- }\r
-\r
- }catch(Exception ex){ex.printStackTrace();}\r
- }\r
-\r
-\r
- public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"),\r
- new String[]{"fa, fasta, fastq", "aln", "pfam", "msf", "pir","blc","jar"},\r
- new String[]{"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
- int value = chooser.showOpenDialog(this);\r
- if(value == JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- String choice = chooser.getSelectedFile().getPath();\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser.getSelectedFile().getParent());\r
- if(chooser.getSelectedFormat().equals("Jalview"))\r
- {\r
- jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", "Jalivew");\r
- Jalview2XML.LoadJalviewAlign(choice);\r
- }\r
- else\r
- {\r
- String format = IdentifyFile.Identify(choice, "File");\r
- jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format);\r
- LoadFile(choice, "File", format);\r
- }\r
- }\r
- }\r
-\r
- public void LoadFile(String file, String protocol, String format)\r
- {\r
- LoadingThread loader = new LoadingThread(file, protocol, format);\r
- loader.start();\r
- }\r
-\r
- class LoadingThread extends Thread\r
- {\r
- String file, protocol, format;\r
-\r
- public LoadingThread(String file, String protocol, String format)\r
- {\r
- this.file = file;\r
- this.protocol = protocol;\r
- this.format = format;\r
- }\r
- public void run()\r
- {\r
- SequenceI [] sequences = null;\r
-\r
- if (FormatAdapter.formats.contains(format))\r
- sequences = FormatAdapter.readFile(file, protocol, format);\r
-\r
- if (sequences != null && sequences.length>0)\r
- {\r
- AlignFrame af = new AlignFrame(new Alignment(sequences));\r
- addInternalFrame(af, file, AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT);\r
- af.currentFileFormat = format;\r
- af.statusBar.setText("Successfully loaded file " + file);\r
- try{\r
- af.setMaximum(Preferences.showFullscreen);\r
- }catch(Exception ex){}\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, and PFAM" // JBPNote - message should be generated through FormatAdapter!\r
- ,"Error loading file",\r
- JOptionPane.WARNING_MESSAGE);\r
-\r
- }\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
- null, null,\r
- "http://www.").toString();\r
- if (url == null)\r
- return;\r
-\r
- String format = IdentifyFile.Identify(url, "URL");\r
-\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();\r
- cap.setForInput();\r
- Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500);\r
- }\r