++
++/**
++ * Displays an undistorted pherogram with {@link PherogramViewPart}.
++ *
++ * @author Ben Stöver
++ *
++ */
++public class ShowPherogramHandler extends AbstractHandler {
++ public static void showPherogram(PherogramComponentModel model) throws PartInitException {
++ PherogramViewPart.createView(model);
++ }
++
++
++ @Override
++ public Object execute(ExecutionEvent event) throws ExecutionException {
++ ISelection currentSelection = HandlerUtil.getCurrentSelection(event);
++ TreeNode treeNodeOfSelection = EditorUtil.getTreeNodeOfSelection(currentSelection);
++ if (treeNodeOfSelection != null && treeNodeOfSelection.getValue() instanceof SingleRead) {
++ //TODO Can the parent node (containing the cut positions) be extracted from SingleRead?
++ try {
++ SingleRead singleRead = (SingleRead)treeNodeOfSelection.getValue();
++ URI uri = null;
++ if (singleRead.getPherogram() != null) { // Pherogram objects without URI are possible.
++ uri = MediaUtils.getFirstMediaRepresentationPart(singleRead.getPherogram()).getUri();
++ }
++
++ if (uri == null) {
++ MessagingUtils.messageDialog("No pherogram available", this,
++ "The selected read does not have an associated pherogram.");
++ }
++ else {
++ showPherogram(new PherogramComponentModel(AlignmentEditor.readPherogram(uri)));
++ }
++ }
++ catch (Exception e) {
++ MessagingUtils.errorDialog("Error", null, e.getLocalizedMessage(), TaxeditorMolecularPlugin.PLUGIN_ID,
++ e, false);
++ }
++ }
++ return null;
++ }
++}
--- /dev/null
-/**\r
-* Copyright (C) 2007 EDIT\r
-* European Distributed Institute of Taxonomy\r
-* http://www.e-taxonomy.eu\r
-*\r
-* The contents of this file are subject to the Mozilla Public License Version 1.1\r
-* See LICENSE.TXT at the top of this package for the full license terms.\r
-*/\r
-\r
-package eu.etaxonomy.taxeditor.molecular.handler;\r
-\r
-\r
-import java.util.Map;\r
-\r
-import org.eclipse.core.commands.ExecutionEvent;\r
-import org.eclipse.core.commands.ExecutionException;\r
-import org.eclipse.jface.resource.ImageDescriptor;\r
-import org.eclipse.ui.IEditorPart;\r
-import org.eclipse.ui.PlatformUI;\r
-import org.eclipse.ui.commands.ICommandService;\r
-import org.eclipse.ui.commands.IElementUpdater;\r
-import org.eclipse.ui.menus.UIElement;\r
-\r
-import eu.etaxonomy.taxeditor.model.AbstractUtility;\r
-import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;\r
-\r
-\r
-\r
-/**\r
- * Switches an {@link AlignmentEditor} between insertion and overwrite mode.\r
- *\r
- * @author Ben Stöver\r
- * @date 04.12.2014\r
- */\r
-public class ToggleInsertOverwriteHandler extends AbstractAlignmentEditorHandler implements IElementUpdater {\r
- public static final String COMMAND_ID =\r
- "eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleInsertOverwrite";\r
-\r
-\r
- private final ImageDescriptor INSERT_DESCRIPTOR = HandlerTools.createImageDescriptor("insert-16x16.png");\r
- private final ImageDescriptor OVERWRITE_DESCRIPTOR = HandlerTools.createImageDescriptor("overwrite-16x16.png");\r
-\r
-\r
- @Override\r
- public void doExecute(ExecutionEvent event, AlignmentEditor editor) throws ExecutionException {\r
- editor.toggleInsertOverwrite();\r
- }\r
-\r
-\r
- @Override\r
- public void updateElement(UIElement element, @SuppressWarnings("rawtypes") Map parameters) {\r
- IEditorPart activeEditor = AbstractUtility.getActiveEditor();\r
- if (activeEditor instanceof AlignmentEditor) {\r
- if (((AlignmentEditor)activeEditor).isInsertMode()) {\r
- element.setIcon(INSERT_DESCRIPTOR);\r
- element.setText("INS");\r
- element.setTooltip("Click to switch to overwrite mode");\r
- }\r
- else {\r
- element.setIcon(OVERWRITE_DESCRIPTOR);\r
- element.setText("OVR");\r
- element.setTooltip("Click to switch to insertion mode");\r
- }\r
- ((ICommandService)PlatformUI.getWorkbench().getService(ICommandService.class)).refreshElements(\r
- ToggleLeftRightInsertionHandler.COMMAND_ID, null);\r
- }\r
- }\r
-}\r
++/**
++* Copyright (C) 2007 EDIT
++* European Distributed Institute of Taxonomy
++* http://www.e-taxonomy.eu
++*
++* The contents of this file are subject to the Mozilla Public License Version 1.1
++* See LICENSE.TXT at the top of this package for the full license terms.
