- });\r
-\r
- windowMenu.add(menuItem);\r
- }\r
-\r
-\r
-\r
- public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- JFileChooser chooser = new JFileChooser(jalview.bin.Cache.LAST_DIRECTORY);\r
- chooser.setDialogTitle("Open local file");\r
- chooser.setToolTipText("Open");\r
- int value = chooser.showOpenDialog(this);\r
- if(value == JFileChooser.APPROVE_OPTION)\r
- {\r
- String choice = chooser.getSelectedFile().getPath();\r
- jalview.bin.Cache.LAST_DIRECTORY = choice;\r
- String format = IdentifyFile.Identify(choice, "File");\r
- LoadFile(choice, "File", format);\r
- }\r
- }\r
-\r
- public void LoadFile(String file, String protocol, String format)\r
- {\r
- SequenceI [] sequences = null;\r
-\r
- if (FormatProperties.contains(format))\r
- sequences = FormatAdapter.read(file, protocol, format);\r
-\r
- if (sequences != null)\r
- {\r
- AlignFrame af = new AlignFrame(new Alignment(sequences));\r
- addInternalFrame(af, file, 700, 500);\r
- af.statusBar.setText("Successfully loaded file " + file);\r
-\r
-\r
- }\r
- else\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop, "Couldn't open file.\n"\r
- + "Formats currently supported are\n"\r
- + "Fasta, MSF, Clustal, BLC, PIR, MSP or PFAM"\r
- ,"Error loading file",\r
- JOptionPane.WARNING_MESSAGE);\r
-\r
- }\r
-\r
- public void inputURLMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- String url = JOptionPane.showInternalInputDialog(Desktop.desktop,"Enter url of input file",\r
- "Input alignment from URL",\r
- JOptionPane.QUESTION_MESSAGE);\r
- if (url == null)\r
- return;\r
-\r
- String format = IdentifyFile.Identify(url, "URL");\r
-\r
- System.out.println(format +" format");\r
- if (format.equals("URL NOT FOUND"))\r
- {\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop,"Couldn't locate " + url,\r
- "URL not found",\r
- JOptionPane.WARNING_MESSAGE);\r
- return;\r
- }\r
-\r
- LoadFile(url, "URL", format);\r
- }\r
-\r
- public void inputTextboxMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(true);\r
- int accept = JOptionPane.showInternalOptionDialog(Desktop.desktop, cap, "Cut & paste Alignment File",\r
- JOptionPane.YES_NO_CANCEL_OPTION,\r
- JOptionPane.PLAIN_MESSAGE,\r
- null,\r
- new Object[]{"Accept", "Cancel", }, null);\r
-\r
-\r
- if(accept == JOptionPane.YES_OPTION)\r
- {\r
- String format = IdentifyFile.Identify(cap.getText(), "Paste");\r
- SequenceI [] sequences = null;\r
-\r
- if (FormatProperties.contains( format ))\r
- sequences = FormatAdapter.read(cap.getText(), "Paste", format);\r
-\r
-\r
- if(sequences!=null)\r
+\r
+\r
+ openFrameCount++;\r
+\r
+ frame.setVisible(true);\r
+ frame.setClosable(true);\r
+ frame.setResizable(resizable);\r
+ frame.setMaximizable(resizable);\r
+ frame.setIconifiable(resizable);\r
+ frame.setFrameIcon(null);\r
+\r
+ if (frame.getX()<1 && frame.getY()<1)\r
+ {\r
+ frame.setLocation(xOffset * openFrameCount, yOffset * ((openFrameCount-1)%10)+yOffset);\r
+ }\r
+\r
+ final JMenuItem menuItem = new JMenuItem(title);\r
+ frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
+ {\r
+ public void internalFrameActivated(javax.swing.event.\r
+ InternalFrameEvent evt)\r
+ {\r
+ JInternalFrame itf = desktop.getSelectedFrame();\r
+ if (itf != null)\r
+ itf.requestFocus();\r
+\r
+ }\r
+\r
+ public void internalFrameClosed(\r
+ javax.swing.event.InternalFrameEvent evt)\r
+ {\r
+ openFrameCount--;\r
+ windowMenu.remove(menuItem);\r
+ JInternalFrame itf = desktop.getSelectedFrame();\r
+ if (itf != null)\r
+ itf.requestFocus();\r
+ }\r
+ ;\r
+ });\r
+\r
+ menuItem.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ try\r
+ {\r
+ frame.setSelected(true);\r
+ frame.setIcon(false);\r
+ }\r
+ catch (java.beans.PropertyVetoException ex)\r
+ {\r
+\r
+ }\r
+ }\r
+ });\r
+\r
+ windowMenu.add(menuItem);\r
+\r
+ desktop.add(frame);\r
+ frame.toFront();\r
+ try{\r
+ frame.setSelected(true);\r
+ frame.requestFocus();\r
+ }catch(java.beans.PropertyVetoException ve)\r
+ {}\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
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\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
