-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 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" <br>
- * <br>
- * 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;
-
- 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()
- {
- 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()
- {
- 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();
- }
- }
-
- /*
- * <param name="PDBfile" value="1gaq.txt PDB|1GAQ|1GAQ|A PDB|1GAQ|1GAQ|B
- * PDB|1GAQ|1GAQ|C">
- *
- * <param name="PDBfile2" value="1gaq.txt A=SEQA B=SEQB C=SEQB">
- *
- * <param name="PDBfile3" value="1q0o Q45135_9MICO">
- */
-
- 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: 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,
- 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 (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;
- }
-}
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
+ */\r
+package jalview.bin;\r
+\r
+import jalview.api.StructureSelectionManagerProvider;\r
+import jalview.appletgui.AlignFrame;\r
+import jalview.appletgui.AlignViewport;\r
+import jalview.appletgui.EmbmenuFrame;\r
+import jalview.appletgui.FeatureSettings;\r
+import jalview.datamodel.Alignment;\r
+import jalview.datamodel.AlignmentI;\r
+import jalview.datamodel.AlignmentOrder;\r
+import jalview.datamodel.ColumnSelection;\r
+import jalview.datamodel.PDBEntry;\r
+import jalview.datamodel.Sequence;\r
+import jalview.datamodel.SequenceGroup;\r
+import jalview.datamodel.SequenceI;\r
+import jalview.io.AnnotationFile;\r
+import jalview.io.AppletFormatAdapter;\r
+import jalview.io.FileParse;\r
+import jalview.io.IdentifyFile;\r
+import jalview.io.JnetAnnotationMaker;\r
+import jalview.javascript.JSFunctionExec;\r
+import jalview.javascript.JalviewLiteJsApi;\r
+import jalview.javascript.JsCallBack;\r
+import jalview.structure.SelectionListener;\r
+import jalview.structure.StructureSelectionManager;\r
+\r
+import java.applet.Applet;\r
+import java.awt.Button;\r
+import java.awt.Color;\r
+import java.awt.Component;\r
+import java.awt.EventQueue;\r
+import java.awt.Font;\r
+import java.awt.Frame;\r
+import java.awt.Graphics;\r
+import java.awt.event.ActionEvent;\r
+import java.awt.event.WindowAdapter;\r
+import java.awt.event.WindowEvent;\r
+import java.io.BufferedReader;\r
+import java.io.InputStreamReader;\r
+import java.net.URL;\r
+import java.util.Hashtable;\r
+import java.util.StringTokenizer;\r
+import java.util.Vector;\r
+\r
+import netscape.javascript.JSObject;\r
+\r
+/**\r
+ * Jalview Applet. Runs in Java 1.18 runtime\r
+ * \r
+ * @author $author$\r
+ * @version $Revision: 1.92 $\r
+ */\r
+public class JalviewLite extends Applet implements\r
+ StructureSelectionManagerProvider, JalviewLiteJsApi\r
+{\r
+\r
+ public StructureSelectionManager getStructureSelectionManager()\r
+ {\r
+ return StructureSelectionManager.getStructureSelectionManager(this);\r
+ }\r
+\r
+ // /////////////////////////////////////////\r
+ // The following public methods maybe called\r
+ // externally, eg via javascript in HTML page\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences()\r
+ */\r
+ public String getSelectedSequences()\r
+ {\r
+ return getSelectedSequencesFrom(getDefaultTargetFrame());\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences(java.lang.String)\r
+ */\r
+ public String getSelectedSequences(String sep)\r
+ {\r
+ return getSelectedSequencesFrom(getDefaultTargetFrame(), sep);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui\r
+ * .AlignFrame)\r
+ */\r
+ public String getSelectedSequencesFrom(AlignFrame alf)\r
+ {\r
+ return getSelectedSequencesFrom(alf, separator); // ""+0x00AC);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui\r
+ * .AlignFrame, java.lang.String)\r
+ */\r
+ public String getSelectedSequencesFrom(AlignFrame alf, String sep)\r
+ {\r
+ StringBuffer result = new StringBuffer("");\r
+ if (sep == null || sep.length() == 0)\r
+ {\r
+ sep = separator; // "+0x00AC;\r
+ }\r
+ if (alf.viewport.getSelectionGroup() != null)\r
+ {\r
+ SequenceI[] seqs = alf.viewport.getSelectionGroup()\r
+ .getSequencesInOrder(alf.viewport.getAlignment());\r
+\r
+ for (int i = 0; i < seqs.length; i++)\r
+ {\r
+ result.append(seqs[i].getName());\r
+ result.append(sep);\r
+ }\r
+ }\r
+\r
+ return result.toString();\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#highlight(java.lang.String,\r
+ * java.lang.String, java.lang.String)\r
+ */\r
+ public void highlight(String sequenceId, String position,\r
+ String alignedPosition)\r
+ {\r
+ highlightIn(getDefaultTargetFrame(), sequenceId, position,\r
+ alignedPosition);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#highlightIn(jalview.appletgui.AlignFrame,\r
+ * java.lang.String, java.lang.String, java.lang.String)\r
+ */\r
+ public void highlightIn(final AlignFrame alf, final String sequenceId,\r
+ final String position, final String alignedPosition)\r
+ {\r
+ // TODO: could try to highlight in all alignments if alf==null\r
+ jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(\r
+ alf.viewport.getAlignment().getSequencesArray());\r
+ final SequenceI sq = matcher.findIdMatch(sequenceId);\r
+ if (sq != null)\r
+ {\r
+ int apos = -1;\r
+ try\r
+ {\r
+ apos = new Integer(position).intValue();\r
+ apos--;\r
+ } catch (NumberFormatException ex)\r
+ {\r
+ return;\r
+ }\r
+ final StructureSelectionManagerProvider me = this;\r
+ final int pos = apos;\r
+ // use vamsas listener to broadcast to all listeners in scope\r
+ if (alignedPosition != null\r
+ && (alignedPosition.trim().length() == 0 || alignedPosition\r
+ .toLowerCase().indexOf("false") > -1))\r
+ {\r
+ java.awt.EventQueue.invokeLater(new Runnable()\r
+ {\r
+ @Override\r
+ public void run()\r
+ {\r
+ StructureSelectionManager.getStructureSelectionManager(me)\r
+ .mouseOverVamsasSequence(sq, sq.findIndex(pos), null);\r
+ }\r
+ });\r
+ }\r
+ else\r
+ {\r
+ java.awt.EventQueue.invokeLater(new Runnable()\r
+ {\r
+ @Override\r
+ public void run()\r
+ {\r
+ StructureSelectionManager.getStructureSelectionManager(me)\r
+ .mouseOverVamsasSequence(sq, pos, null);\r
+ }\r
+ });\r
+ }\r
+ }\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#select(java.lang.String,\r
+ * java.lang.String)\r
+ */\r
+ public void select(String sequenceIds, String columns)\r
+ {\r
+ selectIn(getDefaultTargetFrame(), sequenceIds, columns, separator);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#select(java.lang.String,\r
+ * java.lang.String, java.lang.String)\r
+ */\r
+ public void select(String sequenceIds, String columns, String sep)\r
+ {\r
+ selectIn(getDefaultTargetFrame(), sequenceIds, columns, sep);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#selectIn(jalview.appletgui.AlignFrame,\r
+ * java.lang.String, java.lang.String)\r
+ */\r
+ public void selectIn(AlignFrame alf, String sequenceIds, String columns)\r
+ {\r
+ selectIn(alf, sequenceIds, columns, separator);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#selectIn(jalview.appletgui.AlignFrame,\r
+ * java.lang.String, java.lang.String, java.lang.String)\r
+ */\r
+ public void selectIn(final AlignFrame alf, String sequenceIds,\r
+ String columns, String sep)\r
+ {\r
+ if (sep == null || sep.length() == 0)\r
+ {\r
+ sep = separator;\r
+ }\r
+ else\r
+ {\r
+ if (debug)\r
+ {\r
+ System.err.println("Selecting region using separator string '"\r
+ + separator + "'");\r
+ }\r
+ }\r
+ // deparse fields\r
+ String[] ids = separatorListToArray(sequenceIds, sep);\r
+ String[] cols = separatorListToArray(columns, sep);\r
+ final SequenceGroup sel = new SequenceGroup();\r
+ final ColumnSelection csel = new ColumnSelection();\r
+ AlignmentI al = alf.viewport.getAlignment();\r
+ jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(\r
+ alf.viewport.getAlignment().getSequencesArray());\r
+ int start = 0, end = al.getWidth(), alw = al.getWidth();\r
+ boolean seqsfound = true;\r
+ if (ids != null && ids.length > 0)\r
+ {\r
+ seqsfound = false;\r
+ for (int i = 0; i < ids.length; i++)\r
+ {\r
+ if (ids[i].trim().length() == 0)\r
+ {\r
