2 * Jalview - A Sequence Alignment Editor and Viewer
3 * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
24 import java.awt.event.*;
27 import jalview.appletgui.*;
28 import jalview.datamodel.*;
32 * Jalview Applet. Runs in Java 1.18 runtime
37 public class JalviewLite
43 ///////////////////////////////////////////
44 //The following public methods maybe called
45 //externally, eg via javascript in HTML page
47 * @return list of selected sequences separated by "¬"
49 public String getSelectedSequences()
51 return getSelectedSequencesFrom(getDefaultTargetFrame());
53 public String getSelectedSequencesFrom(AlignFrame alf)
55 StringBuffer result = new StringBuffer("");
57 if (alf.viewport.getSelectionGroup() != null)
59 SequenceI[] seqs = alf.viewport.getSelectionGroup().
61 alf.viewport.getAlignment());
63 for (int i = 0; i < seqs.length; i++)
65 result.append(seqs[i].getName() + "¬");
69 return result.toString();
72 public String getAlignment(String format)
74 return getAlignmentFrom(getDefaultTargetFrame(), format, "true");
76 public String getAlignmentFrom(AlignFrame alf, String format)
78 return getAlignmentFrom(alf, format, "true");
80 public String getAlignment(String format, String suffix)
82 return getAlignmentFrom(getDefaultTargetFrame(), format, suffix);
84 public String getAlignmentFrom(AlignFrame alf, String format, String suffix)
88 boolean seqlimits = suffix.equalsIgnoreCase("true");
90 String reply = new AppletFormatAdapter().formatSequences(format,
91 alf.viewport.getAlignment(), seqlimits);
97 return "Error retrieving alignment in " + format + " format. ";
101 public void loadAnnotation(String annotation)
103 loadAnnotationFrom(getDefaultTargetFrame(), annotation);
105 public void loadAnnotationFrom(AlignFrame alf, String annotation)
107 if (new AnnotationFile().readAnnotationFile(
108 alf.getAlignViewport().getAlignment(), annotation,
109 AppletFormatAdapter.PASTE))
111 alf.alignPanel.fontChanged();
112 alf.alignPanel.setScrollValues(0, 0);
116 alf.parseFeaturesFile(annotation, AppletFormatAdapter.PASTE);
120 public String getFeatures(String format)
122 return getFeaturesFrom(getDefaultTargetFrame(), format);
124 public String getFeaturesFrom(AlignFrame alf, String format)
126 return alf.outputFeatures(false, format);
128 public String getAnnotation()
130 return getAnnotationFrom(getDefaultTargetFrame());
132 public String getAnnotationFrom(AlignFrame alf)
134 return alf.outputAnnotations(false);
136 public AlignFrame newView()
138 return newViewFrom(getDefaultTargetFrame());
140 public AlignFrame newView(String name)
142 return newViewFrom(getDefaultTargetFrame(), name);
145 public AlignFrame newViewFrom(AlignFrame alf)
147 return alf.newView(null);
149 public AlignFrame newViewFrom(AlignFrame alf, String name)
151 return alf.newView(name);
155 * @param text alignment file as a string
156 * @param title window title
157 * @return null or new alignment frame
159 public AlignFrame loadAlignment(String text, String title)
162 String format = new IdentifyFile().Identify(text, AppletFormatAdapter.PASTE);
165 al = new AppletFormatAdapter().readFile(text,
166 AppletFormatAdapter.PASTE,
168 if (al.getHeight() > 0)
170 return new AlignFrame(al, this, title, false);
173 catch (java.io.IOException ex)
175 ex.printStackTrace();
180 ////////////////////////////////////////////////
181 ////////////////////////////////////////////////
185 static int lastFrameX = 200;
186 static int lastFrameY = 200;
187 boolean fileFound = true;
188 String file = "No file";
189 Button launcher = new Button("Start Jalview");
192 * The currentAlignFrame is static, it will change
193 * if and when the user selects a new window.
194 * Note that it will *never* point back to the embedded AlignFrame
195 * if the applet is started as embedded on the page and then afterwards a new view is created.
197 public static AlignFrame currentAlignFrame;
200 * This is the first frame to be displayed, and does not change.
201 * API calls will default to this instance if currentAlignFrame is null.
