2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
3 * Copyright (C) 2008 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 extends Applet
40 // /////////////////////////////////////////
41 // The following public methods maybe called
42 // externally, eg via javascript in HTML page
44 * @return String list of selected sequence IDs, each terminated by "¬"
47 public String getSelectedSequences()
49 return getSelectedSequencesFrom(getDefaultTargetFrame());
54 * separator string or null for default
55 * @return String list of selected sequence IDs, each terminated by sep or
58 public String getSelectedSequences(String sep)
60 return getSelectedSequencesFrom(getDefaultTargetFrame(), sep);
65 * alignframe containing selection
66 * @return String list of selected sequence IDs, each terminated by "¬"
69 public String getSelectedSequencesFrom(AlignFrame alf)
71 return getSelectedSequencesFrom(alf, "¬");
75 * get list of selected sequence IDs separated by given separator
78 * window containing selection
80 * separator string to use - default is "¬"
81 * @return String list of selected sequence IDs, each terminated by the given
84 public String getSelectedSequencesFrom(AlignFrame alf, String sep)
86 StringBuffer result = new StringBuffer("");
87 if (sep == null || sep.length() == 0)
91 if (alf.viewport.getSelectionGroup() != null)
93 SequenceI[] seqs = alf.viewport.getSelectionGroup()
94 .getSequencesInOrder(alf.viewport.getAlignment());
96 for (int i = 0; i < seqs.length; i++)
98 result.append(seqs[i].getName());
103 return result.toString();
107 * get sequences selected in current alignFrame and return their alignment in
108 * format 'format' either with or without suffix
113 * format of alignment file
115 * "true" to append /start-end string to each sequence ID
116 * @return selected sequences as flat file or empty string if there was no
119 public String getSelectedSequencesAsAlignment(String format, String suffix)
121 return getSelectedSequencesAsAlignmentFrom(currentAlignFrame, format,
126 * get sequences selected in alf and return their alignment in format 'format'
127 * either with or without suffix
132 * format of alignment file
134 * "true" to append /start-end string to each sequence ID
135 * @return selected sequences as flat file or empty string if there was no
138 public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
139 String format, String suffix)
143 boolean seqlimits = suffix.equalsIgnoreCase("true");
144 if (alf.viewport.getSelectionGroup() != null)
146 String reply = new AppletFormatAdapter().formatSequences(format,
147 new Alignment(alf.viewport.getSelectionAsNewSequence()),
151 } catch (Exception ex)
153 ex.printStackTrace();
154 return "Error retrieving alignment in " + format + " format. ";
159 public String getAlignment(String format)
161 return getAlignmentFrom(getDefaultTargetFrame(), format, "true");
164 public String getAlignmentFrom(AlignFrame alf, String format)
166 return getAlignmentFrom(alf, format, "true");
169 public String getAlignment(String format, String suffix)
171 return getAlignmentFrom(getDefaultTargetFrame(), format, suffix);
174 public String getAlignmentFrom(AlignFrame alf, String format,
179 boolean seqlimits = suffix.equalsIgnoreCase("true");
181 String reply = new AppletFormatAdapter().formatSequences(format,
182 alf.viewport.getAlignment(), seqlimits);
184 } catch (Exception ex)
186 ex.printStackTrace();
187 return "Error retrieving alignment in " + format + " format. ";
191 public void loadAnnotation(String annotation)
193 loadAnnotationFrom(getDefaultTargetFrame(), annotation);
196 public void loadAnnotationFrom(AlignFrame alf, String annotation)
198 if (new AnnotationFile().readAnnotationFile(alf.getAlignViewport()
199 .getAlignment(), annotation, AppletFormatAdapter.PASTE))
201 alf.alignPanel.fontChanged();
202 alf.alignPanel.setScrollValues(0, 0);
206 alf.parseFeaturesFile(annotation, AppletFormatAdapter.PASTE);
210 public String getFeatures(String format)
212 return getFeaturesFrom(getDefaultTargetFrame(), format);
215 public String getFeaturesFrom(AlignFrame alf, String format)
217 return alf.outputFeatures(false, format);
220 public String getAnnotation()
222 return getAnnotationFrom(getDefaultTargetFrame());
225 public String getAnnotationFrom(AlignFrame alf)
227 return alf.outputAnnotations(false);
230 public AlignFrame newView()
232 return newViewFrom(getDefaultTargetFrame());
235 public AlignFrame newView(String name)
237 return newViewFrom(getDefaultTargetFrame(), name);
240 public AlignFrame newViewFrom(AlignFrame alf)
242 return alf.newView(null);
245 public AlignFrame newViewFrom(AlignFrame alf, String name)
247 return alf.newView(name);
253 * alignment file as a string
256 * @return null or new alignment frame
258 public AlignFrame loadAlignment(String text, String title)
261 String format = new IdentifyFile().Identify(text,
262 AppletFormatAdapter.PASTE);
265 al = new AppletFormatAdapter().readFile(text,
266 AppletFormatAdapter.PASTE, format);
267 if (al.getHeight() > 0)
269 return new AlignFrame(al, this, title, false);
271 } catch (java.io.IOException ex)
273 ex.printStackTrace();
278 // //////////////////////////////////////////////
279 // //////////////////////////////////////////////
281 static int lastFrameX = 200;
283 static int lastFrameY = 200;
285 boolean fileFound = true;
287 String file = "No file";
289 Button launcher = new Button("Start Jalview");
292 * The currentAlignFrame is static, it will change if and when the user
293 * selects a new window. Note that it will *never* point back to the embedded
294 * AlignFrame if the applet is started as embedded on the page and then
295 * afterwards a new view is created.
