--- /dev/null
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+ <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+ <classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
+ <classpathentry exported="true" kind="lib" path="lib/bioinfweb-commons-bio-2-SNAPSHOT.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/bioinfweb-commons-core-2-SNAPSHOT.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/bioinfweb-commons-swing-2-SNAPSHOT.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/bioinfweb-commons-swt-2-SNAPSHOT.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/core-1.9.2-SNAPSHOT.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/libralign-biojava1-0-SNAPSHOT.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/libralign-core-0-SNAPSHOT.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/libralign-swt-0-SNAPSHOT.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/sequencing-1.9.2-SNAPSHOT.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/tic-core-2-SNAPSHOT.jar"/>
+ <classpathentry exported="true" kind="lib" path="lib/tic-swt-2-SNAPSHOT.jar"/>
+ <classpathentry kind="output" path="target/classes"/>
+</classpath>
--- /dev/null
+/target
+.settings/
--- /dev/null
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+ <name>eu.etaxonomy.taxeditor.molecular.lib</name>
+ <comment>The Taxonomic Editor for EDIT's platform for
+ cybertaxonomy. NO_M2ECLIPSE_SUPPORT: Project files created with the maven-eclipse-plugin are not supported in M2Eclipse.</comment>
+ <projects>
+ </projects>
+ <buildSpec>
+ <buildCommand>
+ <name>org.eclipse.pde.ManifestBuilder</name>
+ <arguments>
+ </arguments>
+ </buildCommand>
+ <buildCommand>
+ <name>org.eclipse.pde.SchemaBuilder</name>
+ <arguments>
+ </arguments>
+ </buildCommand>
+ <buildCommand>
+ <name>org.eclipse.jdt.core.javabuilder</name>
+ <arguments>
+ </arguments>
+ </buildCommand>
+ </buildSpec>
+ <natures>
+ <nature>org.eclipse.pde.PluginNature</nature>
+ <nature>org.eclipse.jdt.core.javanature</nature>
+ </natures>
+</projectDescription>
--- /dev/null
+Manifest-Version: 1.0
+Bundle-ManifestVersion: 2
+Bundle-Name: eu.etaxonomy.taxeditor.molecular.lib
+Bundle-SymbolicName: eu.etaxonomy.taxeditor.molecular.lib;singleton:=true
+Bundle-Version: 3.8.0.qualifier
+Bundle-ClassPath: .,
+ lib/bioinfweb-commons-bio-2-SNAPSHOT.jar,
+ lib/bioinfweb-commons-core-2-SNAPSHOT.jar,
+ lib/bioinfweb-commons-swing-2-SNAPSHOT.jar,
+ lib/bioinfweb-commons-swt-2-SNAPSHOT.jar,
+ lib/core-1.9.2-SNAPSHOT.jar,
+ lib/libralign-biojava1-0-SNAPSHOT.jar,
+ lib/libralign-core-0-SNAPSHOT.jar,
+ lib/libralign-swt-0-SNAPSHOT.jar,
+ lib/sequencing-1.9.2-SNAPSHOT.jar,
+ lib/tic-core-2-SNAPSHOT.jar,
+ lib/tic-swt-2-SNAPSHOT.jar
+Export-Package: info.bioinfweb.commons,
+ info.bioinfweb.commons.appversion,
+ info.bioinfweb.commons.beans,
+ info.bioinfweb.commons.bio,
+ info.bioinfweb.commons.changemonitor,
+ info.bioinfweb.commons.collections,
+ info.bioinfweb.commons.collections.observable,
+ info.bioinfweb.commons.graphics,
+ info.bioinfweb.commons.io,
+ info.bioinfweb.commons.log,
+ info.bioinfweb.commons.progress,
+ info.bioinfweb.commons.swing,
+ info.bioinfweb.commons.swing.scrollpaneselector,
+ info.bioinfweb.commons.swt,
+ info.bioinfweb.commons.text,
+ info.bioinfweb.libralign,
+ info.bioinfweb.libralign.actions,
+ info.bioinfweb.libralign.alignmentarea,
+ info.bioinfweb.libralign.alignmentarea.content,
+ info.bioinfweb.libralign.alignmentarea.label,
+ info.bioinfweb.libralign.alignmentarea.order,
+ info.bioinfweb.libralign.alignmentarea.paintsettings,
+ info.bioinfweb.libralign.alignmentarea.rowsarea,
+ info.bioinfweb.libralign.alignmentarea.selection,
+ info.bioinfweb.libralign.alignmentarea.tokenpainter,
+ info.bioinfweb.libralign.dataarea,
+ info.bioinfweb.libralign.dataarea.implementations,
+ info.bioinfweb.libralign.dataarea.implementations.charset,
+ info.bioinfweb.libralign.dataarea.implementations.pherogram,
+ info.bioinfweb.libralign.editsettings,
+ info.bioinfweb.libralign.model,
+ info.bioinfweb.libralign.model.adapters,
+ info.bioinfweb.libralign.model.concatenated,
+ info.bioinfweb.libralign.model.data,
+ info.bioinfweb.libralign.model.events,
+ info.bioinfweb.libralign.model.exception,
+ info.bioinfweb.libralign.model.factory,
+ info.bioinfweb.libralign.model.factory.continuous,
+ info.bioinfweb.libralign.model.implementations,
+ info.bioinfweb.libralign.model.implementations.swingundo,
+ info.bioinfweb.libralign.model.implementations.swingundo.edits,
+ info.bioinfweb.libralign.model.implementations.swingundo.edits.sequence,
+ info.bioinfweb.libralign.model.implementations.swingundo.edits.token,
+ info.bioinfweb.libralign.model.implementations.translation,
+ info.bioinfweb.libralign.model.tokenset,
+ info.bioinfweb.libralign.model.tokenset.continuous,
+ info.bioinfweb.libralign.multiplealignments,
+ info.bioinfweb.libralign.pherogram,
+ info.bioinfweb.libralign.pherogram.distortion,
+ info.bioinfweb.libralign.pherogram.model,
+ info.bioinfweb.libralign.pherogram.provider,
+ info.bioinfweb.libralign.pherogram.view,
+ info.bioinfweb.tic,
+ info.bioinfweb.tic.exception,
+ info.bioinfweb.tic.input,
+ info.bioinfweb.tic.toolkit,
+ info.bioinfweb.tic.toolkit.layoutdata,
+ org.biojava.bibliography,
+ org.biojava.bio,
+ org.biojava.bio.alignment,
+ org.biojava.bio.annodb,
+ org.biojava.bio.chromatogram,
+ org.biojava.bio.chromatogram.graphic,
+ org.biojava.bio.dist,
+ org.biojava.bio.dp,
+ org.biojava.bio.dp.onehead,
+ org.biojava.bio.dp.twohead,
+ org.biojava.bio.molbio,
+ org.biojava.bio.program,
+ org.biojava.bio.program.abi,
+ org.biojava.bio.program.blast2html,
+ org.biojava.bio.program.fastq,
+ org.biojava.bio.program.formats,
+ org.biojava.bio.program.gff,
+ org.biojava.bio.program.gff3,
+ org.biojava.bio.program.hmmer,
+ org.biojava.bio.program.homologene,
+ org.biojava.bio.program.indexdb,
+ org.biojava.bio.program.phred,
+ org.biojava.bio.program.scf,
+ org.biojava.bio.program.ssaha,
+ org.biojava.bio.program.ssbind,
+ org.biojava.bio.program.tagvalue,
+ org.biojava.bio.program.unigene,
+ org.biojava.bio.program.xff,
+ org.biojava.bio.program.xml,
+ org.biojava.bio.proteomics,
+ org.biojava.bio.proteomics.aaindex,
+ org.biojava.bio.search,
+ org.biojava.bio.seq,
+ org.biojava.bio.seq.db,
+ org.biojava.bio.seq.db.biofetch,
+ org.biojava.bio.seq.db.emblcd,
+ org.biojava.bio.seq.db.flat,
+ org.biojava.bio.seq.distributed,
+ org.biojava.bio.seq.filter,
+ org.biojava.bio.seq.homol,
+ org.biojava.bio.seq.impl,
+ org.biojava.bio.seq.io,
+ org.biojava.bio.seq.io.agave,
+ org.biojava.bio.seq.io.filterxml,
+ org.biojava.bio.seq.io.game,
+ org.biojava.bio.seq.io.game12,
+ org.biojava.bio.seq.projection,
+ org.biojava.bio.symbol,
+ org.biojava.bio.taxa,
+ org.biojava.directory,
+ org.biojava.naming,
+ org.biojava.ontology,
+ org.biojava.ontology.io,
+ org.biojava.ontology.obo,
+ org.biojava.stats.svm,
+ org.biojava.stats.svm.tools,
+ org.biojava.utils,
+ org.biojava.utils.automata,
+ org.biojava.utils.cache,
+ org.biojava.utils.candy,
+ org.biojava.utils.io,
+ org.biojava.utils.lsid,
+ org.biojava.utils.math,
+ org.biojava.utils.net,
+ org.biojava.utils.process,
+ org.biojava.utils.regex,
+ org.biojava.utils.stax,
+ org.biojava.utils.walker,
+ org.biojava.utils.xml,
+ org.biojavax,
+ org.biojavax.bio,
+ org.biojavax.bio.alignment,
+ org.biojavax.bio.alignment.blast,
+ org.biojavax.bio.db,
+ org.biojavax.bio.db.ncbi,
+ org.biojavax.bio.seq,
+ org.biojavax.bio.seq.io,
+ org.biojavax.bio.taxa,
+ org.biojavax.bio.taxa.io,
+ org.biojavax.ga,
+ org.biojavax.ga.exception,
+ org.biojavax.ga.functions,
+ org.biojavax.ga.impl,
+ org.biojavax.ga.util,
+ org.biojavax.ontology,
+ org.biojavax.utils,
+ org.jdesktop.swingx.scrollpaneselector
+Bundle-ActivationPolicy: lazy
+Import-Package: javax.swing
+Require-Bundle: org.eclipse.swt
--- /dev/null
+bin.includes = META-INF/,\
+ lib/bioinfweb-commons-bio-2-SNAPSHOT.jar,\
+ lib/bioinfweb-commons-core-2-SNAPSHOT.jar,\
+ lib/bioinfweb-commons-swing-2-SNAPSHOT.jar,\
+ lib/bioinfweb-commons-swt-2-SNAPSHOT.jar,\
+ lib/core-1.9.2-SNAPSHOT.jar,\
+ lib/libralign-biojava1-0-SNAPSHOT.jar,\
+ lib/libralign-core-0-SNAPSHOT.jar,\
+ lib/libralign-swt-0-SNAPSHOT.jar,\
+ lib/sequencing-1.9.2-SNAPSHOT.jar,\
+ lib/tic-core-2-SNAPSHOT.jar,\
+ lib/tic-swt-2-SNAPSHOT.jar
--- /dev/null
+<project>
+ <modelVersion>4.0.0</modelVersion>
+ <groupId>eu.etaxonomy.taxeditor</groupId>
