X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=7fa514710dbf1cfbfeca9faed7d1c98beffe759b;hb=06ce849ffedc7ab10a3c54cda96b9a7dec58c136;hp=30b8d548ce8d89d8f709c206c92a2111abd02cbb;hpb=95e1400e3e807ec4eb7fb23e6d2ae2519416baa3;p=jalview.git diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java index 30b8d54..7fa5147 100644 --- a/src/jalview/bin/JalviewLite.java +++ b/src/jalview/bin/JalviewLite.java @@ -37,6 +37,9 @@ import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.io.AnnotationFile; import jalview.io.AppletFormatAdapter; +import jalview.io.DataSourceType; +import jalview.io.FileFormatI; +import jalview.io.FileFormats; import jalview.io.FileParse; import jalview.io.IdentifyFile; import jalview.io.JPredFile; @@ -48,6 +51,8 @@ import jalview.javascript.JsCallBack; import jalview.javascript.MouseOverStructureListener; import jalview.structure.SelectionListener; import jalview.structure.StructureSelectionManager; +import jalview.util.ColorUtils; +import jalview.util.HttpUtils; import jalview.util.MessageManager; import java.applet.Applet; @@ -63,7 +68,6 @@ import java.awt.event.WindowAdapter; import java.awt.event.WindowEvent; import java.io.BufferedReader; import java.io.IOException; -import java.io.InputStream; import java.io.InputStreamReader; import java.net.URL; import java.util.ArrayList; @@ -101,6 +105,7 @@ public class JalviewLite extends Applet implements * * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences() */ + @Override public String getSelectedSequences() { return getSelectedSequencesFrom(getDefaultTargetFrame()); @@ -111,6 +116,7 @@ public class JalviewLite extends Applet implements * * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences(java.lang.String) */ + @Override public String getSelectedSequences(String sep) { return getSelectedSequencesFrom(getDefaultTargetFrame(), sep); @@ -123,6 +129,7 @@ public class JalviewLite extends Applet implements * jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui * .AlignFrame) */ + @Override public String getSelectedSequencesFrom(AlignFrame alf) { return getSelectedSequencesFrom(alf, separator); // ""+0x00AC); @@ -135,6 +142,7 @@ public class JalviewLite extends Applet implements * jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui * .AlignFrame, java.lang.String) */ + @Override public String getSelectedSequencesFrom(AlignFrame alf, String sep) { StringBuffer result = new StringBuffer(""); @@ -163,6 +171,7 @@ public class JalviewLite extends Applet implements * @see jalview.bin.JalviewLiteJsApi#highlight(java.lang.String, * java.lang.String, java.lang.String) */ + @Override public void highlight(String sequenceId, String position, String alignedPosition) { @@ -176,6 +185,7 @@ public class JalviewLite extends Applet implements * @see jalview.bin.JalviewLiteJsApi#highlightIn(jalview.appletgui.AlignFrame, * java.lang.String, java.lang.String, java.lang.String) */ + @Override public void highlightIn(final AlignFrame alf, final String sequenceId, final String position, final String alignedPosition) { @@ -232,6 +242,7 @@ public class JalviewLite extends Applet implements * @see jalview.bin.JalviewLiteJsApi#select(java.lang.String, * java.lang.String) */ + @Override public void select(String sequenceIds, String columns) { selectIn(getDefaultTargetFrame(), sequenceIds, columns, separator); @@ -243,6 +254,7 @@ public class JalviewLite extends Applet implements * @see jalview.bin.JalviewLiteJsApi#select(java.lang.String, * java.lang.String, java.lang.String) */ + @Override public void select(String sequenceIds, String columns, String sep) { selectIn(getDefaultTargetFrame(), sequenceIds, columns, sep); @@ -254,6 +266,7 @@ public class JalviewLite extends Applet implements * @see