X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=9730eb2d2b15447a7ec2aa80fcb7edb74ff06ff8;hb=e894eb87d40be6e8452d19032ddffe80dad5f804;hp=331e7f53acd348d834572fd50ee2756dca94cd89;hpb=285388369aa586c03977a409a11d44b2ee17be16;p=jalview.git
diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 331e7f5..9730eb2 100755
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -1,329 +1,464 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 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
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-package jalview.bin;
-
-import jalview.appletgui.AlignFrame;
-
-import jalview.datamodel.*;
-
-import jalview.io.*;
-
-import java.applet.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import jalview.appletgui.TreePanel;
-
-
-/**
- * Jalview Applet. Runs in Java 1.18 runtime
- *
- * @author $author$
- * @version $Revision$
- */
-public class JalviewLite extends Applet
-{
- static int lastFrameX = 200;
- static int lastFrameY = 200;
- boolean fileFound = true;
- String file = "No file";
- Button launcher = new Button("Start Jalview");
-
- static AlignFrame currentAlignFrame;
- boolean embedded = false;
-
-
- /**
- * init method for Jalview Applet
- */
- public void init()
- {
- int r = 255;
- int g = 255;
- int b = 255;
- String param = getParameter("RGB");
-
- if (param != null)
- {
- try
- {
- r = Integer.parseInt(param.substring(0, 2), 16);
- g = Integer.parseInt(param.substring(2, 4), 16);
- b = Integer.parseInt(param.substring(4, 6), 16);
- }
- catch (Exception ex)
- {
- r = 255;
- g = 255;
- b = 255;
- }
- }
-
- param = getParameter("label");
- if(param != null)
- launcher.setLabel(param);
-
- this.setBackground(new Color(r, g, b));
-
-
- param = getParameter("features");
- if(param!=null)
- {
- if(param.indexOf("://")==-1)
- param = getCodeBase() + param;
- }
- final String featuresFile = param;
-
- file = getParameter("file");
- if(file.indexOf("://")==-1)
- file = getCodeBase() + file;
-
- final JalviewLite applet = this;
- if(getParameter("embedded")!=null
- && getParameter("embedded").equalsIgnoreCase("true"))
- {
- embedded = true;
- LoadingThread loader = new LoadingThread(file,
- "URL",
- featuresFile,
- applet);
- loader.start();
- }
- else if (file != null)
- {
- add(launcher);
-
- launcher.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- LoadingThread loader = new LoadingThread(file,
- "URL",
- featuresFile,
- applet);
- loader.start();
- }
- });
- }
- else
- {
- file = "NO FILE";
- fileFound = false;
- }
- }
-
-
- public static void main(String [] args)
- {
- if(args.length!=1)
- {
- System.out.println("\nUsage: java -jar jalviewApplet.jar fileName\n");
- System.exit(1);
- }
-
- String format = jalview.io.IdentifyFile.Identify(args[0],"File");
- SequenceI[] sequences = new AppletFormatAdapter().readFile(args[0], "File", format);
-
- if ( (sequences != null) && (sequences.length > 0))
- {
- AlignFrame af = new AlignFrame(new Alignment(sequences), null, args[0]);
- af.statusBar.setText("Successfully loaded file " + args[0]);
- }
- }
-
-
- /**
- * Initialises and displays a new java.awt.Frame
- *
- * @param frame java.awt.Frame to be displayed
- * @param title title of new frame
- * @param width width if new frame
- * @param height height of new frame
- */
- public static void addFrame(final Frame frame, String title, int width,
- int height)
- {
- frame.setLocation(lastFrameX, lastFrameY);
- lastFrameX += 40;
- lastFrameY += 40;
- frame.setSize(width, height);
- frame.setTitle(title);
- frame.addWindowListener(new WindowAdapter()
- {
- public void windowClosing(WindowEvent e)
- {
- if(currentAlignFrame == frame)
- {
- currentAlignFrame = null;
- }
- lastFrameX -=40;
- lastFrameY-=40;