+ <artifactId>eu.etaxonomy.taxeditor.molecular.lib</artifactId>
+ <packaging>eclipse-plugin</packaging>
+
+ <parent>
+ <groupId>eu.etaxonomy</groupId>
+ <artifactId>taxeditor-parent</artifactId>
+ <version>3.8.0-SNAPSHOT</version>
+ </parent>
+
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-dependency-plugin</artifactId>
+ <version>2.4</version>
+ <executions>
+ <execution>
+ <id>copy-dependencies</id>
+ <phase>validate</phase>
+ <goals>
+ <goal>copy-dependencies</goal>
+ </goals>
+ <configuration>
+ <includeArtifactIds>libralign-swt, libralign-core,
+ bioinfweb-commons-swt, bioinfweb-commons-core,
+ bioinfweb-commons-bio, bioinfweb-commons-swing,
+ tic-core, libralign-biojava1, core, sequencing, tic-swt</includeArtifactIds>
+ <outputDirectory>lib</outputDirectory>
+ <overWriteReleases>true</overWriteReleases>
+ <overWriteSnapshots>true</overWriteSnapshots>
+ <excludeTransitive>true</excludeTransitive>
+ </configuration>
+ </execution>
+ <!-- <execution> -->
+ <!-- <id>copy-dependencies-sources</id> -->
+ <!-- <phase>validate</phase> -->
+ <!-- <goals> -->
+ <!-- <goal>copy-dependencies</goal> -->
+ <!-- </goals> -->
+ <!-- <configuration> -->
+ <!-- <classifier>sources</classifier> -->
+ <!-- <includeArtifactIds>cdmlib-commons,cdmlib-model,cdmlib-persistence,cdmlib-remote,cdmlib-print,cdmlib-services,cdmlib-ext,cdmlib-io</includeArtifactIds> -->
+ <!-- <outputDirectory>lib</outputDirectory> -->
+ <!-- <overWriteReleases>true</overWriteReleases> -->
+ <!-- <overWriteSnapshots>true</overWriteSnapshots> -->
+ <!-- <excludeTransitive>true</excludeTransitive> -->
+ <!-- <failOnMissingClassifierArtifact>false</failOnMissingClassifierArtifact> -->
+ <!-- </configuration> -->
+ <!-- </execution> -->
+ </executions>
+ </plugin>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-antrun-plugin</artifactId>
+ <version>1.7</version>
+ <executions>
+ <execution>
+ <id>remove-existing-jars</id>
+ <phase>clean</phase>
+ <goals>
+ <goal>run</goal>
+ </goals>
+ <configuration>
+ <target>
+ <echo>Remove all jars</echo>
+ <delete>
+ <fileset dir="./lib" includes="*" />
+ </delete>
+ </target>
+ </configuration>
+ </execution>
+ <execution>
+ <id>update-snapshot-jar-names</id>
+ <phase>validate</phase>
+ <goals>
+ <goal>run</goal>
+ </goals>
+ <configuration>
+ <target>
+ <echo>Update jars to SNAPSHOT when build with
+ timestamp</echo>
+ <move todir="./lib">
+ <fileset dir="./lib" />
+ <mapper type="regexp"
+ from="(^bioinfweb\-.*\-[0-9]-)[0-9.-]+(\.jar)" to="\1SNAPSHOT\2" />
+ </move>
+ <move todir="./lib">
+ <fileset dir="./lib" />
+ <mapper type="regexp"
+ from="(^libralign\-.*\-[0-9]-)[0-9.-]+(\.jar)" to="\1SNAPSHOT\2" />
+ </move>
+ <move todir="./lib">
+ <fileset dir="./lib" />
+ <mapper type="regexp"
+ from="(^tic\-.*\-[0-9]-)[0-9.-]+(\.jar)" to="\1SNAPSHOT\2" />
+ </move>
+ <move todir="./lib">
+ <fileset dir="./lib" />
+ <mapper type="regexp"
+ from="(^core\-[0-9]\.[0-9]\.[0-9])(\.jar)" to="\1-SNAPSHOT\2" />
+ </move>
+ <move todir="./lib">
+ <fileset dir="./lib" />
+ <mapper type="regexp"
+ from="(^sequencing\-[0-9]\.[0-9]\.[0-9])(\.jar)" to="\1-SNAPSHOT\2" />
+ </move>
+ </target>
+ </configuration>
+ </execution>
+ </executions>
+ </plugin>
+ </plugins>
+ </build>
+
+ <dependencies>
+ <!-- LibrAling -->
+ <dependency>
+ <groupId>info.bioinfweb.libralign</groupId>
+ <artifactId>libralign-core</artifactId>
+ <version>0-SNAPSHOT</version>
+ </dependency>
+ <dependency>
+ <groupId>info.bioinfweb.libralign</groupId>
+ <artifactId>libralign-swt</artifactId>
+ <version>0-SNAPSHOT</version>
+ </dependency>
+ <dependency>
+ <groupId>info.bioinfweb.libralign</groupId>
+ <artifactId>libralign-biojava1</artifactId>
+ <version>0-SNAPSHOT</version>
+ </dependency>
+ <!-- commons -->
+ <dependency>
+ <groupId>info.bioinfweb.commons.java</groupId>
+ <artifactId>bioinfweb-commons-swt</artifactId>
+ <version>2-SNAPSHOT</version>
+ </dependency>
+ <dependency>
+ <groupId>info.bioinfweb.commons.java</groupId>
+ <artifactId>bioinfweb-commons-core</artifactId>
+ <version>2-SNAPSHOT</version>
+ </dependency>
+ <dependency>
+ <groupId>info.bioinfweb.commons.java</groupId>
+ <artifactId>bioinfweb-commons-bio</artifactId>
+ <version>2-SNAPSHOT</version>
+ </dependency>
+ <dependency>
+ <groupId>info.bioinfweb.commons.java</groupId>
+ <artifactId>bioinfweb-commons-swing</artifactId>
+ <version>2-SNAPSHOT</version>
+ </dependency>
+ <!-- tic -->
+ <dependency>
+ <groupId>info.bioinfweb.tic</groupId>
+ <artifactId>tic-core</artifactId>
+ <version>2-SNAPSHOT</version>
+ </dependency>
+ <dependency>
+ <groupId>info.bioinfweb.tic</groupId>
+ <artifactId>tic-swt</artifactId>
+ <version>2-SNAPSHOT</version>
+ </dependency>
+ <!-- biojava -->
+ <dependency>
+ <groupId>org.biojava</groupId>
+ <artifactId>core</artifactId>
+ <version>1.9.2</version>
+ </dependency>
+ <dependency>
+ <groupId>org.biojava</groupId>
+ <artifactId>sequencing</artifactId>
+ <version>1.9.2</version>
+ </dependency>
+ </dependencies>
+
+ <repositories>
+ <repository>
+ <id>bioinfweb-maven-repo</id>
+ <name>bioinfweb repository</name>
+ <url>http://bioinfweb.info/MavenRepository/</url>
+ </repository>
+ </repositories>
+
+</project>
+
--- /dev/null
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+ <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
+ <classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
+ <classpathentry including="**/*.java" kind="src" path="src/main/java"/>
+ <classpathentry kind="output" path="target/classes"/>
+</classpath>
--- /dev/null
+/target
+.settings/
--- /dev/null
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+ <name>eu.etaxonomy.taxeditor.molecular</name>
+ <comment>Provides editors, views and operations for handling molecular data and alignments. NO_M2ECLIPSE_SUPPORT: Project files created with the maven-eclipse-plugin are not supported in M2Eclipse.</comment>
+ <projects>
+ </projects>
+ <buildSpec>
+ <buildCommand>
+ <name>org.eclipse.jdt.core.javabuilder</name>
+ <arguments>
+ </arguments>
+ </buildCommand>
+ <buildCommand>
+ <name>org.eclipse.pde.ManifestBuilder</name>
+ <arguments>
+ </arguments>
+ </buildCommand>
+ <buildCommand>
+ <name>org.eclipse.pde.SchemaBuilder</name>
+ <arguments>
+ </arguments>
+ </buildCommand>
+ </buildSpec>
+ <natures>
+ <nature>org.eclipse.jdt.core.javanature</nature>
+ <nature>org.eclipse.pde.PluginNature</nature>
+ </natures>
+</projectDescription>
--- /dev/null
+Manifest-Version: 1.0
+Bundle-ManifestVersion: 2
+Bundle-Name: Molecular Bundle
+Bundle-SymbolicName: eu.etaxonomy.taxeditor.molecular;singleton:=true
+Bundle-Version: 3.8.0.qualifier
+Bundle-Activator: eu.etaxonomy.taxeditor.molecular.TaxeditorMolecularPlugin
+Require-Bundle: org.eclipse.ui,
+ org.eclipse.core.runtime,
+ org.eclipse.core.expressions,
+ org.eclipse.ui.ide,
+ eu.etaxonomy.taxeditor.bulkeditor,
+ eu.etaxonomy.taxeditor.cdmlib,
+ eu.etaxonomy.taxeditor.editor,
+ eu.etaxonomy.taxeditor.store,
+ eu.etaxonomy.taxeditor.molecular.lib
+Bundle-RequiredExecutionEnvironment: JavaSE-1.6
+Bundle-ActivationPolicy: lazy
+Bundle-Vendor: EDIT
--- /dev/null
+#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
\ No newline at end of file
--- /dev/null
+# Properties file for taxeditor-editor
+Bundle-Vendor.0 = EDIT
+Bundle-Name.0 = EDIT Taxonomischer Editor - Editor Bundle
+command.name.17 = Setze Basionym
+command.name.18 = Entferne Basionym
+editor.name = Multipage Taxon Editor
+editor.name.0 = Editor Taxonname
+editor.name.1 = Bestimmungsschl\u00fcssel
+editor.name.2 = Polytomer Bestimmungsschl\u00fcssel Graph Editor
+editor.name.3 = Polytomer Bestimmungsschl\u00fcssel List Editor
+editor.name.4 = CDM Rechtemanagement
+editor.name.5 = Ansicht Derivate
+view.name = Faktendaten
+view.name.0 = Nutzung
+view.name.1 = Medien
+view.name.2 = Konzeptrelationen
+view.name.3 = Konzeptgraph
+category.name = Taxonomischer Editor
+command.label = Referenz
+command.label.0 = Name
+command.label.1 = Team
+command.label.2 = Person
+command.label.3 = Beleg
+command.label.4 = Faktendaten
+command.label.5 = Medien
+command.label.6 = Konzeptrelationen
+command.label.7 = Konzeptgraph
+command.label.8 = \u00d6ffne Parent
+menu.label = Neue
+command.label.9 = Heterotypisches Synonym
+command.label.10 = Homotypisches Synonym
+command.label.11 = Synonym in Homotypischer Gruppe
+menu.label.0 = \u00c4ndere zu
+command.label.12 = Akzeptiertes Taxon
+command.label.13 = Synonym