203 AlignFrame initialAlignFrame;
205 boolean embedded = false;
207 public boolean jmolAvailable = false;
208 public static boolean debug;
211 * init method for Jalview Applet
215 String dbg = getParameter("debug");
218 debug = dbg.toLowerCase().equals("true");
221 * get the separator parameter if present
223 String sep = getParameter("separator");
230 System.err.println("Separator set to '"+separator+"'");
233 throw new Error("Invalid separator parameter - must be non-zero length");
239 String param = getParameter("RGB");
245 r = Integer.parseInt(param.substring(0, 2), 16);
246 g = Integer.parseInt(param.substring(2, 4), 16);
247 b = Integer.parseInt(param.substring(4, 6), 16);
257 param = getParameter("label");
260 launcher.setLabel(param);
263 this.setBackground(new Color(r, g, b));
265 file = getParameter("file");
269 //Maybe the sequences are added as parameters
270 StringBuffer data = new StringBuffer("PASTE");
272 while ( (file = getParameter("sequence" + i)) != null)
274 data.append(file.toString() + "\n");
277 if (data.length() > 5)
279 file = data.toString();
283 LoadJmolThread jmolAvailable = new LoadJmolThread();
284 jmolAvailable.start();
286 final JalviewLite applet = this;
287 if (getParameter("embedded") != null
288 && getParameter("embedded").equalsIgnoreCase("true"))
291 LoadingThread loader = new LoadingThread(file, applet);
294 else if (file != null)
298 launcher.addActionListener(new java.awt.event.ActionListener()
300 public void actionPerformed(ActionEvent e)
302 LoadingThread loader = new LoadingThread(file,
317 * Initialises and displays a new java.awt.Frame
319 * @param frame java.awt.Frame to be displayed
320 * @param title title of new frame
321 * @param width width if new frame
322 * @param height height of new frame
324 public static void addFrame(final Frame frame, String title, int width,
327 frame.setLocation(lastFrameX, lastFrameY);
330 frame.setSize(width, height);
331 frame.setTitle(title);
332 frame.addWindowListener(new WindowAdapter()
334 public void windowClosing(WindowEvent e)
336 if (frame instanceof AlignFrame)
338 ( (AlignFrame) frame).closeMenuItem_actionPerformed();
340 if (currentAlignFrame == frame)
342 currentAlignFrame = null;
346 frame.setMenuBar(null);
350 public void windowActivated(WindowEvent e)
352 if (frame instanceof AlignFrame)
354 currentAlignFrame = (AlignFrame) frame;
357 System.err.println("Activated window "+frame);
361 super.windowActivated(e);
363 /* Probably not necessary to do this - see TODO above.
365 * @see java.awt.event.WindowAdapter#windowDeactivated(java.awt.event.WindowEvent)
367 public void windowDeactivated(WindowEvent e)
369 if (currentAlignFrame == frame)
371 currentAlignFrame = null;
374 System.err.println("Deactivated window "+frame);
377 super.windowDeactivated(e);
381 frame.setVisible(true);
385 * This paints the background surrounding the "Launch Jalview button"
387 * <br>If file given in parameter not found, displays error message
389 * @param g graphics context
391 public void paint(Graphics g)
395 g.setColor(new Color(200, 200, 200));
396 g.setColor(Color.cyan);
397 g.fillRect(0, 0, getSize().width, getSize().height);
398 g.setColor(Color.red);
399 g.drawString("Jalview can't open file", 5, 15);
400 g.drawString("\"" + file + "\"", 5, 30);
404 g.setColor(Color.black);
405 g.setFont(new Font("Arial", Font.BOLD, 24));
406 g.drawString("Jalview Applet", 50, this.getSize().height / 2 - 30);
407 g.drawString("Loading Data...", 50, this.getSize().height / 2);
412 class LoadJmolThread extends Thread
418 if (!System.getProperty("java.version").startsWith("1.1"))
420 Class.forName("org.jmol.adapter.smarter.SmarterJmolAdapter");
421 jmolAvailable = true;
424 catch (java.lang.ClassNotFoundException ex)
426 System.out.println("Jmol not available - Using MCview for structures");
440 public LoadingThread(String _file,
