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 if (frame instanceof EmbmenuFrame)
348 ((EmbmenuFrame) frame).destroyMenus();
350 frame.setMenuBar(null);
354 public void windowActivated(WindowEvent e)
356 if (frame instanceof AlignFrame)
358 currentAlignFrame = (AlignFrame) frame;
361 System.err.println("Activated window "+frame);
365 super.windowActivated(e);
367 /* Probably not necessary to do this - see TODO above.
369 * @see java.awt.event.WindowAdapter#windowDeactivated(java.awt.event.WindowEvent)
371 public void windowDeactivated(WindowEvent e)
373 if (currentAlignFrame == frame)
375 currentAlignFrame = null;
378 System.err.println("Deactivated window "+frame);
381 super.windowDeactivated(e);
385 frame.setVisible(true);
389 * This paints the background surrounding the "Launch Jalview button"
391 * <br>If file given in parameter not found, displays error message
393 * @param g graphics context
395 public void paint(Graphics g)
399 g.setColor(new Color(200, 200, 200));
400 g.setColor(Color.cyan);
401 g.fillRect(0, 0, getSize().width, getSize().height);
402 g.setColor(Color.red);
403 g.drawString("Jalview can't open file", 5, 15);
404 g.drawString("\"" + file + "\"", 5, 30);
408 g.setColor(Color.black);
409 g.setFont(new Font("Arial", Font.BOLD, 24));
410 g.drawString("Jalview Applet", 50, this.getSize().height / 2 - 30);
411 g.drawString("Loading Data...", 50, this.getSize().height / 2);
416 class LoadJmolThread extends Thread
422 if (!System.getProperty("java.version").startsWith("1.1"))
424 Class.forName("org.jmol.adapter.smarter.SmarterJmolAdapter");
425 jmolAvailable = true;
428 catch (java.lang.ClassNotFoundException ex)
430 System.out.println("Jmol not available - Using MCview for structures");
440 * State variable: File source
444 * State variable: protocol for access to file source
448 * State variable: format of file source
452 private void dbgMsg(String msg)
456 System.err.println(msg);
460 * update the protocol state variable for accessing the datasource
463 * @return possibly updated datasource string
465 public String setProtocolState(String file)
467 if (file.startsWith("PASTE"))
469 file = file.substring(5);
470 protocol = AppletFormatAdapter.PASTE;
472 else if (inArchive(file))
474 protocol = AppletFormatAdapter.CLASSLOADER;
478 file = addProtocol(file);
479 protocol = AppletFormatAdapter.URL;
481 dbgMsg("Protocol identified as '"+protocol+"'");
484 public LoadingThread(String _file,
487 dbgMsg("Loading thread started with:\n>>file\n"+_file+">>endfile");
488 file = setProtocolState(_file);
490 format = new jalview.io.IdentifyFile().Identify(file, protocol);
491 dbgMsg("File identified as '"+format+"'");
500 private void startLoading()
502 dbgMsg("Loading started.");
506 al = new AppletFormatAdapter().readFile(file, protocol,
509 catch (java.io.IOException ex)
511 dbgMsg("File load exception.");
512 ex.printStackTrace();
514 if ( (al != null) && (al.getHeight() > 0))
516 dbgMsg("Successfully loaded file.");
517 initialAlignFrame = new AlignFrame(al,
522 currentAlignFrame = initialAlignFrame;
524 if (protocol == jalview.io.AppletFormatAdapter.PASTE)
526 currentAlignFrame.setTitle("Sequences from " + getDocumentBase());
529 currentAlignFrame.statusBar.setText("Successfully loaded file " + file);
531 String treeFile = applet.getParameter("tree");
532 if (treeFile == null)
534 treeFile = applet.getParameter("treeFile");
537 if (treeFile != null)
541 treeFile = setProtocolState(treeFile);
542 /*if (inArchive(treeFile))
544 protocol = AppletFormatAdapter.CLASSLOADER;
548 protocol = AppletFormatAdapter.URL;
549 treeFile = addProtocol(treeFile);
552 jalview.io.NewickFile fin = new jalview.io.NewickFile(treeFile,
557 if (fin.getTree() != null)
559 currentAlignFrame.loadTree(fin, treeFile);