+ continue;\r
+ }\r
+ SequenceI sq = matcher.findIdMatch(ids[i]);\r
+ if (sq != null)\r
+ {\r
+ seqsfound = true;\r
+ sel.addSequence(sq, false);\r
+ }\r
+ }\r
+ }\r
+ boolean inseqpos = false;\r
+ if (cols != null && cols.length > 0)\r
+ {\r
+ boolean seset = false;\r
+ for (int i = 0; i < cols.length; i++)\r
+ {\r
+ String cl = cols[i].trim();\r
+ if (cl.length() == 0)\r
+ {\r
+ continue;\r
+ }\r
+ int p;\r
+ if ((p = cl.indexOf("-")) > -1)\r
+ {\r
+ int from = -1, to = -1;\r
+ try\r
+ {\r
+ from = new Integer(cl.substring(0, p)).intValue();\r
+ from--;\r
+ } catch (NumberFormatException ex)\r
+ {\r
+ System.err\r
+ .println("ERROR: Couldn't parse first integer in range element column selection string '"\r
+ + cl + "' - format is 'from-to'");\r
+ return;\r
+ }\r
+ try\r
+ {\r
+ to = new Integer(cl.substring(p + 1)).intValue();\r
+ to--;\r
+ } catch (NumberFormatException ex)\r
+ {\r
+ System.err\r
+ .println("ERROR: Couldn't parse second integer in range element column selection string '"\r
+ + cl + "' - format is 'from-to'");\r
+ return;\r
+ }\r
+ if (from >= 0 && to >= 0)\r
+ {\r
+ // valid range\r
+ if (from < to)\r
+ {\r
+ int t = to;\r
+ to = from;\r
+ to = t;\r
+ }\r
+ if (!seset)\r
+ {\r
+ start = from;\r
+ end = to;\r
+ seset = true;\r
+ }\r
+ else\r
+ {\r
+ // comment to prevent range extension\r
+ if (start > from)\r
+ {\r
+ start = from;\r
+ }\r
+ if (end < to)\r
+ {\r
+ end = to;\r
+ }\r
+ }\r
+ for (int r = from; r <= to; r++)\r
+ {\r
+ if (r >= 0 && r < alw)\r
+ {\r
+ csel.addElement(r);\r
+ }\r
+ }\r
+ if (debug)\r
+ {\r
+ System.err.println("Range '" + cl + "' deparsed as [" + from\r
+ + "," + to + "]");\r
+ }\r
+ }\r
+ else\r
+ {\r
+ System.err.println("ERROR: Invalid Range '" + cl\r
+ + "' deparsed as [" + from + "," + to + "]");\r
+ }\r
+ }\r
+ else\r
+ {\r
+ int r = -1;\r
+ try\r
+ {\r
+ r = new Integer(cl).intValue();\r
+ r--;\r
+ } catch (NumberFormatException ex)\r
+ {\r
+ if (cl.toLowerCase().equals("sequence"))\r
+ {\r
+ // we are in the dataset sequence's coordinate frame.\r
+ inseqpos = true;\r
+ }\r
+ else\r
+ {\r
+ System.err\r
+ .println("ERROR: Couldn't parse integer from point selection element of column selection string '"\r
+ + cl + "'");\r
+ return;\r
+ }\r
+ }\r
+ if (r >= 0 && r <= alw)\r
+ {\r
+ if (!seset)\r
+ {\r
+ start = r;\r
+ end = r;\r
+ seset = true;\r
+ }\r
+ else\r
+ {\r
+ // comment to prevent range extension\r
+ if (start > r)\r
+ {\r
+ start = r;\r
+ }\r
+ if (end < r)\r
+ {\r
+ end = r;\r
+ }\r
+ }\r
+ csel.addElement(r);\r
+ if (debug)\r
+ {\r
+ System.err.println("Point selection '" + cl\r
+ + "' deparsed as [" + r + "]");\r
+ }\r
+ }\r
+ else\r
+ {\r
+ System.err.println("ERROR: Invalid Point selection '" + cl\r
+ + "' deparsed as [" + r + "]");\r
+ }\r
+ }\r
+ }\r
+ }\r
+ if (seqsfound)\r
+ {\r
+ // we only propagate the selection when it was the null selection, or the\r
+ // given sequences were found in the alignment.\r
+ if (inseqpos && sel.getSize() > 0)\r
+ {\r
+ // assume first sequence provides reference frame ?\r
+ SequenceI rs = sel.getSequenceAt(0);\r
+ start = rs.findIndex(start);\r
+ end = rs.findIndex(end);\r
+ if (csel != null)\r
+ {\r
+ Vector cs = csel.getSelected();\r
+ csel.clear();\r
+ for (int csi = 0, csiS = cs.size(); csi < csiS; csi++)\r
+ {\r
+ csel.addElement(rs.findIndex(((Integer) cs.elementAt(csi))\r
+ .intValue()));\r
+ }\r
+ }\r
+ }\r
+ sel.setStartRes(start);\r
+ sel.setEndRes(end);\r
+ EventQueue.invokeLater(new Runnable()\r
+ {\r
+ @Override\r
+ public void run()\r
+ {\r
+ alf.select(sel, csel);\r
+ }\r
+ });\r
+ }\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.bin.JalviewLiteJsApi#getSelectedSequencesAsAlignment(java.lang.\r
+ * String, java.lang.String)\r
+ */\r
+ public String getSelectedSequencesAsAlignment(String format, String suffix)\r
+ {\r
+ return getSelectedSequencesAsAlignmentFrom(getDefaultTargetFrame(),\r
+ format, suffix);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.bin.JalviewLiteJsApi#getSelectedSequencesAsAlignmentFrom(jalview\r
+ * .appletgui.AlignFrame, java.lang.String, java.lang.String)\r
+ */\r
+ public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,\r
+ String format, String suffix)\r
+ {\r
+ try\r
+ {\r
+ boolean seqlimits = suffix.equalsIgnoreCase("true");\r
+ if (alf.viewport.getSelectionGroup() != null)\r
+ {\r
+ String reply = new AppletFormatAdapter().formatSequences(format,\r
+ new Alignment(alf.viewport.getSelectionAsNewSequence()),\r
+ seqlimits);\r
+ return reply;\r
+ }\r
+ } catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ return "Error retrieving alignment in " + format + " format. ";\r
+ }\r
+ return "";\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#getAlignmentOrder()\r
+ */\r
+ public String getAlignmentOrder()\r
+ {\r
+ return getAlignmentOrderFrom(getDefaultTargetFrame());\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame\r
+ * )\r
+ */\r
+ public String getAlignmentOrderFrom(AlignFrame alf)\r
+ {\r
+ return getAlignmentOrderFrom(alf, separator);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame\r
+ * , java.lang.String)\r
+ */\r
+ public String getAlignmentOrderFrom(AlignFrame alf, String sep)\r
+ {\r
+ AlignmentI alorder = alf.getAlignViewport().getAlignment();\r
+ String[] order = new String[alorder.getHeight()];\r
+ for (int i = 0; i < order.length; i++)\r
+ {\r
+ order[i] = alorder.getSequenceAt(i).getName();\r
+ }\r
+ return arrayToSeparatorList(order);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#orderBy(java.lang.String,\r
+ * java.lang.String)\r
+ */\r
+ public String orderBy(String order, String undoName)\r
+ {\r
+ return orderBy(order, undoName, separator);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#orderBy(java.lang.String,\r
+ * java.lang.String, java.lang.String)\r
+ */\r
+ public String orderBy(String order, String undoName, String sep)\r
+ {\r
+ return orderAlignmentBy(getDefaultTargetFrame(), order, undoName, sep);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.bin.JalviewLiteJsApi#orderAlignmentBy(jalview.appletgui.AlignFrame,\r
+ * java.lang.String, java.lang.String, java.lang.String)\r
+ */\r
+ public String orderAlignmentBy(AlignFrame alf, String order,\r
+ String undoName, String sep)\r
+ {\r
+ String[] ids = separatorListToArray(order, sep);\r
+ SequenceI[] sqs = null;\r
+ if (ids != null && ids.length > 0)\r
+ {\r
+ jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(\r
+ alf.viewport.getAlignment().getSequencesArray());\r
+ int s = 0;\r
+ sqs = new SequenceI[ids.length];\r
+ for (int i = 0; i < ids.length; i++)\r
+ {\r
+ if (ids[i].trim().length() == 0)\r
+ {\r
+ continue;\r
+ }\r
+ SequenceI sq = matcher.findIdMatch(ids[i]);\r
+ if (sq != null)\r
+ {\r
+ sqs[s++] = sq;\r
+ }\r
+ }\r
+ if (s > 0)\r
+ {\r
+ SequenceI[] sqq = new SequenceI[s];\r
+ System.arraycopy(sqs, 0, sqq, 0, s);\r
+ sqs = sqq;\r
+ }\r
+ else\r
+ {\r
+ sqs = null;\r
+ }\r
+ }\r
+ if (sqs == null)\r
+ {\r
+ return "";\r
+ }\r
+ ;\r
+ final AlignmentOrder aorder = new AlignmentOrder(sqs);\r
+\r
+ if (undoName != null && undoName.trim().length() == 0)\r
+ {\r
+ undoName = null;\r
+ }\r
+ final String _undoName = undoName;\r
+ // TODO: deal with synchronization here: cannot raise any events until after\r
+ // this has returned.\r
+ return alf.sortBy(aorder, _undoName) ? "true" : "";\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#getAlignment(java.lang.String)\r
+ */\r
+ public String getAlignment(String format)\r
+ {\r
+ return getAlignmentFrom(getDefaultTargetFrame(), format, "true");\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame,\r
+ * java.lang.String)\r
+ */\r
+ public String getAlignmentFrom(AlignFrame alf, String format)\r
+ {\r
+ return getAlignmentFrom(alf, format, "true");\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#getAlignment(java.lang.String,\r
+ * java.lang.String)\r
+ */\r
+ public String getAlignment(String format, String suffix)\r
+ {\r
+ return getAlignmentFrom(getDefaultTargetFrame(), format, suffix);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame,\r
