Adjustments to recent changes in LibrAlign.

[taxeditor.git] / eu.etaxonomy.taxeditor.editor / src / main / java / eu / etaxonomy / taxeditor / editor / molecular / AlignmentEditor.java

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;
 
 
+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;
@@ -174,7 +175,8 @@ public class AlignmentEditor extends EditorPart {
                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);
@@ -184,12 +186,12 @@ public class AlignmentEditor extends EditorPart {
 
 
     private AlignmentArea createConsensusHintArea(MultipleAlignmentsContainer container,
-               AlignmentModel<?> sequenceProvider) {
+               AlignmentArea labeledArea) {
 
                AlignmentArea result = new AlignmentArea(container);
                result.setAllowVerticalScrolling(false);
                result.getDataAreas().getBottomAreas().add(
-                               new ConsensusSequenceArea(result.getContentArea(), sequenceProvider));
+                               new ConsensusSequenceArea(result.getContentArea(), labeledArea));
                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.
-               list.add(createConsensusHintArea(alignmentsContainer,
-                               readsArea.getAlignmentModel()));
+               list.add(createConsensusHintArea(alignmentsContainer, readsArea));
 
                registerEditSettingListener(alignmentsContainer);
                }
@@ -230,8 +231,8 @@ public class AlignmentEditor extends EditorPart {
     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();