++*/
++
++package eu.etaxonomy.taxeditor.molecular.handler;
++
++
++import java.util.Map;
++
++import org.eclipse.core.commands.ExecutionEvent;
++import org.eclipse.core.commands.ExecutionException;
++import org.eclipse.jface.resource.ImageDescriptor;
++import org.eclipse.ui.IEditorPart;
++import org.eclipse.ui.PlatformUI;
++import org.eclipse.ui.commands.ICommandService;
++import org.eclipse.ui.commands.IElementUpdater;
++import org.eclipse.ui.menus.UIElement;
++
++import eu.etaxonomy.taxeditor.model.AbstractUtility;
++import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;
++
++
++
++/**
++ * Switches an {@link AlignmentEditor} between insertion and overwrite mode.
++ *
++ * @author Ben Stöver
++ * @date 04.12.2014
++ */
++public class ToggleInsertOverwriteHandler extends AbstractAlignmentEditorHandler implements IElementUpdater {
++ public static final String COMMAND_ID =
++ "eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleInsertOverwrite";
++
++
++ private final ImageDescriptor INSERT_DESCRIPTOR = HandlerTools.createImageDescriptor("insert-16x16.png");
++ private final ImageDescriptor OVERWRITE_DESCRIPTOR = HandlerTools.createImageDescriptor("overwrite-16x16.png");
++
++
++ @Override
++ public void doExecute(ExecutionEvent event, AlignmentEditor editor) throws ExecutionException {
++ editor.toggleInsertOverwrite();
++ }
++
++
++ @Override
++ public void updateElement(UIElement element, @SuppressWarnings("rawtypes") Map parameters) {
++ IEditorPart activeEditor = AbstractUtility.getActiveEditor();
++ if (activeEditor instanceof AlignmentEditor) {
++ if (((AlignmentEditor)activeEditor).isInsertMode()) {
++ element.setIcon(INSERT_DESCRIPTOR);
++ element.setText("INS");
++ element.setTooltip("Click to switch to overwrite mode");
++ }
++ else {
++ element.setIcon(OVERWRITE_DESCRIPTOR);
++ element.setText("OVR");
++ element.setTooltip("Click to switch to insertion mode");
++ }
++ ((ICommandService)PlatformUI.getWorkbench().getService(ICommandService.class)).refreshElements(
++ ToggleLeftRightInsertionHandler.COMMAND_ID, null);
++ }
++ }
++}
--- /dev/null
-/**\r
- * Copyright (C) 2007 EDIT\r
- * European Distributed Institute of Taxonomy\r
- * http://www.e-taxonomy.eu\r
- *\r
- * The contents of this file are subject to the Mozilla Public License Version 1.1\r
- * See LICENSE.TXT at the top of this package for the full license terms.\r
- */\r
-\r
-package eu.etaxonomy.taxeditor.molecular.handler;\r
-\r
-import java.util.Map;\r
-\r
-import org.eclipse.core.commands.ExecutionEvent;\r
-import org.eclipse.core.commands.ExecutionException;\r
-import org.eclipse.jface.resource.ImageDescriptor;\r
-import org.eclipse.ui.IEditorPart;\r
-import org.eclipse.ui.commands.IElementUpdater;\r
-import org.eclipse.ui.menus.UIElement;\r
-\r
-import eu.etaxonomy.taxeditor.model.AbstractUtility;\r
-import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;\r
-\r
-\r
-\r
-/**\r
- * Switches an {@link AlignmentEditor} between insertion in the base sequence to\r
- * the left or to the right.\r
- *\r
- * @author Ben Stöver\r
- * @date 04.12.2014\r
- */\r
-public class ToggleLeftRightInsertionHandler extends AbstractAlignmentEditorHandler implements IElementUpdater {\r
- public static final String COMMAND_ID = "eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleLeftRightInsertion";\r
-\r
-\r
- private final ImageDescriptor INSERT_LEFT_DESCRIPTOR =\r
- HandlerTools.createImageDescriptor("pherogram-insert-left-16x16.png");\r
- private final ImageDescriptor INSERT_RIGHT_DESCRIPTOR =\r
- HandlerTools.createImageDescriptor("pherogram-insert-right-16x16.png");\r
- private final ImageDescriptor INSERT_LEFT_DISABLED_DESCRIPTOR =\r
