X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=7329a6f4f456eb49cbf5c087eb628d6c2ac87030;hb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;hp=9b73944d48ee33072df97fdc7ab813f9e3c02e25;hpb=8aa523a5c524b41c5ed4be23772934ea6b695a90;p=jalview.git
diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 9b73944..7329a6f 100755
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -1,267 +1,1181 @@
-/*
-* 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.*;
-
-
-/**
- * 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;
- static Applet applet;
- boolean fileFound = true;
- String file = "No file";
- Button launcher = new Button("Start Jalview");
-
- /**
- * init method for Jalview Applet
- */
- public void init()
- {
- applet = this;
-
- 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;
- }
- }
-
- AlignFrame.NEW_WINDOW_WIDTH = 700;
- AlignFrame.NEW_WINDOW_HEIGHT = 500;
- try{
- param = applet.getParameter("windowWidth");
- if (param != null)
- {
- int width = Integer.parseInt(param);
- AlignFrame.NEW_WINDOW_WIDTH = width;
- }
- param = applet.getParameter("windowHeight");
- if (param != null)
- {
- int height = Integer.parseInt(param);
- AlignFrame.NEW_WINDOW_HEIGHT = height;
- }
- }catch(Exception ex){}
-
- this.setBackground(new Color(r, g, b));
-
- file = getParameter("file");
-
- if (file != null)
- {
- add(launcher);
- file = applet.getCodeBase() + file;
- launcher.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- String format = jalview.io.IdentifyFile.Identify(file,
- "URL");
- LoadFile(file, "URL", format);
- }
- });
- }
- 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 FormatAdapter().readFile(args[0], "File", format);
-
- if ( (sequences != null) && (sequences.length > 0))
- {
- AlignFrame af = new AlignFrame(new Alignment(sequences), null);
- addFrame(af, args[0], AlignFrame.NEW_WINDOW_WIDTH,
- AlignFrame.NEW_WINDOW_HEIGHT);
- af.statusBar.setText("Successfully loaded file " + args[0]);
- }
- }
-
- /**
- * Displays the given URL in a new browser window
- *
- * @param url URL to display in browser window.
- *
New window will be named "HELP_WINDOW"
- */
- public static void showURL(String url)
- {
- showURL(url, "HELP");
- }
-
- public static void showURL(String url, String target)
- {
- if(applet==null)
- {
- System.out.println("Not running as applet - no browser available.");
- }
- else
- {
- try
- {
- applet.getAppletContext().showDocument(new java.net.URL(url),
- target);
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
- }
-
-
- /**
- * Starts a new LoadingThread for loading an alignment file
- *
- * @param file file name including full path to file
- * @param protocol file or URL or paste
- * @param format Fasta, Clustal, PFAM, MSF, PIR, BLC, Jalview
- */
- public void LoadFile(String file, String protocol, String format)
- {
- LoadingThread loader = new LoadingThread(file, protocol, format, this);
- loader.start();
- }
-
- /**
- * 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)
- {
- frame.dispose();
- }
- });
- frame.setVisible(true);
- }
-
- /**
- * 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);
- }
- }
-
- class LoadingThread extends Thread
- {
- String file;
- String protocol;
- String format;
- JalviewLite jlapplet;
-
- public LoadingThread(String file, String protocol, String format,
- JalviewLite applet)
- {
- this.file = file;
- this.protocol = protocol;
- this.format = format;
- this.jlapplet = applet;
- }
-
- public void run()
- {
- SequenceI[] sequences = null;
- sequences = new FormatAdapter().readFile(file, protocol, format);
-
- if ((sequences != null) && (sequences.length > 0))
- {
- AlignFrame af = new AlignFrame(new Alignment(sequences),
- jlapplet);
- addFrame(af, file, AlignFrame.NEW_WINDOW_WIDTH,
- AlignFrame.NEW_WINDOW_HEIGHT);
- af.statusBar.setText("Successfully loaded file " + file);
- }
- else
- {
- fileFound = false;
- remove(launcher);
- repaint();
- }
- }
- }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 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 java.applet.*;
+
+import java.awt.*;
+import java.awt.event.*;