445 System.err.println("Loading thread started with:\n>>file\n"+_file+">>endfile");
448 if (file.startsWith("PASTE"))
450 file = file.substring(5);
451 protocol = AppletFormatAdapter.PASTE;
453 else if (inArchive(file))
455 protocol = AppletFormatAdapter.CLASSLOADER;
459 file = addProtocol(file);
460 protocol = AppletFormatAdapter.URL;
464 System.err.println("Protocol identified as '"+protocol+"'");
466 format = new jalview.io.IdentifyFile().Identify(file, protocol);
469 System.err.println("File identified as '"+format+"'");
479 private void startLoading()
484 al = new AppletFormatAdapter().readFile(file, protocol,
487 catch (java.io.IOException ex)
489 ex.printStackTrace();
491 if ( (al != null) && (al.getHeight() > 0))
493 initialAlignFrame = new AlignFrame(al,
498 currentAlignFrame = initialAlignFrame;
500 if (protocol == jalview.io.AppletFormatAdapter.PASTE)
502 currentAlignFrame.setTitle("Sequences from " + getDocumentBase());
505 currentAlignFrame.statusBar.setText("Successfully loaded file " + file);
507 String treeFile = applet.getParameter("tree");
508 if (treeFile == null)
510 treeFile = applet.getParameter("treeFile");
513 if (treeFile != null)
517 if (inArchive(treeFile))
519 protocol = AppletFormatAdapter.CLASSLOADER;
523 protocol = AppletFormatAdapter.URL;
524 treeFile = addProtocol(treeFile);
527 jalview.io.NewickFile fin = new jalview.io.NewickFile(treeFile,
532 if (fin.getTree() != null)
534 currentAlignFrame.loadTree(fin, treeFile);
539 ex.printStackTrace();
543 String param = getParameter("features");
546 if (!inArchive(param))
548 param = addProtocol(param);
551 currentAlignFrame.parseFeaturesFile(param, protocol);
554 param = getParameter("showFeatureSettings");
555 if (param != null && param.equalsIgnoreCase("true"))
557 currentAlignFrame.viewport.showSequenceFeatures(true);
558 new FeatureSettings(currentAlignFrame.alignPanel);
561 param = getParameter("annotations");
564 if (!inArchive(param))
566 param = addProtocol(param);
569 new AnnotationFile().readAnnotationFile(
570 currentAlignFrame.viewport.getAlignment(),
574 currentAlignFrame.alignPanel.fontChanged();
575 currentAlignFrame.alignPanel.setScrollValues(0, 0);
579 param = getParameter("jnetfile");
584 if (inArchive(param))
586 protocol = AppletFormatAdapter.CLASSLOADER;
590 protocol = AppletFormatAdapter.URL;
591 param = addProtocol(param);
594 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
596 new JnetAnnotationMaker().add_annotation(predictions,
597 currentAlignFrame.viewport.getAlignment(),
598 0, false); // do not add sequence profile from concise output
599 currentAlignFrame.alignPanel.fontChanged();
600 currentAlignFrame.alignPanel.setScrollValues(0, 0);
604 ex.printStackTrace();
609 <param name="PDBfile" value="1gaq.txt PDB|1GAQ|1GAQ|A PDB|1GAQ|1GAQ|B PDB|1GAQ|1GAQ|C">
611 <param name="PDBfile2" value="1gaq.txt A=SEQA B=SEQB C=SEQB">
613 <param name="PDBfile3" value="1q0o Q45135_9MICO">
617 int pdbFileCount = 0;
619 if (pdbFileCount > 0)
620 param = getParameter("PDBFILE" + pdbFileCount);
622 param = getParameter("PDBFILE");
626 PDBEntry pdb = new PDBEntry();
629 SequenceI[] seqs = null;
630 String [] chains = null;
632 StringTokenizer st = new StringTokenizer(param, " ");
634 if (st.countTokens() < 2)
636 String sequence = applet.getParameter("PDBSEQ");
637 if (sequence != null)
638 seqs = new SequenceI[]
640 (Sequence) currentAlignFrame.
641 getAlignViewport().getAlignment().
647 param = st.nextToken();
648 Vector tmp = new Vector();
649 Vector tmp2 = new Vector();
651 while (st.hasMoreTokens())
653 seqstring = st.nextToken();
654 StringTokenizer st2 = new StringTokenizer(seqstring,"=");
655 if(st2.countTokens()>1)
658 tmp2.addElement(st2.nextToken());
659 seqstring = st2.nextToken();
661 tmp.addElement( (Sequence) currentAlignFrame.
662 getAlignViewport().getAlignment().
