X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=8873cc9afa4a4a78ccaaf5c1892522125ddbccf1;hb=dc26db3406f9e89a291d3f6c6faf2f6920d2035f;hp=c7f4e30d8ba19ad9c0f69d243e1b1dbbcac7dd76;hpb=0861cd5f82d2c302372adc53a97126fccc2bfd30;p=jalview.git diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java index c7f4e30..8873cc9 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; @@ -45,8 +48,11 @@ import jalview.io.NewickFile; import jalview.javascript.JSFunctionExec; import jalview.javascript.JalviewLiteJsApi; 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; @@ -62,9 +68,9 @@ 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; import java.util.Hashtable; import java.util.List; import java.util.StringTokenizer; @@ -78,8 +84,8 @@ import netscape.javascript.JSObject; * @author $author$ * @version $Revision: 1.92 $ */ -public class JalviewLite extends Applet implements - StructureSelectionManagerProvider, JalviewLiteJsApi +public class JalviewLite extends Applet + implements StructureSelectionManagerProvider, JalviewLiteJsApi { private static final String TRUE = "true"; @@ -92,13 +98,14 @@ public class JalviewLite extends Applet implements } // ///////////////////////////////////////// - // The following public methods maybe called + // The following public methods may be called // externally, eg via javascript in HTML page /* * (non-Javadoc) * * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences() */ + @Override public String getSelectedSequences() { return getSelectedSequencesFrom(getDefaultTargetFrame()); @@ -109,6 +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); @@ -121,6 +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); @@ -133,6 +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(""); @@ -161,6 +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) { @@ -174,6 +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) { @@ -186,7 +198,7 @@ public class JalviewLite extends Applet implements int apos = -1; try { - apos = new Integer(position).intValue(); + apos = Integer.valueOf(position).intValue(); apos--; } catch (NumberFormatException ex) { @@ -195,9 +207,8 @@ public class JalviewLite extends Applet implements final StructureSelectionManagerProvider me = this; final int pos = apos; // use vamsas listener to broadcast to all listeners in scope - if (alignedPosition != null - && (alignedPosition.trim().length() == 0 || alignedPosition - .toLowerCase().indexOf("false") > -1)) + if (alignedPosition != null && (alignedPosition.trim().length() == 0 + || alignedPosition.toLowerCase().indexOf("false") > -1)) { java.awt.EventQueue.invokeLater(new Runnable() { @@ -230,6 +241,7 @@ 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); @@ -241,6 +253,7 @@ 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); @@ -252,6 +265,7 @@ 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); @@ -263,6 +277,7 @@ 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) { @@ -322,23 +337,23 @@ public class JalviewLite extends Applet implements int from = -1, to = -1; try { - from = new Integer(cl.substring(0, p)).intValue(); + from = Integer.valueOf(cl.substring(0, p)).intValue(); from--; } catch (NumberFormatException ex) { - System.err - .println("ERROR: Couldn't parse first integer in range element column selection string '" + System.err.println( + "ERROR: Couldn't parse first integer in range element column selection string '" + cl + "' - format is 'from-to'"); return; } try { - to = new Integer(cl.substring(p + 1)).intValue(); + to = Integer.valueOf(cl.substring(p + 1)).intValue(); to--; } catch (NumberFormatException ex) { - System.err - .println("ERROR: Couldn't parse second integer in range element column selection string '" + System.err.println( + "ERROR: Couldn't parse second integer in range element column selection string '" + cl + "' - format is 'from-to'"); return; } @@ -393,7 +408,7 @@ public class JalviewLite extends Applet implements int r = -1; try { - r = new Integer(cl).intValue(); + r = Integer.valueOf(cl).intValue(); r--; } catch (NumberFormatException ex) { @@ -404,8 +419,8 @@ public class JalviewLite extends Applet implements } else { - System.err - .println("ERROR: Couldn't parse integer from point selection element of column selection string '" + System.err.println( + "ERROR: Couldn't parse integer from point selection element of column selection string '" + cl + "'"); return; } @@ -455,14 +470,11 @@ 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); @@ -472,7 +484,8 @@ public class JalviewLite extends Applet implements @Override public void run() { - alf.select(sel, csel); + alf.select(sel, csel, + alf.getAlignViewport().getAlignment().getHiddenColumns()); } }); } @@ -485,7 +498,9 @@ public class JalviewLite extends Applet