+import java.util.*;
+
+import jalview.appletgui.*;
+import jalview.datamodel.*;
+import jalview.io.*;
+
+/**
+ * Jalview Applet. Runs in Java 1.18 runtime
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class JalviewLite extends Applet
+{
+
+ // /////////////////////////////////////////
+ // The following public methods maybe called
+ // externally, eg via javascript in HTML page
+ /**
+ * @return String list of selected sequence IDs, each terminated by "¬"
+ * (¬)
+ */
+ public String getSelectedSequences()
+ {
+ return getSelectedSequencesFrom(getDefaultTargetFrame());
+ }
+
+ /**
+ * @param sep
+ * separator string or null for default
+ * @return String list of selected sequence IDs, each terminated by sep or
+ * ("¬" as default)
+ */
+ public String getSelectedSequences(String sep)
+ {
+ return getSelectedSequencesFrom(getDefaultTargetFrame(), sep);
+ }
+
+ /**
+ * @param alf
+ * alignframe containing selection
+ * @return String list of selected sequence IDs, each terminated by "¬"
+ *
+ */
+ public String getSelectedSequencesFrom(AlignFrame alf)
+ {
+ return getSelectedSequencesFrom(alf, "¬");
+ }
+
+ /**
+ * get list of selected sequence IDs separated by given separator
+ *
+ * @param alf
+ * window containing selection
+ * @param sep
+ * separator string to use - default is "¬"
+ * @return String list of selected sequence IDs, each terminated by the given
+ * separator
+ */
+ public String getSelectedSequencesFrom(AlignFrame alf, String sep)
+ {
+ StringBuffer result = new StringBuffer("");
+ if (sep == null || sep.length() == 0)
+ {
+ sep = "¬";
+ }
+ if (alf.viewport.getSelectionGroup() != null)
+ {
+ SequenceI[] seqs = alf.viewport.getSelectionGroup()
+ .getSequencesInOrder(alf.viewport.getAlignment());
+
+ for (int i = 0; i < seqs.length; i++)
+ {
+ result.append(seqs[i].getName());
+ result.append(sep);
+ }
+ }
+
+ return result.toString();
+ }
+
+ /**
+ * get sequences selected in current alignFrame and return their alignment in
+ * format 'format' either with or without suffix
+ *
+ * @param alf -
+ * where selection is
+ * @param format -
+ * format of alignment file
+ * @param suffix -
+ * "true" to append /start-end string to each sequence ID
+ * @return selected sequences as flat file or empty string if there was no
+ * current selection
+ */
+ public String getSelectedSequencesAsAlignment(String format, String suffix)
+ {
+ return getSelectedSequencesAsAlignmentFrom(currentAlignFrame, format,
+ suffix);
+ }
+
+ /**
+ * get sequences selected in alf and return their alignment in format 'format'
+ * either with or without suffix
+ *
+ * @param alf -
+ * where selection is
+ * @param format -
+ * format of alignment file
+ * @param suffix -
+ * "true" to append /start-end string to each sequence ID
+ * @return selected sequences as flat file or empty string if there was no
+ * current selection
+ */
+ public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
+ String format, String suffix)
+ {
+ try
+ {
+ boolean seqlimits = suffix.equalsIgnoreCase("true");
+ if (alf.viewport.getSelectionGroup() != null)
+ {
+ String reply = new AppletFormatAdapter().formatSequences(format,
+ new Alignment(alf.viewport.getSelectionAsNewSequence()),
+ seqlimits);
+ return reply;
+ }
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ return "Error retrieving alignment in " + format + " format. ";
+ }
+ return "";
+ }
+
+ public String getAlignment(String format)
+ {
+ return getAlignmentFrom(getDefaultTargetFrame(), format, "true");
+ }
+
+ public String getAlignmentFrom(AlignFrame alf, String format)
+ {
+ return getAlignmentFrom(alf, format, "true");
+ }
+
+ public String getAlignment(String format, String suffix)
+ {
+ return getAlignmentFrom(getDefaultTargetFrame(), format, suffix);
+ }
+
+ public String getAlignmentFrom(AlignFrame alf, String format,
+ String suffix)
+ {
+ try
+ {
+ boolean seqlimits = suffix.equalsIgnoreCase("true");
+
+ String reply = new AppletFormatAdapter().formatSequences(format,
+ alf.viewport.getAlignment(), seqlimits);
+ return reply;