- HandlerTools.createImageDescriptor("pherogram-insert-left-disabled-16x16.png");\r
- private final ImageDescriptor INSERT_RIGHT_DISABLED_DESCRIPTOR =\r
- HandlerTools.createImageDescriptor("pherogram-insert-right-disabled-16x16.png");\r
-\r
-\r
- @Override\r
- public void doExecute(ExecutionEvent event, AlignmentEditor editor) throws ExecutionException {\r
- editor.toggleLeftRightInsertionInPherogram();\r
- }\r
-\r
-\r
- @Override\r
- public void updateElement(UIElement element, @SuppressWarnings("rawtypes") Map parameters) {\r
- IEditorPart activeEditor = AbstractUtility.getActiveEditor();\r
- if (activeEditor instanceof AlignmentEditor) {\r
- setBaseEnabled(((AlignmentEditor)activeEditor).isInsertMode());\r
- if (((AlignmentEditor)activeEditor).isInsertLeftInPherogram()) {\r
- element.setIcon(INSERT_LEFT_DESCRIPTOR);\r
- element.setDisabledIcon(INSERT_LEFT_DISABLED_DESCRIPTOR);\r
- element.setText("Left");\r
- element.setTooltip("Switch to insert pherogram distorsions right of future edits.");\r
- }\r
- else {\r
- element.setIcon(INSERT_RIGHT_DESCRIPTOR);\r
- element.setDisabledIcon(INSERT_RIGHT_DISABLED_DESCRIPTOR);\r
- element.setText("Right");\r
- element.setTooltip("Switch to insert pherogram distorsions left of future edits.");\r
- }\r
- }\r
- }\r
-}\r
++/**
++ * Copyright (C) 2007 EDIT
++ * European Distributed Institute of Taxonomy
++ * http://www.e-taxonomy.eu
++ *
++ * The contents of this file are subject to the Mozilla Public License Version 1.1
++ * See LICENSE.TXT at the top of this package for the full license terms.
++ */
++
++package eu.etaxonomy.taxeditor.molecular.handler;
++
++import java.util.Map;
++
++import org.eclipse.core.commands.ExecutionEvent;
++import org.eclipse.core.commands.ExecutionException;
++import org.eclipse.jface.resource.ImageDescriptor;
++import org.eclipse.ui.IEditorPart;
++import org.eclipse.ui.commands.IElementUpdater;
++import org.eclipse.ui.menus.UIElement;
++
++import eu.etaxonomy.taxeditor.model.AbstractUtility;
++import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;
++
++
++
++/**
++ * Switches an {@link AlignmentEditor} between insertion in the base sequence to
++ * the left or to the right.
++ *
++ * @author Ben Stöver
++ * @date 04.12.2014
++ */
++public class ToggleLeftRightInsertionHandler extends AbstractAlignmentEditorHandler implements IElementUpdater {
++ public static final String COMMAND_ID = "eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleLeftRightInsertion";
++
++
++ private final ImageDescriptor INSERT_LEFT_DESCRIPTOR =
++ HandlerTools.createImageDescriptor("pherogram-insert-left-16x16.png");
++ private final ImageDescriptor INSERT_RIGHT_DESCRIPTOR =
++ HandlerTools.createImageDescriptor("pherogram-insert-right-16x16.png");
++ private final ImageDescriptor INSERT_LEFT_DISABLED_DESCRIPTOR =
++ HandlerTools.createImageDescriptor("pherogram-insert-left-disabled-16x16.png");
++ private final ImageDescriptor INSERT_RIGHT_DISABLED_DESCRIPTOR =
++ HandlerTools.createImageDescriptor("pherogram-insert-right-disabled-16x16.png");
++
++
++ @Override
++ public void doExecute(ExecutionEvent event, AlignmentEditor editor) throws ExecutionException {
++ editor.toggleLeftRightInsertionInPherogram();
++ }
++
++
++ @Override
++ public void updateElement(UIElement element, @SuppressWarnings("rawtypes") Map parameters) {
++ IEditorPart activeEditor = AbstractUtility.getActiveEditor();
++ if (activeEditor instanceof AlignmentEditor) {
++ setBaseEnabled(((AlignmentEditor)activeEditor).isInsertMode());
++ if (((AlignmentEditor)activeEditor).isInsertLeftInPherogram()) {
++ element.setIcon(INSERT_LEFT_DESCRIPTOR);
++ element.setDisabledIcon(INSERT_LEFT_DISABLED_DESCRIPTOR);