+command.label.14 = Misapplication
+command.label.15 = L\u00f6schen
+command.label.16 = L\u00f6sche alle leeren Namen
+command.label.17 = Tausche Synonym mit akzeptiertem Namen
+command.label.18 = Zeige Details
+command.label.19 = Speichern
+command.label.20 = Neue Knoten
+command.label.21 = L\u00f6schen
+command.label.22 = Wende Layout an
+command.label.23 = Neue Bestimmungsschl\u00fcsselnummer
+command.label.24 = Neue Alternative
+command.label.25 = Erneuere Knoten
+command.label.26 = L\u00f6schen
+command.label.27 = Neue Faktendaten
+menu.label.1 = Neue
+command.label.28 = Verschiebe Eigenschaften zu Taxon
+command.label.29 = Verschiebe Elemente zu Taxon
+command.label.30 = L\u00f6schen
+command.label.31 = Speichern
+menu.label.2 = Neue Derivate
+command.label.32 = Neue Nutzung
+command.label.33 = Neue Zusammenfassung
+command.label.34 = Neuer Nutzungsdatensatz
+command.label.35 = L\u00f6schen
+command.label.36 = Speichern
+command.label.37 = Neue Bildergalerie
+command.label.38 = Neues Bild
+command.label.39 = Bild nach oben
+command.label.40 = Bild nach unten
+command.label.41 = L\u00f6schen
+command.label.42 = Speichern
+menu.label.3 = Neue
+command.label.43 = \u00d6ffne verbundenes Konzept
+command.label.44 = L\u00f6schen
+command.label.45 = Bearbeite Rechte
+extension.name = Namensbefehle
+category.name.0 = -- Namenseditor
+command.name = \u00d6ffne Elter
+command.name.0 = Erstelle homotypisches Synonym
+command.name.1 = Erstelle heterotypisches Synonym
+command.name.2 = Erstelle Synonym in homotypischer Gruppe
+command.name.3 = \u00c4ndere zu Synonym
+command.name.4 = \u00c4ndere zu akzeptiertem Taxon
+command.name.5 = \u00c4ndere zu Misapplication
+command.name.6 = Tausche Synonym mit akzeptiertem Namen
+
+command.name.7 = Setze Basionym / Originalkombination
+command.name.8 = Entferne Basionym / Originalkombination
+command.name.9 = L\u00f6sche alle leeren Namen
+category.name.1 = -- Fakten
+command.name.10 = Erstelle Beschreibungselement
+command.name.11 = Neue Beschreibung
+command.name.12 = Bewege Beschreibungselement zu Taxon
+command.name.13 = Bewege Beschreibung zu Taxon
+category.name.2 = -- Neue Nutzung
+command.name.14 = Neue Nutzung
+command.name.15 = Neue Zusammenfassung
+command.name.16 = Neuer Nutzungsdatensatz
+category.name.3 = -- Media
+command.name.19 = Bewege Bild nach unten
+command.name.20 = Neue Bildergalerie
+command.name.21 = Neues Bild
+command.name.22 = Bewege Bild nach oben
+category.name.4 = -- Neue Entit\u00e4t
+command.name.23 = Neue Referenz
+command.name.24 = Neuer Name
+command.name.25 = Neues Team
+command.name.26 = Neue Person
+command.name.27 = Neuer Beleg
+category.name.5 = -- Polytomer Bestimmungsschl\u00fcssel
+command.name.28 = Neue Kinderknoten
+command.name.29 = Neuer Geschwisterknoten
+command.name.30 = Knotennummerierung aktualisieren
+command.name.31 = Layout anwenden
+category.name.6 = -- Konzeptbeziehungen
+command.name.32 = Erstelle Konzeptrelationen
+command.name.33 = \u00d6ffne verbundenes Konzept
+category.name.7 = -- Gruppe
+command.name.34 = Bearbeite CDM Rechte
+command.name.35 = \u00d6ffne Derivate Ansicht
+scheme.description = Die Standard Tastenkombinationsschema f\u00fcr den Taxonomischen Editor
+scheme.name = Taxonomic Editor Standard Tastenkombinationen
+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 = Referenz
+command.label.48 = Datenquelle
+command.label.49 = Misapplication
+command.label.50 = Benutze vorhandenes Bild
+command.name.36 = Erstelle Misapplication
+command.name.37 = Benutze vorhandenes Bild
+command.name.38 = \u00d6ffne Checklist Editor
+command.name.39 = Neue Datenquelle
+wizard.name = Specimen Suche/Import
+wizard.description = Sendet eine Anfrage mit den eingegebenen Parametern an den Datenprovider.\nHinweis: Die Anzahl der Anfrageergebnisse sind auf 100 begrenzt.
+command.name.40 = Validierung
+view.name.6 = Validierung
+marker.field.0 = Objekttyp
+marker.field.1 = Objekt
+marker.field.2 = Attribut
+marker.field.3 = Problematischer Wert
+marker.field.4 = Problembeschreibung
+marker.field.5 = Validierer
+marker.field.6 = Entit�tsklasse
+marker.field.7 = Entit�ts ID
+extension.name.0 = Validierungs-Fehler
+command.label.51 = \u00d6ffne Specimen-Editor
+command.label.52 = L\u00f6schen
+command.label.53 = Neue Field Unit
+command.label.54 = L\u00f6schen (mit Kindern)
+command.tooltip = Nur Individuals Associations anzeigen
+command.label.55 = \u00d6ffne zugeh\u00f6rige Specimens
+command.name.41 = Nur Individuals Associations anzeigen
+command.name.42 = \u00d6ffne Taxon Editor
+command.name.43 = Neue Field Unit
+command.name.44 = L\u00f6schen (mit Kindern)
+command.name.46 = Verschiebe Synonym(Homotypische Gruppe) zu neuem Akzeptierten Taxon
+command.label.56 = Verschiebe Synonym(Homotypische Gruppe) zu neuem Akzeptierten Taxon
\ No newline at end of file
--- /dev/null
+#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
\ No newline at end of file
--- /dev/null
+bin.includes = META-INF/,\
+ plugin.xml,\
+ icons/,\
+ OSGI-INF/
--- /dev/null
+<?xml version="1.0" encoding="UTF-8"?>
+<?eclipse version="3.4"?>
+<plugin>
+ <extension
+ point="org.eclipse.ui.editors">
+ <editor
+ class="eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor"
+ default="false"
+ id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor"
+ name="Alignment Editor">
+ </editor>
+ </extension>
+ <extension
+ point="org.eclipse.ui.views">
+ <view
+ allowMultiple="true"
+ class="eu.etaxonomy.taxeditor.molecular.editor.PherogramViewPart"
+ id="eu.etaxonomy.taxeditor.molecular.PherogramView"
+ name="PherogramView"
+ restorable="true">
+ </view>
+ </extension>
+ <extension
+ point="org.eclipse.ui.commands">
+ <command
+ defaultHandler="eu.etaxonomy.taxeditor.molecular.handler.EditSequenceHandler"
+ id="eu.etaxonomy.taxeditor.molecular.editSequence"
+ name="Edit Sequence">
+ </command>
+ <command
+ defaultHandler="eu.etaxonomy.taxeditor.molecular.handler.ShowPherogramHandler"
+ id="eu.etaxonomy.taxeditor.molecular.showPherogram"
+ name="Show Pherogram">
+ </command>
+ <command
+ id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramLeft"
+ name="Cut pherogram left">
+ </command>
+ <command
+ id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramRight"
+ name="Cut pherogram right">
+ </command>
+ <command
+ id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.reverseComplementRows"
+ name="Reverse complement selected rows">
+ </command>
+ <command
+ id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.createConsensus"
+ name="(Re)create consensus sequence">
+ </command>
+ <command
+ id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.updateConsensus"
+ name="Update consensus sequence">
+ </command>
+ <command
+ id="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowProbabilities"
+ name="Toggle show probability values">
+ </command>
+ <command
+ id="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowBaseCallLines"
+ name="Toggle show base call lines">
+ </command>
+ <command
+ id="eu.etaxonomy.taxeditor.molecular.pherogramComponent.changeQualityOutput"
+ name="Change quality output">
+ </command>
+ <command
+ id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram"
+ name="Load Pherogram">
+ </command>
+ <command
+ id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleInsertOverwrite"
+ name="Toggle insert/overwrite">
+ </command>
+ <command
+ id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleLeftRightInsertion"
+ name="Toggle left/right insertion in base call sequence">
+ </command>
+ </extension>
+ <extension
+ point="org.eclipse.ui.menus">
+ <menuContribution
+ locationURI="toolbar:org.eclipse.ui.main.toolbar?after=eu.etaxonomy.taxeditor.navigation.search.toolbar">
+ <toolbar
+ id="eu.etaxonomy.taxeditor.molecular.alignmentToolbar">
+ <command
+ commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleInsertOverwrite"
+ label="Toggle insert/overwrite"
+ style="push">
+ <visibleWhen
+ checkEnabled="true">
+ <with
+ variable="activePartId">
+ <equals
+ value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
+ </equals>
+ </with>
+ </visibleWhen>
+ </command>
+ <command
+ commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleLeftRightInsertion"
+ icon="icons/pherogram-insert-left-16x16.png"
+ style="push">
+ <visibleWhen
+ checkEnabled="true">
+ <with
+ variable="activePartId">
+ <equals