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ return "Error retrieving alignment in " + format + " format. ";
+ }
+ }
+
+ public void loadAnnotation(String annotation)
+ {
+ loadAnnotationFrom(getDefaultTargetFrame(), annotation);
+ }
+
+ public void loadAnnotationFrom(AlignFrame alf, String annotation)
+ {
+ if (new AnnotationFile().readAnnotationFile(alf.getAlignViewport()
+ .getAlignment(), annotation, AppletFormatAdapter.PASTE))
+ {
+ alf.alignPanel.fontChanged();
+ alf.alignPanel.setScrollValues(0, 0);
+ }
+ else
+ {
+ alf.parseFeaturesFile(annotation, AppletFormatAdapter.PASTE);
+ }
+ }
+
+ public String getFeatures(String format)
+ {
+ return getFeaturesFrom(getDefaultTargetFrame(), format);
+ }
+
+ public String getFeaturesFrom(AlignFrame alf, String format)
+ {
+ return alf.outputFeatures(false, format);
+ }
+
+ public String getAnnotation()
+ {
+ return getAnnotationFrom(getDefaultTargetFrame());
+ }
+
+ public String getAnnotationFrom(AlignFrame alf)
+ {
+ return alf.outputAnnotations(false);
+ }
+
+ public AlignFrame newView()
+ {
+ return newViewFrom(getDefaultTargetFrame());
+ }
+
+ public AlignFrame newView(String name)
+ {
+ return newViewFrom(getDefaultTargetFrame(), name);
+ }
+
+ public AlignFrame newViewFrom(AlignFrame alf)
+ {
+ return alf.newView(null);
+ }
+
+ public AlignFrame newViewFrom(AlignFrame alf, String name)
+ {
+ return alf.newView(name);
+ }
+
+ /**
+ *
+ * @param text
+ * alignment file as a string
+ * @param title
+ * window title
+ * @return null or new alignment frame
+ */
+ public AlignFrame loadAlignment(String text, String title)
+ {
+ Alignment al = null;
+
+ String format = new IdentifyFile().Identify(text,
+ AppletFormatAdapter.PASTE);
+ try
+ {
+ al = new AppletFormatAdapter().readFile(text,
+ AppletFormatAdapter.PASTE, format);
+ if (al.getHeight() > 0)
+ {
+ return new AlignFrame(al, this, title, false);
+ }
+ } catch (java.io.IOException ex)
+ {
+ ex.printStackTrace();
+ }
+ return null;
+ }
+
+ // //////////////////////////////////////////////
+ // //////////////////////////////////////////////
+
+ 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. Note that it will *never* point back to the embedded
+ * AlignFrame if the applet is started as embedded on the page and then
+ * afterwards a new view is created.
+ */
+ public static AlignFrame currentAlignFrame;
+
+ /**
+ * This is the first frame to be displayed, and does not change. API calls
+ * will default to this instance if currentAlignFrame is null.
+ */
+ AlignFrame initialAlignFrame;
+
+ boolean embedded = false;
+
+ private boolean checkForJmol = true;
+ private boolean checkedForJmol = false; // ensure we don't check for jmol every time the app is re-inited
+
+ public boolean jmolAvailable = false;
+
+ public static boolean debug;
+
+ /**
+ * init method for Jalview Applet
+ */
+ public void init()
+ {
+ /**
+ * turn on extra applet debugging
+ */
+ String dbg = getParameter("debug");
+ if (dbg != null)
+ {
+ debug = dbg.toLowerCase().equals("true");
+ }
+ /**
+ * if true disable the check for jmol
+ */
+ String chkforJmol = getParameter("nojmol");
+ if (chkforJmol != null)
+ {
+ checkForJmol = !chkforJmol.equals("true");
+ }
+ /**
+ * get the separator parameter if present
+ */
+ String sep = getParameter("separator");
+ if (sep != null)
+ {
+ if (sep.length() > 0)
+ {
+ separator = sep;
+ if (debug)
+ {
+ System.err.println("Separator set to '" + separator + "'");
+ }
+ }
+ else
+ {
+ throw new Error(
+ "Invalid separator parameter - must be non-zero length");
+ }
+ }
+ 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"))
+ {
+ // Launch as embedded applet in page
+ embedded = true;
+ LoadingThread loader = new LoadingThread(file, applet);
+ loader.start();
+ }
+ else if (file != null)
+ {
+ if (getParameter("showbutton") == null
+ || !getParameter("showbutton").equalsIgnoreCase("false"))
+ {
+ // Add the JalviewLite 'Button' to the page
+ add(launcher);
+ launcher.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ LoadingThread loader = new LoadingThread(file, applet);
+ loader.start();
+ }
+ });
+ }
+ else
+ {
+ // Open jalviewLite immediately.
