From 3884b4f508cb45aac19957a70336b61d862a304f Mon Sep 17 00:00:00 2001
From: "b.stoever" <b.stoever@localhost>
Date: Mon, 16 Mar 2015 11:59:21 +0000
Subject: [PATCH] Adjustments to recent changes in LibrAlign.

---
 .../editor/molecular/AlignmentEditor.java     | 23 +++++++++----------
 1 file changed, 11 insertions(+), 12 deletions(-)

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 8fa5d17b3..a2adc2ee8 100644
--- 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);
-- 
2.34.1