/*
* Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
import java.awt.datatransfer.*;
import java.awt.dnd.*;
import java.awt.event.*;
+import java.util.*;
import javax.swing.*;
* @version $Revision$
*/
public class Desktop extends jalview.jbgui.GDesktop
- implements DropTargetListener
+ implements DropTargetListener, ClipboardOwner
{
/** DOCUMENT ME!! */
+ public static Desktop instance;
public static JDesktopPane desktop;
static int openFrameCount = 0;
static final int xOffset = 30;
public static Object [] jalviewClipboard;
+ static int fileLoadingCount= 0;
/**
* Creates a new Desktop object.
*/
public Desktop()
{
+ instance = this;
+ doVamsasClientCheck();
Image image = null;
-
try
{
java.net.URL url = getClass().getResource("/images/logo.gif");
setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
desktop = new JDesktopPane();
desktop.setBackground(Color.white);
- setContentPane(desktop);
+ getContentPane().setLayout(new BorderLayout());
+ getContentPane().add(desktop, BorderLayout.CENTER);
desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
// This line prevents Windows Look&Feel resizing all new windows to maximum
addInternalFrame(frame, "", 750, 160, false);
discoverer=new jalview.ws.Discoverer(); // Only gets started if gui is displayed.
+ }
+
+ private void doVamsasClientCheck() {
+ if (jalview.bin.Cache.vamsasJarsPresent()) {
+ VamsasMenu.setVisible(true);
+ vamsasLoad.setVisible(true);
+ }
}
{}
}
+ public void lostOwnership(Clipboard clipboard, Transferable contents)
+ {
+ Desktop.jalviewClipboard = null;
+ }
+
public void dragEnter(DropTargetDragEvent evt)
{}
for (int i = 0; i < files.size(); i++)
{
String file = files.get(i).toString();
- String protocol = "File";
+ String protocol = FormatAdapter.FILE;
String format = null;
if (file.endsWith(".jar"))
}
else
{
- format = jalview.io.IdentifyFile.Identify(file,
+ format = new IdentifyFile().Identify(file,
protocol);
}
- LoadFile(file, protocol, format);
+
+
+ new FileLoader().LoadFile(file, protocol, format);
+
}
}
catch (Exception ex)
*
* @param e DOCUMENT ME!
*/
- public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)
+ public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)
{
JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
"LAST_DIRECTORY"),
String format = null;
if (chooser.getSelectedFormat().equals("Jalview"))
{
- format = "Jalview";
+ format = "Jalview";
}
else
{
- format = IdentifyFile.Identify(choice, "File");
+ format = new IdentifyFile().Identify(choice, FormatAdapter.FILE);
}
- jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format);
- LoadFile(choice, "File", format);
+ if (viewport != null)
+ new FileLoader().LoadFile(viewport, choice, FormatAdapter.FILE, format);
+ else
+ new FileLoader().LoadFile(choice, FormatAdapter.FILE, format);
}
}
- /**
- * DOCUMENT ME!
- *
- * @param file DOCUMENT ME!
- * @param protocol DOCUMENT ME!
- * @param format DOCUMENT ME!
- */
- public void LoadFile(String file, String protocol, String format)
- {
- FileLoader fileLoader = new FileLoader();
- fileLoader.LoadFile(file, protocol, format);
- }
+
/**
* DOCUMENT ME!
*
* @param e DOCUMENT ME!