jalview.bin.JalviewLiteJsApi#selectIn(jalview.appletgui.AlignFrame, * java.lang.String, java.lang.String) */ + @Override public void selectIn(AlignFrame alf, String sequenceIds, String columns) { selectIn(alf, sequenceIds, columns, separator); @@ -265,6 +278,7 @@ public class JalviewLite extends Applet implements * @see jalview.bin.JalviewLiteJsApi#selectIn(jalview.appletgui.AlignFrame, * java.lang.String, java.lang.String, java.lang.String) */ + @Override public void selectIn(final AlignFrame alf, String sequenceIds, String columns, String sep) { @@ -457,14 +471,11 @@ public class JalviewLite extends Applet implements SequenceI rs = sel.getSequenceAt(0); start = rs.findIndex(start); end = rs.findIndex(end); - if (csel != null) + List cs = new ArrayList(csel.getSelected()); + csel.clear(); + for (Integer selectedCol : cs) { - List cs = csel.getSelected(); - csel.clear(); - for (Integer selectedCol : cs) - { - csel.addElement(rs.findIndex(selectedCol)); - } + csel.addElement(rs.findIndex(selectedCol)); } } sel.setStartRes(start); @@ -487,6 +498,7 @@ public class JalviewLite extends Applet implements * jalview.bin.JalviewLiteJsApi#getSelectedSequencesAsAlignment(java.lang. * String, java.lang.String) */ + @Override public String getSelectedSequencesAsAlignment(String format, String suffix) { return getSelectedSequencesAsAlignmentFrom(getDefaultTargetFrame(), @@ -500,26 +512,29 @@ public class JalviewLite extends Applet implements * jalview.bin.JalviewLiteJsApi#getSelectedSequencesAsAlignmentFrom(jalview * .appletgui.AlignFrame, java.lang.String, java.lang.String) */ + @Override public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf, String format, String suffix) { try { + FileFormatI theFormat = FileFormats.getInstance().forName(format); boolean seqlimits = suffix.equalsIgnoreCase(TRUE); if (alf.viewport.getSelectionGroup() != null) { // JBPNote: getSelectionAsNewSequence behaviour has changed - this // method now returns a full copy of sequence data // TODO consider using getSequenceSelection instead here - String reply = new AppletFormatAdapter().formatSequences(format, + String reply = new AppletFormatAdapter().formatSequences(theFormat, new Alignment(alf.viewport.getSelectionAsNewSequence()), seqlimits); return reply; } - } catch (Exception ex) + } catch (IllegalArgumentException ex) { ex.printStackTrace(); - return "Error retrieving alignment in " + format + " format. "; + return "Error retrieving alignment, possibly invalid format specifier: " + + format; } return ""; } @@ -529,6 +544,7 @@ public class JalviewLite extends Applet implements * * @see jalview.bin.JalviewLiteJsApi#getAlignmentOrder() */ + @Override public String getAlignmentOrder() { return getAlignmentOrderFrom(getDefaultTargetFrame()); @@ -541,6 +557,7 @@ public class JalviewLite extends Applet implements * jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame * ) */ + @Override public String getAlignmentOrderFrom(AlignFrame alf) { return getAlignmentOrderFrom(alf, separator); @@ -553,6 +570,7 @@ public class JalviewLite extends Applet implements * jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame * , java.lang.String) */ + @Override public String getAlignmentOrderFrom(AlignFrame alf, String sep) { AlignmentI alorder = alf.getAlignViewport().getAlignment(); @@ -570,6 +588,7 @@ public class JalviewLite extends Applet implements * @see jalview.bin.JalviewLiteJsApi#orderBy(java.lang.String, * java.lang.String) */ + @Override public String orderBy(String order, String undoName) { return orderBy(order, undoName, separator); @@ -581,6 +600,7 @@ public class JalviewLite extends Applet implements * @see jalview.bin.JalviewLiteJsApi#orderBy(java.lang.String, * java.lang.String, java.lang.String) */ + @Override public String orderBy(String order, String undoName, String sep) { return