import jalview.jbgui.*;\r
import jalview.schemes.*;\r
import jalview.ws.*;\r
-import javax.swing.event.AncestorEvent;\r
+import java.awt.dnd.*;\r
+\r
\r
/**\r
* DOCUMENT ME!\r
* @version $Revision$\r
*/\r
public class AlignFrame\r
- extends GAlignFrame implements ClipboardOwner\r
+ extends GAlignFrame implements ClipboardOwner, DropTargetListener\r
{\r
/** DOCUMENT ME!! */\r
public static final int NEW_WINDOW_WIDTH = 700;\r
viewport = new AlignViewport(al);\r
viewports.add(viewport);\r
\r
+ this.setDropTarget(new java.awt.dnd.DropTarget(this, this));\r
\r
if(viewport.vconsensus==null)\r
{\r
public void setGUINucleotide(boolean nucleotide)\r
{\r
showTranslation.setVisible( nucleotide );\r
- sequenceFeatures.setVisible(!nucleotide );\r
- featureSettings.setVisible( !nucleotide );\r
+ //sequenceFeatures.setVisible(!nucleotide );\r
+ //featureSettings.setVisible( !nucleotide );\r
conservationMenuItem.setVisible( !nucleotide );\r
modifyConservation.setVisible( !nucleotide );\r
\r
}\r
\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param String DOCUMENT ME!\r
- */\r
-\r
- public void parseGroupsFile(String file)\r
- {\r
- try\r
- {\r
- BufferedReader in = new BufferedReader(new FileReader(file));\r
- SequenceI seq = null;\r
- String line, type, desc, token;\r
-\r
- int index, start, end;\r
- StringTokenizer st;\r
- SequenceFeature sf;\r
- FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer();\r
- int lineNo = 0;\r
- while ( (line = in.readLine()) != null)\r
- {\r
- lineNo++;\r
- st = new StringTokenizer(line, "\t");\r
- if (st.countTokens() == 2)\r
- {\r
- type = st.nextToken();\r
- UserColourScheme ucs = new UserColourScheme(st.nextToken());\r
- fr.setColour(type, ucs.findColour("A"));\r
- continue;\r
- }\r
-\r
- while (st.hasMoreElements())\r
- {\r
- desc = st.nextToken();\r
- token = st.nextToken();\r
- if (!token.equals("ID_NOT_SPECIFIED"))\r
- {\r
- index = viewport.alignment.findIndex(viewport.alignment.findName(\r
- token));\r
- st.nextToken();\r
- }\r
- else\r
- {\r
- index = Integer.parseInt(st.nextToken());\r
- }\r
-\r
- start = Integer.parseInt(st.nextToken());\r
- end = Integer.parseInt(st.nextToken());\r
-\r
- seq = viewport.alignment.getSequenceAt(index);\r
- start = seq.findIndex(start) - 1;\r
- end = seq.findIndex(end) - 1;\r
-\r
- type = st.nextToken();\r
-\r
- if (fr.getColour(type) == null)\r
- {\r
- // Probably the old style groups file\r
- UserColourScheme ucs = new UserColourScheme(type);\r
- fr.setColour(type, ucs.findColour("A"));\r
- }\r
-\r
-\r
- sf = new SequenceFeature(type, desc, "", start, end);\r
-\r
- seq.addSequenceFeature(sf);\r
-\r
-\r
- // sg = new SequenceGroup(text, ucs, true, true, false, start, end);\r
- // sg.addSequence(seq, false);\r
-\r
- // viewport.alignment.addGroup(sg);\r
-\r
- }\r
- }\r
-\r
- viewport.showSequenceFeatures = true;\r
-\r
- alignPanel.repaint();\r
-\r
- }\r
- catch (Exception ex)\r
- {\r
- System.out.println("Error parsing groups file: " + ex);\r
- }\r
- }\r
-\r
public void fetchSequence_actionPerformed(ActionEvent e)\r
{\r
new SequenceFetcher(this);\r
newseq.setDatasetSequence(ds);\r
viewport.alignment.getDataset().addSequence(ds);\r
}\r
-\r
+ else\r
+ {\r
+ newseq.setDatasetSequence(sequences[i].getDatasetSequence());\r
+ if(sequences[i].getDatasetSequence().getAnnotation()!=null)\r
+ {\r
+ for(int aa=0; aa<sequences[i].getDatasetSequence().getAnnotation().length; aa++)\r
+ {\r