*/
- public void inputURLMenuItem_actionPerformed(ActionEvent e)
+ public void inputURLMenuItem_actionPerformed(AlignViewport viewport)
{
// This construct allows us to have a wider textfield
// for viewing
JLabel label = new JLabel("Enter URL of Input File");
- JTextField textinput = new JTextField("http://www.", 40);
- JPanel panel = new JPanel(new BorderLayout());
- panel.add(label, BorderLayout.NORTH);
- panel.add(textinput, BorderLayout.SOUTH);
+ final JComboBox history = new JComboBox();
+
+ JPanel panel = new JPanel(new GridLayout(2,1));
+ panel.add(label);
+ panel.add(history);
+ history.setPreferredSize(new Dimension(400,20));
+ history.setEditable(true);
+ history.addItem("http://www.");
+
+ String historyItems = jalview.bin.Cache.getProperty("RECENT_URL");
+ StringTokenizer st;
+
+ if (historyItems != null)
+ {
+ st = new StringTokenizer(historyItems, "\t");
+
+ while (st.hasMoreTokens())
+ {
+ history.addItem(st.nextElement());
+ }
+ }
int reply = JOptionPane.showInternalConfirmDialog(desktop,
panel, "Input Alignment From URL",
return;
}
- String url = textinput.getText();
+ String url = history.getSelectedItem().toString();
if (url.toLowerCase().endsWith(".jar"))
{
- jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", "Jalview");
- Jalview2XML.LoadJalviewAlign(url);
+ if (viewport != null)
+ new FileLoader().LoadFile(viewport, url, FormatAdapter.URL, "Jalview");
+ else
+ new FileLoader().LoadFile(url, FormatAdapter.URL, "Jalview");
}
else
{
-
- String format = IdentifyFile.Identify(url, "URL");
+ String format = new IdentifyFile().Identify(url, FormatAdapter.URL);
if (format.equals("URL NOT FOUND"))
{
return;
}
- LoadFile(url, "URL", format);
+ if (viewport != null)
+ new FileLoader().LoadFile(viewport, url, FormatAdapter.URL, format);
+ else
+ new FileLoader().LoadFile(url, FormatAdapter.URL, format);
}
}
*
* @param e DOCUMENT ME!
*/
- public void inputTextboxMenuItem_actionPerformed(ActionEvent e)
+ public void inputTextboxMenuItem_actionPerformed(AlignViewport viewport)
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
- cap.setForInput();
+ cap.setForInput(viewport);
Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500);
}
"\nFor all issues relating to Jalview, email help@jalview.org" +
"\n\nIf you use JalView, please cite:" +
"\n\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"" +
- "\nBioinformatics, 2004 12;426-7.");
+ "\nBioinformatics, 2004 20;426-7.");
JOptionPane.showInternalMessageDialog(Desktop.desktop,
}
}
+ public void closeAll_actionPerformed(ActionEvent e)
+ {
+ JInternalFrame [] frames = desktop.getAllFrames();
+ for(int i=0; i<frames.length; i++)
+ {
+ try{
+ frames[i].setClosed(true);
+ }catch(java.beans.PropertyVetoException ex){}
+ }
+ }
+
+
/**
* DOCUMENT ME!
*
{
java.io.File choice = chooser.getSelectedFile();
jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
- Jalview2XML.SaveState(choice);
+ new Jalview2XML().SaveState(choice);
}
}
String choice = chooser.getSelectedFile().getAbsolutePath();
jalview.bin.Cache.setProperty("LAST_DIRECTORY",
chooser.getSelectedFile().getParent());
- Jalview2XML.LoadJalviewAlign(choice);
+ new Jalview2XML().LoadJalviewAlign(choice);
}
}
public void inputSequence_actionPerformed(ActionEvent e)
{
- SequenceFetcher sf = new SequenceFetcher(null);
+ new SequenceFetcher(null);
+ }
+
+ JPanel progressPanel;
+
+ public void startLoading(final String fileName)
+ {
+ if (fileLoadingCount == 0)
+ {
+ progressPanel = new JPanel(new BorderLayout());
+ JProgressBar progressBar = new JProgressBar();
+ progressBar.setIndeterminate(true);
+
+ progressPanel.add(new JLabel("Loading File: " + fileName + " "),