implements * jalview.bin.JalviewLiteJsApi#getSelectedSequencesAsAlignment(java.lang. * String, java.lang.String) */ - public String getSelectedSequencesAsAlignment(String format, String suffix) + @Override + public String getSelectedSequencesAsAlignment(String format, + String suffix) { return getSelectedSequencesAsAlignmentFrom(getDefaultTargetFrame(), format, suffix); @@ -498,26 +513,29 @@ 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 ""; } @@ -527,6 +545,7 @@ public class JalviewLite extends Applet implements * * @see jalview.bin.JalviewLiteJsApi#getAlignmentOrder() */ + @Override public String getAlignmentOrder() { return getAlignmentOrderFrom(getDefaultTargetFrame()); @@ -539,6 +558,7 @@ public class JalviewLite extends Applet implements * jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame * ) */ + @Override public String getAlignmentOrderFrom(AlignFrame alf) { return getAlignmentOrderFrom(alf, separator); @@ -551,6 +571,7 @@ 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(); @@ -568,6 +589,7 @@ 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); @@ -579,6 +601,7 @@ 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); @@ -591,6 +614,7 @@ 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) { @@ -647,6 +671,7 @@ 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); @@ -659,6 +684,7 @@ 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); @@ -670,6 +696,7 @@ 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); @@ -682,6 +709,7 @@ 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) { @@ -689,13 +717,15 @@ 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; } } @@ -704,6 +734,7 @@ public class JalviewLite extends Applet implements * * @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String) */ + @Override public void loadAnnotation(String annotation) { loadAnnotationFrom(getDefaultTargetFrame(), annotation); @@ -716,17 +747,18 @@ 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); } } @@ -735,6 +767,7 @@ 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); @@ -747,10 +780,11 @@ 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); } @@ -759,6 +793,7 @@ public class JalviewLite extends Applet implements * * @see jalview.bin.JalviewLiteJsApi#getFeatures(java.lang.String) */ + @Override public String getFeatures(String format) { return getFeaturesFrom(getDefaultTargetFrame(), format); @@ -771,6 +806,7 @@ 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); @@ -781,6 +817,7 @@ public class JalviewLite extends Applet implements * * @see jalview.bin.JalviewLiteJsApi#getAnnotation() */ + @Override public String getAnnotation() { return getAnnotationFrom(getDefaultTargetFrame()); @@ -793,6 +830,7 @@ public class JalviewLite extends Applet implements * jalview.bin.JalviewLiteJsApi#getAnnotationFrom(jalview.appletgui.AlignFrame * ) */ + @Override public String getAnnotationFrom(AlignFrame alf) { return alf.outputAnnotations(false); @@ -803,6 +841,7 @@ public class JalviewLite extends Applet implements * * @see jalview.bin.JalviewLiteJsApi#newView() */ + @Override public AlignFrame newView() { return newViewFrom(getDefaultTargetFrame()); @@ -813,6 +852,7 @@ public class JalviewLite extends Applet implements * * @see jalview.bin.JalviewLiteJsApi#newView(java.lang.String) */ + @Override public AlignFrame newView(String name) { return newViewFrom(getDefaultTargetFrame(), name); @@ -823,6 +863,7 @@ public class JalviewLite extends Applet implements * * @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame) */ + @Override public AlignFrame newViewFrom(AlignFrame alf) { return alf.newView(null); @@ -834,6 +875,7 @@ 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); @@ -845,21 +887,22 @@ 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(); } @@ -871,12 +914,13 @@ public class JalviewLite extends Applet implements * * @see jalview.bin.JalviewLiteJsApi#setMouseoverListener(java.lang.String) */ + @Override public void setMouseoverListener(String listener) { setMouseoverListener(currentAlignFrame, listener); } - private Vector javascriptListeners = new Vector(); + private Vector javascriptListeners = new Vector<>(); /* * (non-Javadoc) @@ -885,6 +929,7 @@ 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) @@ -892,8 +937,8 @@ public class JalviewLite extends Applet implements listener = listener.trim(); if (listener.length() == 0) { - System.err - .println("jalview Javascript error: Ignoring empty function for mouseover listener."); + System.err.println( + "jalview Javascript error: Ignoring empty function for mouseover listener."); return; } } @@ -905,8 +950,9 @@ public class JalviewLite extends Applet implements if (debug) { System.err.println("Added a mouseover listener for " - + ((af == null) ? "All frames" : "Just views