560 dbgMsg("Successfuly imported tree.");
562 dbgMsg("Tree parameter did not resolve to a valid tree.");
567 ex.printStackTrace();
571 String param = getParameter("features");
574 param = setProtocolState(param);
576 currentAlignFrame.parseFeaturesFile(param, protocol);
579 param = getParameter("showFeatureSettings");
580 if (param != null && param.equalsIgnoreCase("true"))
582 currentAlignFrame.viewport.showSequenceFeatures(true);
583 new FeatureSettings(currentAlignFrame.alignPanel);
586 param = getParameter("annotations");
589 param = setProtocolState(param);
591 if (new AnnotationFile().readAnnotationFile(
592 currentAlignFrame.viewport.getAlignment(),
596 currentAlignFrame.alignPanel.fontChanged();
597 currentAlignFrame.alignPanel.setScrollValues(0, 0);
599 System.err.println("Annotations were not added from annotation file '"+param+"'");
604 param = getParameter("jnetfile");
609 param = setProtocolState(param);
610 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
612 JnetAnnotationMaker.add_annotation(predictions,
613 currentAlignFrame.viewport.getAlignment(),
614 0, false); // false==do not add sequence profile from concise output
615 currentAlignFrame.alignPanel.fontChanged();
616 currentAlignFrame.alignPanel.setScrollValues(0, 0);
620 ex.printStackTrace();
625 <param name="PDBfile" value="1gaq.txt PDB|1GAQ|1GAQ|A PDB|1GAQ|1GAQ|B PDB|1GAQ|1GAQ|C">
627 <param name="PDBfile2" value="1gaq.txt A=SEQA B=SEQB C=SEQB">
629 <param name="PDBfile3" value="1q0o Q45135_9MICO">
633 int pdbFileCount = 0;
635 if (pdbFileCount > 0)
636 param = getParameter("PDBFILE" + pdbFileCount);
638 param = getParameter("PDBFILE");
642 PDBEntry pdb = new PDBEntry();
645 SequenceI[] seqs = null;
646 String [] chains = null;
648 StringTokenizer st = new StringTokenizer(param, " ");
650 if (st.countTokens() < 2)
652 String sequence = applet.getParameter("PDBSEQ");
653 if (sequence != null)
654 seqs = new SequenceI[]
656 (Sequence) currentAlignFrame.
657 getAlignViewport().getAlignment().
663 param = st.nextToken();
664 Vector tmp = new Vector();
665 Vector tmp2 = new Vector();
667 while (st.hasMoreTokens())
669 seqstring = st.nextToken();
670 StringTokenizer st2 = new StringTokenizer(seqstring,"=");
671 if(st2.countTokens()>1)
674 tmp2.addElement(st2.nextToken());
675 seqstring = st2.nextToken();
677 tmp.addElement( (Sequence) currentAlignFrame.
678 getAlignViewport().getAlignment().
679 findName(seqstring));
682 seqs = new SequenceI[tmp.size()];
684 if(tmp2.size()==tmp.size())
686 chains = new String[tmp2.size()];
687 tmp2.copyInto(chains);
690 param = setProtocolState(param);
692 if (!jmolAvailable && protocol==AppletFormatAdapter.CLASSLOADER)
694 // TODO: pass PDB file in classloader on to Jmol
695 // This exception preserves the current behaviour where, even if the local pdb file was identified in the class loader
696 protocol = AppletFormatAdapter.URL; // this is probably NOT CORRECT!
697 param = addProtocol(param); //
704 for (int i = 0; i < seqs.length; i++)
706 ( (Sequence) seqs[i]).addPDBId(pdb);
711 new jalview.appletgui.AppletJmol(pdb,
714 currentAlignFrame.alignPanel,
720 new MCview.AppletPDBViewer(pdb,
723 currentAlignFrame.alignPanel,
730 while(pdbFileCount < 10);
732 /////////////////////////////
733 // modify display of features
735 // hide specific groups
736 param = getParameter("hidefeaturegroups");
739 applet.setFeatureGroupState(param, false);
741 // show specific groups
742 param = getParameter("showfeaturegroups");
745 applet.setFeatureGroupState(param, true);
757 * Discovers whether the given file is in the Applet Archive
761 boolean inArchive(String file)
763 //This might throw a security exception in certain browsers
764 //Netscape Communicator for instance.
