Adjustments to recent changes in LibrAlign.

diff --git a/eu.etaxonomy.taxeditor.editor/.classpath b/eu.etaxonomy.taxeditor.editor/.classpath
index f7c4e43f8a11d788866a22c632addd9bd811cc3b..ada5dc9b3c829d3e5c3fce622488b4f5717365d9 100644 (file)
--- a/eu.etaxonomy.taxeditor.editor/.classpath
+++ b/eu.etaxonomy.taxeditor.editor/.classpath
@@ -12,5 +12,6 @@
        <classpathentry exported="true" kind="lib" path="lib/bioinfweb.commons"/>\r
        <classpathentry exported="true" kind="lib" path="lib/LibrAlign" sourcepath="lib/LibrAlign"/>\r
        <classpathentry exported="true" kind="lib" path="lib/commons-lang3-3.1.jar"/>\r
        <classpathentry exported="true" kind="lib" path="lib/bioinfweb.commons"/>\r
        <classpathentry exported="true" kind="lib" path="lib/LibrAlign" sourcepath="lib/LibrAlign"/>\r
        <classpathentry exported="true" kind="lib" path="lib/commons-lang3-3.1.jar"/>\r

+       <classpathentry exported="true" kind="lib" path="lib/JPhyloIO" sourcepath="lib/JPhyloIO"/>\r

        <classpathentry kind="output" path="target/classes"/>\r
 </classpath>\r
        <classpathentry kind="output" path="target/classes"/>\r
 </classpath>\r

diff --git a/eu.etaxonomy.taxeditor.editor/.project b/eu.etaxonomy.taxeditor.editor/.project
index ce8935ac2072251cf6f225298b65070a1a8fc91e..ae393bcbdba6fa4f7375b348031c4bf5cb376b60 100644 (file)
--- a/eu.etaxonomy.taxeditor.editor/.project
+++ b/eu.etaxonomy.taxeditor.editor/.project
@@ -26,6 +26,11 @@
                <nature>org.eclipse.pde.PluginNature</nature>\r
        </natures>\r
        <linkedResources>\r
                <nature>org.eclipse.pde.PluginNature</nature>\r
        </natures>\r
        <linkedResources>\r

+               <link>\r
+                       <name>lib/JPhyloIO</name>\r
+                       <type>2</type>\r
+                       <locationURI>WORKSPACE_LOC/JPhyloIO/bin</locationURI>\r
+               </link>\r

                <link>\r
                        <name>lib/LibrAlign</name>\r
                        <type>2</type>\r
                <link>\r
                        <name>lib/LibrAlign</name>\r
                        <type>2</type>\r

diff --git a/eu.etaxonomy.taxeditor.editor/META-INF/MANIFEST.MF b/eu.etaxonomy.taxeditor.editor/META-INF/MANIFEST.MF
index 14bdc8315c9b1d84a042e31a2e268a2c45a740c9..a9120795f7ed83fed1bc99377cf0cfcb758fddaf 100644 (file)
--- a/eu.etaxonomy.taxeditor.editor/META-INF/MANIFEST.MF
+++ b/eu.etaxonomy.taxeditor.editor/META-INF/MANIFEST.MF
@@ -184,4 +184,5 @@ Bundle-ClassPath: .,
  lib/sequencing-1.8.5.jar,
  lib/bioinfweb.commons/,
  lib/LibrAlign/,
  lib/sequencing-1.8.5.jar,
  lib/bioinfweb.commons/,
  lib/LibrAlign/,

- lib/commons-lang3-3.1.jar
+ lib/commons-lang3-3.1.jar,
+ lib/JPhyloIO/

diff --git a/eu.etaxonomy.taxeditor.editor/build.properties b/eu.etaxonomy.taxeditor.editor/build.properties
index 4d1348ccd3eab89dddb71eb7ae28c6773f567c86..956dd0e7c615eaa094797206385335f56fe914ff 100644 (file)
--- a/eu.etaxonomy.taxeditor.editor/build.properties
+++ b/eu.etaxonomy.taxeditor.editor/build.properties
@@ -13,4 +13,5 @@ bin.includes = META-INF/,\
                lib/sequencing-1.8.5.jar,\
                lib/bioinfweb.commons/,\
                lib/LibrAlign/,\
                lib/sequencing-1.8.5.jar,\
                lib/bioinfweb.commons/,\
                lib/LibrAlign/,\

-               lib/commons-lang3-3.1.jar
+               lib/commons-lang3-3.1.jar,\
+               lib/JPhyloIO/

diff --git a/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/AlignmentEditor.java b/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/AlignmentEditor.java
index 67ce107f535bdf384700b6c430d794f3e34e68f4..057d71e18a17d17b12f19e05b94b7b284efb4b64 100644 (file)
--- a/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/AlignmentEditor.java
+++ b/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/AlignmentEditor.java
@@ -10,6 +10,7 @@
 package eu.etaxonomy.taxeditor.editor.molecular;
 
 
 package eu.etaxonomy.taxeditor.editor.molecular;
 
 

+import info.bioinfweb.jphyloio.events.TokenSetType;

 import info.bioinfweb.libralign.alignmentarea.AlignmentArea;
 import info.bioinfweb.libralign.alignmentarea.selection.SelectionModel;
 import info.bioinfweb.libralign.dataarea.implementations.ConsensusSequenceArea;
 import info.bioinfweb.libralign.alignmentarea.AlignmentArea;
 import info.bioinfweb.libralign.alignmentarea.selection.SelectionModel;
 import info.bioinfweb.libralign.dataarea.implementations.ConsensusSequenceArea;


@@ -174,7 +175,8 @@ public class AlignmentEditor extends EditorPart {
                AlignmentArea result = new AlignmentArea(container);
                result.setAllowVerticalScrolling(allowVerticalScrolling);
 
                AlignmentArea result = new AlignmentArea(container);
                result.setAllowVerticalScrolling(allowVerticalScrolling);
 

-               TokenSet<NucleotideCompound> tokenSet = new BioJavaTokenSet<NucleotideCompound>(new DNACompoundSet(), true);
+               TokenSet<NucleotideCompound> tokenSet = new BioJavaTokenSet<NucleotideCompound>(
+                               TokenSetType.DNA, new DNACompoundSet(), true);  //TODO Should NUCLEOTIDE be used instead?