for " - + af.getAlignViewport().getSequenceSetId())); + + ((af == null) ? "All frames" + : "Just views for " + + af.getAlignViewport().getSequenceSetId())); System.err.println("There are now " + javascriptListeners.size() + " listeners in total."); } @@ -917,6 +963,7 @@ public class JalviewLite extends Applet implements * * @see jalview.bin.JalviewLiteJsApi#setSelectionListener(java.lang.String) */ + @Override public void setSelectionListener(String listener) { setSelectionListener(null, listener); @@ -929,6 +976,7 @@ 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) @@ -936,8 +984,8 @@ public class JalviewLite extends Applet implements listener = listener.trim(); if (listener.length() == 0) { - System.err - .println("jalview Javascript error: Ignoring empty function for selection listener."); + System.err.println( + "jalview Javascript error: Ignoring empty function for selection listener."); return; } } @@ -949,19 +997,26 @@ public class JalviewLite extends Applet implements if (debug) { System.err.println("Added a selection listener for " - + ((af == null) ? "All frames" : "Just views for " - + af.getAlignViewport().getSequenceSetId())); + + ((af == null) ? "All frames" + : "Just views for " + + af.getAlignViewport().getSequenceSetId())); System.err.println("There are now " + javascriptListeners.size() + " listeners in total."); } } - /* - * (non-Javadoc) - * + /** + * Callable from javascript to register a javascript function to pass events + * to a structure viewer. + * + * @param listener + * the name of a javascript function + * @param modelSet + * a token separated list of PDB file names listened for * @see jalview.bin.JalviewLiteJsApi#setStructureListener(java.lang.String, - * java.lang.String) + * java.lang.String) */ + @Override public void setStructureListener(String listener, String modelSet) { if (listener != null) @@ -969,13 +1024,13 @@ public class JalviewLite extends Applet implements listener = listener.trim(); if (listener.length() == 0) { - System.err - .println("jalview Javascript error: Ignoring empty function for selection listener."); + System.err.println( + "jalview Javascript error: Ignoring empty function for selection listener."); return; } } - jalview.javascript.MouseOverStructureListener mol = new jalview.javascript.MouseOverStructureListener( - this, listener, separatorListToArray(modelSet)); + MouseOverStructureListener mol = new MouseOverStructureListener(this, + listener, separatorListToArray(modelSet)); javascriptListeners.addElement(mol); StructureSelectionManager.getStructureSelectionManager(this) .addStructureViewerListener(mol); @@ -995,6 +1050,7 @@ 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) @@ -1010,9 +1066,8 @@ public class JalviewLite extends Applet implements { Object lstn = javascriptListeners.elementAt(ms); JsCallBack lstner = (JsCallBack) lstn; - if ((af == null || lstner.getAlignFrame() == af) - && (listener == null || lstner.getListenerFunction().equals( - listener))) + if ((af == null || lstner.getAlignFrame() == af) && (listener == null + || lstner.getListenerFunction().equals(listener))) { javascriptListeners.removeElement(lstner); msSize--; @@ -1044,12 +1099,14 @@ 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()."); @@ -1106,8 +1163,9 @@ public class JalviewLite extends Applet implements * @see jalview.bin.JalviewLiteJsApi#mouseOverStructure(java.lang.String, * java.lang.String, java.lang.String) */ - public void mouseOverStructure(final String pdbResNum, - final String chain, final String pdbfile) + @Override + public void mouseOverStructure(final String pdbResNum, final String chain, + final String pdbfile) { final StructureSelectionManagerProvider me = this; java.awt.EventQueue.invokeLater(new Runnable() @@ -1118,13 +1176,13 @@ public class JalviewLite extends Applet implements try { StructureSelectionManager.getStructureSelectionManager(me) - .mouseOverStructure(new Integer(pdbResNum).intValue(), + .mouseOverStructure(Integer.valueOf(pdbResNum).intValue(), chain, pdbfile); if (debug) { - System.err.println("mouseOver for '" + pdbResNum - + "' in chain '" + chain + "' in structure '" + pdbfile - + "'"); + System.err + .println("mouseOver for '" + pdbResNum + "' in chain '" + + chain + "' in structure '" + pdbfile + "'"); } } catch (NumberFormatException e) { @@ -1143,6 +1201,7 @@ 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) { @@ -1153,8 +1212,8 @@ public class JalviewLite extends Applet implements { try { - alf.scrollTo(new Integer(topRow).intValue(), new Integer( - leftHandColumn).intValue()); + alf.scrollTo(Integer.valueOf(topRow).intValue(), + Integer.valueOf(leftHandColumn).intValue()); } catch (Exception ex) { @@ -1185,7 +1244,7 @@ public class JalviewLite extends Applet implements { try { - alf.scrollToRow(new Integer(topRow).intValue()); + alf.scrollToRow(Integer.valueOf(topRow).intValue()); } catch (Exception ex) { @@ -1217,12 +1276,12 @@ public class JalviewLite extends Applet implements { try { - alf.scrollToColumn(new Integer(leftHandColumn).intValue()); + alf.scrollToColumn(Integer.valueOf(leftHandColumn).intValue()); } catch (Exception ex) { - System.err - .println("Couldn't parse integer arguments (leftHandColumn='" + System.err.println( + "Couldn't parse integer arguments (leftHandColumn='" + leftHandColumn + "')"); ex.printStackTrace(); } @@ -1296,8 +1355,8 @@ public class JalviewLite extends Applet implements { try { - BufferedReader reader = new BufferedReader(new InputStreamReader( - url.openStream())); + BufferedReader reader = new BufferedReader( + new InputStreamReader(url.openStream())); String line; while ((line = reader.readLine()) != null) { @@ -1345,9 +1404,10 @@ public class JalviewLite extends Applet implements /** * init method for Jalview Applet */ + @Override public void init() { - // remove any handlers that might be hanging around from an earlier instance + debug = TRUE.equalsIgnoreCase(getParameter("debug")); try { if (debug) @@ -1363,30 +1423,24 @@ public class JalviewLite extends Applet implements } catch (Exception ex) { - System.err - .println("Warning: No JalviewLite javascript callbacks available."); + System.err.println( + "Warning: No JalviewLite javascript callbacks available."); if (debug) { ex.printStackTrace(); } } - /** - * turn on extra applet debugging - */ - debug = TRUE.equalsIgnoreCase(getParameter("debug")); + if (debug) { - System.err.println("JalviewLite Version " + getVersion()); System.err.println("Build Date : " + getBuildDate()); System.err.println("Installation : " + getInstallation()); - } String externalsviewer = getParameter("externalstructureviewer"); if (externalsviewer != null) { - useXtrnalSviewer = externalsviewer.trim().toLowerCase() - .equals(TRUE); + useXtrnalSviewer = externalsviewer.trim().toLowerCase().equals(TRUE); } /** * if true disable the check for jmol @@ -1412,7 +1466,8 @@ public class JalviewLite extends Applet implements } else { - throw new Error(MessageManager.getString("error.invalid_separator_parameter")); + throw new Error(MessageManager + .getString("error.invalid_separator_parameter")); } } int r = 255; @@ -1459,7 +1514,7 @@ public class JalviewLite extends Applet implements file = data.toString(); } } - if (TRUE.equalsIgnoreCase(getParameter("enableSplitFrame"))) + if (getDefaultParameter("enableSplitFrame", true)) { file2 = getParameter("file2"); } @@ -1485,6 +1540,7 @@ 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, @@ -1568,8 +1624,8 @@ public class JalviewLite extends Applet implements { // do onInit with the JS executor thread new JSFunctionExec(this).executeJavascriptFunction(true, - initjscallback, null, "Calling oninit callback '" - + initjscallback + "'."); + initjscallback, null, + "Calling oninit callback '" + initjscallback + "'."); } catch (Exception e) { System.err.println("Exception when executing _oninit callback '" @@ -1607,6 +1663,7 @@ public class JalviewLite extends Applet implements frame.setTitle(title); frame.addWindowListener(new WindowAdapter() { + @Override public void windowClosing(WindowEvent e) { if (frame instanceof AlignFrame) @@ -1631,6 +1688,7 @@ public class JalviewLite extends Applet implements frame.dispose(); } + @Override public void windowActivated(WindowEvent e) { if (frame instanceof AlignFrame) @@ -1668,6 +1726,7 @@ public class JalviewLite extends Applet implements * @param g * graphics context */ + @Override public void paint(Graphics g) { if (!fileFound) @@ -1677,8 +1736,8 @@ public class JalviewLite extends Applet implements g.fillRect(0, 0, getSize().width, getSize().height); g.setColor(Color.red); g.drawString( - MessageManager.getString("label.jalview_cannot_open_file"), - 5, 15); + MessageManager.getString("label.jalview_cannot_open_file"), 5, + 15); g.drawString("\"" + file + "\"", 5, 30); } else if (embedded) @@ -1719,6 +1778,7 @@ public class JalviewLite extends Applet implements { private boolean running = false; + @Override public void run() { if (running || checkedForJmol) @@ -1737,8 +1797,8 @@ public class JalviewLite extends Applet implements } if (!jmolAvailable) { - System.out - .println("Jmol not available - Using MCview for structures"); + System.out.println( + "Jmol not available - Using MCview for structures"); } } catch (java.lang.ClassNotFoundException ex) { @@ -1749,8 +1809,8 @@ public class JalviewLite extends Applet implements jmolAvailable = false; if (debug) { - System.err - .println("Skipping Jmol check. Will use MCView (probably)"); + System.err.println( + "Skipping Jmol check. Will