+ value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
+ </equals>
+ </with>
+ </visibleWhen>
+ </command>
+ </toolbar>
+ </menuContribution>
+ <menuContribution
+ allPopups="false"
+ locationURI="menu:org.eclipse.ui.main.menu">
+ <menu
+ label="Alignment Editor">
+ <command
+ commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram"
+ style="push">
+ </command>
+ <command
+ commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramLeft"
+ id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramLeft"
+ name="Cut pherogram left">
+ </command>
+ <command
+ commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramRight"
+ id="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramRight"
+ style="push">
+ </command>
+ <command
+ commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.reverseComplementRows"
+ mnemonic="r"
+ style="push">
+ </command>
+ <command
+ commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.createConsensus"
+ style="push">
+ </command>
+ <command
+ commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.updateConsensus"
+ style="push">
+ </command>
+ <visibleWhen
+ checkEnabled="true">
+ <with
+ variable="activePartId">
+ <equals
+ value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
+ </equals>
+ </with>
+ </visibleWhen>
+ </menu>
+ <menu
+ label="Pherogram View">
+ <command
+ commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.changeQualityOutput"
+ style="push">
+ </command>
+ <command
+ commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowProbabilities"
+ style="push">
+ </command>
+ <command
+ commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowBaseCallLines"
+ style="push">
+ </command>
+ <visibleWhen
+ checkEnabled="true">
+ <with
+ variable="activePartId">
+ <equals
+ value="eu.etaxonomy.taxeditor.molecular.PherogramView">
+ </equals>
+ </with>
+ </visibleWhen>
+ </menu>
+ </menuContribution>
+ <menuContribution
+ locationURI="popup:eu.etaxonomy.taxeditor.editor.view.derivate.DerivateView?before=eu.etaxonomy.taxeditor.editor.view.derivate.DerivateContextMenu">
+ <command
+ commandId="eu.etaxonomy.taxeditor.molecular.editSequence"
+ label="Edit Sequence"
+ style="push">
+ <visibleWhen
+ checkEnabled="true">
+ <reference
+ definitionId="isSequence">
+ </reference>
+ </visibleWhen>
+ </command>
+ <command
+ commandId="eu.etaxonomy.taxeditor.molecular.showPherogram"
+ label="Show Pherogram"
+ style="push">
+ <visibleWhen
+ checkEnabled="true">
+ <reference
+ definitionId="isSingleRead">
+ </reference>
+ </visibleWhen>
+ </command>
+ </menuContribution>
+ </extension>
+ <extension
+ point="org.eclipse.ui.handlers">
+ <handler
+ class="eu.etaxonomy.taxeditor.molecular.handler.LoadPherogramHandler"
+ commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram">
+ <activeWhen>
+ <with
+ variable="activePartId">
+ <equals
+ value="eu.etaxonomy.taxeditor.molecular.AlignmentEditor">
+ </equals>
+ </with>
+ </activeWhen>
+ </handler>
+ <handler
+ class="eu.etaxonomy.taxeditor.molecular.handler.ToggleInsertOverwriteHandler"
+ commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleInsertOverwrite">
+ </handler>
+ <handler
+ class="eu.etaxonomy.taxeditor.molecular.handler.ToggleLeftRightInsertionHandler"
+ commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.toggleLeftRightInsertion">
+ </handler>
+ <handler
+ class="eu.etaxonomy.taxeditor.molecular.handler.CutPherogramLeftHandler"
+ commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramLeft">
+ </handler>
+ <handler
+ class="eu.etaxonomy.taxeditor.molecular.handler.CutPherogramRightHandler"
+ commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.cutPherogramRight">
+ </handler>
+ <handler
+ class="eu.etaxonomy.taxeditor.molecular.handler.ReverseComplementHandler"
+ commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.reverseComplementRows">
+ </handler>
+ <handler
+ class="eu.etaxonomy.taxeditor.molecular.handler.CreateConsensusSequenceHandler"
+ commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.createConsensus">
+ </handler>
+ <handler
+ class="eu.etaxonomy.taxeditor.molecular.handler.UpdateConsensusSequenceHandler"
+ commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.updateConsensus">
+ </handler>
+ <handler
+ class="eu.etaxonomy.taxeditor.molecular.handler.ToggleShowPherogramProbabilitiesHandler"
+ commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowProbabilities">
+ </handler>
+ <handler
+ class="eu.etaxonomy.taxeditor.molecular.handler.ToggleShowPherogramBaseCallLinesHandler"
+ commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.toggleShowBaseCallLines">
+ </handler>
+ <handler
+ class="eu.etaxonomy.taxeditor.molecular.handler.ChangePherogramQualityOutputType"
+ commandId="eu.etaxonomy.taxeditor.molecular.pherogramComponent.changeQualityOutput">
+ </handler>
+ </extension>
+ <extension
+ point="org.eclipse.core.expressions.definitions">
+ <definition
+ id="isSequence">
+ <with
+ variable="selection">
+ <test
+ property="eu.etaxonomy.taxeditor.molecular.SpecimenPropertyTester.isSequence">
+ </test>
+ </with>
+ </definition>
+ <definition
+ id="isSingleRead">
+ <with
+ variable="selection">
+ <test
+ property="eu.etaxonomy.taxeditor.molecular.SpecimenPropertyTester.isSingleRead">
+ </test>
+ </with>
+ </definition>
+ </extension>
+ <extension
+ point="org.eclipse.core.expressions.propertyTesters">
+ <propertyTester
+ class="eu.etaxonomy.taxeditor.molecular.handler.SpecimenPropertyTester"
+ id="eu.etaxonomy.taxeditor.molecular.SpecimenPropertyTester"
+ namespace="eu.etaxonomy.taxeditor.molecular.SpecimenPropertyTester"
+ properties="isSequence,isSingleRead"
+ type="org.eclipse.jface.viewers.IStructuredSelection">
+ </propertyTester>
+ </extension>
+ <extension
+ point="org.eclipse.ui.bindings">
+ <scheme
+ description="%scheme.description"
+ id="eu.etaxonomy.taxeditor.bindings.scheme.default"
+ name="%scheme.name">
+ </scheme>
+ <key
+ commandId="eu.etaxonomy.taxeditor.molecular.AlignmentEditor.loadPherogram"
+ schemeId="eu.etaxonomy.taxeditor.bindings.scheme.default"
+ sequence="M1+O">
+ </key>
+ </extension>
+
+</plugin>
--- /dev/null
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+
+ <parent>
+ <groupId>eu.etaxonomy</groupId>
+ <artifactId>taxeditor-parent</artifactId>
+ <version>3.8.0-SNAPSHOT</version>
+ </parent>
+
+ <modelVersion>4.0.0</modelVersion>
+ <artifactId>eu.etaxonomy.taxeditor.molecular</artifactId>
+ <packaging>eclipse-plugin</packaging>
+
+ <name>Molecular Bundle</name>
+ <description>Provides editors, views and operations for handling molecular data and alignments</description>
+
+</project>
--- /dev/null
+package eu.etaxonomy.taxeditor.molecular;
+
+import org.eclipse.ui.plugin.AbstractUIPlugin;
+import org.osgi.framework.BundleContext;
+
+/**
+ * The activator class controls the plug-in life cycle
+ */
+public class TaxeditorMolecularPlugin extends AbstractUIPlugin {
+
+ // The plug-in ID
+ public static final String PLUGIN_ID = "eu.etaxonomy.taxeditor.molecular"; //$NON-NLS-1$
+
+ // The shared instance
+ private static TaxeditorMolecularPlugin plugin;
+
+ /**
+ * The constructor
+ */
+ public TaxeditorMolecularPlugin() {
+ }
+
+ @Override
+ public void start(BundleContext context) throws Exception {
+ super.start(context);
+ plugin = this;
+ }
+
+ @Override
+ public void stop(BundleContext context) throws Exception {
+ plugin = null;
+ super.stop(context);
+ }
+
+ /**
+ * Returns the shared instance
+ *
+ * @return the shared instance
+ */
+ public static TaxeditorMolecularPlugin getDefault() {
+ return plugin;
+ }
+
+}
--- /dev/null
+// $Id$
+/**
+* Copyright (C) 2014 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.alignmentarea.AlignmentArea;
+import info.bioinfweb.libralign.alignmentarea.selection.SelectionModel;
+import info.bioinfweb.libralign.alignmentarea.tokenpainter.NucleotideTokenPainter;
+import info.bioinfweb.libralign.dataarea.implementations.ConsensusSequenceArea;
+import info.bioinfweb.libralign.dataarea.implementations.SequenceIndexArea;
+import info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramArea;
+import info.bioinfweb.libralign.editsettings.EditSettingsChangeEvent;
+import info.bioinfweb.libralign.editsettings.EditSettingsListener;
+import info.bioinfweb.libralign.model.AlignmentModel;
+import info.bioinfweb.libralign.model.AlignmentModelChangeListener;
+import info.bioinfweb.libralign.model.AlignmentModelUtils;