663 findName(seqstring));
666 seqs = new SequenceI[tmp.size()];
668 if(tmp2.size()==tmp.size())
670 chains = new String[tmp2.size()];
671 tmp2.copyInto(chains);
675 if (inArchive(param) && !jmolAvailable)
677 protocol = AppletFormatAdapter.CLASSLOADER;
681 protocol = AppletFormatAdapter.URL;
682 param = addProtocol(param);
689 for (int i = 0; i < seqs.length; i++)
691 ( (Sequence) seqs[i]).addPDBId(pdb);
696 new jalview.appletgui.AppletJmol(pdb,
699 currentAlignFrame.alignPanel,
705 new MCview.AppletPDBViewer(pdb,
708 currentAlignFrame.alignPanel,
715 while(pdbFileCount < 10);
717 /////////////////////////////
718 // modify display of features
720 // hide specific groups
721 param = getParameter("hidefeaturegroups");
724 applet.setFeatureGroupState(param, false);
726 // show specific groups
727 param = getParameter("showfeaturegroups");
730 applet.setFeatureGroupState(param, true);
742 * Discovers whether the given file is in the Applet Archive
746 boolean inArchive(String file)
748 //This might throw a security exception in certain browsers
749 //Netscape Communicator for instance.
752 return (getClass().getResourceAsStream("/" + file) != null);
756 System.out.println("Exception checking resources: " + file + " " + ex);
761 String addProtocol(String file)
763 if (file.indexOf("://") == -1)
765 file = getCodeBase() + file;
772 * @return the default alignFrame acted on by the public applet methods.
773 * May return null with an error message on System.err indicating the fact.
775 protected AlignFrame getDefaultTargetFrame()
777 if (currentAlignFrame!=null)
779 return currentAlignFrame;
781 if (initialAlignFrame!=null)
783 return initialAlignFrame;
785 System.err.println("Implementation error: Jalview Applet API cannot work out which AlignFrame to use.");
789 * separator used for separatorList
791 protected String separator = "|"; // this is a safe(ish) separator - tabs don't work for firefox
793 * parse the string into a list
795 * @return elements separated by separator
797 public String[] separatorListToArray(String list)
799 int seplen = separator.length();
800 if (list==null || list.equals(""))
802 java.util.Vector jv = new Vector();
804 while ((pos=list.indexOf(separator,cp))>cp)
806 jv.addElement(list.substring(cp,pos));
809 if (cp<list.length())
811 jv.addElement(list.substring(cp));
814 { String[] v = new String[jv.size()];
815 for (int i=0; i<v.length; i++)
817 v[i] = (String) jv.elementAt(i);
819 jv.removeAllElements();
822 System.err.println("Array from '"+separator+"' separated List:\n"+v.length);
823 for (int i=0; i<v.length;i++)
825 System.err.println("item "+i+" '"+v[i]+"'");
832 System.err.println("Empty Array from '"+separator+"' separated List");
837 * concatenate the list with separator
839 * @return concatenated string
841 public String arrayToSeparatorList(String[] list)
843 StringBuffer v = new StringBuffer();
846 for (int i=0,iSize=list.length-1;i<iSize;i++)
854 if (list[list.length-1]!=null)
855 { v.append(list[list.length-1]);
859 System.err.println("Returning '"+separator+"' separated List:\n");
860 System.err.println(v);
866 System.err.println("Returning empty '"+separator+"' separated List\n");
872 * @see jalview.appletgui.AlignFrame#getFeatureGroups()
874 public String getFeatureGroups()
876 String lst = arrayToSeparatorList(getDefaultTargetFrame().getFeatureGroups());
880 * @param alf alignframe to get feature groups on
882 * @see jalview.appletgui.AlignFrame#getFeatureGroups()
884 public String getFeatureGroupsOn(AlignFrame alf)
886 String lst = arrayToSeparatorList(alf.getFeatureGroups());
892 * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean)
894 public String getFeatureGroupsOfState(boolean visible)
896 return arrayToSeparatorList(getDefaultTargetFrame().getFeatureGroupsOfState(visible));
899 * @param alf align frame to get groups of state visible
902 * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean)
904 public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)
906 return arrayToSeparatorList(alf.getFeatureGroupsOfState(visible));
908 * @param groups tab separated list of group names
909 * @param state true or false
910 * @see jalview.appletgui.AlignFrame#setFeatureGroupState(java.lang.String[], boolean)
912 public void setFeatureGroupStateOn(AlignFrame alf, String groups, boolean state)
914 boolean st = state;//!(state==null || state.equals("") || state.toLowerCase().equals("false"));
915 alf.setFeatureGroupState(separatorListToArray(groups), st);
917 public void setFeatureGroupState(String groups, boolean state)
919 setFeatureGroupStateOn(getDefaultTargetFrame(), groups, state);
922 * List separator string
923 * @return the separator
925 public String getSeparator()
930 * List separator string
931 * @param separator the separator to set
933 public void setSeparator(String separator)
935 this.separator = separator;