use MCView (probably)"); } } checkedForJmol = true; @@ -1768,7 +1828,7 @@ 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 @@ -1788,27 +1848,72 @@ public class JalviewLite extends Applet implements * update the protocol state variable for accessing the datasource located * by file. * - * @param file + * @param path * @return possibly updated datasource string */ - public String setProtocolState(String file) + public String resolveFileProtocol(String path) { - if (file.startsWith("PASTE")) + /* + * is it paste data? + */ + if (path.startsWith("PASTE")) { - file = file.substring(5); - protocol = AppletFormatAdapter.PASTE; + protocol = DataSourceType.PASTE; + return path.substring(5); } - else if (inArchive(file)) + + /* + * is it a URL? + */ + if (path.indexOf("://") != -1) { - protocol = AppletFormatAdapter.CLASSLOADER; + protocol = DataSourceType.URL; + return path; } - else + + /* + * try relative to document root + */ + URL documentBase = getDocumentBase(); + String withDocBase = resolveUrlForLocalOrAbsolute(path, documentBase); + if (HttpUtils.isValidUrl(withDocBase)) + { + if (debug) + { + System.err.println("Prepended document base '" + documentBase + + "' to make: '" + withDocBase + "'"); + } + protocol = DataSourceType.URL; + return withDocBase; + } + + /* + * try relative to codebase (if different to document base) + */ + URL codeBase = getCodeBase(); + String withCodeBase = applet.resolveUrlForLocalOrAbsolute(path, + codeBase); + if (!withCodeBase.equals(withDocBase) + && HttpUtils.isValidUrl(withCodeBase)) + { + protocol = DataSourceType.URL; + if (debug) + { + System.err.println("Prepended codebase '" + codeBase + + "' to make: '" + withCodeBase + "'"); + } + return withCodeBase; + } + + /* + * try locating by classloader; try this last so files in the directory + * are resolved using document base + */ + if (inArchive(path)) { - file = addProtocol(file); - protocol = AppletFormatAdapter.URL; + protocol = DataSourceType.CLASSLOADER; } - dbgMsg("Protocol identified as '" + protocol + "'"); - return file; + return path; } public LoadingThread(String file, String file2, JalviewLite _applet) @@ -1818,6 +1923,7 @@ public class JalviewLite extends Applet implements applet = _applet; } + @Override public void run() { LoadJmolThread jmolchecker = new LoadJmolThread(); @@ -1842,7 +1948,8 @@ public class JalviewLite extends Applet implements */ private void startLoading() { - dbgMsg("Loading thread started with:\n>>file\n" + _file + ">>endfile"); + dbgMsg("Loading thread started with:\n>>file\n" + _file + + ">>endfile"); dbgMsg("Loading started."); @@ -1884,8 +1991,11 @@ public class JalviewLite extends Applet implements { AlignmentI al1 = af.viewport.getAlignment(); AlignmentI al2 = af2.viewport.getAlignment(); - if (AlignmentUtils.isMappable(al1, al2)) + AlignmentI cdna = al1.isNucleotide() ? al1 : al2; + AlignmentI prot = al1.isNucleotide() ? al2 : al1; + if (AlignmentUtils.mapProteinAlignmentToCdna(prot, cdna)) { + al2.alignAs(al1); SplitFrame sf = new SplitFrame(af, af2); sf.addToDisplay(embedded, JalviewLite.this); return; @@ -1915,13 +2025,15 @@ public class JalviewLite extends Applet implements { return null; } - String resolvedFile = setProtocolState(fileParam); - String format = new IdentifyFile().Identify(resolvedFile, protocol); - dbgMsg("File identified as '" + format + "'"); + String resolvedFile = resolveFileProtocol(fileParam); AlignmentI al = null; try { - al = new AppletFormatAdapter().readFile(resolvedFile, protocol, format); + 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)) { dbgMsg("Successfully loaded file."); @@ -1936,10 +2048,10 @@ 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[] + newAlignFrame.setTitle(MessageManager + .formatMessage("label.sequences_from", new Object[] { applet.getDocumentBase().toString() })); } @@ -1968,8 +2080,8 @@ public class JalviewLite extends Applet implements dbgMsg(">>>Dump finished."); } catch (Exception e) { - System.err - .println("Exception when trying to dump the content of the file parameter."); + System.err.println( + "Exception when trying to dump the content of the file parameter."); e.printStackTrace(); } } @@ -1992,8 +2104,8 @@ public class JalviewLite extends Applet implements * related to JAL-434 */ - applet.setAlignPdbStructures(getDefaultParameter("alignpdbfiles", - false)); + applet.setAlignPdbStructures( + getDefaultParameter("alignpdbfiles", false)); /* * @@ -2009,9 +2121,11 @@ public class JalviewLite extends Applet implements Vector pdbs = new Vector(); // create a lazy matcher if we're asked to jalview.analysis.SequenceIdMatcher matcher = (applet - .getDefaultParameter("relaxedidmatch", false)) ? new