+ BorderLayout.WEST);
+
+ progressPanel.add(progressBar, BorderLayout.CENTER);
+
+ instance.getContentPane().add(progressPanel, BorderLayout.SOUTH);
+ }
+ fileLoadingCount++;
+ validate();
+ }
+
+ public void stopLoading()
+ {
+ fileLoadingCount--;
+ if (fileLoadingCount < 1)
+ {
+ if(progressPanel!=null)
+ {
+ this.getContentPane().remove(progressPanel);
+ progressPanel = null;
+ }
+ fileLoadingCount = 0;
+ }
+ validate();
+ }
+
+ public static int getViewCount(String viewId)
+ {
+ int count = 0;
+ JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+ for (int t = 0; t < frames.length; t++)
+ {
+ if (frames[t] instanceof AlignFrame)
+ {
+ AlignFrame af = (AlignFrame) frames[t];
+ for(int a=0; a<af.alignPanels.size(); a++)
+ {
+ if(viewId.equals(
+ ((AlignmentPanel)af.alignPanels.elementAt(a)).av.getSequenceSetId() )
+ )
+ count ++;
+ }
+ }
+ }
+
+ return count;
+ }
+
+ public void explodeViews(AlignFrame af)
+ {
+ int size = af.alignPanels.size();
+ if(size<2)
+ return;
+
+ for(int i=0; i<size; i++)
+ {
+ AlignmentPanel ap = (AlignmentPanel)af.alignPanels.elementAt(i);
+ AlignFrame newaf = new AlignFrame(ap);
+ if(ap.av.explodedPosition!=null)
+ newaf.setBounds(ap.av.explodedPosition);
+
+ ap.av.gatherViewsHere = false;
+
+ addInternalFrame(newaf, af.getTitle(),
+ AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ }
+
+ af.alignPanels.clear();
+ af.closeMenuItem_actionPerformed(true);
+
+ }
+
+ public void gatherViews(AlignFrame source)
+ {
+ source.viewport.gatherViewsHere = true;
+ source.viewport.explodedPosition = source.getBounds();
+ JInternalFrame[] frames = desktop.getAllFrames();
+ String viewId = source.viewport.sequenceSetID;
+
+ for (int t = 0; t < frames.length; t++)
+ {
+ if (frames[t] instanceof AlignFrame && frames[t] != source)
+ {
+ AlignFrame af = (AlignFrame) frames[t];
+ boolean gatherThis = false;
+ for (int a = 0; a < af.alignPanels.size(); a++)
+ {
+ AlignmentPanel ap = (AlignmentPanel) af.alignPanels.elementAt(a);
+ if (viewId.equals(ap.av.getSequenceSetId()))
+ {
+ gatherThis = true;
+ ap.av.gatherViewsHere = false;
+ ap.av.explodedPosition = af.getBounds();
+ source.addAlignmentPanel(ap, false);
+ }
+ }
+
+ if (gatherThis)
+ {
+ af.alignPanels.clear();
+ af.closeMenuItem_actionPerformed(true);
+ }
+ }
+ }
+
+ }
+
+ jalview.gui.VamsasClient v_client=null;
+ public void vamsasLoad_actionPerformed(ActionEvent e)
+ {
+ if (v_client==null) {
+ // Start a session.
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+ getProperty("LAST_DIRECTORY"));
+
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle("Load Vamsas file");
+ chooser.setToolTipText("Import");
+
+ int value = chooser.showOpenDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ v_client = new jalview.gui.VamsasClient(this,
+ chooser.getSelectedFile());
+ this.vamsasLoad.setText("Session Update");
+ this.vamsasStop.setVisible(true);
+ v_client.initial_update();
+ v_client.startWatcher();
+ }
+ } else {
+ // store current data in session.
+ v_client.push_update();
+ }
+ }
+ public void vamsasStop_actionPerformed(ActionEvent e) {
+ if (v_client!=null) {
+ v_client.end_session();
+ v_client=null;
+ this.vamsasStop.setVisible(false);
+ this.vamsasLoad.setText("Start Vamsas Session...");
+ }
+ }
+ /**
+ * hide vamsas user gui bits when a vamsas document event is being handled.
+ * @param b true to hide gui, false to reveal gui
+ */
+ public void setVamsasUpdate(boolean b) {
+ jalview.bin.Cache.log.debug("Setting gui for Vamsas update "+(b ? "in progress" : "finished"));
+ vamsasLoad.setVisible(!b);
+ vamsasStop.setVisible(!b);
+
}
}
git://source.jalview.org / jalview.git / blobdiff