767 boolean rtn = (getClass().getResourceAsStream("/" + file) != null);
769 { System.err.println("Resource '"+file+"' was "+(rtn ? "" : "not") +" located by classloader.");
775 System.out.println("Exception checking resources: " + file + " " + ex);
780 String addProtocol(String file)
782 if (file.indexOf("://") == -1)
784 file = getCodeBase() + file;
787 System.err.println("Prepended codebase for resource: '"+file+"'");
795 * @return the default alignFrame acted on by the public applet methods.
796 * May return null with an error message on System.err indicating the fact.
798 protected AlignFrame getDefaultTargetFrame()
800 if (currentAlignFrame!=null)
802 return currentAlignFrame;
804 if (initialAlignFrame!=null)
806 return initialAlignFrame;
808 System.err.println("Implementation error: Jalview Applet API cannot work out which AlignFrame to use.");
812 * separator used for separatorList
814 protected String separator = "|"; // this is a safe(ish) separator - tabs don't work for firefox
816 * parse the string into a list
818 * @return elements separated by separator
820 public String[] separatorListToArray(String list)
822 int seplen = separator.length();
823 if (list==null || list.equals(""))
825 java.util.Vector jv = new Vector();
827 while ((pos=list.indexOf(separator,cp))>cp)
829 jv.addElement(list.substring(cp,pos));
832 if (cp<list.length())
834 jv.addElement(list.substring(cp));
837 { String[] v = new String[jv.size()];
838 for (int i=0; i<v.length; i++)
840 v[i] = (String) jv.elementAt(i);
842 jv.removeAllElements();
845 System.err.println("Array from '"+separator+"' separated List:\n"+v.length);
846 for (int i=0; i<v.length;i++)
848 System.err.println("item "+i+" '"+v[i]+"'");
855 System.err.println("Empty Array from '"+separator+"' separated List");
860 * concatenate the list with separator
862 * @return concatenated string
864 public String arrayToSeparatorList(String[] list)
866 StringBuffer v = new StringBuffer();
869 for (int i=0,iSize=list.length-1;i<iSize;i++)
877 if (list[list.length-1]!=null)
878 { v.append(list[list.length-1]);
882 System.err.println("Returning '"+separator+"' separated List:\n");
883 System.err.println(v);
889 System.err.println("Returning empty '"+separator+"' separated List\n");
895 * @see jalview.appletgui.AlignFrame#getFeatureGroups()
897 public String getFeatureGroups()
899 String lst = arrayToSeparatorList(getDefaultTargetFrame().getFeatureGroups());
903 * @param alf alignframe to get feature groups on
905 * @see jalview.appletgui.AlignFrame#getFeatureGroups()
907 public String getFeatureGroupsOn(AlignFrame alf)
909 String lst = arrayToSeparatorList(alf.getFeatureGroups());
915 * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean)
917 public String getFeatureGroupsOfState(boolean visible)
919 return arrayToSeparatorList(getDefaultTargetFrame().getFeatureGroupsOfState(visible));
922 * @param alf align frame to get groups of state visible
925 * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean)
927 public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)
929 return arrayToSeparatorList(alf.getFeatureGroupsOfState(visible));
931 * @param groups tab separated list of group names
932 * @param state true or false
933 * @see jalview.appletgui.AlignFrame#setFeatureGroupState(java.lang.String[], boolean)
935 public void setFeatureGroupStateOn(AlignFrame alf, String groups, boolean state)
937 boolean st = state;//!(state==null || state.equals("") || state.toLowerCase().equals("false"));
938 alf.setFeatureGroupState(separatorListToArray(groups), st);
940 public void setFeatureGroupState(String groups, boolean state)
942 setFeatureGroupStateOn(getDefaultTargetFrame(), groups, state);
945 * List separator string
946 * @return the separator
948 public String getSeparator()
953 * List separator string
954 * @param separator the separator to set
956 public void setSeparator(String separator)
958 this.separator = separator;