+import info.bioinfweb.libralign.model.adapters.StringAdapter;
+import info.bioinfweb.libralign.model.events.SequenceChangeEvent;
+import info.bioinfweb.libralign.model.events.SequenceRenamedEvent;
+import info.bioinfweb.libralign.model.events.TokenChangeEvent;
+import info.bioinfweb.libralign.model.implementations.PackedAlignmentModel;
+import info.bioinfweb.libralign.model.tokenset.CharacterTokenSet;
+import info.bioinfweb.libralign.model.tokenset.TokenSet;
+import info.bioinfweb.libralign.multiplealignments.AlignmentAreaList;
+import info.bioinfweb.libralign.multiplealignments.MultipleAlignmentsContainer;
+import info.bioinfweb.libralign.pherogram.model.PherogramAreaModel;
+import info.bioinfweb.libralign.pherogram.model.ShiftChange;
+import info.bioinfweb.libralign.pherogram.provider.BioJavaPherogramProvider;
+import info.bioinfweb.libralign.pherogram.provider.PherogramProvider;
+import info.bioinfweb.libralign.pherogram.provider.ReverseComplementPherogramProvider;
+import info.bioinfweb.tic.SWTComponentFactory;
+
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.URI;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
+
+import org.biojava.bio.chromatogram.ChromatogramFactory;
+import org.biojava.bio.chromatogram.UnsupportedChromatogramFormatException;
+import org.eclipse.core.runtime.IProgressMonitor;
+import org.eclipse.swt.SWT;
+import org.eclipse.swt.widgets.Composite;
+import org.eclipse.ui.IActionBars;
+import org.eclipse.ui.IEditorInput;
+import org.eclipse.ui.IEditorPart;
+import org.eclipse.ui.IEditorSite;
+import org.eclipse.ui.PartInitException;
+import org.eclipse.ui.PlatformUI;
+import org.eclipse.ui.commands.ICommandService;
+import org.eclipse.ui.part.EditorPart;
+
+import eu.etaxonomy.cdm.api.conversation.ConversationHolder;
+import eu.etaxonomy.cdm.api.service.molecular.ISequenceService;
+import eu.etaxonomy.cdm.model.media.MediaUtils;
+import eu.etaxonomy.cdm.model.molecular.Sequence;
+import eu.etaxonomy.cdm.model.molecular.SequenceString;
+import eu.etaxonomy.cdm.model.molecular.SingleRead;
+import eu.etaxonomy.cdm.model.molecular.SingleReadAlignment;
+import eu.etaxonomy.cdm.model.molecular.SingleReadAlignment.Shift;
+import eu.etaxonomy.taxeditor.model.MessagingUtils;
+import eu.etaxonomy.taxeditor.molecular.TaxeditorMolecularPlugin;
+import eu.etaxonomy.taxeditor.molecular.handler.ToggleInsertOverwriteHandler;
+import eu.etaxonomy.taxeditor.molecular.handler.ToggleLeftRightInsertionHandler;
+import eu.etaxonomy.taxeditor.store.CdmStore;
+import eu.etaxonomy.taxeditor.view.derivateSearch.DerivateLabelProvider;
+
+
+
+/**
+ * Editor component to edit a contig alignment used to combine different overlapping pherograms from Sanger sequencing to
+ * a consensus sequence.
+ * <p>
+ * The contained GUI components used to edit the alignment come from <a href="http://bioinfweb.info/LibrAlign/">LibrAlign</a>.
+ *
+ * @author Ben Stöver
+ * @author pplitzner
+ * @date 04.08.2014
+ */
+public class AlignmentEditor extends EditorPart {
+ public static final String ID = "eu.etaxonomy.taxeditor.molecular.AlignmentEditor";
+
+ public static final int READS_AREA_INDEX = 1;
+ public static final int EDITABLE_CONSENSUS_AREA_INDEX = READS_AREA_INDEX + 1;
+ public static final int CONSENSUS_HINT_AREA_INDEX = EDITABLE_CONSENSUS_AREA_INDEX + 1;
+ public static final int PHEROGRAM_AREA_INDEX = 0;
+ public static final int CONSENSUS_DATA_AREA_INDEX = 0;
+ public static final String DEFAULT_READ_NAME_PREFIX = "Read ";
+ public static final String CONSENSUS_NAME = "Consensus";
+
+
+ private final ConversationHolder conversationHolder;
+
+ private final AlignmentModelChangeListener DIRTY_LISTENER = new AlignmentModelChangeListener() {
+ @Override
+ public <T> void afterTokenChange(TokenChangeEvent<T> e) {
+ setDirty();
+ }
+
+ @Override
+ public <T> void afterSequenceRenamed(SequenceRenamedEvent<T> e) {
+ setDirty();
+ }
+
+ @Override
+ public <T> void afterSequenceChange(SequenceChangeEvent<T> e) {
+ setDirty();
+ }
+
+ @Override
+ public <T, U> void afterProviderChanged(AlignmentModel<T> oldProvider,
+ AlignmentModel<U> newProvider) { // Not expected.
+
+ setDirty();
+ }
+ };
+
+ private MultipleAlignmentsContainer alignmentsContainer = null;
+ private final Map<Integer, SingleReadAlignment> cdmMap = new TreeMap<Integer, SingleReadAlignment>(); //TODO Move this to ContigSequenceDataProvider
+ private boolean dirty = false;
+
+
+ public AlignmentEditor() {
+ super();
+ conversationHolder = CdmStore.createConversation();
+ //conversationHolder = null;
+ }
+
+
+ private void refreshToolbarElement(String id) {
+ ICommandService commandService =
+ (ICommandService)PlatformUI.getWorkbench().getActiveWorkbenchWindow().getService(ICommandService.class);
+ if (commandService != null) {
+ commandService.refreshElements(id, Collections.EMPTY_MAP);
+ }
+ }
+
+
+ private void registerEditSettingListener(MultipleAlignmentsContainer container) {
+ container.getEditSettings().addListener(new EditSettingsListener() {
+ @Override
+ public void workingModeChanged(EditSettingsChangeEvent e) {} // Currently nothing to do
+
+ @Override
+ public void insertLeftInDataAreaChanged(EditSettingsChangeEvent e) {
+ updateStatusBar();
+ refreshToolbarElement(ToggleLeftRightInsertionHandler.COMMAND_ID);
+ }
+
+ @Override
+ public void insertChanged(EditSettingsChangeEvent e) {
+ updateStatusBar();
+ refreshToolbarElement(ToggleInsertOverwriteHandler.COMMAND_ID);
+ }
+ });
+ }
+
+
+ private AlignmentArea createIndexArea(MultipleAlignmentsContainer container, AlignmentArea labeledArea) {
+ AlignmentArea result = new AlignmentArea(container);
+ result.setAllowVerticalScrolling(false);
+ result.getDataAreas().getTopAreas().add(new SequenceIndexArea(result.getContentArea(), labeledArea));
+ return result;
+ }
+
+
+ private AlignmentArea createEditableAlignmentArea(MultipleAlignmentsContainer container, boolean allowVerticalScrolling) {
+ AlignmentArea result = new AlignmentArea(container);
+ result.setAllowVerticalScrolling(allowVerticalScrolling);
+
+ CharacterTokenSet tokenSet = CharacterTokenSet.newDNAInstance(); //TODO Should NUCLEOTIDE be used instead?
+ AlignmentModel<Character> provider = new PackedAlignmentModel<Character>(tokenSet);
+ result.setAlignmentModel(provider, false);
+ provider.getChangeListeners().add(DIRTY_LISTENER);
+ result.getPaintSettings().getTokenPainterList().set(0, new NucleotideTokenPainter());
+
+ return result;
+ }
+
+
+ private AlignmentArea createConsensusHintArea(MultipleAlignmentsContainer container,
+ AlignmentArea labeledArea) {
+
+ AlignmentArea result = new AlignmentArea(container);
+ result.setAllowVerticalScrolling(false);
+ result.getDataAreas().getBottomAreas().add(
+ new ConsensusSequenceArea(result.getContentArea(), labeledArea));
+ return result;
+ }
+
+
+ private MultipleAlignmentsContainer getAlignmentsContainer() {
+ if (alignmentsContainer == null) {
+ alignmentsContainer = new MultipleAlignmentsContainer();
+
+ AlignmentAreaList list = alignmentsContainer.getAlignmentAreas();
+ AlignmentArea readsArea = createEditableAlignmentArea(alignmentsContainer, true);
+ list.add(createIndexArea(alignmentsContainer, readsArea));
+ list.add(readsArea); // Make sure READS_AREA_INDEX is correct.
+ list.add(createEditableAlignmentArea(alignmentsContainer, false)); // Make sure COMSENSUS_AREA_INDEX is correct.
+ list.add(createConsensusHintArea(alignmentsContainer, readsArea));
+
+ registerEditSettingListener(alignmentsContainer);
+ }
+ return alignmentsContainer;
+ }
+
+
+ public AlignmentArea getReadsArea() {
+ return getAlignmentsContainer().getAlignmentAreas().get(READS_AREA_INDEX);
+ }
+
+
+ private AlignmentArea getEditableConsensusArea() {
+ return getAlignmentsContainer().getAlignmentAreas().get(EDITABLE_CONSENSUS_AREA_INDEX);
+ }
+
+
+ public boolean hasPherogram(int sequenceID) {
+ return getReadsArea().getDataAreas().getSequenceAreas(sequenceID).size() > PHEROGRAM_AREA_INDEX;
+ }
+
+
+ public PherogramArea getPherogramArea(int sequenceID) {
+ if (hasPherogram(sequenceID)) {
+ return (PherogramArea)getReadsArea().getDataAreas().getSequenceAreas(sequenceID).get(PHEROGRAM_AREA_INDEX);
+ }
+ else {
+ return null;
+ }
+ }
+
+
+ private ConsensusSequenceArea getConsensusHintDataArea() {
+ return (ConsensusSequenceArea)getAlignmentsContainer().getAlignmentAreas().
+ get(CONSENSUS_HINT_AREA_INDEX).getDataAreas().getBottomAreas().