jalview.analysis.SequenceIdMatcher( - alignFrame.getAlignViewport().getAlignment() - .getSequencesArray()) : null; + .getDefaultParameter("relaxedidmatch", false)) + ? new jalview.analysis.SequenceIdMatcher( + alignFrame.getAlignViewport().getAlignment() + .getSequencesArray()) + : null; String param; do @@ -2040,18 +2154,18 @@ public class JalviewLite extends Applet implements String sequence = applet.getParameter("PDBSEQ"); if (sequence != null) { - seqs = new SequenceI[] - { matcher == null ? (Sequence) alignFrame.getAlignViewport() - .getAlignment().findName(sequence) : matcher - .findIdMatch(sequence) }; + seqs = new SequenceI[] { matcher == null + ? (Sequence) alignFrame.getAlignViewport() + .getAlignment().findName(sequence) + : matcher.findIdMatch(sequence) }; } } else { param = st.nextToken(); - Vector tmp = new Vector(); - Vector tmp2 = new Vector(); + List tmp = new ArrayList<>(); + List tmp2 = new ArrayList<>(); while (st.hasMoreTokens()) { @@ -2060,39 +2174,23 @@ public class JalviewLite extends Applet implements if (st2.countTokens() > 1) { // This is the chain - tmp2.addElement(st2.nextToken()); + tmp2.add(st2.nextToken()); seqstring = st2.nextToken(); } - tmp.addElement(matcher == null ? (Sequence) alignFrame - .getAlignViewport().getAlignment() - .findName(seqstring) : matcher.findIdMatch(seqstring)); + tmp.add(matcher == null + ? (Sequence) alignFrame.getAlignViewport() + .getAlignment().findName(seqstring) + : matcher.findIdMatch(seqstring)); } - seqs = new SequenceI[tmp.size()]; - tmp.copyInto(seqs); + seqs = tmp.toArray(new SequenceI[tmp.size()]); if (tmp2.size() == tmp.size()) { - chains = new String[tmp2.size()]; - tmp2.copyInto(chains); + chains = tmp2.toArray(new String[tmp2.size()]); } } - param = setProtocolState(param); - - if (// !jmolAvailable - // && - protocol == AppletFormatAdapter.CLASSLOADER && !useXtrnalSviewer) - { - // Re: JAL-357 : the bug isn't a problem if we are using an - // external viewer! - // 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); // - } - + param = resolveFileProtocol(param); + // TODO check JAL-357 for files in a jar (CLASSLOADER) pdb.setFile(param); if (seqs != null) @@ -2102,8 +2200,9 @@ public class JalviewLite extends Applet implements if (seqs[i] != null) { ((Sequence) seqs[i]).addPDBId(pdb); - StructureSelectionManager.getStructureSelectionManager( - applet).registerPDBEntry(pdb); + StructureSelectionManager + .getStructureSelectionManager(applet) + .registerPDBEntry(pdb); } else { @@ -2111,8 +2210,8 @@ public class JalviewLite extends Applet implements { // 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 " + System.err.println( + "Warning: Possible input parsing error: Null sequence for attachment of PDB (sequence " + i + ")"); } } @@ -2125,8 +2224,7 @@ 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 }); } } } @@ -2139,7 +2237,8 @@ public class JalviewLite extends Applet implements PDBEntry[] pdb = new PDBEntry[pdbs.size()]; String[][] chains = new String[pdbs.size()][]; String[] protocols = new String[pdbs.size()]; - for (int pdbsi = 0, pdbsiSize = pdbs.size(); pdbsi < pdbsiSize; pdbsi++) + for (int pdbsi = 0, pdbsiSize = pdbs + .size(); pdbsi < pdbsiSize; pdbsi++) { Object[] o = (Object[]) pdbs.elementAt(pdbsi); pdb[pdbsi] = (PDBEntry) o[0]; @@ -2165,21 +2264,23 @@ 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 { - param = setProtocolState(param); + param = resolveFileProtocol(param); JPredFile predictions = new JPredFile(param, protocol); JnetAnnotationMaker.add_annotation(predictions, alignFrame.viewport.getAlignment(), 0, false); // false == do not add sequence profile from concise output - SequenceI repseq = alignFrame.viewport.getAlignment() - .getSequenceAt(0); - alignFrame.viewport.getAlignment().setSeqrep(repseq); - ColumnSelection cs = new ColumnSelection(); - cs.hideInsertionsFor(repseq); - alignFrame.viewport.setColumnSelection(cs); + + alignFrame.viewport.getAlignment().setupJPredAlignment(); + alignFrame.alignPanel.fontChanged(); alignFrame.alignPanel.setScrollValues(0, 0); result = true; @@ -2204,7 +2305,7 @@ public class JalviewLite extends Applet implements String param = applet.getParameter("annotations"); if (param != null) { - param = setProtocolState(param); + param = resolveFileProtocol(param); if (new AnnotationFile().annotateAlignmentView(alignFrame.viewport, param, protocol)) @@ -2215,8 +2316,8 @@ public class JalviewLite extends Applet implements } else { - System.err - .println("Annotations were not added from annotation file '" + System.err.println( + "Annotations were not added from annotation file '" + param + "'"); } } @@ -2257,7 +2358,7 @@ public class JalviewLite extends Applet implements param = applet.getParameter("features"); if (param != null) { - param = setProtocolState(param); + param = resolveFileProtocol(param); result = alignFrame.parseFeaturesFile(param, protocol); } @@ -2287,14 +2388,14 @@ public class JalviewLite extends Applet implements { if (debug) { - System.err - .println("Attempting to load T-COFFEE score file from the scoreFile parameter"); + System.err.println( + "Attempting to load T-COFFEE score file from the scoreFile parameter"); } result = alignFrame.loadScoreFile(sScoreFile); if (!result) { - System.err - .println("Failed to parse T-COFFEE parameter as a valid score file ('" + System.err.println( + "Failed to parse T-COFFEE parameter as a valid score file ('" + sScoreFile + "')"); } } catch (Exception e) @@ -2326,7 +2427,7 @@ public class JalviewLite extends Applet implements { try { - treeFile = setProtocolState(treeFile); + treeFile = resolveFileProtocol(treeFile); NewickFile fin = new NewickFile(treeFile, protocol); fin.parse(); @@ -2351,113 +2452,29 @@ public class JalviewLite extends Applet implements /** * Discovers whether the given file is in the Applet Archive * - * @param file + * @param f * String * @return boolean */ - boolean inArchive(String file) + boolean inArchive(String f) { // This might throw a security exception in certain browsers // Netscape Communicator for instance. try { - boolean rtn = (getClass().getResourceAsStream("/" + file) != null); + boolean rtn = (getClass().getResourceAsStream("/" + f) != null); if (debug) { - System.err.println("Resource '" + file + "' was " - + (rtn ? "" : "not") + " located by classloader."); + System.err.println("Resource '" + f + "' was " + + (rtn ? "" : "not ") + "located by classloader."); } return rtn; } catch (Exception ex) { - System.out.println("Exception checking resources: " + file + " " - + 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 file - * @return - */ - String addProtocol(final String file) - { - if (file.indexOf("://") == -1) - { - /* - * Try relative to document base - */ - String url = applet.resolveUrlForLocalOrAbsolute(file, - getDocumentBase()); - if (urlExists(url)) - { - if (debug) - { - System.err.println("Prepended document base for resource: '" - + file + "'"); - } - return url; - } - - /* - * Try relative to codebase - */ - url = applet.resolveUrlForLocalOrAbsolute(file, getCodeBase()); - if (urlExists(url)) - { - if (debug) - { - System.err.println("Prepended codebase for resource: '" + file - + "'"); - } - return url; - } - } - - /* - * Not resolved, leave unchanged - */ - return file; - } - - /** - * 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; - } } /** @@ -2475,8 +2492,8 @@ public class JalviewLite extends Applet implements { return initialAlignFrame; } - System.err - .println("Implementation error: Jalview Applet API cannot work out which AlignFrame to use."); + System.err.println( + "Implementation error: Jalview Applet API cannot work out which AlignFrame to use."); return null; } @@ -2510,9 +2527,9 @@ public class JalviewLite extends Applet implements * @param separator * @return elements separated by separator */ - public String[] separatorListToArray(String list, String separator) + public static String[] separatorListToArray(String list, String separator) { - // note separator local variable intentionally masks object field + // TODO use StringUtils version (slightly different...) int seplen = separator.length(); if (list == null || list.equals("") || list.equals(separator)) { @@ -2554,8 +2571,8 @@ public class JalviewLite extends Applet implements } if (debug) { - System.err.println("Empty Array from '" + separator - + "' separated List"); + System.err.println( + "Empty Array from '" + separator + "' separated List"); } return null; } @@ -2578,8 +2595,9 @@ public class JalviewLite extends Applet implements * @param separator * @return concatenated string */ - public String arrayToSeparatorList(String[] list, String separator) + public static String arrayToSeparatorList(String[] list, String separator) { + // TODO use StringUtils version StringBuffer v = new StringBuffer(); if (list != null && list.length > 0) { @@ -2596,16 +2614,16 @@ public class JalviewLite extends Applet implements } if (debug) { - System.err.println("Returning '" + separator - + "' separated List:\n"); + 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"); + System.err.println( + "Returning empty '" + separator + "' separated List\n"); } return "" + separator; } @@ -2615,10 +2633,11 @@ public class JalviewLite extends Applet implements * * @see jalview.bin.JalviewLiteJsApi#getFeatureGroups() */ + @Override public String getFeatureGroups() { - String lst = arrayToSeparatorList(getDefaultTargetFrame() - .getFeatureGroups()); + String lst = arrayToSeparatorList( + getDefaultTargetFrame().getFeatureGroups()); return lst; } @@ -2629,6 +2648,7 @@ public class JalviewLite extends Applet