++ element.setText("Left");
++ element.setTooltip("Switch to insert pherogram distorsions right of future edits.");
++ }
++ else {
++ element.setIcon(INSERT_RIGHT_DESCRIPTOR);
++ element.setDisabledIcon(INSERT_RIGHT_DISABLED_DESCRIPTOR);
++ element.setText("Right");
++ element.setTooltip("Switch to insert pherogram distorsions left of future edits.");
++ }
++ }
++ }
++}
--- /dev/null
-// $Id$\r
-/**\r
-* Copyright (C) 2015 EDIT\r
-* European Distributed Institute of Taxonomy\r
-* http://www.e-taxonomy.eu\r
-*\r
-* The contents of this file are subject to the Mozilla Public License Version 1.1\r
-* See LICENSE.TXT at the top of this package for the full license terms.\r
-*/\r
-package eu.etaxonomy.taxeditor.molecular.handler;\r
-\r
-\r
-import info.bioinfweb.libralign.pherogram.PherogramComponent;\r
-\r
-import org.eclipse.core.commands.ExecutionEvent;\r
-import org.eclipse.core.commands.ExecutionException;\r
-\r
-\r
-\r
-/**\r
- * @author BenStoever\r
- * @date 23.06.2015\r
- *\r
- */\r
-public class ToggleShowPherogramBaseCallLinesHandler extends AbstractPherogramComponentHandler {\r
- @Override\r
- public void doExecute(ExecutionEvent event, PherogramComponent component) throws ExecutionException {\r
- component.getFormats().toggleShowBaseCallLines();\r
- }\r
-}\r
++// $Id$
++/**
++* Copyright (C) 2015 EDIT
++* European Distributed Institute of Taxonomy
++* http://www.e-taxonomy.eu
++*
++* The contents of this file are subject to the Mozilla Public License Version 1.1
++* See LICENSE.TXT at the top of this package for the full license terms.
++*/
++package eu.etaxonomy.taxeditor.molecular.handler;
++
++
++import info.bioinfweb.libralign.pherogram.PherogramComponent;
++
++import org.eclipse.core.commands.ExecutionEvent;
++import org.eclipse.core.commands.ExecutionException;
++
++
++
++/**
++ * @author BenStoever
++ * @date 23.06.2015
++ *
++ */
++public class ToggleShowPherogramBaseCallLinesHandler extends AbstractPherogramComponentHandler {
++ @Override
++ public void doExecute(ExecutionEvent event, PherogramComponent component) throws ExecutionException {
++ component.getFormats().toggleShowBaseCallLines();
++ }
++}
--- /dev/null
-// $Id$\r
-/**\r
-* Copyright (C) 2015 EDIT\r
-* European Distributed Institute of Taxonomy\r
-* http://www.e-taxonomy.eu\r
-*\r
-* The contents of this file are subject to the Mozilla Public License Version 1.1\r
-* See LICENSE.TXT at the top of this package for the full license terms.\r
-*/\r
-package eu.etaxonomy.taxeditor.molecular.handler;\r
-\r
-\r
-import info.bioinfweb.libralign.pherogram.PherogramComponent;\r
-\r
-import org.eclipse.core.commands.ExecutionEvent;\r
-import org.eclipse.core.commands.ExecutionException;\r
-\r
-import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;\r
-import eu.etaxonomy.taxeditor.molecular.editor.PherogramViewPart;\r
-\r
-\r
-\r
-\r
-/**\r
- * Toggles whether probability values (substitution, overcall and undercall) should be displayed\r
- * in pherogram areas of {@link AlignmentEditor} or {@link PherogramViewPart}.\r
- *\r
- * @author Ben Stöver\r
- * @date 23.06.2015\r
- */\r
-public class ToggleShowPherogramProbabilitiesHandler extends AbstractPherogramComponentHandler {\r
- @Override\r
- public void doExecute(ExecutionEvent event, PherogramComponent component) throws ExecutionException {\r
- component.getFormats().toggleShowProbabilityValues();\r
- }\r
-}\r
++// $Id$
++/**
++* Copyright (C) 2015 EDIT
++* European Distributed Institute of Taxonomy
++* http://www.e-taxonomy.eu
++*
++* The contents of this file are subject to the Mozilla Public License Version 1.1
++* See LICENSE.TXT at the top of this package for the full license terms.