+ LoadingThread loader = new LoadingThread(file, applet);
+ loader.start();
+ }
+ }
+ else
+ {
+ // jalview initialisation with no alignment. loadAlignment() method can
+ // still be called to open new alignments.
+ file = "NO FILE";
+ fileFound = false;
+ }
+ }
+
+ /**
+ * 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 (frame instanceof AlignFrame)
+ {
+ ((AlignFrame) frame).closeMenuItem_actionPerformed();
+ }
+ if (currentAlignFrame == frame)
+ {
+ currentAlignFrame = null;
+ }
+ lastFrameX -= 40;
+ lastFrameY -= 40;
+ if (frame instanceof EmbmenuFrame)
+ {
+ ((EmbmenuFrame) frame).destroyMenus();
+ }
+ frame.setMenuBar(null);
+ frame.dispose();
+ }
+
+ public void windowActivated(WindowEvent e)
+ {
+ if (frame instanceof AlignFrame)
+ {
+ currentAlignFrame = (AlignFrame) frame;
+ if (debug)
+ {
+ System.err.println("Activated window " + frame);
+ }
+ }
+ // be good.
+ super.windowActivated(e);
+ }
+ /*
+ * Probably not necessary to do this - see TODO above. (non-Javadoc)
+ *
+ * @see java.awt.event.WindowAdapter#windowDeactivated(java.awt.event.WindowEvent)
+ *
+ * public void windowDeactivated(WindowEvent e) { if (currentAlignFrame ==
+ * frame) { currentAlignFrame = null; if (debug) {
+ * System.err.println("Deactivated window "+frame); } }
+ * super.windowDeactivated(e); }
+ */
+ });
+ frame.setVisible(true);
+ }
+
+ /**
+ * 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.getSize().height / 2 - 30);
+ g.drawString("Loading Data...", 50, this.getSize().height / 2);
+ }
+ }
+
+ class LoadJmolThread extends Thread
+ {
+ private boolean running=false;
+
+ public void run()
+ {
+ if (running || checkedForJmol) {
+ return;
+ }
+ running=true;
+ if (checkForJmol)
+ {
+ try
+ {
+ if (!System.getProperty("java.version").startsWith("1.1"))
+ {
+ Class.forName("org.jmol.adapter.smarter.SmarterJmolAdapter");
+ jmolAvailable = true;
+ }
+ if (!jmolAvailable)
+ {
+ System.out
+ .println("Jmol not available - Using MCview for structures");
+ }
+ } catch (java.lang.ClassNotFoundException ex)
+ {
+ }
+ }
+ else
+ {
+ jmolAvailable = false;
+ if (debug)
+ {
+ System.err
+ .println("Skipping Jmol check. Will use MCView (probably)");
+ }
+ }
+ checkedForJmol=true;
+ running=false;
+ }
+
+ public boolean notFinished()
+ {
+ return running || !checkedForJmol;
+ }
+ }
+
+ class LoadingThread extends Thread
+ {
+ /**
+ * State variable: File source
+ */
+ String file;
+
+ /**
+ * State variable: protocol for access to file source
+ */
+ String protocol;
+
+ /**
+ * State variable: format of file source
+ */
+ String format;
+ String _file;
+ JalviewLite applet;
+ private void dbgMsg(String msg)
+ {
+ if (applet.debug)
+ {
+ System.err.println(msg);
+ }
+ }
+
+ /**
+ * update the protocol state variable for accessing the datasource located
+ * by file.
+ *
+ * @param file
+ * @return possibly updated datasource string
+ */
+ public String setProtocolState(String 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;
+ }
+ dbgMsg("Protocol identified as '" + protocol + "'");
+ return file;
+ }
+
+ public LoadingThread(String _file, JalviewLite _applet)
+ {
+ this._file=_file;
+ applet = _applet;
+ }
+
+ public void run()
+ {
+ LoadJmolThread jmolchecker = new LoadJmolThread();
+ jmolchecker.start();
+ while (jmolchecker.notFinished())
+ {
+ // wait around until the Jmol check is complete.