297 public static AlignFrame currentAlignFrame;
300 * This is the first frame to be displayed, and does not change. API calls
301 * will default to this instance if currentAlignFrame is null.
303 AlignFrame initialAlignFrame;
305 boolean embedded = false;
307 private boolean checkForJmol = true;
309 public boolean jmolAvailable = false;
311 public static boolean debug;
314 * init method for Jalview Applet
319 * turn on extra applet debugging
321 String dbg = getParameter("debug");
324 debug = dbg.toLowerCase().equals("true");
327 * if true disable the check for jmol
329 String chkforJmol = getParameter("nojmol");
330 if (chkforJmol != null)
332 checkForJmol = !chkforJmol.equals("true");
335 * get the separator parameter if present
337 String sep = getParameter("separator");
340 if (sep.length() > 0)
345 System.err.println("Separator set to '" + separator + "'");
351 "Invalid separator parameter - must be non-zero length");
357 String param = getParameter("RGB");
363 r = Integer.parseInt(param.substring(0, 2), 16);
364 g = Integer.parseInt(param.substring(2, 4), 16);
365 b = Integer.parseInt(param.substring(4, 6), 16);
366 } catch (Exception ex)
374 param = getParameter("label");
377 launcher.setLabel(param);
380 this.setBackground(new Color(r, g, b));
382 file = getParameter("file");
386 // Maybe the sequences are added as parameters
387 StringBuffer data = new StringBuffer("PASTE");
389 while ((file = getParameter("sequence" + i)) != null)
391 data.append(file.toString() + "\n");
394 if (data.length() > 5)
396 file = data.toString();
400 LoadJmolThread jmolAvailable = new LoadJmolThread();
401 jmolAvailable.start();
403 final JalviewLite applet = this;
404 if (getParameter("embedded") != null
405 && getParameter("embedded").equalsIgnoreCase("true"))
407 // Launch as embedded applet in page
409 LoadingThread loader = new LoadingThread(file, applet);
412 else if (file != null)
414 if (getParameter("showbutton") == null
415 || !getParameter("showbutton").equalsIgnoreCase("false"))
417 // Add the JalviewLite 'Button' to the page
419 launcher.addActionListener(new java.awt.event.ActionListener()
421 public void actionPerformed(ActionEvent e)
423 LoadingThread loader = new LoadingThread(file, applet);
430 // Open jalviewLite immediately.
431 LoadingThread loader = new LoadingThread(file, applet);
437 // jalview initialisation with no alignment. loadAlignment() method can
438 // still be called to open new alignments.