orderAlignmentBy(getDefaultTargetFrame(), order, undoName, sep); @@ -593,6 +613,7 @@ public class JalviewLite extends Applet implements * jalview.bin.JalviewLiteJsApi#orderAlignmentBy(jalview.appletgui.AlignFrame, * java.lang.String, java.lang.String, java.lang.String) */ + @Override public String orderAlignmentBy(AlignFrame alf, String order, String undoName, String sep) { @@ -649,6 +670,7 @@ public class JalviewLite extends Applet implements * * @see jalview.bin.JalviewLiteJsApi#getAlignment(java.lang.String) */ + @Override public String getAlignment(String format) { return getAlignmentFrom(getDefaultTargetFrame(), format, TRUE); @@ -661,6 +683,7 @@ public class JalviewLite extends Applet implements * jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame, * java.lang.String) */ + @Override public String getAlignmentFrom(AlignFrame alf, String format) { return getAlignmentFrom(alf, format, TRUE); @@ -672,6 +695,7 @@ public class JalviewLite extends Applet implements * @see jalview.bin.JalviewLiteJsApi#getAlignment(java.lang.String, * java.lang.String) */ + @Override public String getAlignment(String format, String suffix) { return getAlignmentFrom(getDefaultTargetFrame(), format, suffix); @@ -684,6 +708,7 @@ public class JalviewLite extends Applet implements * jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame, * java.lang.String, java.lang.String) */ + @Override public String getAlignmentFrom(AlignFrame alf, String format, String suffix) { @@ -691,13 +716,15 @@ public class JalviewLite extends Applet implements { boolean seqlimits = suffix.equalsIgnoreCase(TRUE); - String reply = new AppletFormatAdapter().formatSequences(format, + FileFormatI theFormat = FileFormats.getInstance().forName(format); + String reply = new AppletFormatAdapter().formatSequences(theFormat, alf.viewport.getAlignment(), seqlimits); return reply; - } catch (Exception ex) + } catch (IllegalArgumentException ex) { ex.printStackTrace(); - return "Error retrieving alignment in " + format + " format. "; + return "Error retrieving alignment, possibly invalid format specifier: " + + format; } } @@ -706,6 +733,7 @@ public class JalviewLite extends Applet implements * * @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String) */ + @Override public void loadAnnotation(String annotation) { loadAnnotationFrom(getDefaultTargetFrame(), annotation); @@ -718,17 +746,18 @@ public class JalviewLite extends Applet implements * jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame * , java.lang.String) */ + @Override public void loadAnnotationFrom(AlignFrame alf, String annotation) { if (new AnnotationFile().annotateAlignmentView(alf.getAlignViewport(), - annotation, AppletFormatAdapter.PASTE)) + annotation, DataSourceType.PASTE)) { alf.alignPanel.fontChanged(); alf.alignPanel.setScrollValues(0, 0); } else { - alf.parseFeaturesFile(annotation, AppletFormatAdapter.PASTE); + alf.parseFeaturesFile(annotation, DataSourceType.PASTE); } } @@ -737,6 +766,7 @@ public class JalviewLite extends Applet implements * * @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String) */ + @Override public void loadFeatures(String features, boolean autoenabledisplay) { loadFeaturesFrom(getDefaultTargetFrame(), features, autoenabledisplay); @@ -749,10 +779,11 @@ public class JalviewLite extends Applet implements * jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame * , java.lang.String) */ + @Override public boolean loadFeaturesFrom(AlignFrame alf, String features, boolean autoenabledisplay) { - return alf.parseFeaturesFile(features, AppletFormatAdapter.PASTE, + return alf.parseFeaturesFile(features, DataSourceType.PASTE, autoenabledisplay); } @@ -761,6 +792,7 @@ public class JalviewLite extends Applet implements * * @see