implements * jalview.bin.JalviewLiteJsApi#getFeatureGroupsOn(jalview.appletgui.AlignFrame * ) */ + @Override public String getFeatureGroupsOn(AlignFrame alf) { String lst = arrayToSeparatorList(alf.getFeatureGroups()); @@ -2640,10 +2660,11 @@ public class JalviewLite extends Applet implements * * @see jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfState(boolean) */ + @Override public String getFeatureGroupsOfState(boolean visible) { - return arrayToSeparatorList(getDefaultTargetFrame() - .getFeatureGroupsOfState(visible)); + return arrayToSeparatorList( + getDefaultTargetFrame().getFeatureGroupsOfState(visible)); } /* @@ -2653,6 +2674,7 @@ 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)); @@ -2664,6 +2686,7 @@ 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) { @@ -2685,6 +2708,7 @@ 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); @@ -2695,6 +2719,7 @@ public class JalviewLite extends Applet implements * * @see jalview.bin.JalviewLiteJsApi#getSeparator() */ + @Override public String getSeparator() { return separator; @@ -2705,6 +2730,7 @@ 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) @@ -2736,7 +2762,7 @@ public class JalviewLite extends Applet implements { return def; } - if (stn.toLowerCase().equals(TRUE)) + if (TRUE.equalsIgnoreCase(stn)) { return true; } @@ -2749,6 +2775,7 @@ 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) { @@ -2765,14 +2792,15 @@ public class JalviewLite extends Applet implements return alignPdbStructures; } + @Override public void start() { // callInitCallback(); } - private Hashtable jshashes = new Hashtable(); + private Hashtable jshashes = new Hashtable<>(); - private Hashtable> jsmessages = new Hashtable>(); + private Hashtable> jsmessages = new Hashtable<>(); public void setJsMessageSet(String messageclass, String viewId, String[] colcommands) @@ -2780,7 +2808,7 @@ public class JalviewLite extends Applet implements Hashtable msgset = jsmessages.get(messageclass); if (msgset == null) { - msgset = new Hashtable(); + msgset = new Hashtable<>(); jsmessages.put(messageclass, msgset); } msgset.put(viewId, colcommands); @@ -2798,6 +2826,7 @@ 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); @@ -2865,22 +2894,13 @@ 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() @@ -2897,27 +2917,60 @@ public class JalviewLite extends Applet implements * form a complete URL given a path to a resource and a reference location on * the same server * - * @param url + * @param targetPath * - an absolute path on the same server as localref or a document * located relative to localref * @param localref * - a URL on the same server as url * @return a complete URL for the resource located by url */ - private String resolveUrlForLocalOrAbsolute(String url, URL localref) + private String resolveUrlForLocalOrAbsolute(String targetPath, + URL localref) { - String codebase = localref.toString(); - if (url.indexOf("/") == 0) + String resolvedPath = ""; + if (targetPath.startsWith("/")) { - url = codebase.substring(0, codebase.length() - - localref.getFile().length()) - + url; + 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. + * www.jalview.org/examples/index.html#applets?a=b is trimmed to + * www.jalview.org/examples/ + */ + String urlPath = localref.toString(); + String directoryPath = urlPath; + int lastSeparator = directoryPath.lastIndexOf("/"); + if (lastSeparator > 0) + { + directoryPath = directoryPath.substring(0, lastSeparator + 1); + } + + if (targetPath.startsWith("/")) + { + /* + * construct absolute URL to a file on the server - this is not allowed? + */ + // String localfile = localref.getFile(); + // resolvedPath = urlPath.substring(0, + // urlPath.length() - localfile.length()) + // + targetPath; + resolvedPath = directoryPath + targetPath.substring(1); } else { - url = localref + url; + resolvedPath = directoryPath + targetPath; + } + if (debug) + { + System.err.println( + "resolveUrlForLocalOrAbsolute returning " + resolvedPath); } - return url; + return resolvedPath; } /** @@ -2937,17 +2990,15 @@ public class JalviewLite extends Applet implements // form valid URL // Should really use docbase, not codebase. URL prepend; - url = resolveUrlForLocalOrAbsolute( - url, - prepend = getDefaultParameter("resolvetocodebase", false) ? getDocumentBase() - : getCodeBase()); + url = resolveUrlForLocalOrAbsolute(url, + prepend = getDefaultParameter("resolvetocodebase", false) + ? getCodeBase() + : getDocumentBase()); if (debug) { - System.err - .println("Show url (prepended " - + prepend - + " - toggle resolvetocodebase if code/docbase resolution is wrong): " - + url); + System.err.println("Show url (prepended " + prepend + + " - toggle resolvetocodebase if code/docbase resolution is wrong): " + + url); } } else