++*/
++package eu.etaxonomy.taxeditor.molecular.handler;
++
++
++import info.bioinfweb.libralign.pherogram.PherogramComponent;
++
++import org.eclipse.core.commands.ExecutionEvent;
++import org.eclipse.core.commands.ExecutionException;
++
++import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;
++import eu.etaxonomy.taxeditor.molecular.editor.PherogramViewPart;
++
++
++
++
++/**
++ * Toggles whether probability values (substitution, overcall and undercall) should be displayed
++ * in pherogram areas of {@link AlignmentEditor} or {@link PherogramViewPart}.
++ *
++ * @author Ben Stöver
++ * @date 23.06.2015
++ */
++public class ToggleShowPherogramProbabilitiesHandler extends AbstractPherogramComponentHandler {
++ @Override
++ public void doExecute(ExecutionEvent event, PherogramComponent component) throws ExecutionException {
++ component.getFormats().toggleShowProbabilityValues();
++ }
++}
--- /dev/null
-/**\r
-* Copyright (C) 2007 EDIT\r
-* European Distributed Institute of Taxonomy\r
-* http://www.e-taxonomy.eu\r
-*\r
-* The contents of this file are subject to the Mozilla Public License Version 1.1\r
-* See LICENSE.TXT at the top of this package for the full license terms.\r
-*/\r
-package eu.etaxonomy.taxeditor.molecular.handler;\r
-\r
-\r
-import org.eclipse.core.commands.ExecutionEvent;\r
-import org.eclipse.core.commands.ExecutionException;\r
-\r
-import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;\r
-\r
-\r
-\r
-\r
-public class UpdateConsensusSequenceHandler extends AbstractAlignmentEditorHandler {\r
- @Override\r
- public void doExecute(ExecutionEvent event, AlignmentEditor editor) throws ExecutionException {\r
- editor.updateConsensusSequence();\r
- }\r
-}\r
++/**
++* Copyright (C) 2007 EDIT
++* European Distributed Institute of Taxonomy
++* http://www.e-taxonomy.eu
++*
++* The contents of this file are subject to the Mozilla Public License Version 1.1
++* See LICENSE.TXT at the top of this package for the full license terms.
++*/
++package eu.etaxonomy.taxeditor.molecular.handler;
++
++
++import org.eclipse.core.commands.ExecutionEvent;
++import org.eclipse.core.commands.ExecutionException;
++
++import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;
++
++
++
++
++public class UpdateConsensusSequenceHandler extends AbstractAlignmentEditorHandler {
++ @Override
++ public void doExecute(ExecutionEvent event, AlignmentEditor editor) throws ExecutionException {
++ editor.updateConsensusSequence();
++ }
++}
--- /dev/null
-// $Id$\r
-/**\r
- * Copyright (C) 2015 EDIT\r
- * European Distributed Institute of Taxonomy\r
- * http://www.e-taxonomy.eu\r
- *\r
- * The contents of this file are subject to the Mozilla Public License Version 1.1\r
- * See LICENSE.TXT at the top of this package for the full license terms.\r
- */\r
-/**\r
- * Contains handlers that trigger actions in an active instance of\r
- * {@link main.java.eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor}. Handlers opening\r
- * an alignment editor or pherogram view are not contained in here.\r
- *\r
- * @author Ben Stöver\r
- */\r
++// $Id$
++/**
++ * Copyright (C) 2015 EDIT
++ * European Distributed Institute of Taxonomy
++ * http://www.e-taxonomy.eu
++ *
++ * The contents of this file are subject to the Mozilla Public License Version 1.1
++ * See LICENSE.TXT at the top of this package for the full license terms.
++ */
++/**
++ * Contains handlers that trigger actions in an active instance of
++ * {@link main.java.eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor}. Handlers opening
++ * an alignment editor or pherogram view are not contained in here.
++ *
++ * @author Ben Stöver
++ */
+ package eu.etaxonomy.taxeditor.molecular.handler;
BGBM BDI Projects / taxeditor.git / commitdiff