+ * java.lang.String, java.lang.String)\r
+ */\r
+ public String getAlignmentFrom(AlignFrame alf, String format,\r
+ String suffix)\r
+ {\r
+ try\r
+ {\r
+ boolean seqlimits = suffix.equalsIgnoreCase("true");\r
+\r
+ String reply = new AppletFormatAdapter().formatSequences(format,\r
+ alf.viewport.getAlignment(), seqlimits);\r
+ return reply;\r
+ } catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ return "Error retrieving alignment in " + format + " format. ";\r
+ }\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String)\r
+ */\r
+ public void loadAnnotation(String annotation)\r
+ {\r
+ loadAnnotationFrom(getDefaultTargetFrame(), annotation);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame\r
+ * , java.lang.String)\r
+ */\r
+ public void loadAnnotationFrom(AlignFrame alf, String annotation)\r
+ {\r
+ if (new AnnotationFile().readAnnotationFile(alf.getAlignViewport()\r
+ .getAlignment(), annotation, AppletFormatAdapter.PASTE))\r
+ {\r
+ alf.alignPanel.fontChanged();\r
+ alf.alignPanel.setScrollValues(0, 0);\r
+ }\r
+ else\r
+ {\r
+ alf.parseFeaturesFile(annotation, AppletFormatAdapter.PASTE);\r
+ }\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#getFeatures(java.lang.String)\r
+ */\r
+ public String getFeatures(String format)\r
+ {\r
+ return getFeaturesFrom(getDefaultTargetFrame(), format);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.bin.JalviewLiteJsApi#getFeaturesFrom(jalview.appletgui.AlignFrame,\r
+ * java.lang.String)\r
+ */\r
+ public String getFeaturesFrom(AlignFrame alf, String format)\r
+ {\r
+ return alf.outputFeatures(false, format);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#getAnnotation()\r
+ */\r
+ public String getAnnotation()\r
+ {\r
+ return getAnnotationFrom(getDefaultTargetFrame());\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.bin.JalviewLiteJsApi#getAnnotationFrom(jalview.appletgui.AlignFrame\r
+ * )\r
+ */\r
+ public String getAnnotationFrom(AlignFrame alf)\r
+ {\r
+ return alf.outputAnnotations(false);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#newView()\r
+ */\r
+ public AlignFrame newView()\r
+ {\r
+ return newViewFrom(getDefaultTargetFrame());\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#newView(java.lang.String)\r
+ */\r
+ public AlignFrame newView(String name)\r
+ {\r
+ return newViewFrom(getDefaultTargetFrame(), name);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame)\r
+ */\r
+ public AlignFrame newViewFrom(AlignFrame alf)\r
+ {\r
+ return alf.newView(null);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame,\r
+ * java.lang.String)\r
+ */\r
+ public AlignFrame newViewFrom(AlignFrame alf, String name)\r
+ {\r
+ return alf.newView(name);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#loadAlignment(java.lang.String,\r
+ * java.lang.String)\r
+ */\r
+ public AlignFrame loadAlignment(String text, String title)\r
+ {\r
+ Alignment al = null;\r
+\r
+ String format = new IdentifyFile().Identify(text,\r
+ AppletFormatAdapter.PASTE);\r
+ try\r
+ {\r
+ al = new AppletFormatAdapter().readFile(text,\r
+ AppletFormatAdapter.PASTE, format);\r
+ if (al.getHeight() > 0)\r
+ {\r
+ return new AlignFrame(al, this, title, false);\r
+ }\r
+ } catch (java.io.IOException ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ return null;\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#setMouseoverListener(java.lang.String)\r
+ */\r
+ public void setMouseoverListener(String listener)\r
+ {\r
+ setMouseoverListener(currentAlignFrame, listener);\r
+ }\r
+\r
+ private Vector<jalview.javascript.JSFunctionExec> javascriptListeners = new Vector<jalview.javascript.JSFunctionExec>();\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.bin.JalviewLiteJsApi#setMouseoverListener(jalview.appletgui.AlignFrame\r
+ * , java.lang.String)\r
+ */\r
+ public void setMouseoverListener(AlignFrame af, String listener)\r
+ {\r
+ if (listener != null)\r
+ {\r
+ listener = listener.trim();\r
+ if (listener.length() == 0)\r
+ {\r
+ System.err\r
+ .println("jalview Javascript error: Ignoring empty function for mouseover listener.");\r
+ return;\r
+ }\r
+ }\r
+ jalview.javascript.MouseOverListener mol = new jalview.javascript.MouseOverListener(\r
+ this, af, listener);\r
+ javascriptListeners.addElement(mol);\r
+ StructureSelectionManager.getStructureSelectionManager(this)\r
+ .addStructureViewerListener(mol);\r
+ if (debug)\r
+ {\r
+ System.err.println("Added a mouseover listener for "\r
+ + ((af == null) ? "All frames" : "Just views for "\r
+ + af.getAlignViewport().getSequenceSetId()));\r
+ System.err.println("There are now " + javascriptListeners.size()\r
+ + " listeners in total.");\r
+ }\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#setSelectionListener(java.lang.String)\r
+ */\r
+ public void setSelectionListener(String listener)\r
+ {\r
+ setSelectionListener(null, listener);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.bin.JalviewLiteJsApi#setSelectionListener(jalview.appletgui.AlignFrame\r
+ * , java.lang.String)\r
+ */\r
+ public void setSelectionListener(AlignFrame af, String listener)\r
+ {\r
+ if (listener != null)\r
+ {\r
+ listener = listener.trim();\r
+ if (listener.length() == 0)\r
+ {\r
+ System.err\r
+ .println("jalview Javascript error: Ignoring empty function for selection listener.");\r
+ return;\r
+ }\r
+ }\r
+ jalview.javascript.JsSelectionSender mol = new jalview.javascript.JsSelectionSender(\r
+ this, af, listener);\r
+ javascriptListeners.addElement(mol);\r
+ StructureSelectionManager.getStructureSelectionManager(this)\r
+ .addSelectionListener(mol);\r
+ if (debug)\r
+ {\r
+ System.err.println("Added a selection listener for "\r
+ + ((af == null) ? "All frames" : "Just views for "\r
+ + af.getAlignViewport().getSequenceSetId()));\r
+ System.err.println("There are now " + javascriptListeners.size()\r
+ + " listeners in total.");\r
+ }\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#setStructureListener(java.lang.String,\r
+ * java.lang.String)\r
+ */\r
+ public void setStructureListener(String listener, String modelSet)\r
+ {\r
+ if (listener != null)\r
+ {\r
+ listener = listener.trim();\r
+ if (listener.length() == 0)\r
+ {\r
+ System.err\r
+ .println("jalview Javascript error: Ignoring empty function for selection listener.");\r
+ return;\r
+ }\r
+ }\r
+ jalview.javascript.MouseOverStructureListener mol = new jalview.javascript.MouseOverStructureListener(\r
+ this, listener, separatorListToArray(modelSet));\r
+ javascriptListeners.addElement(mol);\r
+ StructureSelectionManager.getStructureSelectionManager(this)\r
+ .addStructureViewerListener(mol);\r
+ if (debug)\r
+ {\r
+ System.err.println("Added a javascript structure viewer listener '"\r
+ + listener + "'");\r
+ System.err.println("There are now " + javascriptListeners.size()\r
+ + " listeners in total.");\r
+ }\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.bin.JalviewLiteJsApi#removeJavascriptListener(jalview.appletgui\r
+ * .AlignFrame, java.lang.String)\r
+ */\r
+ public void removeJavascriptListener(AlignFrame af, String listener)\r
+ {\r
+ if (listener != null)\r
+ {\r
+ listener = listener.trim();\r
+ if (listener.length() == 0)\r
+ {\r
+ listener = null;\r
+ }\r
+ }\r
+ boolean rprt = false;\r
+ for (int ms = 0, msSize = javascriptListeners.size(); ms < msSize;)\r
+ {\r
+ Object lstn = javascriptListeners.elementAt(ms);\r
+ JsCallBack lstner = (JsCallBack) lstn;\r
+ if ((af == null || lstner.getAlignFrame() == af)\r
+ && (listener == null || lstner.getListenerFunction().equals(\r
+ listener)))\r
+ {\r
+ javascriptListeners.removeElement(lstner);\r
+ msSize--;\r
+ if (lstner instanceof SelectionListener)\r
+ {\r
+ StructureSelectionManager.getStructureSelectionManager(this)\r
+ .removeSelectionListener((SelectionListener) lstner);\r
+ }\r
+ else\r
+ {\r
+ StructureSelectionManager.getStructureSelectionManager(this)\r
+ .removeStructureViewerListener(lstner, null);\r
+ }\r
+ rprt = debug;\r
+ if (debug)\r
+ {\r