- frame.setMenuBar(null);
- frame.dispose();
- }
- public void windowActivated(WindowEvent e)
- {
- if(frame instanceof AlignFrame)
- currentAlignFrame = (AlignFrame)frame;
- }
-
- });
- frame.setVisible(true);
- }
-
- public String getAlignment(String format)
- {
- return getAlignment(format, "true");
- }
-
- public String getAlignment(String format, String suffix)
- {
- try
- {
- boolean seqlimits = suffix.equalsIgnoreCase("true");
-
- String reply = new AppletFormatAdapter().formatSequences(format,
- currentAlignFrame.viewport.getAlignment().getSequences(), seqlimits);
- return reply;
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- return "Error retrieving alignment in " + format + " format. ";
- }
- }
-
- /**
- * This paints the background surrounding the "Launch Jalview button"
- *
- *
If file given in parameter not found, displays error message
- *
- * @param g graphics context
- */
- public void paint(Graphics g)
- {
- if (!fileFound)
- {
- g.setColor(new Color(200, 200, 200));
- g.setColor(Color.cyan);
- g.fillRect(0, 0, getSize().width, getSize().height);
- g.setColor(Color.red);
- g.drawString("Jalview can't open file", 5, 15);
- g.drawString("\"" + file + "\"", 5, 30);
- }
- else if(embedded)
- {
- g.setColor(Color.black);
- g.setFont(new Font("Arial", Font.BOLD, 24));
- g.drawString("Jalview Applet", 50, this.size().height/2 -30);
- g.drawString("Loading Data...", 50, this.size().height/2);
- }
-
-
- }
-
- class LoadingThread extends Thread
- {
- String file;
- String protocol;
- String format;
- String featuresFile;
- JalviewLite applet;
-
- public LoadingThread(String file,
- String protocol,
- String features,
- JalviewLite applet)
- {
- this.file = file;
- this.protocol = protocol;
- format = jalview.io.IdentifyFile.Identify(file, "URL");
- featuresFile = features;
- this.applet = applet;
- }
-
- public void run()
- {
- SequenceI[] sequences = null;
- sequences = new AppletFormatAdapter().readFile(file, protocol, format);
-
- if ((sequences != null) && (sequences.length > 0))
- {
- currentAlignFrame = new AlignFrame(new Alignment(sequences),
- applet, file);
- if (embedded)
- currentAlignFrame.setEmbedded();
-
- currentAlignFrame.statusBar.setText("Successfully loaded file " + file);
-
- if (featuresFile != null)
- currentAlignFrame.parseFeaturesFile(featuresFile);
-
- String treeFile = applet.getParameter("treeFile");
- if (treeFile != null)
- {
- try
- {
- jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.
- getCodeBase() + treeFile, "URL");
- fin.parse();
-
- if (fin.getTree() != null)
- {
- TreePanel tp = null;
- tp = new TreePanel(currentAlignFrame.viewport,
- currentAlignFrame.viewport.getAlignment().getSequences(),
- fin, "FromFile", applet.getCodeBase() + treeFile);
- addFrame(tp, treeFile, 600, 500);
- currentAlignFrame.addTreeMenuItem(tp, treeFile);
- }
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
-
-
- String pdbfile = applet.getParameter("PDBFILE");
- if(pdbfile!=null)
- {
- if(pdbfile.indexOf("://")==-1)
- pdbfile = getCodeBase() + pdbfile;
-
- String sequence = applet.getParameter("PDBSEQ");
-
- if(sequence!=null)
- {
- new MCview.AppletPDBViewer(pdbfile, "URL",
- (Sequence)currentAlignFrame.getAlignViewport().getAlignment().findName(sequence),
- currentAlignFrame.getSeqcanvas());
- }
-
- }
- }
- else
- {
- fileFound = false;
- remove(launcher);
- repaint();
- }
- }
- }
-}
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* 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
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
+package jalview.bin;
+
+import jalview.appletgui.AlignFrame;
+
+import jalview.datamodel.*;
+
+import jalview.io.*;
+
+import java.applet.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+