jalview.bin.JalviewLiteJsApi#getFeatures(java.lang.String) */ + @Override public String getFeatures(String format) { return getFeaturesFrom(getDefaultTargetFrame(), format); @@ -773,6 +805,7 @@ public class JalviewLite extends Applet implements * jalview.bin.JalviewLiteJsApi#getFeaturesFrom(jalview.appletgui.AlignFrame, * java.lang.String) */ + @Override public String getFeaturesFrom(AlignFrame alf, String format) { return alf.outputFeatures(false, format); @@ -783,6 +816,7 @@ public class JalviewLite extends Applet implements * * @see jalview.bin.JalviewLiteJsApi#getAnnotation() */ + @Override public String getAnnotation() { return getAnnotationFrom(getDefaultTargetFrame()); @@ -795,6 +829,7 @@ public class JalviewLite extends Applet implements * jalview.bin.JalviewLiteJsApi#getAnnotationFrom(jalview.appletgui.AlignFrame * ) */ + @Override public String getAnnotationFrom(AlignFrame alf) { return alf.outputAnnotations(false); @@ -805,6 +840,7 @@ public class JalviewLite extends Applet implements * * @see jalview.bin.JalviewLiteJsApi#newView() */ + @Override public AlignFrame newView() { return newViewFrom(getDefaultTargetFrame()); @@ -815,6 +851,7 @@ public class JalviewLite extends Applet implements * * @see jalview.bin.JalviewLiteJsApi#newView(java.lang.String) */ + @Override public AlignFrame newView(String name) { return newViewFrom(getDefaultTargetFrame(), name); @@ -825,6 +862,7 @@ public class JalviewLite extends Applet implements * * @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame) */ + @Override public AlignFrame newViewFrom(AlignFrame alf) { return alf.newView(null); @@ -836,6 +874,7 @@ public class JalviewLite extends Applet implements * @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame, * java.lang.String) */ + @Override public AlignFrame newViewFrom(AlignFrame alf, String name) { return alf.newView(name); @@ -847,21 +886,22 @@ public class JalviewLite extends Applet implements * @see jalview.bin.JalviewLiteJsApi#loadAlignment(java.lang.String, * java.lang.String) */ + @Override public AlignFrame loadAlignment(String text, String title) { AlignmentI al = null; - String format = new IdentifyFile().Identify(text, - AppletFormatAdapter.PASTE); try { - al = new AppletFormatAdapter().readFile(text, - AppletFormatAdapter.PASTE, format); + FileFormatI format = new IdentifyFile().identify(text, + DataSourceType.PASTE); + al = new AppletFormatAdapter().readFile(text, DataSourceType.PASTE, + format); if (al.getHeight() > 0) { return new AlignFrame(al, this, title, false); } - } catch (java.io.IOException ex) + } catch (IOException ex) { ex.printStackTrace(); } @@ -873,6 +913,7 @@ public class JalviewLite extends Applet implements * * @see jalview.bin.JalviewLiteJsApi#setMouseoverListener(java.lang.String) */ + @Override public void setMouseoverListener(String listener) { setMouseoverListener(currentAlignFrame, listener); @@ -887,6 +928,7 @@ public class JalviewLite extends Applet implements * jalview.bin.JalviewLiteJsApi#setMouseoverListener(jalview.appletgui.AlignFrame * , java.lang.String) */ + @Override public void setMouseoverListener(AlignFrame af, String listener) { if (listener != null) @@ -919,6 +961,7 @@ public class JalviewLite extends Applet implements * * @see jalview.bin.JalviewLiteJsApi#setSelectionListener(java.lang.String) */ + @Override public void setSelectionListener(String listener) { setSelectionListener(null, listener); @@ -931,6 +974,7 @@ public class JalviewLite extends Applet implements * jalview.bin.JalviewLiteJsApi#setSelectionListener(jalview.appletgui.AlignFrame * , java.lang.String) */ + @Override public void setSelectionListener(AlignFrame af, String listener) { if (listener != null) @@ -969,6 +1013,7 @@ public class JalviewLite extends Applet implements * @see