445 * Initialises and displays a new java.awt.Frame
448 * java.awt.Frame to be displayed
454 * height of new frame
456 public static void addFrame(final Frame frame, String title, int width,
459 frame.setLocation(lastFrameX, lastFrameY);
462 frame.setSize(width, height);
463 frame.setTitle(title);
464 frame.addWindowListener(new WindowAdapter()
466 public void windowClosing(WindowEvent e)
468 if (frame instanceof AlignFrame)
470 ((AlignFrame) frame).closeMenuItem_actionPerformed();
472 if (currentAlignFrame == frame)
474 currentAlignFrame = null;
478 if (frame instanceof EmbmenuFrame)
480 ((EmbmenuFrame) frame).destroyMenus();
482 frame.setMenuBar(null);
486 public void windowActivated(WindowEvent e)
488 if (frame instanceof AlignFrame)
490 currentAlignFrame = (AlignFrame) frame;
493 System.err.println("Activated window " + frame);
497 super.windowActivated(e);
500 * Probably not necessary to do this - see TODO above. (non-Javadoc)
502 * @see java.awt.event.WindowAdapter#windowDeactivated(java.awt.event.WindowEvent)
504 * public void windowDeactivated(WindowEvent e) { if (currentAlignFrame ==
505 * frame) { currentAlignFrame = null; if (debug) {
506 * System.err.println("Deactivated window "+frame); } }
507 * super.windowDeactivated(e); }
510 frame.setVisible(true);
514 * This paints the background surrounding the "Launch Jalview button" <br>
516 * If file given in parameter not found, displays error message
521 public void paint(Graphics g)
525 g.setColor(new Color(200, 200, 200));
526 g.setColor(Color.cyan);
527 g.fillRect(0, 0, getSize().width, getSize().height);
528 g.setColor(Color.red);
529 g.drawString("Jalview can't open file", 5, 15);
530 g.drawString("\"" + file + "\"", 5, 30);
534 g.setColor(Color.black);
535 g.setFont(new Font("Arial", Font.BOLD, 24));
536 g.drawString("Jalview Applet", 50, this.getSize().height / 2 - 30);
537 g.drawString("Loading Data...", 50, this.getSize().height / 2);
541 class LoadJmolThread extends Thread
549 if (!System.getProperty("java.version").startsWith("1.1"))
551 Class.forName("org.jmol.adapter.smarter.SmarterJmolAdapter");
552 jmolAvailable = true;
557 .println("Jmol not available - Using MCview for structures");
559 } catch (java.lang.ClassNotFoundException ex)
565 jmolAvailable = false;
569 .println("Skipping Jmol check. Will use MCView (probably)");
575 class LoadingThread extends Thread
578 * State variable: File source
583 * State variable: protocol for access to file source
588 * State variable: format of file source
594 private void dbgMsg(String msg)
598 System.err.println(msg);
603 * update the protocol state variable for accessing the datasource located
607 * @return possibly updated datasource string
609 public String setProtocolState(String file)
611 if (file.startsWith("PASTE"))
613 file = file.substring(5);
614 protocol = AppletFormatAdapter.PASTE;
616 else if (inArchive(file))
618 protocol = AppletFormatAdapter.CLASSLOADER;
622 file = addProtocol(file);
623 protocol = AppletFormatAdapter.URL;
625 dbgMsg("Protocol identified as '" + protocol + "'");
629 public LoadingThread(String _file, JalviewLite _applet)
631 dbgMsg("Loading thread started with:\n>>file\n" + _file + ">>endfile");
632 file = setProtocolState(_file);
634 format = new jalview.io.IdentifyFile().Identify(file, protocol);
635 dbgMsg("File identified as '" + format + "'");
644 private void startLoading()
646 dbgMsg("Loading started.");
650 al = new AppletFormatAdapter().readFile(file, protocol, format);
651 } catch (java.io.IOException ex)
653 dbgMsg("File load exception.");
654 ex.printStackTrace();
656 if ((al != null) && (al.getHeight() > 0))
658 dbgMsg("Successfully loaded file.");
659 initialAlignFrame = new AlignFrame(al, applet, file, embedded);
661 currentAlignFrame = initialAlignFrame;
663 if (protocol == jalview.io.AppletFormatAdapter.PASTE)
665 currentAlignFrame.setTitle("Sequences from " + getDocumentBase());
668 currentAlignFrame.statusBar.setText("Successfully loaded file "
671 String treeFile = applet.getParameter("tree");
672 if (treeFile == null)
674 treeFile = applet.getParameter("treeFile");
677 if (treeFile != null)
681 treeFile = setProtocolState(treeFile);
683 * if (inArchive(treeFile)) { protocol =
684 * AppletFormatAdapter.CLASSLOADER; } else { protocol =