+ for (int i = 0; i < files.size(); i++)\r
+ {\r
+ String file = files.get(i).toString();\r
+ String protocol = FormatAdapter.FILE;\r
+ String format = null;\r
+\r
+ if (file.endsWith(".jar"))\r
+ {\r
+ format = "Jalview";\r
+\r
+ }\r
+ else\r
+ {\r
+ format = new IdentifyFile().Identify(file,\r
+ protocol);\r
+ }\r
+ LoadFile(file, protocol, format);\r
+ }\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
+ "LAST_DIRECTORY"),\r
+ new String[]\r
+ {\r
+ "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",\r
+ "jar"\r
+ },\r
+ new String[]\r
+ {\r
+ "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"\r
+ }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));\r
+\r
+ chooser.setFileView(new JalviewFileView());\r
+ chooser.setDialogTitle("Open local file");\r
+ chooser.setToolTipText("Open");\r
+\r
+ int value = chooser.showOpenDialog(this);\r
+\r
+ if (value == JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
+ String choice = chooser.getSelectedFile().getPath();\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
+ chooser.getSelectedFile().getParent());\r
+\r
+ String format = null;\r
+ if (chooser.getSelectedFormat().equals("Jalview"))\r
+ {\r
+ format = "Jalview";\r
+ }\r
+ else\r
+ {\r
+ format = new IdentifyFile().Identify(choice, FormatAdapter.FILE);\r
+ }\r
+\r
+ jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format);\r
+ LoadFile(choice, FormatAdapter.FILE, format);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param file DOCUMENT ME!\r
+ * @param protocol DOCUMENT ME!\r
+ * @param format DOCUMENT ME!\r
+ */\r
+ public void LoadFile(String file, String protocol, String format)\r
+ {\r
+ FileLoader fileLoader = new FileLoader();\r
+ fileLoader.LoadFile(file, protocol, format);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void inputURLMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ // This construct allows us to have a wider textfield\r
+ // for viewing\r
+ JLabel label = new JLabel("Enter URL of Input File");\r
+ JTextField textinput = new JTextField("http://www.", 40);\r
+ JPanel panel = new JPanel(new BorderLayout());\r
+ panel.add(label, BorderLayout.NORTH);\r
+ panel.add(textinput, BorderLayout.SOUTH);\r
+\r
+\r
+ int reply = JOptionPane.showInternalConfirmDialog(desktop,\r
+ panel, "Input Alignment From URL",\r
+ JOptionPane.OK_CANCEL_OPTION );\r
+\r
+\r
+ if (reply != JOptionPane.OK_OPTION )\r
+ {\r
+ return;\r
+ }\r
+\r
+ String url = textinput.getText();\r
+\r
+ if (url.toLowerCase().endsWith(".jar"))\r
+ {\r
+ jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", "Jalview");\r
+ new Jalview2XML().LoadJalviewAlign(url);\r
+ }\r
+ else\r
+ {\r
+\r
+ String format = new IdentifyFile().Identify(url, FormatAdapter.URL);\r
+\r
+ if (format.equals("URL NOT FOUND"))\r
+ {\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ "Couldn't locate " + url,\r
+ "URL not found",\r
+ JOptionPane.WARNING_MESSAGE);\r
+\r
+ return;\r
+ }\r
+\r
+ LoadFile(url, FormatAdapter.URL, format);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void inputTextboxMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
+ cap.setForInput();\r
+ Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500);\r
+ }\r
+\r
+ /*\r
+ * Exit the program\r
+ */\r
+ public void quit()\r
+ {\r
+ jalview.bin.Cache.setProperty("SCREEN_X", getBounds().x + "");\r
+ jalview.bin.Cache.setProperty("SCREEN_Y", getBounds().y + "");\r
+ jalview.bin.Cache.setProperty("SCREEN_WIDTH", getWidth() + "");\r
+ jalview.bin.Cache.setProperty("SCREEN_HEIGHT", getHeight() + "");\r
+ System.exit(0);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void aboutMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ StringBuffer message = new StringBuffer("JalView version " +\r
+ jalview.bin.Cache.getProperty(\r
+ "VERSION") +\r
+ "; last updated: " +\r
+ jalview.bin.\r
+ Cache.getDefault("BUILD_DATE", "unknown"));\r
+\r
+ if (!jalview.bin.Cache.getProperty("LATEST_VERSION").equals(\r
+ jalview.bin.Cache.getProperty("VERSION")))\r