+ System.err.println("Removed listener '" + listener + "'");\r
+ }\r
+ }\r
+ else\r
+ {\r
+ ms++;\r
+ }\r
+ }\r
+ if (rprt)\r
+ {\r
+ System.err.println("There are now " + javascriptListeners.size()\r
+ + " listeners in total.");\r
+ }\r
+ }\r
+\r
+ public void stop()\r
+ {\r
+ System.err.println("Applet " + getName() + " stop().");\r
+ tidyUp();\r
+ }\r
+\r
+ public void destroy()\r
+ {\r
+ System.err.println("Applet " + getName() + " destroy().");\r
+ tidyUp();\r
+ }\r
+\r
+ private void tidyUp()\r
+ {\r
+ removeAll();\r
+ if (currentAlignFrame != null && currentAlignFrame.viewport != null\r
+ && currentAlignFrame.viewport.applet != null)\r
+ {\r
+ AlignViewport av = currentAlignFrame.viewport;\r
+ currentAlignFrame.closeMenuItem_actionPerformed();\r
+ av.applet = null;\r
+ currentAlignFrame = null;\r
+ }\r
+ if (javascriptListeners != null)\r
+ {\r
+ while (javascriptListeners.size() > 0)\r
+ {\r
+ jalview.javascript.JSFunctionExec mol = javascriptListeners\r
+ .elementAt(0);\r
+ javascriptListeners.removeElement(mol);\r
+ if (mol instanceof SelectionListener)\r
+ {\r
+ StructureSelectionManager.getStructureSelectionManager(this)\r
+ .removeSelectionListener((SelectionListener) mol);\r
+ }\r
+ else\r
+ {\r
+ StructureSelectionManager.getStructureSelectionManager(this)\r
+ .removeStructureViewerListener(mol, null);\r
+ }\r
+ mol.jvlite = null;\r
+ }\r
+ }\r
+ if (jsFunctionExec != null)\r
+ {\r
+ jsFunctionExec.stopQueue();\r
+ jsFunctionExec.jvlite = null;\r
+ }\r
+ initialAlignFrame = null;\r
+ jsFunctionExec = null;\r
+ javascriptListeners = null;\r
+ StructureSelectionManager.release(this);\r
+ }\r
+\r
+ private jalview.javascript.JSFunctionExec jsFunctionExec;\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#mouseOverStructure(java.lang.String,\r
+ * java.lang.String, java.lang.String)\r
+ */\r
+ public void mouseOverStructure(final String pdbResNum,\r
+ final String chain, final String pdbfile)\r
+ {\r
+ final StructureSelectionManagerProvider me = this;\r
+ java.awt.EventQueue.invokeLater(new Runnable()\r
+ {\r
+ @Override\r
+ public void run()\r
+ {\r
+ try\r
+ {\r
+ StructureSelectionManager.getStructureSelectionManager(me)\r
+ .mouseOverStructure(new Integer(pdbResNum).intValue(),\r
+ chain, pdbfile);\r
+ if (debug)\r
+ {\r
+ System.err.println("mouseOver for '" + pdbResNum\r
+ + "' in chain '" + chain + "' in structure '" + pdbfile\r
+ + "'");\r
+ }\r
+ } catch (NumberFormatException e)\r
+ {\r
+ System.err.println("Ignoring invalid residue number string '"\r
+ + pdbResNum + "'");\r
+ }\r
+\r
+ }\r
+ });\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.bin.JalviewLiteJsApi#scrollViewToIn(jalview.appletgui.AlignFrame,\r
+ * java.lang.String, java.lang.String)\r
+ */\r
+ public void scrollViewToIn(final AlignFrame alf, final String topRow,\r
+ final String leftHandColumn)\r
+ {\r
+ java.awt.EventQueue.invokeLater(new Runnable()\r
+ {\r
+ @Override\r
+ public void run()\r
+ {\r
+ try\r
+ {\r
+ alf.scrollTo(new Integer(topRow).intValue(), new Integer(\r
+ leftHandColumn).intValue());\r
+\r
+ } catch (Exception ex)\r
+ {\r
+ System.err.println("Couldn't parse integer arguments (topRow='"\r
+ + topRow + "' and leftHandColumn='" + leftHandColumn\r
+ + "')");\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+ });\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.javascript.JalviewLiteJsApi#scrollViewToRowIn(jalview.appletgui\r
+ * .AlignFrame, java.lang.String)\r
+ */\r
+ @Override\r
+ public void scrollViewToRowIn(final AlignFrame alf, final String topRow)\r
+ {\r
+\r
+ java.awt.EventQueue.invokeLater(new Runnable()\r
+ {\r
+ @Override\r
+ public void run()\r
+ {\r
+ try\r
+ {\r
+ alf.scrollToRow(new Integer(topRow).intValue());\r
+\r
+ } catch (Exception ex)\r
+ {\r
+ System.err.println("Couldn't parse integer arguments (topRow='"\r
+ + topRow + "')");\r
+ ex.printStackTrace();\r
+ }\r
+\r
+ }\r
+ });\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.javascript.JalviewLiteJsApi#scrollViewToColumnIn(jalview.appletgui\r
+ * .AlignFrame, java.lang.String)\r
+ */\r
+ @Override\r
+ public void scrollViewToColumnIn(final AlignFrame alf,\r
+ final String leftHandColumn)\r
+ {\r
+ java.awt.EventQueue.invokeLater(new Runnable()\r
+ {\r
+\r
+ @Override\r
+ public void run()\r
+ {\r
+ try\r
+ {\r
+ alf.scrollToColumn(new Integer(leftHandColumn).intValue());\r
+\r
+ } catch (Exception ex)\r
+ {\r
+ System.err\r
+ .println("Couldn't parse integer arguments (leftHandColumn='"\r
+ + leftHandColumn + "')");\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+ });\r
+\r
+ }\r
+\r
+ // //////////////////////////////////////////////\r
+ // //////////////////////////////////////////////\r
+\r
+ public static int lastFrameX = 200;\r
+\r
+ public static int lastFrameY = 200;\r
+\r
+ boolean fileFound = true;\r
+\r
+ String file = "No file";\r
+\r
+ Button launcher = new Button("Start Jalview");\r
+\r
+ /**\r
+ * The currentAlignFrame is static, it will change if and when the user\r
+ * selects a new window. Note that it will *never* point back to the embedded\r
+ * AlignFrame if the applet is started as embedded on the page and then\r
+ * afterwards a new view is created.\r
+ */\r
+ public AlignFrame currentAlignFrame = null;\r
+\r
+ /**\r
+ * This is the first frame to be displayed, and does not change. API calls\r
+ * will default to this instance if currentAlignFrame is null.\r
+ */\r
+ AlignFrame initialAlignFrame = null;\r
+\r
+ boolean embedded = false;\r
+\r
+ private boolean checkForJmol = true;\r
+\r
+ private boolean checkedForJmol = false; // ensure we don't check for jmol\r
+\r
+ // every time the app is re-inited\r
+\r
+ public boolean jmolAvailable = false;\r
+\r
+ private boolean alignPdbStructures = false;\r
+\r
+ /**\r
+ * use an external structure viewer exclusively (no jmols or MCViews will be\r
+ * opened by JalviewLite itself)\r
+ */\r
+ public boolean useXtrnalSviewer = false;\r
+\r
+ public static boolean debug = false;\r
+\r
+ static String builddate = null, version = null;\r
+\r
+ private static void initBuildDetails()\r
+ {\r
+ if (builddate == null)\r
+ {\r
+ builddate = "unknown";\r
+ version = "test";\r
+ java.net.URL url = JalviewLite.class\r
+ .getResource("/.build_properties");\r
+ if (url != null)\r
+ {\r
+ try\r
+ {\r
+ BufferedReader reader = new BufferedReader(new InputStreamReader(\r
+ url.openStream()));\r
+ String line;\r
+ while ((line = reader.readLine()) != null)\r
+ {\r
+ if (line.indexOf("VERSION") > -1)\r
+ {\r
+ version = line.substring(line.indexOf("=") + 1);\r
+ }\r
+ if (line.indexOf("BUILD_DATE") > -1)\r
+ {\r
+ builddate = line.substring(line.indexOf("=") + 1);\r
+ }\r
+ }\r
+ } catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ public static String getBuildDate()\r
+ {\r
+ initBuildDetails();\r
+ return builddate;\r
+ }\r
+\r
+ public static String getVersion()\r
+ {\r
+ initBuildDetails();\r
+ return version;\r
+ }\r
+\r
+ // public JSObject scriptObject = null;\r
+\r
+ /**\r
+ * init method for Jalview Applet\r
+ */\r
+ public void init()\r
+ {\r
+ // remove any handlers that might be hanging around from an earlier instance\r
+ try\r
+ {\r
+ if (debug)\r
+ {\r
+ System.err.println("Applet context is '"\r
+ + getAppletContext().getClass().toString() + "'");\r
+ }\r
+ JSObject scriptObject = JSObject.getWindow(this);\r
+ if (debug && scriptObject != null)\r
+ {\r
+ System.err.println("Applet has Javascript callback support.");\r
+ }\r
+\r
+ } catch (Exception ex)\r
+ {\r
+ System.err\r
+ .println("Warning: No JalviewLite javascript callbacks available.");\r
+ if (debug)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+ /**\r
+ * turn on extra applet debugging\r
+ */\r
+ String dbg = getParameter("debug");\r
+ if (dbg != null)\r
+ {\r
+ debug = dbg.toLowerCase().equals("true");\r
+ }\r
+ if (debug)\r
+ {\r
+\r
+ System.err.println("JalviewLite Version " + getVersion());\r
+ System.err.println("Build Date : " + getBuildDate());\r
+\r
+ }\r
+ String externalsviewer = getParameter("externalstructureviewer");\r