+ get(CONSENSUS_DATA_AREA_INDEX);
+ }
+
+
+ @Deprecated //TODO Remove as soon as testing period is over
+ private void createTestContents() {
+ // Just for testing:
+ try {
+ addRead(new File("D:/Users/BenStoever/ownCloud/Dokumente/Projekte/EDITor/Quelltexte/LibrAlign branch/Repository/eu.etaxonomy.taxeditor.editor/src/main/resources/AlignmentTestData/JR430_JR-P01.ab1").toURI(), false);
+ //addRead(new File("D:/Users/BenStoever/ownCloud/Dokumente/Projekte/EDITor/Quelltexte/LibrAlign branch/Repository/eu.etaxonomy.taxeditor.editor/src/main/resources/AlignmentTestData/JR444_JR-P05.ab1").toURI(), false);
+ addRead(new File("D:/Users/BenStoever/ownCloud/Dokumente/Projekte/EDITor/Quelltexte/LibrAlign branch/Repository/eu.etaxonomy.taxeditor.editor/src/main/resources/AlignmentTestData/Test_qualityScore.scf").toURI(), false);
+
+ // Add test consensus sequence:
+ AlignmentModel consensusModel = getEditableConsensusArea().getAlignmentModel();
+ int id = consensusModel.addSequence(CONSENSUS_NAME);
+ Collection<Object> tokens = new ArrayList<Object>(); // First save tokens in a collection to avoid GUI updated for each token.
+ tokens.add(consensusModel.getTokenSet().tokenByRepresentation("A"));
+ tokens.add(consensusModel.getTokenSet().tokenByRepresentation("C"));
+ tokens.add(consensusModel.getTokenSet().tokenByRepresentation("G"));
+ tokens.add(consensusModel.getTokenSet().tokenByRepresentation("T"));
+ consensusModel.insertTokensAt(id, 0, tokens);
+ }
+ catch (Exception e) {
+ throw new RuntimeException(e);
+ }
+ }
+
+
+ private void readCDMData(Sequence sequenceNode) {
+ //TODO If called from somewhere else than createPartControl() the editorInput needs to be checked and previous contents need to be cleared (or updated).
+
+ // Add reads:
+ for (SingleReadAlignment singleReadAlignment : sequenceNode.getSingleReadAlignments()) {
+ try {
+ SingleRead pherogramInfo = singleReadAlignment.getSingleRead();
+ URI uri = null;
+ if (pherogramInfo.getPherogram() != null) {
+ uri = MediaUtils.getFirstMediaRepresentationPart(pherogramInfo.getPherogram()).getUri();
+ }
+ int id = addRead(DerivateLabelProvider.getDerivateText(pherogramInfo, conversationHolder),
+ uri,
+ singleReadAlignment.isReverseComplement(),
+ singleReadAlignment.getEditedSequence(),
+ singleReadAlignment.getFirstSeqPosition(),
+ singleReadAlignment.getLeftCutPosition(),
+ singleReadAlignment.getRightCutPosition(),
+ singleReadAlignment.getShifts());
+ cdmMap.put(id, singleReadAlignment);
+ }
+ catch (Exception e) { // Usually due to an error while trying to read the pherogram (e.g. due to an unsupported format or an invalid URI).
+ MessagingUtils.errorDialog("Error", null, "A single read was skipped because of the following error:\n\n" +
+ e.getLocalizedMessage(), TaxeditorMolecularPlugin.PLUGIN_ID, e, false);
+ }
+ }
+
+ // Set consensus sequence:
+ AlignmentModel consensusProvider = getEditableConsensusArea().getAlignmentModel();
+ int id = consensusProvider.addSequence(CONSENSUS_NAME);
+ consensusProvider.insertTokensAt(id, 0, AlignmentModelUtils.charSequenceToTokenList(
+ sequenceNode.getConsensusSequence().getString(), consensusProvider.getTokenSet()));
+ //TODO Can the consensus sequence also be null? / Should it be created here, if nothing is in the DB?
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.eclipse.ui.part.WorkbenchPart#createPartControl(org.eclipse.swt.widgets.Composite)
+ */
+ @Override
+ public void createPartControl(Composite parent) {
+ SWTComponentFactory.getInstance().getSWTComponent(getAlignmentsContainer(), parent, SWT.NONE);
+ updateStatusBar();
+
+ if (getEditorInput() instanceof AlignmentEditorInput) {
+ if (((AlignmentEditorInput)getEditorInput()).getSequenceNodeUuid() != null) {
+ Sequence sequenceNode = CdmStore.getService(ISequenceService.class).load(((AlignmentEditorInput)getEditorInput()).getSequenceNodeUuid());
+ //re-load into the current session if it is already persisted in the DB
+ if(sequenceNode!=null && sequenceNode.getId()!=0){
+ sequenceNode = CdmStore.getService(ISequenceService.class).load(sequenceNode.getUuid());
+ }
+ readCDMData(sequenceNode);
+ }
+ else {
+ createTestContents(); // This case will removed after the test phase and an exception should probably be thrown.
+ }
+ }
+ else {
+ throw new IllegalArgumentException("The editor input must have the type " +
+ AlignmentEditorInput.class.getCanonicalName()); //TODO What should be done here?
+ }
+ }
+
+
+ private void updateStatusBar() {
+ IActionBars bars = getEditorSite().getActionBars();
+ bars.getStatusLineManager().setMessage("Edit mode: " +
+ (getReadsArea().getEditSettings().isInsert() ? "Insert" : "Overwrite") + " " +
+ "Insertion in pherogram: " +
+ (getReadsArea().getEditSettings().isInsertLeftInDataArea() ? "Left" : "Right"));
+ }
+
+
+ private SingleReadAlignment.Shift[] convertToCDMShifts(PherogramAreaModel model) {
+ Iterator<ShiftChange> iterator = model.shiftChangeIterator();
+ List<Shift> shifts = new ArrayList<SingleReadAlignment.Shift>();
+ while (iterator.hasNext()) {
+ ShiftChange shiftChange = iterator.next();
+ shifts.add(new SingleReadAlignment.Shift(shiftChange.getBaseCallIndex(), shiftChange.getShiftChange()));
+ }
+ return shifts.toArray(new Shift[]{});
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.eclipse.ui.part.EditorPart#doSave(org.eclipse.core.runtime.IProgressMonitor)
+ */
+ @Override
+ public void doSave(IProgressMonitor monitor) {
+ if (getEditorInput() instanceof AlignmentEditorInput) {
+ String taskName = "Saving alignment";
+ monitor.beginTask(taskName, 3);
+
+ //re-loading sequence to avoid session conflicts
+ Sequence sequenceNode = CdmStore.getService(ISequenceService.class).load(((AlignmentEditorInput)getEditorInput()).getSequenceNodeUuid());
+ StringAdapter stringProvider = new StringAdapter(getEditableConsensusArea().getAlignmentModel(), false); // Throws an exception if a token has more than one character.
+
+ // Write consensus sequence:
+ SequenceString consensusSequenceObj = sequenceNode.getConsensusSequence();
+ String newConsensusSequence = stringProvider.getSequence(
+ getEditableConsensusArea().getAlignmentModel().sequenceIDByName(CONSENSUS_NAME));
+ if (consensusSequenceObj == null) {
+ sequenceNode.setConsensusSequence(SequenceString.NewInstance(newConsensusSequence));
+ }
+ else {
+ consensusSequenceObj.setString(newConsensusSequence);
+ }
+
+ // Write single reads:
+ stringProvider.setUnderlyingProvider(getReadsArea().getAlignmentModel());
+ sequenceNode.getSingleReadAlignments().retainAll(cdmMap.values()); // Remove all reads that are not in the alignment anymore.
+ Iterator<Integer> iterator = getReadsArea().getAlignmentModel().sequenceIDIterator();
+ while (iterator.hasNext()) {
+ int id = iterator.next();
+ SingleReadAlignment singleRead = cdmMap.get(id);
+ if (singleRead == null) {
+ throw new InternalError("Creating new reads from AlignmentEditor not implemented.");
+ //TODO Create new read object. => Shall it be allowed to add reads in the alignment editor which are not represented in the CDM tree before the alignment editor is saved?
+ //singleRead = SingleReadAlignment.NewInstance(consensusSequence, singleRead, shifts, editedSequence);
+ }
+
+ singleRead.setEditedSequence(stringProvider.getSequence(id));
+
+ PherogramArea pherogramArea = getPherogramArea(id);
+ if (pherogramArea != null) {
+ PherogramAreaModel model = pherogramArea.getModel();
+ singleRead.setReverseComplement(model.getPherogramProvider() instanceof ReverseComplementPherogramProvider); // Works only if ReverseComplementPherogramProvider instances are not nested.
+ singleRead.setShifts(convertToCDMShifts(getPherogramArea(id).getModel()));
+ singleRead.setFirstSeqPosition(model.getFirstSeqPos());
+ singleRead.setLeftCutPosition(model.getLeftCutPosition());
+ singleRead.setRightCutPosition(model.getRightCutPosition());
+ }
+ }
+
+ if (!conversationHolder.isBound()) {
+ conversationHolder.bind();
+ }
+ monitor.worked(1);
+
+ // Commit the conversation and start a new transaction immediately:
+ conversationHolder.commit(true);
+ monitor.worked(1);
+
+ dirty = false;
+ monitor.worked(1);
+ monitor.done();
+ firePropertyChange(PROP_DIRTY);
+ }
+ else {
+ //TODO Throw exception as soon as testing period which allows unlinked AlignmentEditor is over.
+ }
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.eclipse.ui.part.EditorPart#doSaveAs()
+ */
+ @Override
+ public void doSaveAs() {}
+
+
+ /* (non-Javadoc)
+ * @see org.eclipse.ui.part.EditorPart#init(org.eclipse.ui.IEditorSite, org.eclipse.ui.IEditorInput)
+ */
+ @Override
+ public void init(IEditorSite site, IEditorInput input) throws PartInitException {
+ setSite(site);
+ setInput(input);
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.eclipse.ui.part.EditorPart#isDirty()
+ */
+ @Override
+ public boolean isDirty() {
+ return dirty;
+ }
+
+
+ private void setDirty() {
+ dirty = true;
+ firePropertyChange(IEditorPart.PROP_DIRTY);
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.eclipse.ui.part.EditorPart#isSaveAsAllowed()
+ */
+ @Override
+ public boolean isSaveAsAllowed() {
+ return false; // "Save as" not allowed.
