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 8fa5d17b3566af2c72b7d751a27c669d7973a74d..a2adc2ee82c93f29a5480fd47e9d1ea1e8d24b1e 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
@@ -109,7 +109,7 @@ public class AlignmentEditor extends EditorPart {
     private AlignmentArea createIndexArea(MultipleAlignmentsContainer container) {
                AlignmentArea result = new AlignmentArea(container);
                result.setAllowVerticalScrolling(false);
-               result.getContentArea().getDataAreas().getTopAreas().add(new SequenceIndexArea(result.getContentArea()));
+               result.getDataAreas().getTopAreas().add(new SequenceIndexArea(result.getContentArea()));
                return result;
     }
     
@@ -120,7 +120,7 @@ public class AlignmentEditor extends EditorPart {
 
                TokenSet<NucleotideCompound> tokenSet = new BioJavaTokenSet<NucleotideCompound>(new DNACompoundSet(), true);
                SequenceDataProvider<NucleotideCompound> provider = new PackedSequenceDataProvider<NucleotideCompound>(tokenSet);
-               result.getContentArea().setSequenceProvider(provider, false);
+               result.setSequenceProvider(provider, false);
                
                return result;
        }
@@ -131,7 +131,7 @@ public class AlignmentEditor extends EditorPart {
        
                AlignmentArea result = new AlignmentArea(container);
                result.setAllowVerticalScrolling(false);
-               result.getContentArea().getDataAreas().getBottomAreas().add(
+               result.getDataAreas().getBottomAreas().add(
                                new ConsensusSequenceArea(result.getContentArea(), sequenceProvider));
                return result;
     }
@@ -147,7 +147,7 @@ public class AlignmentEditor extends EditorPart {
                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.getContentArea().getSequenceProvider()));
+                               readsArea.getSequenceProvider()));
                
                registerEditSettingListener(alignmentsContainer);
                }
@@ -179,7 +179,7 @@ public class AlignmentEditor extends EditorPart {
                        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());
                        
                        // Add test consensus sequence:
-                       SequenceDataProvider consensusProvider = getConsensusArea().getContentArea().getSequenceProvider();
+                       SequenceDataProvider consensusProvider = getConsensusArea().getSequenceProvider();
                        int id = consensusProvider.addSequence("Consensus");
                        Collection<Object> tokens = new ArrayList<Object>();  // First save tokens in a collection to avoid GUI updated for each token.
                        tokens.add(consensusProvider.getTokenSet().tokenByKeyChar('A'));
@@ -197,9 +197,9 @@ public class AlignmentEditor extends EditorPart {
     private void updateStatusBar() {
         IActionBars bars = getEditorSite().getActionBars();
         bars.getStatusLineManager().setMessage("Edit mode: " + 
-                       (getReadsArea().getContentArea().getEditSettings().isInsert() ? "Insert" : "Overwrite") + "  " +
+                       (getReadsArea().getEditSettings().isInsert() ? "Insert" : "Overwrite") + "  " +
                        "Insertion in pherogram: " +
-                       (getReadsArea().getContentArea().getEditSettings().isInsertLeftInDataArea() ? "Left" : "Right"));
+                       (getReadsArea().getEditSettings().isInsertLeftInDataArea() ? "Left" : "Right"));
     }
 
     
@@ -292,7 +292,7 @@ public class AlignmentEditor extends EditorPart {
        
        private String newReadName() {
                int index = 1;
-               while (getReadsArea().getContentArea().getSequenceProvider().sequenceIDByName(DEFAULT_READ_NAME_PREFIX + index) 
+               while (getReadsArea().getSequenceProvider().sequenceIDByName(DEFAULT_READ_NAME_PREFIX + index) 
                                != SequenceDataProvider.NO_SEQUENCE_FOUND) {
                        
                        index++;
@@ -307,8 +307,7 @@ public class AlignmentEditor extends EditorPart {
     
     
     public void addRead(String name, URI pherogramURI) throws IOException, UnsupportedChromatogramFormatException {
-               AlignmentContentArea contentArea = getReadsArea().getContentArea();
-               SequenceDataProvider provider = contentArea.getSequenceProvider();
+               SequenceDataProvider provider = getReadsArea().getSequenceProvider();
                PherogramProvider pherogramProvider = readPherogram(pherogramURI);  // Must happen before a sequence is added, because it might throw an exception.
                
         // Create sequence:
@@ -324,9 +323,9 @@ public class AlignmentEditor extends EditorPart {
                provider.insertTokensAt(id, 0, tokens);
                
                // Add data area:
-               PherogramArea pherogramArea = new PherogramArea(contentArea, pherogramProvider);
+               PherogramArea pherogramArea = new PherogramArea(getReadsArea().getContentArea(), pherogramProvider);
                pherogramArea.addMouseListener(new PherogramMouseListener(pherogramURI));
-               contentArea.getDataAreas().getSequenceAreas(id).add(pherogramArea);
+               getReadsArea().getDataAreas().getSequenceAreas(id).add(pherogramArea);
                
                // Save source URI:
                uriMap.put(id, pherogramURI);