+ if (externalsviewer != null)\r
+ {\r
+ useXtrnalSviewer = externalsviewer.trim().toLowerCase()\r
+ .equals("true");\r
+ }\r
+ /**\r
+ * if true disable the check for jmol\r
+ */\r
+ String chkforJmol = getParameter("nojmol");\r
+ if (chkforJmol != null)\r
+ {\r
+ checkForJmol = !chkforJmol.equals("true");\r
+ }\r
+ /**\r
+ * get the separator parameter if present\r
+ */\r
+ String sep = getParameter("separator");\r
+ if (sep != null)\r
+ {\r
+ if (sep.length() > 0)\r
+ {\r
+ separator = sep;\r
+ if (debug)\r
+ {\r
+ System.err.println("Separator set to '" + separator + "'");\r
+ }\r
+ }\r
+ else\r
+ {\r
+ throw new Error(\r
+ "Invalid separator parameter - must be non-zero length");\r
+ }\r
+ }\r
+ int r = 255;\r
+ int g = 255;\r
+ int b = 255;\r
+ String param = getParameter("RGB");\r
+\r
+ if (param != null)\r
+ {\r
+ try\r
+ {\r
+ r = Integer.parseInt(param.substring(0, 2), 16);\r
+ g = Integer.parseInt(param.substring(2, 4), 16);\r
+ b = Integer.parseInt(param.substring(4, 6), 16);\r
+ } catch (Exception ex)\r
+ {\r
+ r = 255;\r
+ g = 255;\r
+ b = 255;\r
+ }\r
+ }\r
+ param = getParameter("label");\r
+ if (param != null)\r
+ {\r
+ launcher.setLabel(param);\r
+ }\r
+\r
+ setBackground(new Color(r, g, b));\r
+\r
+ file = getParameter("file");\r
+\r
+ if (file == null)\r
+ {\r
+ // Maybe the sequences are added as parameters\r
+ StringBuffer data = new StringBuffer("PASTE");\r
+ int i = 1;\r
+ while ((file = getParameter("sequence" + i)) != null)\r
+ {\r
+ data.append(file.toString() + "\n");\r
+ i++;\r
+ }\r
+ if (data.length() > 5)\r
+ {\r
+ file = data.toString();\r
+ }\r
+ }\r
+\r
+ final JalviewLite jvapplet = this;\r
+ if (getParameter("embedded") != null\r
+ && getParameter("embedded").equalsIgnoreCase("true"))\r
+ {\r
+ // Launch as embedded applet in page\r
+ embedded = true;\r
+ LoadingThread loader = new LoadingThread(file, jvapplet);\r
+ loader.start();\r
+ }\r
+ else if (file != null)\r
+ {\r
+ if (getParameter("showbutton") == null\r
+ || !getParameter("showbutton").equalsIgnoreCase("false"))\r
+ {\r
+ // Add the JalviewLite 'Button' to the page\r
+ add(launcher);\r
+ launcher.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ LoadingThread loader = new LoadingThread(file, jvapplet);\r
+ loader.start();\r
+ }\r
+ });\r
+ }\r
+ else\r
+ {\r
+ // Open jalviewLite immediately.\r
+ LoadingThread loader = new LoadingThread(file, jvapplet);\r
+ loader.start();\r
+ }\r
+ }\r
+ else\r
+ {\r
+ // jalview initialisation with no alignment. loadAlignment() method can\r
+ // still be called to open new alignments.\r
+ file = "NO FILE";\r
+ fileFound = false;\r
+ // callInitCallback();\r
+ }\r
+ }\r
+\r
+ private void callInitCallback()\r
+ {\r
+ String initjscallback = getParameter("oninit");\r
+ if (initjscallback == null)\r
+ {\r
+ return;\r
+ }\r
+ initjscallback = initjscallback.trim();\r
+ if (initjscallback.length() > 0)\r
+ {\r
+ JSObject scriptObject = null;\r
+ try\r
+ {\r
+ scriptObject = JSObject.getWindow(this);\r
+ } catch (Exception ex)\r
+ {\r
+ }\r
+ ;\r
+ if (scriptObject != null)\r
+ {\r
+ try\r
+ {\r
+ // do onInit with the JS executor thread\r
+ new JSFunctionExec(this).executeJavascriptFunction(true,\r
+ initjscallback, null, "Calling oninit callback '"\r
+ + initjscallback + "'.");\r
+ } catch (Exception e)\r
+ {\r
+ System.err.println("Exception when executing _oninit callback '"\r
+ + initjscallback + "'.");\r
+ e.printStackTrace();\r
+ }\r
+ }\r
+ else\r
+ {\r
+ System.err.println("Not executing _oninit callback '"\r
+ + initjscallback + "' - no scripting allowed.");\r
+ }\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Initialises and displays a new java.awt.Frame\r
+ * \r
+ * @param frame\r
+ * java.awt.Frame to be displayed\r
+ * @param title\r
+ * title of new frame\r
+ * @param width\r
+ * width if new frame\r
+ * @param height\r
+ * height of new frame\r
+ */\r
+ public static void addFrame(final Frame frame, String title, int width,\r
+ int height)\r
+ {\r
+ frame.setLocation(lastFrameX, lastFrameY);\r
+ lastFrameX += 40;\r
+ lastFrameY += 40;\r
+ frame.setSize(width, height);\r
+ frame.setTitle(title);\r
+ frame.addWindowListener(new WindowAdapter()\r
+ {\r
+ public void windowClosing(WindowEvent e)\r
+ {\r
+ if (frame instanceof AlignFrame)\r
+ {\r
+ AlignViewport vp = ((AlignFrame) frame).viewport;\r
+ ((AlignFrame) frame).closeMenuItem_actionPerformed();\r
+ if (vp.applet.currentAlignFrame == frame)\r
+ {\r
+ vp.applet.currentAlignFrame = null;\r
+ }\r
+ vp.applet = null;\r
+ vp = null;\r
+\r
+ }\r
+ lastFrameX -= 40;\r
+ lastFrameY -= 40;\r
+ if (frame instanceof EmbmenuFrame)\r
+ {\r
+ ((EmbmenuFrame) frame).destroyMenus();\r
+ }\r
+ frame.setMenuBar(null);\r
+ frame.dispose();\r
+ }\r
+\r
+ public void windowActivated(WindowEvent e)\r
+ {\r
+ if (frame instanceof AlignFrame)\r
+ {\r
+ ((AlignFrame) frame).viewport.applet.currentAlignFrame = (AlignFrame) frame;\r
+ if (debug)\r
+ {\r
+ System.err.println("Activated window " + frame);\r
+ }\r
+ }\r
+ // be good.\r
+ super.windowActivated(e);\r
+ }\r
+ /*\r
+ * Probably not necessary to do this - see TODO above. (non-Javadoc)\r
+ * \r
+ * @see\r
+ * java.awt.event.WindowAdapter#windowDeactivated(java.awt.event.WindowEvent\r
+ * )\r
+ * \r
+ * public void windowDeactivated(WindowEvent e) { if (currentAlignFrame ==\r
+ * frame) { currentAlignFrame = null; if (debug) {\r
+ * System.err.println("Deactivated window "+frame); } }\r
+ * super.windowDeactivated(e); }\r
+ */\r
+ });\r
+ frame.setVisible(true);\r
+ }\r
+\r
+ /**\r
+ * This paints the background surrounding the "Launch Jalview button" <br>\r
+ * <br>\r
+ * If file given in parameter not found, displays error message\r
+ * \r
+ * @param g\r
+ * graphics context\r
+ */\r
+ public void paint(Graphics g)\r
+ {\r
+ if (!fileFound)\r
+ {\r
+ g.setColor(new Color(200, 200, 200));\r
+ g.setColor(Color.cyan);\r
+ g.fillRect(0, 0, getSize().width, getSize().height);\r
+ g.setColor(Color.red);\r
+ g.drawString("Jalview can't open file", 5, 15);\r
+ g.drawString("\"" + file + "\"", 5, 30);\r
+ }\r
+ else if (embedded)\r
+ {\r
+ g.setColor(Color.black);\r
+ g.setFont(new Font("Arial", Font.BOLD, 24));\r
+ g.drawString("Jalview Applet", 50, getSize().height / 2 - 30);\r
+ g.drawString("Loading Data...", 50, getSize().height / 2);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * get all components associated with the applet of the given type\r
+ * \r
+ * @param class1\r
+ * @return\r
+ */\r
+ public Vector getAppletWindow(Class class1)\r
+ {\r
+ Vector wnds = new Vector();\r
+ Component[] cmp = getComponents();\r
+ if (cmp != null)\r
+ {\r
+ for (int i = 0; i < cmp.length; i++)\r
+ {\r
+ if (class1.isAssignableFrom(cmp[i].getClass()))\r
+ {\r
+ wnds.addElement(cmp);\r
+ }\r
+ }\r
+ }\r
+ return wnds;\r
+ }\r
+\r
+ class LoadJmolThread extends Thread\r
+ {\r
+ private boolean running = false;\r
+\r
+ public void run()\r
+ {\r
+ if (running || checkedForJmol)\r
+ {\r
+ return;\r
+ }\r
+ running = true;\r
+ if (checkForJmol)\r
+ {\r
+ try\r
+ {\r
+ if (!System.getProperty("java.version").startsWith("1.1"))\r
+ {\r
+ Class.forName("org.jmol.adapter.smarter.SmarterJmolAdapter");\r
+ jmolAvailable = true;\r
+ }\r
+ if (!jmolAvailable)\r
+ {\r
+ System.out\r
+ .println("Jmol not available - Using MCview for structures");\r
+ }\r
+ } catch (java.lang.ClassNotFoundException ex)\r
+ {\r
+ }\r
+ }\r
+ else\r
+ {\r
+ jmolAvailable = false;\r
+ if (debug)\r
+ {\r
+ System.err\r
+ .println("Skipping Jmol check. Will use MCView (probably)");\r
+ }\r
+ }\r
+ checkedForJmol = true;\r
+ running = false;\r
+ }\r
+\r
+ public boolean notFinished()\r
+ {\r
+ return running || !checkedForJmol;\r
+ }\r
+ }\r
+\r
+ class LoadingThread extends Thread\r
+ {\r
+ /**\r
+ * State variable: File source\r
+ */\r
+ String file;\r
+\r
+ /**\r
+ * State variable: protocol for access to file source\r
+ */\r
+ String protocol;\r
+\r
+ /**\r
+ * State variable: format of file source\r
+ */\r
+ String format;\r
+\r
+ String _file;\r
+\r
+ JalviewLite applet;\r
+\r