jalview.bin.JalviewLiteJsApi#setStructureListener(java.lang.String, * java.lang.String) */ + @Override public void setStructureListener(String listener, String modelSet) { if (listener != null) @@ -1002,6 +1047,7 @@ public class JalviewLite extends Applet implements * jalview.bin.JalviewLiteJsApi#removeJavascriptListener(jalview.appletgui * .AlignFrame, java.lang.String) */ + @Override public void removeJavascriptListener(AlignFrame af, String listener) { if (listener != null) @@ -1051,12 +1097,14 @@ public class JalviewLite extends Applet implements } } + @Override public void stop() { System.err.println("Applet " + getName() + " stop()."); tidyUp(); } + @Override public void destroy() { System.err.println("Applet " + getName() + " destroy()."); @@ -1113,6 +1161,7 @@ public class JalviewLite extends Applet implements * @see jalview.bin.JalviewLiteJsApi#mouseOverStructure(java.lang.String, * java.lang.String, java.lang.String) */ + @Override public void mouseOverStructure(final String pdbResNum, final String chain, final String pdbfile) { @@ -1150,6 +1199,7 @@ public class JalviewLite extends Applet implements * jalview.bin.JalviewLiteJsApi#scrollViewToIn(jalview.appletgui.AlignFrame, * java.lang.String, java.lang.String) */ + @Override public void scrollViewToIn(final AlignFrame alf, final String topRow, final String leftHandColumn) { @@ -1489,6 +1539,7 @@ public class JalviewLite extends Applet implements add(launcher); launcher.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { LoadingThread loader = new LoadingThread(file, file2, @@ -1611,6 +1662,7 @@ public class JalviewLite extends Applet implements frame.setTitle(title); frame.addWindowListener(new WindowAdapter() { + @Override public void windowClosing(WindowEvent e) { if (frame instanceof AlignFrame) @@ -1635,6 +1687,7 @@ public class JalviewLite extends Applet implements frame.dispose(); } + @Override public void windowActivated(WindowEvent e) { if (frame instanceof AlignFrame) @@ -1672,6 +1725,7 @@ public class JalviewLite extends Applet implements * @param g * graphics context */ + @Override public void paint(Graphics g) { if (!fileFound) @@ -1723,6 +1777,7 @@ public class JalviewLite extends Applet implements { private boolean running = false; + @Override public void run() { if (running || checkedForJmol) @@ -1772,7 +1827,7 @@ public class JalviewLite extends Applet implements /** * State variable: protocol for access to file source */ - String protocol; + DataSourceType protocol; String _file; // alignment file or URL spec @@ -1802,7 +1857,7 @@ public class JalviewLite extends Applet implements */ if (path.startsWith("PASTE")) { - protocol = AppletFormatAdapter.PASTE; + protocol = DataSourceType.PASTE; return path.substring(5); } @@ -1811,7 +1866,7 @@ public class JalviewLite extends Applet implements */ if (path.indexOf("://") != -1) { - protocol = AppletFormatAdapter.URL; + protocol = DataSourceType.URL; return path; } @@ -1820,14 +1875,14 @@ public class JalviewLite extends Applet implements */ URL documentBase = getDocumentBase(); String withDocBase = resolveUrlForLocalOrAbsolute(path, documentBase); - if (urlExists(withDocBase)) + if (HttpUtils.isValidUrl(withDocBase)) { if (debug) { System.err.println("Prepended document base '" + documentBase + "' to make: '" + withDocBase + "'"); } - protocol = AppletFormatAdapter.URL; + protocol = DataSourceType.URL; return withDocBase; } @@ -1837,9 +1892,10 @@ public class JalviewLite extends Applet implements URL codeBase = getCodeBase(); String withCodeBase = applet.resolveUrlForLocalOrAbsolute(path, codeBase); - if (!withCodeBase.equals(withDocBase) && urlExists(withCodeBase)) + if (!withCodeBase.equals(withDocBase) + && HttpUtils.isValidUrl(withCodeBase)) { - protocol = AppletFormatAdapter.URL; + protocol = DataSourceType.URL; if (debug) { System.err.println("Prepended codebase '" + codeBase @@ -1854,7 +1910,7 @@ public class JalviewLite extends Applet implements */ if (inArchive(path)) { - protocol = AppletFormatAdapter.CLASSLOADER; + protocol = DataSourceType.CLASSLOADER; } return path; } @@ -1866,6 +1922,7 @@ public class JalviewLite extends Applet implements applet = _applet; } + @Override public void run() { LoadJmolThread jmolchecker = new LoadJmolThread(); @@ -1967,11 +2024,12 @@ public class JalviewLite extends Applet implements return null; } String resolvedFile = resolveFileProtocol(fileParam); - String format = new IdentifyFile().Identify(resolvedFile, protocol); - dbgMsg("File identified as '" + format + "'"); AlignmentI al = null; try { + FileFormatI format = new IdentifyFile().identify(resolvedFile, + protocol); + dbgMsg("File identified as '" + format + "'"); al = new AppletFormatAdapter().readFile(resolvedFile, protocol, format); if ((al != null) && (al.getHeight() > 0)) @@ -1988,7 +2046,7 @@ public class JalviewLite extends Applet implements // update the focus. currentAlignFrame = newAlignFrame; - if (protocol == AppletFormatAdapter.PASTE) + if (protocol == DataSourceType.PASTE) { newAlignFrame.setTitle(MessageManager.formatMessage( "label.sequences_from", new Object[] { applet @@ -2159,8 +2217,7 @@ public class JalviewLite extends Applet implements } else { - pdbs.addElement(new Object[] { pdb, seqs, chains, - new String(protocol) }); + pdbs.addElement(new Object[] { pdb, seqs, chains, protocol }); } } } @@ -2199,6 +2256,11 @@ public class JalviewLite extends Applet implements { boolean result = false; String param = applet.getParameter("jnetfile"); + if (param == null) + { + // jnet became jpred around 2016 + param = applet.getParameter("jpredfile"); + } if (param != null) { try @@ -2404,97 +2466,10 @@ public class JalviewLite extends Applet implements return rtn; } catch (Exception ex) { - System.out.println("Exception checking resources: " + f + " " - + ex); + System.out.println("Exception checking resources: " + f + " " + ex); return false; } } - - /** - * If the file is not already in URL format, tries to locate it by resolving - * as a URL. - * - * @param f - * @return - */ - String addProtocol(final String f) - { - if (f.indexOf("://") != -1) - { - // already has URL format - return f; - } - - /* - * Try relative to document base - */ - URL documentBase = getDocumentBase(); - System.err.println("Trying documentbase: " + documentBase); - String url = applet.resolveUrlForLocalOrAbsolute(f, documentBase); - if (urlExists(url)) - { - if (true/* debug */) - { - System.err.println("Prepended document base '" + documentBase - + "' to make: '" + url + "'"); - } - return url; - } - - /* - * Try relative to codebase - */ - URL codeBase = getCodeBase(); - System.err.println("Trying codebase: " + codeBase); - url = applet.resolveUrlForLocalOrAbsolute(f, codeBase); - if (urlExists(url)) - { - if (true/* debug */) - { - System.err.println("Prepended codebase '" + codeBase - + "' to make: '" + url + "'"); - } - return url; - } - - return f; - } - - /** - * Returns true if an input stream can be opened on the specified URL, else - * false. - * - * @param url - * @return - */ - private boolean urlExists(String url) - { - InputStream is = null; - try - { - is = new URL(url).openStream(); - if (is != null) - { - return true; - } - } catch (Exception x) - { - // ignore - } finally - { - if (is != null) - { - try - { - is.close(); - } catch (IOException e) - { - // ignore - } - } - } - return false; - } } /** @@ -2653,6 +2628,7 @@ public class JalviewLite extends Applet implements * * @see jalview.bin.JalviewLiteJsApi#getFeatureGroups() */ + @Override public String getFeatureGroups() { String lst = arrayToSeparatorList(getDefaultTargetFrame() @@ -2667,6 +2643,7 @@ public class JalviewLite extends Applet implements * jalview.bin.JalviewLiteJsApi#getFeatureGroupsOn(jalview.appletgui.AlignFrame * ) */ + @Override public String getFeatureGroupsOn(AlignFrame alf) { String lst = arrayToSeparatorList(alf.getFeatureGroups()); @@ -2678,6 +2655,7 @@ public class JalviewLite extends Applet implements * * @see jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfState(boolean) */ + @Override public String getFeatureGroupsOfState(boolean visible) { return arrayToSeparatorList(getDefaultTargetFrame() @@ -2691,6 +2669,7 @@ public class JalviewLite extends Applet implements * jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfStateOn(jalview.appletgui * .AlignFrame, boolean) */ + @Override public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible) { return arrayToSeparatorList(alf.getFeatureGroupsOfState(visible)); @@ -2702,6 +2681,7 @@ public class JalviewLite extends Applet implements * @see jalview.bin.JalviewLiteJsApi#setFeatureGroupStateOn(jalview.appletgui. * AlignFrame, java.lang.String, boolean) */ + @Override public void setFeatureGroupStateOn(final AlignFrame alf, final String groups, boolean state) { @@ -2723,6 +2703,7 @@ public class JalviewLite extends Applet implements * @see jalview.bin.JalviewLiteJsApi#setFeatureGroupState(java.lang.String, * boolean) */ + @Override public void setFeatureGroupState(String groups, boolean state) { setFeatureGroupStateOn(getDefaultTargetFrame(), groups, state); @@ -2733,6 +2714,7 @@ public class JalviewLite extends Applet implements * * @see jalview.bin.JalviewLiteJsApi#getSeparator() */ + @Override public String getSeparator() { return separator; @@ -2743,6 +2725,7 @@ public class JalviewLite extends Applet implements * * @see jalview.bin.JalviewLiteJsApi#setSeparator(java.lang.String) */ + @Override public void setSeparator(String separator) { if (separator == null || separator.length() < 1) @@ -2787,6 +2770,7 @@ public class JalviewLite extends Applet implements * @see jalview.bin.JalviewLiteJsApi#addPdbFile(jalview.appletgui.AlignFrame, * java.lang.String, java.lang.String, java.lang.String) */ + @Override public boolean addPdbFile(AlignFrame alFrame, String sequenceId, String pdbEntryString, String pdbFile) { @@ -2803,6 +2787,7 @@ public class JalviewLite extends Applet implements return alignPdbStructures; } + @Override public void start() { // callInitCallback(); @@ -2836,6 +2821,7 @@ public class JalviewLite extends Applet implements * @see jalview.bin.JalviewLiteJsApi#getJsMessage(java.lang.String, * java.lang.String) */ + @Override public String getJsMessage(String messageclass, String viewId) { Hashtable msgset = jsmessages.get(messageclass); @@ -2903,22 +2889,13 @@ public class JalviewLite extends Applet implements { return defcolour; } - Color col = jalview.schemes.ColourSchemeProperty - .getAWTColorFromName(colprop); + Color col = ColorUtils.parseColourString(colprop); if (col == null) { - try - { - col = new jalview.schemes.UserColourScheme(colprop).findColour('A'); - } catch (Exception ex) - { - System.err.println("Couldn't parse '" + colprop - + "' as a colour for " + colparam); - col = null; - } + System.err.println("Couldn't parse '" + colprop + + "' as a colour for " + colparam); } return (col == null) ? defcolour : col; - } public void openJalviewHelpUrl() @@ -2946,6 +2923,15 @@ public class JalviewLite extends Applet implements URL localref) { String resolvedPath = ""; + if (targetPath.startsWith("/")) + { + String codebase = localref.toString(); + String localfile = localref.getFile(); + resolvedPath = codebase.substring(0, + codebase.length() - localfile.length()) + + targetPath; + return resolvedPath; + } /* * get URL path and strip off any trailing file e.g.