+ try { Thread.sleep(2); } catch (Exception e) {};
+ }
+ startLoading();
+ }
+
+ private void startLoading()
+ {
+ AlignFrame newAlignFrame;
+ dbgMsg("Loading thread started with:\n>>file\n" + _file + ">>endfile");
+ file = setProtocolState(_file);
+
+ format = new jalview.io.IdentifyFile().Identify(file, protocol);
+ dbgMsg("File identified as '" + format + "'");
+ dbgMsg("Loading started.");
+ Alignment al = null;
+ try
+ {
+ al = new AppletFormatAdapter().readFile(file, protocol, format);
+ } catch (java.io.IOException ex)
+ {
+ dbgMsg("File load exception.");
+ ex.printStackTrace();
+ }
+ if ((al != null) && (al.getHeight() > 0))
+ {
+ dbgMsg("Successfully loaded file.");
+ newAlignFrame = new AlignFrame(al, applet, file, embedded);
+ if (initialAlignFrame==null)
+ {
+ initialAlignFrame = newAlignFrame;
+ }
+ // update the focus.
+ currentAlignFrame = newAlignFrame;
+
+ if (protocol == jalview.io.AppletFormatAdapter.PASTE)
+ {
+ newAlignFrame.setTitle("Sequences from " + getDocumentBase());
+ }
+
+ newAlignFrame.statusBar.setText("Successfully loaded file "
+ + file);
+
+ String treeFile = applet.getParameter("tree");
+ if (treeFile == null)
+ {
+ treeFile = applet.getParameter("treeFile");
+ }
+
+ if (treeFile != null)
+ {
+ try
+ {
+ treeFile = setProtocolState(treeFile);
+ /*
+ * 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)
+ {
+ newAlignFrame.loadTree(fin, treeFile);
+ dbgMsg("Successfuly imported tree.");
+ }
+ else
+ {
+ dbgMsg("Tree parameter did not resolve to a valid tree.");
+ }
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ String param = getParameter("features");
+ if (param != null)
+ {
+ param = setProtocolState(param);
+
+ newAlignFrame.parseFeaturesFile(param, protocol);
+ }
+
+ param = getParameter("showFeatureSettings");
+ if (param != null && param.equalsIgnoreCase("true"))
+ {
+ newAlignFrame.viewport.showSequenceFeatures(true);
+ new FeatureSettings(newAlignFrame.alignPanel);
+ }
+
+ param = getParameter("annotations");
+ if (param != null)
+ {
+ param = setProtocolState(param);
+
+ if (new AnnotationFile().readAnnotationFile(
+ newAlignFrame.viewport.getAlignment(), param,
+ protocol))
+ {
+ newAlignFrame.alignPanel.fontChanged();
+ newAlignFrame.alignPanel.setScrollValues(0, 0);
+ }
+ else
+ {
+ System.err
+ .println("Annotations were not added from annotation file '"
+ + param + "'");
+ }
+
+ }
+
+ param = getParameter("jnetfile");
+ if (param != null)
+ {
+ try
+ {
+ param = setProtocolState(param);
+ jalview.io.JPredFile predictions = new jalview.io.JPredFile(
+ param, protocol);
+ JnetAnnotationMaker.add_annotation(predictions,
+ newAlignFrame.viewport.getAlignment(), 0, false); // false==do
+ // not
+ // add
+ // sequence
+ // profile
+ // from
+ // concise
+ // output
+ newAlignFrame.alignPanel.fontChanged();
+ newAlignFrame.alignPanel.setScrollValues(0, 0);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ /*
+ *
+ *
+ *
+ *
+ *
+ */
+
+ int pdbFileCount = 0;
+ do
+ {
+ if (pdbFileCount > 0)
+ param = getParameter("PDBFILE" + pdbFileCount);
+ else
+ param = getParameter("PDBFILE");
+
+ if (param != null)
+ {
+ PDBEntry pdb = new PDBEntry();
+
+ String seqstring;
+ SequenceI[] seqs = null;
+ String[] chains = null;
+
+ StringTokenizer st = new StringTokenizer(param, " ");
+
+ if (st.countTokens() < 2)
+ {
+ String sequence = applet.getParameter("PDBSEQ");
+ if (sequence != null)
+ seqs = new SequenceI[]
+ { (Sequence) newAlignFrame.getAlignViewport()
+ .getAlignment().findName(sequence) };
+
+ }
+ else
+ {
+ param = st.nextToken();
+ Vector tmp = new Vector();
+ Vector tmp2 = new Vector();
+
+ while (st.hasMoreTokens())
+ {
+ seqstring = st.nextToken();
+ StringTokenizer st2 = new StringTokenizer(seqstring, "=");
+ if (st2.countTokens() > 1)
+ {
+ // This is the chain
+ tmp2.addElement(st2.nextToken());
+ seqstring = st2.nextToken();
+ }
+ tmp.addElement((Sequence) newAlignFrame
+ .getAlignViewport().getAlignment().findName(
+ seqstring));
+ }
+
+ seqs = new SequenceI[tmp.size()];
+ tmp.copyInto(seqs);
+ if (tmp2.size() == tmp.size())
+ {
+ chains = new String[tmp2.size()];
+ tmp2.copyInto(chains);
+ }
+ }
+ param = setProtocolState(param);
+
+ if (// !jmolAvailable
+ // &&
+ protocol == AppletFormatAdapter.CLASSLOADER)
+ {
+ // TODO: verify this Re:
+ // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
+ // This exception preserves the current behaviour where, even if
+ // the local pdb file was identified in the class loader
+ protocol = AppletFormatAdapter.URL; // this is probably NOT
+ // CORRECT!
