X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=c7cc4f3b990aa6c163cfc6c6d3bb98c6b9c5e75d;hb=d6ad9619070895df810de190dd202b1698632438;hp=c9ec3918e3f65231aced553aeaf2cc9372c6ed6d;hpb=9344c308a62c48e2ddedd12247edab74e581c2e7;p=jalview.git
diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index c9ec391..c7cc4f3 100755
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -1,249 +1,1034 @@
-/*
-* 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;
- }
- }
-
- 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 = 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 = 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
+ * Copyright (C) 2007 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;
+
+ public boolean jmolAvailable = false;
+ public static boolean debug;
+
+ /**
+ * init method for Jalview Applet
+ */
+ public void init()
+ {
+ String dbg = getParameter("debug");
+ if (dbg!=null)
+ {
+ debug = dbg.toLowerCase().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();
+ }
+ }
+
+ LoadJmolThread jmolAvailable = new LoadJmolThread();
+ jmolAvailable.start();
+
+ 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;
+ }
+ }
+
+
+ /**
+ * 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
+ {
+ public void run()
+ {
+ try
+ {
+ if (!System.getProperty("java.version").startsWith("1.1"))
+ {
+ Class.forName("org.jmol.adapter.smarter.SmarterJmolAdapter");
+ jmolAvailable = true;
+ }
+ }
+ catch (java.lang.ClassNotFoundException ex)
+ {
+ System.out.println("Jmol not available - Using MCview for structures");
+ }
+ }
+ }
+
+
+ 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;
+ 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)
+ {
+ 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+"'");
+ applet = _applet;
+ }
+
+ public void run()
+ {
+ startLoading();
+ }
+
+ private void startLoading()
+ {
+ 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.");
+ initialAlignFrame = new AlignFrame(al,
+ applet,
+ file,
+ embedded);
+ // update the focus.
+ currentAlignFrame = initialAlignFrame;
+
+ if (protocol == jalview.io.AppletFormatAdapter.PASTE)
+ {
+ currentAlignFrame.setTitle("Sequences from " + getDocumentBase());
+ }
+
+ currentAlignFrame.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)
+ {
+ currentAlignFrame.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);
+
+ currentAlignFrame.parseFeaturesFile(param, protocol);
+ }
+
+ param = getParameter("showFeatureSettings");
+ if (param != null && param.equalsIgnoreCase("true"))
+ {
+ currentAlignFrame.viewport.showSequenceFeatures(true);
+ new FeatureSettings(currentAlignFrame.alignPanel);
+ }
+
+ param = getParameter("annotations");
+ if (param != null)
+ {
+ param = setProtocolState(param);
+
+ if (new AnnotationFile().readAnnotationFile(
+ currentAlignFrame.viewport.getAlignment(),
+ param,
+ protocol))
+ {
+ currentAlignFrame.alignPanel.fontChanged();
+ currentAlignFrame.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,
+ currentAlignFrame.viewport.getAlignment(),
+ 0, false); // false==do not add sequence profile from concise output
+ currentAlignFrame.alignPanel.fontChanged();
+ currentAlignFrame.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) currentAlignFrame.
+ 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) currentAlignFrame.
+ 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: pass PDB file in classloader on to Jmol
+ // 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,
+ currentAlignFrame.alignPanel,
+ protocol);
+ lastFrameX += 40;
+ lastFrameY+=40;
+ }
+ else
+ new MCview.AppletPDBViewer(pdb,
+ seqs,
+ chains,
+ currentAlignFrame.alignPanel,
+ protocol);
+ }
+ }
+
+ pdbFileCount++;
+ }
+ while(pdbFileCount < 10);
+
+ /////////////////////////////
+ // modify display of features
+ //
+ // hide specific groups
+ param = getParameter("hidefeaturegroups");
+ if (param != null)
+ {
+ applet.setFeatureGroupState(param, false);
+ }
+ // show specific groups
+ param = getParameter("showfeaturegroups");
+ if (param != null)
+ {
+ applet.setFeatureGroupState(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 (cp0)
+ { String[] v = new String[jv.size()];
+ for (int i=0; i