From: b.stoever <b.stoever@localhost>
Date: Mon, 27 Oct 2014 15:33:59 +0000 (+0000)
Subject: Basic implementation for LoadPherogramHandler added. (Imported data is currently... 
X-Git-Tag: 3.8.0^2~59^2~107
X-Git-Url: https://dev.e-taxonomy.eu/gitweb/taxeditor.git/commitdiff_plain/79ef938c5180a070265be8e76d3f2e1cd19b4307

Basic implementation for LoadPherogramHandler added. (Imported data is currently not displayed due to currently unimplemented support for adding sequences and data areas during runtime in LibrAlign.)
---

diff --git a/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/LoadPherogramHandler.java b/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/LoadPherogramHandler.java
index 2ffa2ca70..61addf4e5 100644
--- a/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/LoadPherogramHandler.java
+++ b/eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/LoadPherogramHandler.java
@@ -9,6 +9,17 @@
 package eu.etaxonomy.taxeditor.editor.handler;
 
 
+import info.bioinfweb.libralign.AlignmentArea;
+import info.bioinfweb.libralign.AlignmentContentArea;
+import info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramArea;
+import info.bioinfweb.libralign.pherogram.BioJavaPherogramProvider;
+import info.bioinfweb.libralign.sequenceprovider.SequenceDataProvider;
+
+import java.io.File;
+import java.io.IOException;
+
+import org.biojava.bio.chromatogram.ChromatogramFactory;
+import org.biojava.bio.chromatogram.UnsupportedChromatogramFormatException;
 import org.eclipse.core.commands.AbstractHandler;
 import org.eclipse.core.commands.ExecutionEvent;
 import org.eclipse.core.commands.ExecutionException;
@@ -17,6 +28,7 @@ import org.eclipse.ui.IEditorPart;
 
 import eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor;
 import eu.etaxonomy.taxeditor.model.AbstractUtility;
+import eu.etaxonomy.taxeditor.model.MessagingUtils;
 
 
 
@@ -27,19 +39,71 @@ import eu.etaxonomy.taxeditor.model.AbstractUtility;
  * @author pplitzner
  * @date 16.10.2014
  */
-public class LoadPherogramHandler extends AbstractHandler{
+public class LoadPherogramHandler extends AbstractHandler {
+	public static final String DEFAULT_READ_NAME_PREFIX = "Read ";
+	
+	
+	private String newReadName(SequenceDataProvider provider) {
+		int index = 1;
+		while (provider.sequenceIDByName(DEFAULT_READ_NAME_PREFIX + index) != SequenceDataProvider.NO_SEQUENCE_FOUND) {
+			index++;
+		}
+		return DEFAULT_READ_NAME_PREFIX + index;
+	}
+	
+	
+	private void addPherogram(AlignmentContentArea contentArea, File pherogram) 
+			throws IOException, UnsupportedChromatogramFormatException {
+		
+		SequenceDataProvider provider = contentArea.getSequenceProvider();
+		BioJavaPherogramProvider pherogramProvider = new BioJavaPherogramProvider(ChromatogramFactory.create(pherogram));  // Must happen before a sequence is added, because it might throw an exception.
+		String name = newReadName(provider);
+		
+        // Create sequence:
+		provider.addSequence(name);
+		int id = provider.sequenceIDByName(name);
+		
+		// Copy base call sequence into alignment:
+		for (int i = 0; i < pherogramProvider.getSequenceLength(); i++) {
+			provider.insertTokenAt(id, i, provider.getTokenSet().tokenByKeyChar(
+					pherogramProvider.getBaseCall(i).getUpperedBase().charAt(0)));
+		}
+		
+		// Add data area:
+		PherogramArea pherogramArea = new PherogramArea(contentArea, pherogramProvider);
+		contentArea.getDataAreas().getSequenceAreas(id).add(pherogramArea);
+	}
+	
+	
     /* (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;
+        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();
-            System.out.println(path);
-//            alignmentEditor.getAlignmentArea().getSelection()
+            if (path != null) {
+            	try {
+            		addPherogram(alignmentEditor.getReadsArea().getContentArea(), new File(path));
+            	}
+            	catch (UnsupportedChromatogramFormatException e) {
+                    MessagingUtils.errorDialog("Unsupported format", this, "The format of the pherogram file \"" + path + 
+                    		"\" is not supported. (Only AB1 and SCF are supported.)", "eu.etaxonomy.taxeditor.editor", e, false);  //TODO set pluginID
+            	}
+            	catch (IOException e) {
+                    MessagingUtils.errorDialog("Unsupported format", this, 
+                    		"An IO error occurred while trying to read the file \"" + path + "\".", 
+                    		"/eu.etaxonomy.taxeditor.editor", e, false);  //TODO set pluginID
+            	}
+            }
         }
         return null;
     }
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 b4863284c..3efa522e0 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
@@ -56,10 +56,10 @@ import org.eclipse.ui.part.EditorPart;
 public class AlignmentEditor extends EditorPart {
     public static final String ID = "eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor";
 
-    private AlignmentArea alignmentArea;
+    private AlignmentArea readsArea;
 
 
-	private AlignmentArea createAlignmentArea() {
+	private AlignmentArea createReadsArea() {
 		try {
 			AlignmentArea result = new AlignmentArea();
 			AlignmentContentArea contentArea = result.getContentArea();
@@ -114,13 +114,18 @@ public class AlignmentEditor extends EditorPart {
 	}
 
 
-    /* (non-Javadoc)
+    public AlignmentArea getReadsArea() {
+		return readsArea;
+	}
+
+
+	/* (non-Javadoc)
      * @see org.eclipse.ui.part.WorkbenchPart#createPartControl(org.eclipse.swt.widgets.Composite)
      */
     @Override
     public void createPartControl(Composite parent) {
-    	alignmentArea = createAlignmentArea();
-		Composite alignmentWidget = alignmentArea.createSWTWidget(parent, SWT.NONE);
+    	readsArea = createReadsArea();
+		Composite alignmentWidget = readsArea.createSWTWidget(parent, SWT.NONE);
 		//getSite().setSelectionProvider(provider)
     }