+ param = addProtocol(param); //
+ }
+
+ pdb.setFile(param);
+
+ if (seqs != null)
+ {
+ for (int i = 0; i < seqs.length; i++)
+ {
+ if (seqs[i] != null)
+ {
+ ((Sequence) seqs[i]).addPDBId(pdb);
+ }
+ else
+ {
+ if (JalviewLite.debug)
+ {
+ // this may not really be a problem but we give a warning
+ // anyway
+ System.err
+ .println("Warning: Possible input parsing error: Null sequence for attachment of PDB (sequence "
+ + i + ")");
+ }
+ }
+ }
+
+ if (jmolAvailable)
+ {
+ new jalview.appletgui.AppletJmol(pdb, seqs, chains,
+ newAlignFrame.alignPanel, protocol);
+ lastFrameX += 40;
+ lastFrameY += 40;
+ }
+ else
+ new MCview.AppletPDBViewer(pdb, seqs, chains,
+ newAlignFrame.alignPanel, protocol);
+ }
+ }
+
+ pdbFileCount++;
+ } while (pdbFileCount < 10);
+
+ // ///////////////////////////
+ // modify display of features
+ //
+ // hide specific groups
+ param = getParameter("hidefeaturegroups");
+ if (param != null)
+ {
+ applet.setFeatureGroupStateOn(newAlignFrame,param, false);
+ }
+ // show specific groups
+ param = getParameter("showfeaturegroups");
+ if (param != null)
+ {
+ applet.setFeatureGroupStateOn(newAlignFrame,param, true);
+ }
+ }
+ 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
+ {
+ boolean rtn = (getClass().getResourceAsStream("/" + file) != null);
+ if (debug)
+ {
+ System.err.println("Resource '" + file + "' was "
+ + (rtn ? "" : "not") + " located by classloader.");
+ }
+ return rtn;
+ } catch (Exception ex)
+ {
+ System.out.println("Exception checking resources: " + file + " "
+ + ex);
+ return false;
+ }
+ }
+
+ String addProtocol(String file)
+ {
+ if (file.indexOf("://") == -1)
+ {
+ file = getCodeBase() + file;
+ if (debug)
+ {
+ System.err.println("Prepended codebase for resource: '" + file
+ + "'");
+ }
+ }
+
+ return file;
+ }
+ }
+
+ /**
+ * @return the default alignFrame acted on by the public applet methods. May
+ * return null with an error message on System.err indicating the
+ * fact.
