+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ new HTMLOutput(viewport,\r
+ alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),\r
+ alignPanel.seqPanel.seqCanvas.getFeatureRenderer());\r
+ }\r
+\r
+ public void createImageMap(File file, String image)\r
+ {\r
+ alignPanel.makePNGImageMap(file, image);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void createPNG(File f)\r
+ {\r
+ alignPanel.makePNG(f);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void createEPS(File f)\r
+ {\r
+ alignPanel.makeEPS(f);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void printMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ //Putting in a thread avoids Swing painting problems\r
+ PrintThread thread = new PrintThread();\r
+ thread.start();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void closeMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ try\r
+ {\r
+ PaintRefresher.components.remove(viewport.alignment);\r
+ this.setClosed(true);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ void updateEditMenuBar()\r
+ {\r
+ if (historyList.size() > 0)\r
+ {\r
+ undoMenuItem.setEnabled(true);\r
+\r
+ HistoryItem hi = (HistoryItem) historyList.peek();\r
+ undoMenuItem.setText("Undo " + hi.getDescription());\r
+ }\r
+ else\r
+ {\r
+ undoMenuItem.setEnabled(false);\r
+ undoMenuItem.setText("Undo");\r
+ }\r
+\r
+ if (redoList.size() > 0)\r
+ {\r
+ redoMenuItem.setEnabled(true);\r
+\r
+ HistoryItem hi = (HistoryItem) redoList.peek();\r
+ redoMenuItem.setText("Redo " + hi.getDescription());\r
+ }\r
+ else\r
+ {\r
+ redoMenuItem.setEnabled(false);\r
+ redoMenuItem.setText("Redo");\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param hi DOCUMENT ME!\r
+ */\r
+ public void addHistoryItem(HistoryItem hi)\r
+ {\r
+ historyList.push(hi);\r
+ updateEditMenuBar();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void undoMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ HistoryItem hi = (HistoryItem) historyList.pop();\r
+ redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,\r
+ HistoryItem.HIDE));\r
+ restoreHistoryItem(hi);\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void redoMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ HistoryItem hi = (HistoryItem) redoList.pop();\r
+ restoreHistoryItem(hi);\r
+ updateEditMenuBar();\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
+ }\r
+\r
+ // used by undo and redo\r
+ void restoreHistoryItem(HistoryItem hi)\r
+ {\r
+ if (hi.getType() == HistoryItem.SORT)\r
+ {\r
+ for (int i = 0; i < hi.getSequences().size(); i++)\r
+ {\r
+ viewport.alignment.getSequences().setElementAt(hi.getSequences()\r
+ .elementAt(i),\r
+ i);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ for (int i = 0; i < hi.getSequences().size(); i++)\r
+ {\r
+ SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);\r
+\r
+ if (restore.getLength() == 0)\r
+ {\r
+ restore.setSequence(hi.getHidden().elementAt(i).toString());\r
+ viewport.alignment.getSequences().insertElementAt(restore,\r
+ hi.getAlignIndex(i));\r
+ }\r
+ else\r
+ {\r
+ restore.setSequence(hi.getHidden().elementAt(i).toString());\r
+ }\r
+ }\r
+\r
+ if (hi.getType() == HistoryItem.PASTE)\r
+ {\r
+ for (int i = viewport.alignment.getHeight() - 1;\r
+ i > (hi.getSequences().size() - 1); i--)\r
+ {\r
+ viewport.alignment.deleteSequence(i);\r
+ }\r
+ }\r
+ }\r
+\r
+ updateEditMenuBar();\r
+\r
+ viewport.firePropertyChange("alignment", null,\r
+ viewport.getAlignment().getSequences());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param up DOCUMENT ME!\r
+ */\r
+ public void moveSelectedSequences(boolean up)\r
+ {\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
+\r
+ if (sg == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ if (up)\r
+ {\r
+ for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
+ {\r
+ SequenceI seq = viewport.alignment.getSequenceAt(i);\r
+\r
+ if (!sg.sequences.contains(seq))\r
+ {\r
+ continue;\r
+ }\r
+\r
+ SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
+\r
+ if (sg.sequences.contains(temp))\r
+ {\r
+ continue;\r
+ }\r
+\r