+/**
+ * Jalview Applet. Runs in Java 1.18 runtime
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class JalviewLite extends Applet
+{
+ static int lastFrameX = 200;
+ static int lastFrameY = 200;
+ boolean fileFound = true;
+ String file = "No file";
+ Button launcher = new Button("Start Jalview");
+
+ //The currentAlignFrame is static, it will change
+ //if and when the user selects a new window
+ static AlignFrame currentAlignFrame;
+
+ //This is the first frame to be displayed, and does not change
+ AlignFrame initialAlignFrame;
+
+ boolean embedded = false;
+
+
+ /**
+ * init method for Jalview Applet
+ */
+ public void init()
+ {
+ int r = 255;
+ int g = 255;
+ int b = 255;
+ String param = getParameter("RGB");
+
+ if (param != null)
+ {
+ try
+ {
+ r = Integer.parseInt(param.substring(0, 2), 16);
+ g = Integer.parseInt(param.substring(2, 4), 16);
+ b = Integer.parseInt(param.substring(4, 6), 16);
+ }
+ catch (Exception ex)
+ {
+ r = 255;
+ g = 255;
+ b = 255;
+ }
+ }
+
+ param = getParameter("label");
+ if(param != null)
+ launcher.setLabel(param);
+
+ this.setBackground(new Color(r, g, b));
+
+ file = getParameter("file");
+
+ if(file==null)
+ {
+ //Maybe the sequences are added as parameters
+ StringBuffer data = new StringBuffer("PASTE");
+ int i=1;
+ while( (file=getParameter("sequence"+i))!=null)
+ {
+ data.append(file.toString()+"\n");
+ i++;
+ }
+ if(data.length()>5)
+ file = data.toString();
+ }
+
+ final JalviewLite applet = this;
+ if(getParameter("embedded")!=null
+ && getParameter("embedded").equalsIgnoreCase("true"))
+ {
+ embedded = true;
+ LoadingThread loader = new LoadingThread(file, applet);
+ loader.start();
+ }
+ else if (file != null)
+ {
+ add(launcher);
+
+ launcher.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ LoadingThread loader = new LoadingThread(file,
+ applet);
+ loader.start();
+ }
+ });
+ }
+ else
+ {
+ file = "NO FILE";
+ fileFound = false;
+ }
+ }
+
+
+ public static void main(String [] args)
+ {
+ if(args.length!=1)
+ {
+ System.out.println("\nUsage: java -jar jalviewApplet.jar fileName\n");
+ System.exit(1);
+ }
+
+ String format = new jalview.io.IdentifyFile().Identify(args[0],AppletFormatAdapter.FILE);
+
+ SequenceI[] sequences = null;
+ try{
+ sequences = new AppletFormatAdapter().readFile(args[0], AppletFormatAdapter.FILE, format);
+ }catch(java.io.IOException ex)
+ {
+ ex.printStackTrace();
+ }
+ if ( (sequences != null) && (sequences.length > 0))
+ {
+ AlignFrame af = new AlignFrame(new Alignment(sequences), null, args[0], false);
+ af.statusBar.setText("Successfully loaded file " + args[0]);
+ }
+ }
+
+
+ /**
+ * Initialises and displays a new java.awt.Frame
+ *
+ * @param frame java.awt.Frame to be displayed
+ * @param title title of new frame
+ * @param width width if new frame
+ * @param height height of new frame
+ */
+ public static void addFrame(final Frame frame, String title, int width,
+ int height)
+ {
+ frame.setLocation(lastFrameX, lastFrameY);
+ lastFrameX += 40;
+ lastFrameY += 40;
+ frame.setSize(width, height);
+ frame.setTitle(title);
+ frame.addWindowListener(new WindowAdapter()
+ {
+ public void windowClosing(WindowEvent e)
+ {
+ if(currentAlignFrame == frame)
+ {
+ currentAlignFrame = null;
+ }
+ lastFrameX -=40;
+ lastFrameY -=40;
+ frame.setMenuBar(null);
+ frame.dispose();
+ }
+ public void windowActivated(WindowEvent e)
+ {
+ if(frame instanceof AlignFrame)
+ currentAlignFrame = (AlignFrame)frame;
+ }
+
+ });
+ frame.setVisible(true);
+ }
+
+ public String getSelectedSequences()
+ {
+ StringBuffer result = new StringBuffer("");
+
+ if(initialAlignFrame.viewport.getSelectionGroup()!=null)
+ {
+ SequenceI[] seqs = initialAlignFrame.viewport.getSelectionGroup().