685 * AppletFormatAdapter.URL; treeFile = addProtocol(treeFile); }
687 jalview.io.NewickFile fin = new jalview.io.NewickFile(treeFile,
692 if (fin.getTree() != null)
694 currentAlignFrame.loadTree(fin, treeFile);
695 dbgMsg("Successfuly imported tree.");
699 dbgMsg("Tree parameter did not resolve to a valid tree.");
701 } catch (Exception ex)
703 ex.printStackTrace();
707 String param = getParameter("features");
710 param = setProtocolState(param);
712 currentAlignFrame.parseFeaturesFile(param, protocol);
715 param = getParameter("showFeatureSettings");
716 if (param != null && param.equalsIgnoreCase("true"))
718 currentAlignFrame.viewport.showSequenceFeatures(true);
719 new FeatureSettings(currentAlignFrame.alignPanel);
722 param = getParameter("annotations");
725 param = setProtocolState(param);
727 if (new AnnotationFile().readAnnotationFile(
728 currentAlignFrame.viewport.getAlignment(), param,
731 currentAlignFrame.alignPanel.fontChanged();
732 currentAlignFrame.alignPanel.setScrollValues(0, 0);
737 .println("Annotations were not added from annotation file '"
743 param = getParameter("jnetfile");
748 param = setProtocolState(param);
749 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
751 JnetAnnotationMaker.add_annotation(predictions,
752 currentAlignFrame.viewport.getAlignment(), 0, false); // false==do
760 currentAlignFrame.alignPanel.fontChanged();
761 currentAlignFrame.alignPanel.setScrollValues(0, 0);
762 } catch (Exception ex)
764 ex.printStackTrace();
769 * <param name="PDBfile" value="1gaq.txt PDB|1GAQ|1GAQ|A PDB|1GAQ|1GAQ|B
772 * <param name="PDBfile2" value="1gaq.txt A=SEQA B=SEQB C=SEQB">
774 * <param name="PDBfile3" value="1q0o Q45135_9MICO">
777 int pdbFileCount = 0;
780 if (pdbFileCount > 0)
781 param = getParameter("PDBFILE" + pdbFileCount);
783 param = getParameter("PDBFILE");
787 PDBEntry pdb = new PDBEntry();
790 SequenceI[] seqs = null;
791 String[] chains = null;
793 StringTokenizer st = new StringTokenizer(param, " ");
795 if (st.countTokens() < 2)
797 String sequence = applet.getParameter("PDBSEQ");
798 if (sequence != null)
799 seqs = new SequenceI[]
800 { (Sequence) currentAlignFrame.getAlignViewport()
801 .getAlignment().findName(sequence) };
806 param = st.nextToken();
807 Vector tmp = new Vector();
808 Vector tmp2 = new Vector();
810 while (st.hasMoreTokens())
812 seqstring = st.nextToken();
813 StringTokenizer st2 = new StringTokenizer(seqstring, "=");
814 if (st2.countTokens() > 1)
817 tmp2.addElement(st2.nextToken());
818 seqstring = st2.nextToken();
820 tmp.addElement((Sequence) currentAlignFrame
821 .getAlignViewport().getAlignment().findName(
825 seqs = new SequenceI[tmp.size()];
827 if (tmp2.size() == tmp.size())
829 chains = new String[tmp2.size()];
830 tmp2.copyInto(chains);
833 param = setProtocolState(param);
835 if (// !jmolAvailable
837 protocol == AppletFormatAdapter.CLASSLOADER)
839 // TODO: verify this Re:
840 // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
841 // This exception preserves the current behaviour where, even if
842 // the local pdb file was identified in the class loader
843 protocol = AppletFormatAdapter.URL; // this is probably NOT
845 param = addProtocol(param); //
852 for (int i = 0; i < seqs.length; i++)
856 ((Sequence) seqs[i]).addPDBId(pdb);
860 if (JalviewLite.debug)
862 // this may not really be a problem but we give a warning
865 .println("Warning: Possible input parsing error: Null sequence for attachment of PDB (sequence "
873 new jalview.appletgui.AppletJmol(pdb, seqs, chains,
874 currentAlignFrame.alignPanel, protocol);
879 new MCview.AppletPDBViewer(pdb, seqs, chains,
880 currentAlignFrame.alignPanel, protocol);
885 } while (pdbFileCount < 10);
887 // ///////////////////////////
888 // modify display of features
890 // hide specific groups
891 param = getParameter("hidefeaturegroups");
894 applet.setFeatureGroupState(param, false);
896 // show specific groups
897 param = getParameter("showfeaturegroups");
900 applet.setFeatureGroupState(param, true);
912 * Discovers whether the given file is in the Applet Archive
918 boolean inArchive(String file)
920 // This might throw a security exception in certain browsers
921 // Netscape Communicator for instance.