+ */
+ protected AlignFrame getDefaultTargetFrame()
+ {
+ if (currentAlignFrame != null)
+ {
+ return currentAlignFrame;
+ }
+ if (initialAlignFrame != null)
+ {
+ return initialAlignFrame;
+ }
+ System.err
+ .println("Implementation error: Jalview Applet API cannot work out which AlignFrame to use.");
+ return null;
+ }
+
+ /**
+ * separator used for separatorList
+ */
+ protected String separator = "|"; // this is a safe(ish) separator - tabs
+
+ // don't work for firefox
+
+ /**
+ * parse the string into a list
+ *
+ * @param list
+ * @return elements separated by separator
+ */
+ public String[] separatorListToArray(String list)
+ {
+ int seplen = separator.length();
+ if (list == null || list.equals(""))
+ return null;
+ java.util.Vector jv = new Vector();
+ int cp = 0, pos;
+ while ((pos = list.indexOf(separator, cp)) > cp)
+ {
+ jv.addElement(list.substring(cp, pos));
+ cp = pos + seplen;
+ }
+ if (cp < list.length())
+ {
+ jv.addElement(list.substring(cp));
+ }
+ if (jv.size() > 0)
+ {
+ String[] v = new String[jv.size()];
+ for (int i = 0; i < v.length; i++)
+ {
+ v[i] = (String) jv.elementAt(i);
+ }
+ jv.removeAllElements();
+ if (debug)
+ {
+ System.err.println("Array from '" + separator
+ + "' separated List:\n" + v.length);
+ for (int i = 0; i < v.length; i++)
+ {
+ System.err.println("item " + i + " '" + v[i] + "'");
+ }
+ }
+ return v;
+ }
+ if (debug)
+ {
+ System.err.println("Empty Array from '" + separator
+ + "' separated List");
+ }
+ return null;
+ }
+
+ /**
+ * concatenate the list with separator
+ *
+ * @param list
+ * @return concatenated string
+ */
+ public String arrayToSeparatorList(String[] list)
+ {
+ StringBuffer v = new StringBuffer();
+ if (list != null)
+ {
+ for (int i = 0, iSize = list.length - 1; i < iSize; i++)
+ {
+ if (list[i] != null)
+ {
+ v.append(list[i]);
+ }
+ v.append(separator);
+ }
+ if (list[list.length - 1] != null)
+ {
+ v.append(list[list.length - 1]);
+ }
+ if (debug)
+ {
+ System.err.println("Returning '" + separator
+ + "' separated List:\n");
+ System.err.println(v);
+ }
+ return v.toString();
+ }
+ if (debug)
+ {
+ System.err.println("Returning empty '" + separator
+ + "' separated List\n");
+ }
+ return "";
+ }
+
+ /**
+ * @return
+ * @see jalview.appletgui.AlignFrame#getFeatureGroups()
+ */
+ public String getFeatureGroups()
+ {
+ String lst = arrayToSeparatorList(getDefaultTargetFrame()
+ .getFeatureGroups());
+ return lst;
+ }
+
+ /**
+ * @param alf
+ * alignframe to get feature groups on
+ * @return
+ * @see jalview.appletgui.AlignFrame#getFeatureGroups()
+ */
+ public String getFeatureGroupsOn(AlignFrame alf)
+ {
+ String lst = arrayToSeparatorList(alf.getFeatureGroups());
+ return lst;
+ }
+
+ /**
+ * @param visible
+ * @return
+ * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean)
+ */
+ public String getFeatureGroupsOfState(boolean visible)
+ {
+ return arrayToSeparatorList(getDefaultTargetFrame()
+ .getFeatureGroupsOfState(visible));
+ }
+
+ /**
+ * @param alf
+ * align frame to get groups of state visible
+ * @param visible
+ * @return
+ * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean)
+ */
+ public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)
+ {
+ return arrayToSeparatorList(alf.getFeatureGroupsOfState(visible));
+ }
+
+ /**
+ * @param groups
+ * tab separated list of group names
+ * @param state
+ * true or false
+ * @see jalview.appletgui.AlignFrame#setFeatureGroupState(java.lang.String[],
+ * boolean)
+ */
+ public void setFeatureGroupStateOn(AlignFrame alf, String groups,
+ boolean state)
+ {
+ boolean st = state;// !(state==null || state.equals("") ||
+ // state.toLowerCase().equals("false"));
+ alf.setFeatureGroupState(separatorListToArray(groups), st);
+ }
+
+ public void setFeatureGroupState(String groups, boolean state)
+ {
+ setFeatureGroupStateOn(getDefaultTargetFrame(), groups, state);
+ }
+
+ /**
+ * List separator string
+ *
+ * @return the separator
+ */
+ public String getSeparator()
+ {
+ return separator;
+ }
+
+ /**
+ * List separator string
+ *
+ * @param separator
+ * the separator to set
+ */
+ public void setSeparator(String separator)
+ {
+ this.separator = separator;
+ }
+}