+ viewport.alignment.addAnnotation(sequences[i].getDatasetSequence().getAnnotation()[aa]);\r
+ }\r
+ }\r
+ }\r
}\r
viewport.setEndSeq(viewport.alignment.getHeight());\r
viewport.alignment.getWidth();\r
}\r
catch (Exception ex)\r
{\r
+ ex.printStackTrace();\r
+ System.out.println("Exception whilst pasting: "+ex);\r
// could be anything being pasted in here\r
}\r
\r
viewport.getColumnSelection().clear();\r
viewport.setSelectionGroup(null);\r
alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);\r
+ alignPanel.idPanel.idCanvas.searchResults = null;\r
alignPanel.annotationPanel.activeRes = null;\r
PaintRefresher.Refresh(null, viewport.alignment);\r
}\r
if(alignPanel.overviewPanel!=null)\r
alignPanel.overviewPanel.updateOverviewImage();\r
\r
+ viewport.alignment.adjustSequenceAnnotations();\r
+\r
alignPanel.repaint();\r
}\r
\r
{\r
addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,\r
HistoryItem.HIDE));\r
-\r
- SequenceI current;\r
- int Width = viewport.getAlignment().getWidth();\r
-\r
- for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
- i++)\r
- {\r
- current = viewport.getAlignment().getSequenceAt(i);\r
-\r
- if (current.getLength() < Width)\r
- {\r
- current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
- }\r
- }\r
-\r
- alignmentChanged();\r
+ if (viewport.getAlignment().padGaps())\r
+ alignmentChanged();\r
}\r
\r
/**\r
new FontChooser(alignPanel);\r
}\r
\r
+ public void smoothFont_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.antiAlias = smoothFont.isSelected();\r
+ alignPanel.annotationPanel.image = null;\r
+ alignPanel.repaint();\r
+ }\r
+\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
{\r
viewport.showSequenceFeatures(sequenceFeatures.isSelected());\r
\r
- if (viewport.showSequenceFeatures)\r
+ if (viewport.showSequenceFeatures && !viewport.alignment.isNucleotide())\r
{\r
new SequenceFeatureFetcher(viewport.\r
alignment,\r
changeColour(new NucleotideColourScheme());\r
}\r
\r
+ public void annotationColour_actionPerformed(ActionEvent e)\r
+ {\r
+ new AnnotationColourChooser(viewport, alignPanel);\r
+ }\r
+\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
viewport = (AlignViewport)viewports.elementAt(index);\r
alignPanel = (AlignmentPanel)alignPanels.elementAt(index);\r
}*/\r
+\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param String DOCUMENT ME!\r
+ */\r
+public boolean parseGroupsFile(String file)\r
+{\r
+ try\r
+ {\r
+ BufferedReader in = new BufferedReader(new FileReader(file));\r
+ SequenceI seq = null;\r
+ String line, type, desc, token;\r
+\r
+ int index, start, end;\r
+ StringTokenizer st;\r
+ SequenceFeature sf;\r
+ int lineNo = 0;\r
+ while ( (line = in.readLine()) != null)\r
+ {\r
+ lineNo++;\r
+ st = new StringTokenizer(line, "\t");\r
+ if (st.countTokens() == 2)\r
+ {\r
+ type = st.nextToken();\r
+ UserColourScheme ucs = new UserColourScheme(st.nextToken());\r
+ alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(type, ucs.findColour("A"));\r
+ continue;\r
+ }\r
+\r
+ while (st.hasMoreElements())\r
+ {\r
+ desc = st.nextToken();\r
+ token = st.nextToken();\r
+ if (!token.equals("ID_NOT_SPECIFIED"))\r
+ {\r
+ index = viewport.alignment.findIndex(viewport.alignment.findName(token));\r
+ st.nextToken();\r
+ }\r
+ else\r
+ {\r
+ index = Integer.parseInt(st.nextToken());\r
+ }\r
+\r
+ start = Integer.parseInt(st.nextToken());\r
+ end = Integer.parseInt(st.nextToken());\r
+\r
+ seq = viewport.alignment.getSequenceAt(index);\r