+ private void dbgMsg(String msg)\r
+ {\r
+ if (applet.debug)\r
+ {\r
+ System.err.println(msg);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * update the protocol state variable for accessing the datasource located\r
+ * by file.\r
+ * \r
+ * @param file\r
+ * @return possibly updated datasource string\r
+ */\r
+ public String setProtocolState(String file)\r
+ {\r
+ if (file.startsWith("PASTE"))\r
+ {\r
+ file = file.substring(5);\r
+ protocol = AppletFormatAdapter.PASTE;\r
+ }\r
+ else if (inArchive(file))\r
+ {\r
+ protocol = AppletFormatAdapter.CLASSLOADER;\r
+ }\r
+ else\r
+ {\r
+ file = addProtocol(file);\r
+ protocol = AppletFormatAdapter.URL;\r
+ }\r
+ dbgMsg("Protocol identified as '" + protocol + "'");\r
+ return file;\r
+ }\r
+\r
+ public LoadingThread(String _file, JalviewLite _applet)\r
+ {\r
+ this._file = _file;\r
+ applet = _applet;\r
+ }\r
+\r
+ public void run()\r
+ {\r
+ LoadJmolThread jmolchecker = new LoadJmolThread();\r
+ jmolchecker.start();\r
+ while (jmolchecker.notFinished())\r
+ {\r
+ // wait around until the Jmol check is complete.\r
+ try\r
+ {\r
+ Thread.sleep(2);\r
+ } catch (Exception e)\r
+ {\r
+ }\r
+ ;\r
+ }\r
+ startLoading();\r
+ // applet.callInitCallback();\r
+ }\r
+\r
+ private void startLoading()\r
+ {\r
+ AlignFrame newAlignFrame;\r
+ dbgMsg("Loading thread started with:\n>>file\n" + _file + ">>endfile");\r
+ file = setProtocolState(_file);\r
+\r
+ format = new jalview.io.IdentifyFile().Identify(file, protocol);\r
+ dbgMsg("File identified as '" + format + "'");\r
+ dbgMsg("Loading started.");\r
+ Alignment al = null;\r
+ try\r
+ {\r
+ al = new AppletFormatAdapter().readFile(file, protocol, format);\r
+ } catch (java.io.IOException ex)\r
+ {\r
+ dbgMsg("File load exception.");\r
+ ex.printStackTrace();\r
+ if (debug)\r
+ {\r
+ try\r
+ {\r
+ FileParse fp = new FileParse(file, protocol);\r
+ String ln = null;\r
+ dbgMsg(">>>Dumping contents of '" + file + "' " + "("\r
+ + protocol + ")");\r
+ while ((ln = fp.nextLine()) != null)\r
+ {\r
+ dbgMsg(ln);\r
+ }\r
+ dbgMsg(">>>Dump finished.");\r
+ } catch (Exception e)\r
+ {\r
+ System.err\r
+ .println("Exception when trying to dump the content of the file parameter.");\r
+ e.printStackTrace();\r
+ }\r
+ }\r
+ }\r
+ if ((al != null) && (al.getHeight() > 0))\r
+ {\r
+ dbgMsg("Successfully loaded file.");\r
+ newAlignFrame = new AlignFrame(al, applet, file, embedded);\r
+ if (initialAlignFrame == null)\r
+ {\r
+ initialAlignFrame = newAlignFrame;\r
+ }\r
+ // update the focus.\r
+ currentAlignFrame = newAlignFrame;\r
+\r
+ if (protocol == jalview.io.AppletFormatAdapter.PASTE)\r
+ {\r
+ newAlignFrame.setTitle("Sequences from "\r
+ + applet.getDocumentBase());\r
+ }\r
+\r
+ newAlignFrame.statusBar.setText("Successfully loaded file " + file);\r
+\r
+ String treeFile = applet.getParameter("tree");\r
+ if (treeFile == null)\r
+ {\r
+ treeFile = applet.getParameter("treeFile");\r
+ }\r
+\r
+ if (treeFile != null)\r
+ {\r
+ try\r
+ {\r
+ treeFile = setProtocolState(treeFile);\r
+ /*\r
+ * if (inArchive(treeFile)) { protocol =\r
+ * AppletFormatAdapter.CLASSLOADER; } else { protocol =\r
+ * AppletFormatAdapter.URL; treeFile = addProtocol(treeFile); }\r
+ */\r
+ jalview.io.NewickFile fin = new jalview.io.NewickFile(treeFile,\r
+ protocol);\r
+\r
+ fin.parse();\r
+\r
+ if (fin.getTree() != null)\r
+ {\r
+ newAlignFrame.loadTree(fin, treeFile);\r
+ dbgMsg("Successfuly imported tree.");\r
+ }\r
+ else\r
+ {\r
+ dbgMsg("Tree parameter did not resolve to a valid tree.");\r
+ }\r
+ } catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+\r
+ String param = applet.getParameter("features");\r
+ if (param != null)\r
+ {\r
+ param = setProtocolState(param);\r
+\r
+ newAlignFrame.parseFeaturesFile(param, protocol);\r
+ }\r
+\r
+ param = applet.getParameter("showFeatureSettings");\r
+ if (param != null && param.equalsIgnoreCase("true"))\r
+ {\r
+ newAlignFrame.viewport.showSequenceFeatures(true);\r
+ new FeatureSettings(newAlignFrame.alignPanel);\r
+ }\r
+\r
+ param = applet.getParameter("annotations");\r
+ if (param != null)\r
+ {\r
+ param = setProtocolState(param);\r
+\r
+ if (new AnnotationFile().readAnnotationFile(\r
+ newAlignFrame.viewport.getAlignment(), param, protocol))\r
+ {\r
+ newAlignFrame.alignPanel.fontChanged();\r
+ newAlignFrame.alignPanel.setScrollValues(0, 0);\r
+ }\r
+ else\r
+ {\r
+ System.err\r
+ .println("Annotations were not added from annotation file '"\r
+ + param + "'");\r
+ }\r
+\r
+ }\r
+\r
+ param = applet.getParameter("jnetfile");\r
+ if (param != null)\r
+ {\r
+ try\r
+ {\r
+ param = setProtocolState(param);\r
+ jalview.io.JPredFile predictions = new jalview.io.JPredFile(\r
+ param, protocol);\r
+ JnetAnnotationMaker.add_annotation(predictions,\r
+ newAlignFrame.viewport.getAlignment(), 0, false); // false==do\r
+ // not\r
+ // add\r
+ // sequence\r
+ // profile\r
+ // from\r
+ // concise\r
+ // output\r
+ newAlignFrame.alignPanel.fontChanged();\r
+ newAlignFrame.alignPanel.setScrollValues(0, 0);\r
+ } catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+ /*\r
+ * <param name="alignpdbfiles" value="false/true"/> Undocumented for 2.6\r
+ * - related to JAL-434\r
+ */\r
+ applet.setAlignPdbStructures(getDefaultParameter("alignpdbfiles",\r
+ false));\r
+ /*\r
+ * <param name="PDBfile" value="1gaq.txt PDB|1GAQ|1GAQ|A PDB|1GAQ|1GAQ|B\r
+ * PDB|1GAQ|1GAQ|C">\r
+ * \r
+ * <param name="PDBfile2" value="1gaq.txt A=SEQA B=SEQB C=SEQB">\r
+ * \r
+ * <param name="PDBfile3" value="1q0o Q45135_9MICO">\r
+ */\r
+\r
+ int pdbFileCount = 0;\r
+ // Accumulate pdbs here if they are heading for the same view (if\r
+ // alignPdbStructures is true)\r
+ Vector pdbs = new Vector();\r
+ // create a lazy matcher if we're asked to\r
+ jalview.analysis.SequenceIdMatcher matcher = (applet\r
+ .getDefaultParameter("relaxedidmatch", false)) ? new jalview.analysis.SequenceIdMatcher(\r
+ newAlignFrame.getAlignViewport().getAlignment()\r
+ .getSequencesArray()) : null;\r
+\r
+ do\r
+ {\r
+ if (pdbFileCount > 0)\r
+ {\r
+ param = applet.getParameter("PDBFILE" + pdbFileCount);\r
+ }\r
+ else\r
+ {\r
+ param = applet.getParameter("PDBFILE");\r
+ }\r
+\r
+ if (param != null)\r
+ {\r
+ PDBEntry pdb = new PDBEntry();\r
+\r
+ String seqstring;\r
+ SequenceI[] seqs = null;\r
+ String[] chains = null;\r
+\r
+ StringTokenizer st = new StringTokenizer(param, " ");\r
+\r
+ if (st.countTokens() < 2)\r
+ {\r
+ String sequence = applet.getParameter("PDBSEQ");\r
+ if (sequence != null)\r
+ seqs = new SequenceI[]\r
+ { matcher == null ? (Sequence) newAlignFrame\r
+ .getAlignViewport().getAlignment()\r
+ .findName(sequence) : matcher.findIdMatch(sequence) };\r
+\r
+ }\r
+ else\r
+ {\r
+ param = st.nextToken();\r
+ Vector tmp = new Vector();\r
+ Vector tmp2 = new Vector();\r
+\r
+ while (st.hasMoreTokens())\r
+ {\r
+ seqstring = st.nextToken();\r
+ StringTokenizer st2 = new StringTokenizer(seqstring, "=");\r
+ if (st2.countTokens() > 1)\r
+ {\r
+ // This is the chain\r
+ tmp2.addElement(st2.nextToken());\r
+ seqstring = st2.nextToken();\r
+ }\r
+ tmp.addElement(matcher == null ? (Sequence) newAlignFrame\r
+ .getAlignViewport().getAlignment()\r
+ .findName(seqstring) : matcher\r
+ .findIdMatch(seqstring));\r
+ }\r
+\r
+ seqs = new SequenceI[tmp.size()];\r
+ tmp.copyInto(seqs);\r
+ if (tmp2.size() == tmp.size())\r
+ {\r
+ chains = new String[tmp2.size()];\r
+ tmp2.copyInto(chains);\r
+ }\r
+ }\r
+ param = setProtocolState(param);\r
+\r
+ if (// !jmolAvailable\r
+ // &&\r
+ protocol == AppletFormatAdapter.CLASSLOADER\r
+ && !useXtrnalSviewer)\r
+ {\r
+ // Re: JAL-357 : the bug isn't a problem if we are using an\r
+ // external viewer!\r
+ // TODO: verify this Re:\r
+ // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605\r
+ // This exception preserves the current behaviour where, even if\r
+ // the local pdb file was identified in the class loader\r
+ protocol = AppletFormatAdapter.URL; // this is probably NOT\r
+ // CORRECT!\r
+ param = addProtocol(param); //\r
+ }\r
+\r
+ pdb.setFile(param);\r
+\r
