eu.etaxonomy.taxeditor.molecular/src/main/java/eu/etaxonomy/taxeditor/molecular/handler/AlignmentEditorPasteHandler.java

   1 package eu.etaxonomy.taxeditor.molecular.handler;
   2
   3
   4 import info.bioinfweb.libralign.alignmentarea.AlignmentArea;
   5 import info.bioinfweb.libralign.alignmentarea.order.SequenceOrder;
   6 import info.bioinfweb.libralign.alignmentarea.selection.SelectionModel;
   7 import info.bioinfweb.libralign.model.AlignmentModel;
   8 import info.bioinfweb.libralign.model.utils.AlignmentModelUtils;
   9
  10 import java.util.ArrayList;
  11 import java.util.List;
  12 import java.util.Map;
  13 import java.util.Scanner;
  14
  15 import org.eclipse.core.commands.ExecutionEvent;
  16 import org.eclipse.jface.dialogs.MessageDialog;
  17 import org.eclipse.swt.dnd.TextTransfer;
  18 import org.eclipse.ui.commands.IElementUpdater;
  19 import org.eclipse.ui.handlers.HandlerUtil;
  20 import org.eclipse.ui.menus.UIElement;
  21
  22 import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;
  23
  24
  25
  26 /**
  27  * Handler that pastes the current contents of the clipboard into an active instance of {@link AlignmentEditor}.
  28  *
  29  * @author Ben Stöver
  30  * @date 26.08.2015
  31  */
  32 public class AlignmentEditorPasteHandler extends AbstractFocusedAlignmentAreaHandler implements IElementUpdater {
  33         private void pasteString(AlignmentArea area, String sequenceID, String content) {
  34                 area.getActionProvider().deleteSelection();  // Overwrite selected tokens.
  35                 area.getActionProvider().elongateSequence(sequenceID, area.getSelection().getCursorColumn());
  36
  37                 @SuppressWarnings("unchecked")
  38                 AlignmentModel<Object> alignmentModel = (AlignmentModel<Object>)area.getAlignmentModel();
  39                 alignmentModel.insertTokensAt(sequenceID, area.getSelection().getCursorColumn(),
  40                                 AlignmentModelUtils.charSequenceToTokenList(content, alignmentModel.getTokenSet(),
  41                                                 true, alignmentModel.getTokenSet().getGapToken()));
  42         }
  43
  44
  45         @Override
  46         protected void doExecute2(ExecutionEvent event, AlignmentEditor editor, AlignmentArea focusedArea) {
  47                 SelectionModel selection = focusedArea.getSelection();
  48                 String clipboardText = (String)editor.CLIPBOARD.getContents(TextTransfer.getInstance());
  49                 if (clipboardText != null) {
  50                         List<String> lines = new ArrayList<String>();
  51                         Scanner scanner = new Scanner(clipboardText);
  52                         try {
  53                                 while (scanner.hasNext()) {
  54                                         lines.add(scanner.nextLine());
  55                                 }
  56                                 if (lines.get(lines.size() - 1).equals("")) {
  57                                         lines.remove(lines.size() - 1);
  58                                 }
  59                         }
  60                         finally {
  61                                 scanner.close();
  62                         }
  63
  64                         if (!lines.isEmpty()) { //TODO Can lines be empty? (Can an empty string "" be copied to the clipboard?)
  65                                 if (selection.getCursorHeight() == 1) {  // If the consensus sequence is focused, this is the only possible case.
  66                                         String sequenceID = focusedArea.getSequenceOrder().idByIndex(selection.getCursorRow());
  67                                         if (lines.size() == 1) {
  68                                                 pasteString(focusedArea, sequenceID, lines.get(0));
  69                                         }
  70                                         else {
  71                                                 MessageDialog dialog = new MessageDialog(HandlerUtil.getActiveWorkbenchWindow(event).getShell(),  //TODO Can the window be null?
  72                                                                 "Pasting multiple lines", null,
  73                                                                 "The text to be pasted contains mutlitple lines (" + lines.size() +
  74                                                                 ") although the current cursor height is one. What do you want to do?",
  75                                                                 MessageDialog.QUESTION,
  76                                                                 new String[]{"Ingnore line breaks and paste as one sequence",
  77                                                                                 "Only paste the first line from the clipboard", "Cancel"},
  78                                                                 0);
  79                                                 //TODO Does the dialog have to be disposed in some way?
  80
  81                                                 switch (dialog.open()) {
  82                                                         case 0:  // Paste all lines in one sequence.
  83                                                                 pasteString(focusedArea, sequenceID, clipboardText);
  84                                                                 break;
  85                                                         case 1:  // Paste only first line.
  86                                                                 pasteString(focusedArea, sequenceID, lines.get(0));
  87                                                                 break;
  88                                                 }
  89                                         }
  90                                 }
  91                                 else {
  92                                         if (selection.getCursorHeight() == lines.size()) {
  93                                                 SequenceOrder order = focusedArea.getSequenceOrder();
  94                                                 for (int i = 0; i < selection.getCursorHeight(); i++) {
  95                                                         pasteString(focusedArea, order.idByIndex(selection.getCursorRow() + i), lines.get(i));  // Multiple calls of deleteSelection() in here are unnecessary, but should have no effect.
  96                                                 }
  97                                         }
  98                                         else {
  99                                                 MessageDialog.openError(HandlerUtil.getActiveWorkbenchWindow(event).getShell(),  //TODO Can the window be null?
 100                                                                 "Unable to paste multiple lines",
 101                                                                 "The current cursor height (" + selection.getCursorHeight() +
 102                                                                 ") does not match the number of lines to be pasted (" + lines.size() + ")." +
 103                                                                 System.getProperty("line.separator") + System.getProperty("line.separator") +
 104                                                                 "You can either change the cursor height accordingly or set the cursor height to one "
 105                                                                 + "allowing you to paste all lines from the clipboad into one sequence.");
 106                                         }
 107                                 }
 108                         }
 109                 }
 110         }
 111
 112
 113         @Override
 114         public boolean isEnabled() {
 115                 AlignmentEditor editor = getActiveAlignmentEditor();
 116                 if (editor != null) {
 117                         AlignmentArea focusedArea = editor.getFocusedArea();
 118                         return (focusedArea != null);
 119                 }
 120                 else {
 121                         return false;
 122                 }
 123         }
 124
 125
 126         @Override
 127         public void updateElement(UIElement element, @SuppressWarnings("rawtypes") Map parameters) {
 128                 setBaseEnabled(isEnabled());
 129     }
 130 }