+ }
+
+
+ @Override
+ public void setFocus() {
+ if(conversationHolder!=null){
+ conversationHolder.bind();
+ }
+ }
+
+
+ public boolean isInsertMode() {
+ return getAlignmentsContainer().getEditSettings().isInsert();
+ }
+
+
+ public boolean isInsertLeftInPherogram() {
+ return getAlignmentsContainer().getEditSettings().isInsertLeftInDataArea();
+ }
+
+
+ public void toggleLeftRightInsertionInPherogram() {
+ getAlignmentsContainer().getEditSettings().toggleInsertLeftInDataArea();
+ }
+
+
+ public void toggleInsertOverwrite() {
+ getAlignmentsContainer().getEditSettings().toggleInsert();
+ }
+
+
+ private String cutPherogram(boolean left) {
+ SelectionModel selection = getReadsArea().getSelection();
+ if (selection.getCursorHeight() != 1) {
+ return "Cutting pherograms is only possible if exactly one row is selected.";
+ }
+ else {
+ PherogramArea pherogramArea =
+ getPherogramArea(getReadsArea().getSequenceOrder().idByIndex(selection.getCursorRow()));
+ if (pherogramArea == null) {
+ return "There is no pherogram attached to the current sequence.";
+ }
+ else {
+ if (left) {
+ if (pherogramArea.setLeftCutPositionBySelection()) {
+ return null;
+ }
+ else {
+ return "The left end of the selection lies outside the pherogram attached to this sequence.";
+ }
+ }
+ else {
+ if (pherogramArea.setRightCutPositionBySelection()) {
+ return null;
+ }
+ else {
+ return "The right end of the selection lies outside the pherogram attached to this sequence.";
+ }
+ }
+ }
+ }
+ }
+
+
+ public String cutPherogramLeft() {
+ return cutPherogram(true);
+ }
+
+
+ public String cutPherogramRight() {
+ return cutPherogram(false);
+ }
+
+
+ public void reverseComplementSelectedSequences() {
+ SelectionModel selection = getReadsArea().getSelection();
+ AlignmentModel<?> model = getReadsArea().getAlignmentModel();
+ for (int row = selection.getFirstRow(); row < selection.getFirstRow() + selection.getCursorHeight(); row++) {
+ int sequenceID = getReadsArea().getSequenceOrder().idByIndex(row);
+ PherogramArea area = getPherogramArea(sequenceID);
+ PherogramAreaModel pherogramAlignmentModel = area.getModel();
+ AlignmentModelUtils.reverseComplement(model, sequenceID,
+ pherogramAlignmentModel.editableIndexByBaseCallIndex(
+ pherogramAlignmentModel.getLeftCutPosition()).getBeforeValidIndex(),
+ pherogramAlignmentModel.editableIndexByBaseCallIndex(
+ pherogramAlignmentModel.getRightCutPosition()).getAfterValidIndex());
+ pherogramAlignmentModel.reverseComplement();
+ }
+ }
+
+
+ /**
+ * Recreates the whole consensus sequence from all single read sequences. The previous consensus
+ * sequence is overwritte.
+ */
+ @SuppressWarnings("unchecked")
+ public <T> void createConsensusSequence() {
+ ConsensusSequenceArea area = getConsensusHintDataArea();
+ AlignmentModel<T> model = (AlignmentModel<T>)getEditableConsensusArea().getAlignmentModel();
+ int sequenceID = model.sequenceIDIterator().next(); // There is always one sequence contained.
+ int length = getReadsArea().getAlignmentModel().getMaxSequenceLength();
+
+ Collection<T> tokens = new ArrayList<T>(length);
+ for (int column = 0; column < length; column++) {
+ tokens.add(model.getTokenSet().tokenByRepresentation(area.getConsensusToken(column)));
+ }
+
+ model.removeTokensAt(sequenceID, 0, model.getSequenceLength(sequenceID));
+ model.insertTokensAt(sequenceID, 0, tokens);
+ }
+
+
+ /**
+ * Updates the current consensus sequence by replacing gaps by the according consensus tokens
+ * calculated from the single read sequences and extends the consensus sequence if necessary.
+ */
+ @SuppressWarnings("unchecked")
+ public <T> void updateConsensusSequence() {
+ ConsensusSequenceArea area = getConsensusHintDataArea();
+ AlignmentModel<T> model = (AlignmentModel<T>)getEditableConsensusArea().getAlignmentModel();
+ TokenSet<T> tokenSet = model.getTokenSet();
+ int sequenceID = model.sequenceIDIterator().next(); // There is always one sequence contained.
+ int currentConsensusLength = model.getSequenceLength(sequenceID);
+ int overallLength = getReadsArea().getAlignmentModel().getMaxSequenceLength();
+
+ // Replace gaps by new information:
+ for (int column = 0; column < currentConsensusLength; column++) {
+ if (tokenSet.isGapToken(model.getTokenAt(sequenceID, column))) {
+ T newToken = tokenSet.tokenByRepresentation(area.getConsensusToken(column));
+ if (!tokenSet.isGapToken(newToken)) {
+ model.setTokenAt(sequenceID, column, newToken);
+ }
+ }
+ }
+
+ // Append additional tokens:
+ if (overallLength > currentConsensusLength) {
+ Collection<T> tokens = new ArrayList<T>(overallLength);
+ for (int column = currentConsensusLength; column < overallLength; column++) {
+ tokens.add(tokenSet.tokenByRepresentation(area.getConsensusToken(column)));
+ }
+ model.appendTokens(sequenceID, tokens);
+ }
+ }
+
+
+ public static PherogramProvider readPherogram(URI uri) throws IOException, UnsupportedChromatogramFormatException {
+ PherogramProvider result;
+ InputStream stream = uri.toURL().openStream();
+ try {
+ result = new BioJavaPherogramProvider(ChromatogramFactory.create(stream));
+ }
+ finally {
+ stream.close();
+ }
+ return result;
+ }
+
+
+ private String newReadName() {
+ int index = 1;
+ while (getReadsArea().getAlignmentModel().sequenceIDByName(DEFAULT_READ_NAME_PREFIX + index)
+ != AlignmentModel.NO_SEQUENCE_FOUND) {
+
+ index++;
+ }
+ return DEFAULT_READ_NAME_PREFIX + index;
+ }
+
+
+ public void addRead(URI pherogramURI, boolean reverseComplemented) throws IOException, UnsupportedChromatogramFormatException {
+ addRead(newReadName(), pherogramURI, reverseComplemented, null, null, null, null, null);
+ }
+
+
+ /**
+ * Adds a new sequence with attached phergram data area to the reads alignment.
+ * <p>
+ * If {@code null} is specified as {@code editedSequence} the base call sequence from the pherogram will
+ * be set as the edited sequence. If {@code null} is specified as {@code shifts} no shifts between the edited
+ * and the base calls sequence are assumed.
+ *
+ * @param name the name of the new sequence
+ * @param pherogramURI the URI where the associated pherogram file is located
+ * @param reverseComplemented Specify {@code true} here, if the reverse complement of the pherogram data should
+ * be added, {@code false} otherwise.
+ * @param editedSequence the edited version of the base call sequence (May be {@code null}.)
+ * @param shifts the alignment information that links the edited and the base call sequence (May be {@code null}.)
+ * @return the sequence ID of the added read
+ * @throws IOException if an error occurred when trying to read the pherogram file
+ * @throws UnsupportedChromatogramFormatException if the format of the pherogram file is not supported
+ */
+ public int addRead(String name, URI pherogramURI, boolean reverseComplemented, String editedSequence,
+ Integer firstSeqPos, Integer leftCutPos, Integer rightCutPos, SingleReadAlignment.Shift[] shifts)
+ throws IOException, UnsupportedChromatogramFormatException {
+
+ AlignmentModel provider = getReadsArea().getAlignmentModel();
+ PherogramProvider pherogramProvider = null;
+ if (pherogramURI != null) {
+ pherogramProvider = readPherogram(pherogramURI); // Must happen before a sequence is added, because it might throw an exception.
+ if (reverseComplemented) {
+ pherogramProvider = new ReverseComplementPherogramProvider(pherogramProvider);
+ }
+ }
+
+ // Create sequence:
+ provider.addSequence(name);
+ int id = provider.sequenceIDByName(name);
+
+ // Set edited sequence:
+ Collection<Object> tokens = null; // First save tokens in a collection to avoid GUI updated for each token.
+ if (editedSequence != null) {
+ tokens = AlignmentModelUtils.charSequenceToTokenList(editedSequence, provider.getTokenSet());
+ }
+ else if (pherogramProvider != null) { // Copy base call sequence into alignment:
+ tokens = new ArrayList<Object>();
+ for (int i = 0; i < pherogramProvider.getSequenceLength(); i++) {
+ tokens.add(provider.getTokenSet().tokenByRepresentation(
+ Character.toString(pherogramProvider.getBaseCall(i))));
+ }
+ setDirty();
+ }
+
+ if (tokens != null) { // If either an edited sequence or a pherogram URI was provided.