+ if (seqs != null)\r
+ {\r
+ for (int i = 0; i < seqs.length; i++)\r
+ {\r
+ if (seqs[i] != null)\r
+ {\r
+ ((Sequence) seqs[i]).addPDBId(pdb);\r
+ }\r
+ else\r
+ {\r
+ if (JalviewLite.debug)\r
+ {\r
+ // this may not really be a problem but we give a warning\r
+ // anyway\r
+ System.err\r
+ .println("Warning: Possible input parsing error: Null sequence for attachment of PDB (sequence "\r
+ + i + ")");\r
+ }\r
+ }\r
+ }\r
+\r
+ if (!alignPdbStructures)\r
+ {\r
+ newAlignFrame.newStructureView(applet, pdb, seqs, chains,\r
+ protocol);\r
+ }\r
+ else\r
+ {\r
+ pdbs.addElement(new Object[]\r
+ { pdb, seqs, chains, new String(protocol) });\r
+ }\r
+ }\r
+ }\r
+\r
+ pdbFileCount++;\r
+ } while (param != null || pdbFileCount < 10);\r
+ if (pdbs.size() > 0)\r
+ {\r
+ SequenceI[][] seqs = new SequenceI[pdbs.size()][];\r
+ PDBEntry[] pdb = new PDBEntry[pdbs.size()];\r
+ String[][] chains = new String[pdbs.size()][];\r
+ String[] protocols = new String[pdbs.size()];\r
+ for (int pdbsi = 0, pdbsiSize = pdbs.size(); pdbsi < pdbsiSize; pdbsi++)\r
+ {\r
+ Object[] o = (Object[]) pdbs.elementAt(pdbsi);\r
+ pdb[pdbsi] = (PDBEntry) o[0];\r
+ seqs[pdbsi] = (SequenceI[]) o[1];\r
+ chains[pdbsi] = (String[]) o[2];\r
+ protocols[pdbsi] = (String) o[3];\r
+ }\r
+ newAlignFrame.alignedStructureView(applet, pdb, seqs, chains,\r
+ protocols);\r
+\r
+ }\r
+ // ///////////////////////////\r
+ // modify display of features\r
+ //\r
+ // hide specific groups\r
+ param = applet.getParameter("hidefeaturegroups");\r
+ if (param != null)\r
+ {\r
+ applet.setFeatureGroupStateOn(newAlignFrame, param, false);\r
+ }\r
+ // show specific groups\r
+ param = applet.getParameter("showfeaturegroups");\r
+ if (param != null)\r
+ {\r
+ applet.setFeatureGroupStateOn(newAlignFrame, param, true);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ fileFound = false;\r
+ applet.remove(launcher);\r
+ applet.repaint();\r
+ }\r
+ callInitCallback();\r
+ }\r
+\r
+ /**\r
+ * Discovers whether the given file is in the Applet Archive\r
+ * \r
+ * @param file\r
+ * String\r
+ * @return boolean\r
+ */\r
+ boolean inArchive(String file)\r
+ {\r
+ // This might throw a security exception in certain browsers\r
+ // Netscape Communicator for instance.\r
+ try\r
+ {\r
+ boolean rtn = (getClass().getResourceAsStream("/" + file) != null);\r
+ if (debug)\r
+ {\r
+ System.err.println("Resource '" + file + "' was "\r
+ + (rtn ? "" : "not") + " located by classloader.");\r
+ }\r
+ return rtn;\r
+ } catch (Exception ex)\r
+ {\r
+ System.out.println("Exception checking resources: " + file + " "\r
+ + ex);\r
+ return false;\r
+ }\r
+ }\r
+\r
+ String addProtocol(String file)\r
+ {\r
+ if (file.indexOf("://") == -1)\r
+ {\r
+ String fl = applet.resolveUrlForLocalOrAbsolute(file,\r
+ getDocumentBase());\r
+ try\r
+ {\r
+ if (new java.net.URL(fl).openStream() != null)\r
+ {\r
+ if (debug)\r
+ {\r
+ System.err.println("Prepended document base for resource: '"\r
+ + file + "'");\r
+ }\r
+ return fl;\r
+ }\r
+ } catch (Exception x)\r
+ {\r
+ }\r
+ ;\r
+ fl = applet.resolveUrlForLocalOrAbsolute(file, getCodeBase());\r
+ try\r
+ {\r
+ if (new java.net.URL(fl).openStream() != null)\r
+ {\r
+ if (debug)\r
+ {\r
+ System.err.println("Prepended codebase for resource: '"\r
+ + file + "'");\r
+ }\r
+ return fl;\r
+ }\r
+ } catch (Exception x)\r
+ {\r
+ }\r
+ ;\r
+\r
+ }\r
+\r
+ return file;\r
+ }\r
+ }\r
+\r
+ /**\r
+ * @return the default alignFrame acted on by the public applet methods. May\r
+ * return null with an error message on System.err indicating the\r
+ * fact.\r
+ */\r
+ public AlignFrame getDefaultTargetFrame()\r
+ {\r
+ if (currentAlignFrame != null)\r
+ {\r
+ return currentAlignFrame;\r
+ }\r
+ if (initialAlignFrame != null)\r
+ {\r
+ return initialAlignFrame;\r
+ }\r
+ System.err\r
+ .println("Implementation error: Jalview Applet API cannot work out which AlignFrame to use.");\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * separator used for separatorList\r
+ */\r
+ protected String separator = "" + ((char) 0x00AC); // the default used to be\r
+ // '|' but many sequence\r
+ // IDS include pipes.\r
+\r
+ /**\r
+ * set to enable the URL based javascript execution mechanism\r
+ */\r
+ public boolean jsfallbackEnabled = false;\r
+\r
+ /**\r
+ * parse the string into a list\r
+ * \r
+ * @param list\r
+ * @return elements separated by separator\r
+ */\r
+ public String[] separatorListToArray(String list)\r
+ {\r
+ return separatorListToArray(list, separator);\r
+ }\r
+\r
+ /**\r
+ * parse the string into a list\r
+ * \r
+ * @param list\r
+ * @param separator\r
+ * @return elements separated by separator\r
+ */\r
+ public String[] separatorListToArray(String list, String separator)\r
+ {\r
+ // note separator local variable intentionally masks object field\r
+ int seplen = separator.length();\r
+ if (list == null || list.equals("") || list.equals(separator))\r
+ return null;\r
+ java.util.Vector jv = new Vector();\r
+ int cp = 0, pos;\r
+ while ((pos = list.indexOf(separator, cp)) > cp)\r
+ {\r
+ jv.addElement(list.substring(cp, pos));\r
+ cp = pos + seplen;\r
+ }\r
+ if (cp < list.length())\r
+ {\r
+ String c = list.substring(cp);\r
+ if (!c.equals(separator))\r
+ {\r
+ jv.addElement(c);\r
+ }\r
+ }\r
+ if (jv.size() > 0)\r
+ {\r
+ String[] v = new String[jv.size()];\r
+ for (int i = 0; i < v.length; i++)\r
+ {\r
+ v[i] = (String) jv.elementAt(i);\r
+ }\r
+ jv.removeAllElements();\r
+ if (debug)\r
+ {\r
+ System.err.println("Array from '" + separator\r
+ + "' separated List:\n" + v.length);\r
+ for (int i = 0; i < v.length; i++)\r
+ {\r
+ System.err.println("item " + i + " '" + v[i] + "'");\r
+ }\r
+ }\r
+ return v;\r
+ }\r
+ if (debug)\r
+ {\r
+ System.err.println("Empty Array from '" + separator\r
+ + "' separated List");\r
+ }\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * concatenate the list with separator\r
+ * \r
+ * @param list\r
+ * @return concatenated string\r
+ */\r
+ public String arrayToSeparatorList(String[] list)\r
+ {\r
+ return arrayToSeparatorList(list, separator);\r
+ }\r
+\r
+ /**\r
+ * concatenate the list with separator\r
+ * \r
+ * @param list\r
+ * @param separator\r
+ * @return concatenated string\r
+ */\r
+ public String arrayToSeparatorList(String[] list, String separator)\r
+ {\r
+ StringBuffer v = new StringBuffer();\r
+ if (list != null && list.length > 0)\r
+ {\r
+ for (int i = 0, iSize = list.length; i < iSize; i++)\r
+ {\r
+ if (list[i] != null)\r
+ {\r
+ if (i > 0)\r
+ {\r
+ v.append(separator);\r
+ }\r
+ v.append(list[i]);\r
+ }\r
+ }\r
+ if (debug)\r
+ {\r
+ System.err.println("Returning '" + separator\r
+ + "' separated List:\n");\r
+ System.err.println(v);\r
+ }\r
+ return v.toString();\r
+ }\r
+ if (debug)\r
+ {\r
+ System.err.println("Returning empty '" + separator\r
+ + "' separated List\n");\r
+ }\r
+ return "" + separator;\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#getFeatureGroups()\r
+ */\r
+ public String getFeatureGroups()\r
+ {\r
+ String lst = arrayToSeparatorList(getDefaultTargetFrame()\r
+ .getFeatureGroups());\r
+ return lst;\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.bin.JalviewLiteJsApi#getFeatureGroupsOn(jalview.appletgui.AlignFrame\r
+ * )\r
+ */\r
+ public String getFeatureGroupsOn(AlignFrame alf)\r
+ {\r
+ String lst = arrayToSeparatorList(alf.getFeatureGroups());\r
+ return lst;\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfState(boolean)\r
+ */\r
+ public String getFeatureGroupsOfState(boolean visible)\r
+ {\r
+ return arrayToSeparatorList(getDefaultTargetFrame()\r
+ .getFeatureGroupsOfState(visible));\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfStateOn(jalview.appletgui\r
+ * .AlignFrame, boolean)\r
+ */\r
+ public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)\r
+ {\r
+ return arrayToSeparatorList(alf.getFeatureGroupsOfState(visible));\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#setFeatureGroupStateOn(jalview.appletgui.\r
+ * AlignFrame, java.lang.String, boolean)\r
+ */\r
+ public void setFeatureGroupStateOn(final AlignFrame alf,\r