+ getSequencesInOrder(
+ initialAlignFrame.viewport.getAlignment());
+
+ for (int i = 0; i < seqs.length; i++)
+ result.append(seqs[i].getName() + "¬");
+ }
+
+ return result.toString();
+ }
+
+ public String getAlignment(String format)
+ {
+ return getAlignment(format, "true");
+ }
+
+ public String getAlignment(String format, String suffix)
+ {
+ try
+ {
+ boolean seqlimits = suffix.equalsIgnoreCase("true");
+
+ String reply = new AppletFormatAdapter().formatSequences(format,
+ currentAlignFrame.viewport.getAlignment().getSequences(), seqlimits);
+ return reply;
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ return "Error retrieving alignment in " + format + " format. ";
+ }
+ }
+
+ /**
+ * This paints the background surrounding the "Launch Jalview button"
+ *
+ *
If file given in parameter not found, displays error message
+ *
+ * @param g graphics context
+ */
+ public void paint(Graphics g)
+ {
+ if (!fileFound)
+ {
+ g.setColor(new Color(200, 200, 200));
+ g.setColor(Color.cyan);
+ g.fillRect(0, 0, getSize().width, getSize().height);
+ g.setColor(Color.red);
+ g.drawString("Jalview can't open file", 5, 15);
+ g.drawString("\"" + file + "\"", 5, 30);
+ }
+ else if(embedded)
+ {
+ g.setColor(Color.black);
+ g.setFont(new Font("Arial", Font.BOLD, 24));
+ g.drawString("Jalview Applet", 50, this.size().height/2 -30);
+ g.drawString("Loading Data...", 50, this.size().height/2);
+ }
+
+
+ }
+
+ class LoadingThread extends Thread
+ {
+ String file;
+ String protocol;
+ String format;
+ JalviewLite applet;
+
+ public LoadingThread(String _file,
+ JalviewLite _applet)
+ {
+ file = _file;
+ if(file.startsWith("PASTE"))
+ {
+ file = file.substring(5);
+ protocol = AppletFormatAdapter.PASTE;
+ }
+ else if(inArchive(file))
+ protocol = AppletFormatAdapter.CLASSLOADER;
+ else
+ {
+ file = addProtocol(file);
+ protocol = AppletFormatAdapter.URL;
+ }
+ format = new jalview.io.IdentifyFile().Identify(file, protocol);
+ applet = _applet;
+ }
+
+ public void run()
+ {
+ SequenceI[] sequences = null;
+ try{
+ sequences = new AppletFormatAdapter().readFile(file, protocol,
+ format);
+ }catch(java.io.IOException ex)
+ {
+ ex.printStackTrace();
+ }
+ if ((sequences != null) && (sequences.length > 0))
+ {
+ currentAlignFrame = new AlignFrame(new Alignment(sequences),
+ applet,
+ file,
+ embedded);
+
+ if(protocol==jalview.io.AppletFormatAdapter.PASTE)
+ currentAlignFrame.setTitle("Sequences from "+getDocumentBase());
+
+ initialAlignFrame = currentAlignFrame;
+
+ currentAlignFrame.statusBar.setText("Successfully loaded file " + file);
+
+
+ String treeFile = applet.getParameter("tree");
+ if(treeFile==null)
+ treeFile = applet.getParameter("treeFile");
+
+ if (treeFile != null)
+ {
+ try
+ {
+ if(inArchive(treeFile))
+ protocol = AppletFormatAdapter.CLASSLOADER;
+ else
+ {