+ provider.insertTokensAt(id, 0, tokens);
+ // Create pherogram area:
+ PherogramArea pherogramArea = new PherogramArea(getReadsArea().getContentArea(),
+ new PherogramAreaModel(pherogramProvider));
+
+ // Set position properties and shifts:
+ PherogramAreaModel model = pherogramArea.getModel();
+ if ((firstSeqPos != null) && (leftCutPos != null)) {
+ model.setFirstSeqLeftCutPos(firstSeqPos, leftCutPos);
+ }
+ if (rightCutPos != null) {
+ model.setRightCutPosition(rightCutPos);
+ }
+ if ((shifts != null) && (shifts.length > 0)) {
+ for (int i = 0; i < shifts.length; i++) {
+ model.addShiftChange(shifts[i].position, shifts[i].shift);
+ }
+ setDirty();
+ }
+
+ // Add pherogram area to GUI:
+ pherogramArea.addMouseListener(new PherogramMouseListener(pherogramArea));
+ getReadsArea().getDataAreas().getSequenceAreas(id).add(pherogramArea);
+ }
+
+ return id;
+ }
+}
\ No newline at end of file
--- /dev/null
+// $Id$
+/**
+* Copyright (C) 2014 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 java.util.UUID;
+
+import org.eclipse.jface.resource.ImageDescriptor;
+import org.eclipse.ui.IEditorInput;
+import org.eclipse.ui.IPersistableElement;
+
+
+
+/**
+ * @author pplitzner
+ * @author Ben Stöver
+ * @date 04.08.2014
+ */
+public class AlignmentEditorInput implements IEditorInput {
+ private static final String name = "AlignmentEditor";
+
+
+ private final UUID sequenceNodeUuid;
+
+
+ public AlignmentEditorInput(UUID sequenceNodeUuid) {
+ super();
+ this.sequenceNodeUuid = sequenceNodeUuid;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.eclipse.core.runtime.IAdaptable#getAdapter(java.lang.Class)
+ */
+ @Override
+ public Object getAdapter(Class adapter) {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.eclipse.ui.IEditorInput#exists()
+ */
+ @Override
+ public boolean exists() {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.eclipse.ui.IEditorInput#getImageDescriptor()
+ */
+ @Override
+ public ImageDescriptor getImageDescriptor() {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.eclipse.ui.IEditorInput#getName()
+ */
+ @Override
+ public String getName() {
+ return name;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.eclipse.ui.IEditorInput#getPersistable()
+ */
+ @Override
+ public IPersistableElement getPersistable() {
+ return null;
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.eclipse.ui.IEditorInput#getToolTipText()
+ */
+ @Override
+ public String getToolTipText() {
+ return name;
+ }
+
+
+ /**
+ * Returns the {@link UUID} of the sequence CDM node that should be edited by the {@link AlignmentEditor} this object
+ * is used with.
+ *
+ * @return the uuid of the CDM node to work on
+ */
+ public UUID getSequenceNodeUuid() {
+ return sequenceNodeUuid;
+ }
+
+
+ @Override
+ public int hashCode() {
+ final int prime = 31;
+ int result = 1;
+ result = prime * result
+ + ((sequenceNodeUuid == null) ? 0 : sequenceNodeUuid.hashCode());
+ return result;
+ }
+
+
+ @Override
+ public boolean equals(Object obj) {
+ if (this == obj) {
+ return true;
+ }
+ if (obj == null) {
+ return false;
+ }
+ if (getClass() != obj.getClass()) {
+ return false;
+ }
+ AlignmentEditorInput other = (AlignmentEditorInput) obj;
+ if (sequenceNodeUuid == null) {
+ if (other.sequenceNodeUuid != null) {
+ return false;
+ }
+ } else if (!sequenceNodeUuid.equals(other.sequenceNodeUuid)) {
+ return false;
+ }
+ return true;
+ }
+}
--- /dev/null
+/**
+* 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
+/**
+* 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
+// $Id$
+/**
+* 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
+// $Id$
+/**
+* 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
+// $Id$
+/**
+* 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
+/**
+* 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
+// $Id$
+/**
+* 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
+// $Id$
+/**
+* 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
+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.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.molecular.Sequence;
+import eu.etaxonomy.taxeditor.editor.EditorUtil;
+import eu.etaxonomy.taxeditor.molecular.TaxeditorMolecularPlugin;
+import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;
+import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditorInput;
+
+
+
+/**
+ * Opens the alignment editor from the CDM tree.
+ *
+ * @author Ben Stöver
+ * @author pplitzner
+ */
+public class EditSequenceHandler extends AbstractHandler {
+
+ org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(EditSequenceHandler.class);
+
+ @Override
+ public Object execute(ExecutionEvent event) throws ExecutionException {
+ ISelection currentSelection = HandlerUtil.getCurrentSelection(event);
+ TreeNode treeNodeOfSelection = EditorUtil.getTreeNodeOfSelection(currentSelection);
+ if(treeNodeOfSelection != null && treeNodeOfSelection.getValue() instanceof Sequence){
+ AlignmentEditorInput input = new AlignmentEditorInput(((Sequence)treeNodeOfSelection.getValue()).getUuid()); //TODO Should there always be a new instance created here? What if the specified CDM node is already opened in an AlignmentEditor? => Possible create Singleton that keeps instances by sequence objects in a map.
+ try {
+ TaxeditorMolecularPlugin.getDefault().getWorkbench()
+ .getActiveWorkbenchWindow().getActivePage().openEditor(input, AlignmentEditor.ID);
+ }
+ catch (PartInitException e) {
+ logger.error("Could not open AlignmentEditor", e);
+ }
+ }
+ return null;
+ }
+}
--- /dev/null
+// $Id$
+/**
+* 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
+/**
+* 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.io.File;
+import java.io.IOException;
+
+import org.biojava.bio.chromatogram.UnsupportedChromatogramFormatException;
+import org.eclipse.core.commands.AbstractHandler;
+import org.eclipse.core.commands.ExecutionEvent;
+import org.eclipse.core.commands.ExecutionException;
+import org.eclipse.swt.widgets.FileDialog;
+import org.eclipse.ui.IEditorPart;
+
+import eu.etaxonomy.taxeditor.model.AbstractUtility;
+import eu.etaxonomy.taxeditor.model.MessagingUtils;
+import eu.etaxonomy.taxeditor.molecular.TaxeditorMolecularPlugin;
+import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;
+
+
+
+/**
+ * Handler that loads an additional read into the contig alignment displayed by an instance of {@link AlignmentEditor}.
+ *
+ * @author Ben Stöver
+ * @author pplitzner
+ */
+public class LoadPherogramHandler extends AbstractHandler {
+ //TODO Change so that also URIs which do not point to files can be specified.
+
+ /* (non-Javadoc)
+ * @see org.eclipse.core.commands.IHandler#execute(org.eclipse.core.commands.ExecutionEvent)
+ */
+ @Override
+ public Object execute(ExecutionEvent event) throws ExecutionException {
+ IEditorPart activeEditor = AbstractUtility.getActiveEditor();
+ if (activeEditor instanceof AlignmentEditor) {
+ AlignmentEditor alignmentEditor = (AlignmentEditor)activeEditor;
+
+ FileDialog fileDialog = new FileDialog(alignmentEditor.getSite().getShell());
+ fileDialog.setText("Import pherogram into contig alignment");
+ fileDialog.setFilterNames(new String[]{"All supported formats", "AB1 pherogram files", "SCF pherogram files", "All files"});
+ fileDialog.setFilterExtensions(new String[]{"*.ab1;*.scf", "*.ab1", "*.scf", "*.*"});
+
+ String path = fileDialog.open();
+ if (path != null) {
+ try {
+ alignmentEditor.addRead(new File(path).toURI(), false);
+ }
+ catch (UnsupportedChromatogramFormatException e) {
+ MessagingUtils.errorDialog("Unsupported format", this, "The format of the pherogram file \"" + path +
+ "\" is not supported. (Only AB1 and SCF are supported.)", TaxeditorMolecularPlugin.PLUGIN_ID, e, false); //TODO set pluginID
+ }
+ catch (IOException e) {
+ MessagingUtils.errorDialog("Unsupported format", this,
+ "An IO error occurred while trying to read the file \"" + path + "\".",
+ TaxeditorMolecularPlugin.PLUGIN_ID, e, false); //TODO set pluginID
+ }
+ }
+ }
+ return null;
+ }
+}
--- /dev/null
+/**
+* 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;
+
+
+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
+package eu.etaxonomy.taxeditor.molecular.handler;
+
+
+import org.eclipse.core.expressions.PropertyTester;
+import org.eclipse.jface.viewers.IStructuredSelection;
+import org.eclipse.jface.viewers.TreeNode;
+
+import eu.etaxonomy.cdm.model.molecular.Sequence;
+import eu.etaxonomy.cdm.model.molecular.SingleRead;
+import eu.etaxonomy.taxeditor.editor.EditorUtil;
+
+
+
+/**
+ * Tests types of specimens to add items to the context menu.
+ *
+ * @author pplitzner
+ * @author BenStoever
+ */
+public class SpecimenPropertyTester extends PropertyTester {
+ private static final String SEQUENCE = "isSequence";
+ private static final String SINGLE_READ = "isSingleRead";
+
+
+ public SpecimenPropertyTester() {}
+
+
+ /* (non-Javadoc)
+ * @see org.eclipse.core.expressions.IPropertyTester#test(java.lang.Object, java.lang.String, java.lang.Object[], java.lang.Object)
+ */
+ /** {@inheritDoc} */
+ @Override
+ public boolean test(Object receiver, String property, Object[] args, Object expectedValue) {
+ if (receiver instanceof IStructuredSelection) {
+ IStructuredSelection selection = (IStructuredSelection) receiver;
+ TreeNode treeNodeOfSelection = EditorUtil.getTreeNodeOfSelection(selection);
+ if (treeNodeOfSelection!=null) {
+ if (SEQUENCE.equals(property)) {
+ return isSequence(treeNodeOfSelection.getValue());
+ }
+ else if (SINGLE_READ.equals(property)) {
+ return isSingleReadAlignment(treeNodeOfSelection.getValue());
+ }
+ }
+ }
+ return false;
+ }
+
+
+ private boolean isSequence(Object object) {
+ return (object instanceof Sequence);
+ }
+
+
+ private boolean isSingleReadAlignment(Object object) {
+ return (object instanceof SingleRead);
+ }
+}
--- /dev/null
+/**
+* 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
+/**
+ * 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
+// $Id$
+/**
+* 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
+// $Id$
+/**
+* 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
+/**
+* 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
+// $Id$
+/**
+ * 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;
\ No newline at end of file
BGBM BDI Projects / taxeditor.git / commitdiff