+ final String groups, boolean state)\r
+ {\r
+ final boolean st = state;// !(state==null || state.equals("") ||\r
+ // state.toLowerCase().equals("false"));\r
+ java.awt.EventQueue.invokeLater(new Runnable()\r
+ {\r
+ @Override\r
+ public void run()\r
+ {\r
+ alf.setFeatureGroupState(separatorListToArray(groups), st);\r
+ }\r
+ });\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#setFeatureGroupState(java.lang.String,\r
+ * boolean)\r
+ */\r
+ public void setFeatureGroupState(String groups, boolean state)\r
+ {\r
+ setFeatureGroupStateOn(getDefaultTargetFrame(), groups, state);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#getSeparator()\r
+ */\r
+ public String getSeparator()\r
+ {\r
+ return separator;\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#setSeparator(java.lang.String)\r
+ */\r
+ public void setSeparator(String separator)\r
+ {\r
+ if (separator == null || separator.length() < 1)\r
+ {\r
+ // reset to default\r
+ separator = "" + ((char) 0x00AC);\r
+ }\r
+ this.separator = separator;\r
+ if (debug)\r
+ {\r
+ System.err.println("Default Separator now: '" + separator + "'");\r
+ }\r
+ }\r
+\r
+ /**\r
+ * get boolean value of applet parameter 'name' and return default if\r
+ * parameter is not set\r
+ * \r
+ * @param name\r
+ * name of paremeter\r
+ * @param def\r
+ * the value to return otherwise\r
+ * @return true or false\r
+ */\r
+ public boolean getDefaultParameter(String name, boolean def)\r
+ {\r
+ String stn;\r
+ if ((stn = getParameter(name)) == null)\r
+ {\r
+ return def;\r
+ }\r
+ if (stn.toLowerCase().equals("true"))\r
+ {\r
+ return true;\r
+ }\r
+ return false;\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#addPdbFile(jalview.appletgui.AlignFrame,\r
+ * java.lang.String, java.lang.String, java.lang.String)\r
+ */\r
+ public boolean addPdbFile(AlignFrame alFrame, String sequenceId,\r
+ String pdbEntryString, String pdbFile)\r
+ {\r
+ return alFrame.addPdbFile(sequenceId, pdbEntryString, pdbFile);\r
+ }\r
+\r
+ protected void setAlignPdbStructures(boolean alignPdbStructures)\r
+ {\r
+ this.alignPdbStructures = alignPdbStructures;\r
+ }\r
+\r
+ public boolean isAlignPdbStructures()\r
+ {\r
+ return alignPdbStructures;\r
+ }\r
+\r
+ public void start()\r
+ {\r
+ // callInitCallback();\r
+ }\r
+\r
+ private Hashtable<String, long[]> jshashes = new Hashtable<String, long[]>();\r
+\r
+ private Hashtable<String, Hashtable<String, String[]>> jsmessages = new Hashtable<String, Hashtable<String, String[]>>();\r
+\r
+ public void setJsMessageSet(String messageclass, String viewId,\r
+ String[] colcommands)\r
+ {\r
+ Hashtable<String, String[]> msgset = jsmessages.get(messageclass);\r
+ if (msgset == null)\r
+ {\r
+ msgset = new Hashtable<String, String[]>();\r
+ jsmessages.put(messageclass, msgset);\r
+ }\r
+ msgset.put(viewId, colcommands);\r
+ long[] l = new long[colcommands.length];\r
+ for (int i = 0; i < colcommands.length; i++)\r
+ {\r
+ l[i] = colcommands[i].hashCode();\r
+ }\r
+ jshashes.put(messageclass + "|" + viewId, l);\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see jalview.bin.JalviewLiteJsApi#getJsMessage(java.lang.String,\r
+ * java.lang.String)\r
+ */\r
+ public String getJsMessage(String messageclass, String viewId)\r
+ {\r
+ Hashtable<String, String[]> msgset = jsmessages.get(messageclass);\r
+ if (msgset != null)\r
+ {\r
+ String[] msgs = msgset.get(viewId);\r
+ if (msgs != null)\r
+ {\r
+ for (int i = 0; i < msgs.length; i++)\r
+ {\r
+ if (msgs[i] != null)\r
+ {\r
+ String m = msgs[i];\r
+ msgs[i] = null;\r
+ return m;\r
+ }\r
+ }\r
+ }\r
+ }\r
+ return "";\r
+ }\r
+\r
+ public boolean isJsMessageSetChanged(String string, String string2,\r
+ String[] colcommands)\r
+ {\r
+ long[] l = jshashes.get(string + "|" + string2);\r
+ if (l == null && colcommands != null)\r
+ {\r
+ return true;\r
+ }\r
+ for (int i = 0; i < colcommands.length; i++)\r
+ {\r
+ if (l[i] != colcommands[i].hashCode())\r
+ {\r
+ return true;\r
+ }\r
+ }\r
+ return false;\r
+ }\r
+\r
+ private Vector jsExecQueue = new Vector();\r
+\r
+ public Vector getJsExecQueue()\r
+ {\r
+ return jsExecQueue;\r
+ }\r
+\r
+ public void setExecutor(JSFunctionExec jsFunctionExec2)\r
+ {\r
+ jsFunctionExec = jsFunctionExec2;\r
+ }\r
+\r
+ /**\r
+ * return the given colour value parameter or the given default if parameter\r
+ * not given\r
+ * \r
+ * @param colparam\r
+ * @param defcolour\r
+ * @return\r
+ */\r
+ public Color getDefaultColourParameter(String colparam, Color defcolour)\r
+ {\r
+ String colprop = getParameter(colparam);\r
+ if (colprop == null || colprop.trim().length() == 0)\r
+ {\r
+ return defcolour;\r
+ }\r
+ Color col = jalview.schemes.ColourSchemeProperty\r
+ .getAWTColorFromName(colprop);\r
+ if (col == null)\r
+ {\r
+ try\r
+ {\r
+ col = new jalview.schemes.UserColourScheme(colprop).findColour('A');\r
+ } catch (Exception ex)\r
+ {\r
+ System.err.println("Couldn't parse '" + colprop\r
+ + "' as a colour for " + colparam);\r
+ col = null;\r
+ }\r
+ }\r
+ return (col == null) ? defcolour : col;\r
+\r
+ }\r
+\r
+ public void openJalviewHelpUrl()\r
+ {\r
+ String helpUrl = getParameter("jalviewhelpurl");\r
+ if (helpUrl == null || helpUrl.trim().length() < 5)\r
+ {\r
+ helpUrl = "http://www.jalview.org/help.html";\r
+ }\r
+ showURL(helpUrl, "HELP");\r
+ }\r
+\r
+ /**\r
+ * form a complete URL given a path to a resource and a reference location on\r
+ * the same server\r
+ * \r
+ * @param url\r
+ * - an absolute path on the same server as localref or a document\r
+ * located relative to localref\r
+ * @param localref\r
+ * - a URL on the same server as url\r
+ * @return a complete URL for the resource located by url\r
+ */\r
+ private String resolveUrlForLocalOrAbsolute(String url, URL localref)\r
+ {\r
+ String codebase = localref.toString();\r
+ if (url.indexOf("/") == 0)\r
+ {\r
+ url = codebase.substring(0, codebase.length()\r
+ - localref.getFile().length())\r
+ + url;\r
+ }\r
+ else\r
+ {\r
+ url = localref + url;\r
+ }\r
+ return url;\r
+ }\r
+\r
+ /**\r
+ * open a URL in the browser - resolving it according to relative refs and\r
+ * coping with javascript: protocol if necessary.\r
+ * \r
+ * @param url\r
+ * @param target\r
+ */\r
+ public void showURL(String url, String target)\r
+ {\r
+ try\r
+ {\r
+ if (url.indexOf(":") == -1)\r
+ {\r
+ // TODO: verify (Bas Vroling bug) prepend codebase or server URL to\r
+ // form valid URL\r
+ // Should really use docbase, not codebase.\r
+ URL prepend;\r
+ url = resolveUrlForLocalOrAbsolute(\r
+ url,\r
+ prepend = getDefaultParameter("resolvetocodebase", false) ? getDocumentBase()\r
+ : getCodeBase());\r
+ if (debug)\r
+ {\r
+ System.err\r
+ .println("Show url (prepended "\r
+ + prepend\r
+ + " - toggle resolvetocodebase if code/docbase resolution is wrong): "\r
+ + url);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ if (debug)\r
+ {\r
+ System.err.println("Show url: " + url);\r
+ }\r
+ }\r
+ if (url.indexOf("javascript:") == 0)\r
+ {\r
+ // no target for the javascript context\r
+ getAppletContext().showDocument(new java.net.URL(url));\r
+ }\r
+ else\r
+ {\r
+ getAppletContext().showDocument(new java.net.URL(url), target);\r
+ }\r
+ } catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+\r
+ /**\r
+ * bind structures in a viewer to any matching sequences in an alignFrame (use\r
+ * sequenceIds to limit scope of search to specific sequences)\r
+ * \r
+ * @param alFrame\r
+ * @param viewer\r
+ * @param sequenceIds\r
+ * @return TODO: consider making an exception structure for indicating when\r
+ * binding fails public SequenceStructureBinding\r
+ * addStructureViewInstance( AlignFrame alFrame, Object viewer, String\r
+ * sequenceIds) {\r
+ * \r
+ * if (sequenceIds != null && sequenceIds.length() > 0) { return\r
+ * alFrame.addStructureViewInstance(viewer,\r
+ * separatorListToArray(sequenceIds)); } else { return\r
+ * alFrame.addStructureViewInstance(viewer, null); } // return null; }\r
+ */\r
+}\r
git://source.jalview.org / jalview.git / blobdiff