Basic implementation for LoadPherogramHandler added. (Imported data is currently...

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 2ffa2ca709e2ca5a35aa4242675b7b2a9a3abd15..61addf4e55850d8d06f7bd51fe2fac57e7811ed6 100644 (file)
--- 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 b4863284ce34de651ea0cb65cf03f4f997bb91af..3efa522e0c3a333e37757ac505ed05510a164ca5 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
@@ -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)
     }