                AlignmentModel<NucleotideCompound> provider = new PackedAlignmentModel<NucleotideCompound>(tokenSet);
                result.setAlignmentModel(provider, false);
                provider.getChangeListeners().add(DIRTY_LISTENER);
                AlignmentModel<NucleotideCompound> provider = new PackedAlignmentModel<NucleotideCompound>(tokenSet);
                result.setAlignmentModel(provider, false);
                provider.getChangeListeners().add(DIRTY_LISTENER);


@@ -184,12 +186,12 @@ public class AlignmentEditor extends EditorPart {
 
 
     private AlignmentArea createConsensusHintArea(MultipleAlignmentsContainer container,
 
 
     private AlignmentArea createConsensusHintArea(MultipleAlignmentsContainer container,

-               AlignmentModel<?> sequenceProvider) {
+               AlignmentArea labeledArea) {

 
                AlignmentArea result = new AlignmentArea(container);
                result.setAllowVerticalScrolling(false);
                result.getDataAreas().getBottomAreas().add(
 
                AlignmentArea result = new AlignmentArea(container);
                result.setAllowVerticalScrolling(false);
                result.getDataAreas().getBottomAreas().add(

-                               new ConsensusSequenceArea(result.getContentArea(), sequenceProvider));
+                               new ConsensusSequenceArea(result.getContentArea(), labeledArea));

                return result;
     }
 
                return result;
     }
 


@@ -203,8 +205,7 @@ public class AlignmentEditor extends EditorPart {
                AlignmentArea readsArea = createEditableAlignmentArea(alignmentsContainer, true);
                list.add(readsArea);  // Make sure READS_AREA_INDEX is correct.
                list.add(createEditableAlignmentArea(alignmentsContainer, false));  // Make sure COMSENSUS_AREA_INDEX is correct.
                AlignmentArea readsArea = createEditableAlignmentArea(alignmentsContainer, true);
                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.getAlignmentModel()));
+               list.add(createConsensusHintArea(alignmentsContainer, readsArea));

 
                registerEditSettingListener(alignmentsContainer);
                }
 
                registerEditSettingListener(alignmentsContainer);
                }


@@ -230,8 +231,8 @@ public class AlignmentEditor extends EditorPart {
     private void createTestContents() {
                // Just for testing:
                try {
     private void createTestContents() {
                // Just for testing:
                try {

-                       addRead(new File("D:/Users/BenStoever/Documents/Studium/Projekte/Promotion/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/Documents/Studium/Projekte/Promotion/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/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);

 
                        // Add test consensus sequence:
                        AlignmentModel consensusProvider = getConsensusArea().getAlignmentModel();
 
                        // Add test consensus sequence:
                        AlignmentModel consensusProvider = getConsensusArea().getAlignmentModel();

diff --git a/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/ContigSequenceDataProvider.java b/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/ContigSequenceDataProvider.java
index 6b93861b8dd54ed2d246070985509977c3df0ee6..2139f628ffa8605b853df68e7e4233188bbe85d2 100644 (file)
--- a/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/ContigSequenceDataProvider.java
+++ b/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/ContigSequenceDataProvider.java
@@ -13,6 +13,7 @@ package eu.etaxonomy.taxeditor.editor.molecular;
 import org.biojava3.core.sequence.compound.NucleotideCompound;\r
 \r
 import info.bioinfweb.commons.bio.biojava3.core.sequence.compound.AlignmentAmbiguityDNACompoundSet;\r
 import org.biojava3.core.sequence.compound.NucleotideCompound;\r
 \r
 import info.bioinfweb.commons.bio.biojava3.core.sequence.compound.AlignmentAmbiguityDNACompoundSet;\r

+import info.bioinfweb.jphyloio.events.TokenSetType;\r

 import info.bioinfweb.libralign.model.AlignmentModel;\r
 import info.bioinfweb.libralign.model.implementations.PackedAlignmentModel;\r
 import info.bioinfweb.libralign.model.tokenset.BioJavaTokenSet;\r
 import info.bioinfweb.libralign.model.AlignmentModel;\r
 import info.bioinfweb.libralign.model.implementations.PackedAlignmentModel;\r
 import info.bioinfweb.libralign.model.tokenset.BioJavaTokenSet;\r


@@ -30,7 +31,8 @@ public class ContigSequenceDataProvider extends PackedAlignmentModel<NucleotideC
 \r
        \r
        public ContigSequenceDataProvider() {\r
 \r
        \r
        public ContigSequenceDataProvider() {\r

-               super(new BioJavaTokenSet<NucleotideCompound>(AlignmentAmbiguityDNACompoundSet.getAlignmentAmbiguityDNACompoundSet(), true));\r
+               super(new BioJavaTokenSet<NucleotideCompound>(TokenSetType.NUCLEOTIDE, \r
+                               AlignmentAmbiguityDNACompoundSet.getAlignmentAmbiguityDNACompoundSet(), true));\r

        }\r
        \r
        \r
        }\r
        \r
        \r