924 boolean rtn = (getClass().getResourceAsStream("/" + file) != null);
927 System.err.println("Resource '" + file + "' was "
928 + (rtn ? "" : "not") + " located by classloader.");
931 } catch (Exception ex)
933 System.out.println("Exception checking resources: " + file + " "
939 String addProtocol(String file)
941 if (file.indexOf("://") == -1)
943 file = getCodeBase() + file;
946 System.err.println("Prepended codebase for resource: '" + file
956 * @return the default alignFrame acted on by the public applet methods. May
957 * return null with an error message on System.err indicating the
960 protected AlignFrame getDefaultTargetFrame()
962 if (currentAlignFrame != null)
964 return currentAlignFrame;
966 if (initialAlignFrame != null)
968 return initialAlignFrame;
971 .println("Implementation error: Jalview Applet API cannot work out which AlignFrame to use.");
976 * separator used for separatorList
978 protected String separator = "|"; // this is a safe(ish) separator - tabs
980 // don't work for firefox
983 * parse the string into a list
986 * @return elements separated by separator
988 public String[] separatorListToArray(String list)
990 int seplen = separator.length();
991 if (list == null || list.equals(""))
993 java.util.Vector jv = new Vector();
995 while ((pos = list.indexOf(separator, cp)) > cp)
997 jv.addElement(list.substring(cp, pos));
1000 if (cp < list.length())
1002 jv.addElement(list.substring(cp));
1006 String[] v = new String[jv.size()];
1007 for (int i = 0; i < v.length; i++)
1009 v[i] = (String) jv.elementAt(i);
1011 jv.removeAllElements();
1014 System.err.println("Array from '" + separator
1015 + "' separated List:\n" + v.length);
1016 for (int i = 0; i < v.length; i++)
1018 System.err.println("item " + i + " '" + v[i] + "'");
1025 System.err.println("Empty Array from '" + separator
1026 + "' separated List");
1032 * concatenate the list with separator
1035 * @return concatenated string
1037 public String arrayToSeparatorList(String[] list)
1039 StringBuffer v = new StringBuffer();
1042 for (int i = 0, iSize = list.length - 1; i < iSize; i++)
1044 if (list[i] != null)
1048 v.append(separator);
1050 if (list[list.length - 1] != null)
1052 v.append(list[list.length - 1]);
1056 System.err.println("Returning '" + separator
1057 + "' separated List:\n");
1058 System.err.println(v);
1060 return v.toString();
1064 System.err.println("Returning empty '" + separator
1065 + "' separated List\n");
1072 * @see jalview.appletgui.AlignFrame#getFeatureGroups()
1074 public String getFeatureGroups()
1076 String lst = arrayToSeparatorList(getDefaultTargetFrame()
1077 .getFeatureGroups());
1083 * alignframe to get feature groups on
1085 * @see jalview.appletgui.AlignFrame#getFeatureGroups()
1087 public String getFeatureGroupsOn(AlignFrame alf)
1089 String lst = arrayToSeparatorList(alf.getFeatureGroups());
1096 * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean)
1098 public String getFeatureGroupsOfState(boolean visible)
1100 return arrayToSeparatorList(getDefaultTargetFrame()
1101 .getFeatureGroupsOfState(visible));
1106 * align frame to get groups of state visible
1109 * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean)
1111 public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)
1113 return arrayToSeparatorList(alf.getFeatureGroupsOfState(visible));
1118 * tab separated list of group names
1121 * @see jalview.appletgui.AlignFrame#setFeatureGroupState(java.lang.String[],
1124 public void setFeatureGroupStateOn(AlignFrame alf, String groups,
1127 boolean st = state;// !(state==null || state.equals("") ||
1128 // state.toLowerCase().equals("false"));
1129 alf.setFeatureGroupState(separatorListToArray(groups), st);
1132 public void setFeatureGroupState(String groups, boolean state)
1134 setFeatureGroupStateOn(getDefaultTargetFrame(), groups, state);
1138 * List separator string
1140 * @return the separator
1142 public String getSeparator()
1148 * List separator string
1151 * the separator to set
1153 public void setSeparator(String separator)
1155 this.separator = separator;