+ viewport.alignment.getSequences().setElementAt(temp, i);\r
+ viewport.alignment.getSequences().setElementAt(seq, i - 1);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
+ {\r
+ SequenceI seq = viewport.alignment.getSequenceAt(i);\r
+\r
+ if (!sg.sequences.contains(seq))\r
+ {\r
+ continue;\r
+ }\r
+\r
+ SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
+\r
+ if (sg.sequences.contains(temp))\r
+ {\r
+ continue;\r
+ }\r
+\r
+ viewport.alignment.getSequences().setElementAt(temp, i);\r
+ viewport.alignment.getSequences().setElementAt(seq, i + 1);\r
+ }\r
+ }\r
+\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ public void lostOwnership(Clipboard clipboard, Transferable contents)\r
+ {\r
+ Desktop.jalviewClipboard = null;\r
+ }\r
+\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void copy_actionPerformed(ActionEvent e)\r
+ {\r
+ if (viewport.getSelectionGroup() == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
+\r
+ Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
+\r
+ Hashtable orderedSeqs = new Hashtable();\r
+ SequenceI[] seqs = new SequenceI[sg.getSize()];\r
+\r
+ for (int i = 0; i < sg.getSize(); i++)\r
+ {\r
+ SequenceI seq = sg.getSequenceAt(i);\r
+ int index = viewport.alignment.findIndex(seq);\r
+ orderedSeqs.put(index + "", seq);\r
+ }\r
+\r
+ int index = 0, startRes, endRes;\r
+ char ch;\r
+\r
+ for (int i = 0; i < sg.getSize(); i++)\r
+ {\r
+ SequenceI seq = null;\r
+\r
+ while (seq == null)\r
+ {\r
+ if (orderedSeqs.containsKey(index + ""))\r
+ {\r
+ seq = (SequenceI) orderedSeqs.get(index + "");\r
+ index++;\r
+\r
+ break;\r
+ }\r
+ else\r
+ {\r
+ index++;\r
+ }\r
+ }\r
+\r
+ //FIND START RES\r
+ //Returns residue following index if gap\r
+ startRes = seq.findPosition(sg.getStartRes());\r
+\r
+ //FIND END RES\r
+ //Need to find the residue preceeding index if gap\r
+ endRes = 0;\r
+\r
+ for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)\r
+ {\r
+ ch = seq.getCharAt(j);\r
+ if (!jalview.util.Comparison.isGap( (ch)))\r
+ {\r
+ endRes++;\r
+ }\r
+ }\r
+\r
+ if (endRes > 0)\r
+ {\r
+ endRes += seq.getStart() - 1;\r
+ }\r
+\r
+ seqs[i] = new Sequence(seq.getName(),\r
+ seq.getSequence(sg.getStartRes(), sg.getEndRes() + 1),\r
+ startRes,\r
+ endRes);\r
+ seqs[i].setDescription(seq.getDescription());\r
+ seqs[i].setDBRef(seq.getDBRef());\r
+ seqs[i].setSequenceFeatures(seq.getSequenceFeatures());\r
+ seqs[i].setDatasetSequence(seq.getDatasetSequence());\r
+\r
+ }\r
+\r
+ FastaFile ff = new FastaFile();\r
+ ff.addJVSuffix( viewport.showJVSuffix );\r
+ c.setContents(new StringSelection( ff.print(seqs)), this);\r
+ Desktop.jalviewClipboard = new Object[]{seqs, viewport.alignment.getDataset()};\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void pasteNew_actionPerformed(ActionEvent e)\r
+ {\r
+ paste(true);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void pasteThis_actionPerformed(ActionEvent e)\r
+ {\r
+ addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,\r
+ HistoryItem.PASTE));\r
+ paste(false);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param newAlignment DOCUMENT ME!\r
+ */\r
+ void paste(boolean newAlignment)\r
+ {\r
+ try\r
+ {\r
+ Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
+ Transferable contents = c.getContents(this);\r
+\r
+ if (contents == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ String str = (String) contents.getTransferData(DataFlavor.stringFlavor);\r
+ if(str.length()<1)\r
+ return;\r
+\r
+ String format = IdentifyFile.Identify(str, "Paste");\r
+ SequenceI[] sequences;\r
+\r
+ if(Desktop.jalviewClipboard!=null)\r
+ {\r
+ // The clipboard was filled from within Jalview, we must use the sequences\r
+ // And dataset from the copied alignment\r
+ sequences = (SequenceI[])Desktop.jalviewClipboard[0];\r
+ }\r
+ else\r
+ {\r
+ sequences = new FormatAdapter().readFile(str, "Paste", format);\r
+ }\r
+\r
+ if (newAlignment)\r
+ {\r
+\r
+ Alignment alignment = new Alignment(sequences);\r
+\r
+ if(Desktop.jalviewClipboard!=null)\r
+ alignment.setDataset( (Alignment)Desktop.jalviewClipboard[1] );\r
+ else\r
+ alignment.setDataset( null );\r
+\r