+ protocol = AppletFormatAdapter.URL;
+ treeFile = addProtocol(treeFile);
+ }
+
+ jalview.io.NewickFile fin = new jalview.io.NewickFile(treeFile, protocol);
+
+ fin.parse();
+
+ if (fin.getTree() != null)
+ {
+ currentAlignFrame.loadTree(fin, treeFile);
+ }
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ String param = getParameter("features");
+ if (param != null)
+ {
+ if( !inArchive(param) )
+ param = addProtocol( param );
+
+ currentAlignFrame.parseFeaturesFile(param, protocol);
+ }
+
+ param = getParameter("showFeatureSettings");
+ if(param !=null && param.equalsIgnoreCase("true"))
+ {
+ currentAlignFrame.viewport.showSequenceFeatures(true);
+ currentAlignFrame.featureSettings_actionPerformed();
+ }
+
+ param = getParameter("annotations");
+ if (param != null)
+ {
+ if( !inArchive(param) )
+ param = addProtocol( param );
+
+ new AnnotationFile().readAnnotationFile(
+ currentAlignFrame.viewport.getAlignment(),
+ param);
+
+ currentAlignFrame.alignPanel.fontChanged();
+ currentAlignFrame.alignPanel.setScrollValues(0,0);
+
+ }
+
+ param = getParameter("jnetfile");
+ if (param != null)
+ {
+ try
+ {
+ if (inArchive(param))
+ protocol = AppletFormatAdapter.CLASSLOADER;
+ else
+ {
+ protocol = AppletFormatAdapter.URL;
+ param = addProtocol(param);
+ }
+
+ jalview.io.JPredFile predictions = new jalview.io.JPredFile(
+ param, protocol);
+ new JnetAnnotationMaker().add_annotation(predictions,
+ currentAlignFrame.viewport.getAlignment(),
+ 0,false); // do not add sequence profile from concise output
+ currentAlignFrame.alignPanel.fontChanged();
+ currentAlignFrame.alignPanel.setScrollValues(0, 0);
+ } catch (Exception ex) {
+ ex.printStackTrace();
+ }
+ }
+
+
+ String pdbfile = applet.getParameter("PDBFILE");
+ if(pdbfile!=null)
+ {
+ if( inArchive(pdbfile) )
+ protocol = AppletFormatAdapter.CLASSLOADER;
+ else
+ {
+ protocol = AppletFormatAdapter.URL;
+ pdbfile = addProtocol(pdbfile);
+ }
+
+ String sequence = applet.getParameter("PDBSEQ");
+
+ if(sequence!=null)
+ {
+ new MCview.AppletPDBViewer(pdbfile, protocol,
+ (Sequence)currentAlignFrame.getAlignViewport().getAlignment().findName(sequence),
+ currentAlignFrame.getSeqcanvas());
+ }
+
+ }
+ }
+ else
+ {
+ fileFound = false;
+ remove(launcher);
+ repaint();
+ }
+ }
+
+ /**
+ * Discovers whether the given file is in the Applet Archive
+ * @param file String
+ * @return boolean
+ */
+ boolean inArchive(String file)
+ {
+ //This might throw a security exception in certain browsers
+ //Netscape Communicator for instance.
+ try{
+ return (getClass().getResourceAsStream("/" + file) != null);
+ }catch(Exception ex)
+ {
+ System.out.println("Exception checking resources: "+file+" "+ex);
+ return false;
+ }
+ }
+
+ String addProtocol(String file)
+ {
+ if (file.indexOf("://") == -1)
+ file = getCodeBase() + file;
+
+ return file;
+ }
+
+ }
+}