+\r
+ type = st.nextToken();\r
+\r
+ if (alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(type) == null)\r
+ {\r
+ // Probably the old style groups file\r
+ UserColourScheme ucs = new UserColourScheme(type);\r
+ alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(type, ucs.findColour("A"));\r
+ }\r
+\r
+ sf = new SequenceFeature(type, desc, "", start, end);\r
+\r
+ seq.getDatasetSequence().addSequenceFeature(sf);\r
+ }\r
+ }\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ System.out.println("Error parsing groups file: " + ex);\r
+ return false;\r
+ }\r
+\r
+ viewport.showSequenceFeatures = true;\r
+ alignPanel.repaint();\r
+ return true;\r
+}\r
+\r
+public void dragEnter(DropTargetDragEvent evt)\r
+{}\r
+\r
+public void dragExit(DropTargetEvent evt)\r
+{}\r
+\r
+public void dragOver(DropTargetDragEvent evt)\r
+{}\r
+\r
+public void dropActionChanged(DropTargetDragEvent evt)\r
+{}\r
+\r
+public void drop(DropTargetDropEvent evt)\r
+{\r
+ Transferable t = evt.getTransferable();\r
+ java.util.List files = null;\r
+\r
+ try\r
+ {\r
+ DataFlavor uriListFlavor = new DataFlavor("text/uri-list;class=java.lang.String");\r
+ if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))\r
+ {\r
+ //Works on Windows and MacOSX\r
+ evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);\r
+ files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);\r
+ }\r
+ else if (t.isDataFlavorSupported(uriListFlavor))\r
+ {\r
+ // This is used by Unix drag system\r
+ evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);\r
+ String data = (String) t.getTransferData(uriListFlavor);\r
+ files = new java.util.ArrayList(1);\r
+ for (java.util.StringTokenizer st = new java.util.StringTokenizer(\r
+ data,\r
+ "\r\n");\r
+ st.hasMoreTokens(); )\r
+ {\r
+ String s = st.nextToken();\r
+ if (s.startsWith("#"))\r
+ {\r
+ // the line is a comment (as per the RFC 2483)\r
+ continue;\r
+ }\r
+\r
+ java.net.URI uri = new java.net.URI(s);\r
+ java.io.File file = new java.io.File(uri);\r
+ files.add(file);\r
+ }\r
+ }\r
+ }\r
+ catch (Exception e)\r
+ {\r
+ e.printStackTrace();\r
+ }\r
+\r
+ if (files != null)\r
+ {\r
+ try\r
+ {\r
+ boolean isAnnotation = false;\r
+\r
+ for (int i = 0; i < files.size(); i++)\r
+ {\r
+ String file = files.get(i).toString();\r
+\r
+ isAnnotation = new AnnotationReader().readAnnotationFile(viewport.alignment, file);\r
+\r
+ if( !isAnnotation )\r
+ {\r
+ boolean isGroupsFile = parseGroupsFile(file);\r
+ if (!isGroupsFile)\r
+ {\r
+ String protocol = "File";\r
+ String format = jalview.io.IdentifyFile.Identify(file, protocol);\r
+ SequenceI[] sequences = new FormatAdapter().readFile(file, protocol, format);\r
+\r
+ FastaFile ff = new FastaFile();\r
+ Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
+ c.setContents(new StringSelection(ff.print(sequences)), this);\r
+\r
+ this.paste(false);\r
+\r
+ }\r
+ }\r
+ }\r
+\r
+ if(isAnnotation)\r
+ {\r
+ int height = alignPanel.annotationPanel.adjustPanelHeight();\r
+ alignPanel.annotationScroller.setPreferredSize(\r
+ new Dimension(alignPanel.annotationScroller.getWidth(),\r
+ height));\r
+\r
+ alignPanel.annotationSpaceFillerHolder.setPreferredSize(new Dimension(\r
+ alignPanel.annotationSpaceFillerHolder.getWidth(),\r
+ height));\r
+\r
+ alignPanel.addNotify();\r
+ }\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+}\r
+\r
}\r
git://source.jalview.org / jalview.git / blobdiff