From: BobHanson Date: Tue, 2 Jun 2020 00:32:42 +0000 (-0500) Subject: JAL-3626 from JAL-3253-applet web page embedding X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=51b0b157926ed477cb558ca5971126bf9fccbd31;p=jalview.git JAL-3626 from JAL-3253-applet web page embedding --- diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index cdd8cc1..98dc039 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -20,10 +20,22 @@ */ package jalview.bin; +import jalview.api.AlignCalcWorkerI; +import jalview.api.AlignViewportI; +import jalview.api.JalviewApp; +import jalview.api.StructureSelectionManagerProvider; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; import jalview.ext.so.SequenceOntology; import jalview.gui.AlignFrame; +import jalview.gui.AlignmentPanel; +import jalview.gui.CalculationChooser; import jalview.gui.Desktop; import jalview.gui.PromptUserConfig; +import jalview.gui.StructureViewer; import jalview.io.AppletFormatAdapter; import jalview.io.BioJsHTMLOutput; import jalview.io.DataSourceType; @@ -35,12 +47,19 @@ import jalview.io.HtmlSvgOutput; import jalview.io.IdentifyFile; import jalview.io.NewickFile; import jalview.io.gff.SequenceOntologyFactory; +import jalview.javascript.JSFunctionExec; +import jalview.javascript.MouseOverStructureListener; +import jalview.renderer.seqfeatures.FeatureRenderer; import jalview.schemes.ColourSchemeI; import jalview.schemes.ColourSchemeProperty; +import jalview.structure.SelectionSource; +import jalview.structure.VamsasSource; import jalview.util.MessageManager; import jalview.util.Platform; import jalview.ws.jws2.Jws2Discoverer; +import netscape.javascript.JSObject; +import java.applet.AppletContext; import java.io.BufferedReader; import java.io.File; import java.io.FileOutputStream; @@ -58,6 +77,7 @@ import java.security.PermissionCollection; import java.security.Permissions; import java.security.Policy; import java.util.HashMap; +import java.util.Hashtable; import java.util.Map; import java.util.Vector; import java.util.logging.ConsoleHandler; @@ -87,7 +107,7 @@ import groovy.util.GroovyScriptEngine; * @author $author$ * @version $Revision$ */ -public class Jalview +public class Jalview implements JalviewJSApi { static { @@ -102,6 +122,39 @@ public class Jalview public static AlignFrame currentAlignFrame; + public boolean isJavaAppletTag; + + public String appletResourcePath; + + JalviewAppLoader appLoader; + + protected JSFunctionExec jsFunctionExec; + + private boolean noCalculation, noMenuBar, noStatus; + + private boolean noAnnotation; + + public boolean getStartCalculations() + { + return !noCalculation; + } + + public boolean getAllowMenuBar() + { + return !noMenuBar; + } + + public boolean getShowStatus() + { + return !noStatus; + } + + public boolean getShowAnnotation() + { + return !noAnnotation; + } + + static { if (!Platform.isJS()) @@ -202,53 +255,14 @@ public class Jalview */ public static void main(String[] args) { -// setLogging(); // BH - for event debugging in JavaScript - instance = new Jalview(); - instance.doMain(args); -} - - private static void logClass(String name) - { - // BH - for event debugging in JavaScript - ConsoleHandler consoleHandler = new ConsoleHandler(); - consoleHandler.setLevel(Level.ALL); - Logger logger = Logger.getLogger(name); - logger.setLevel(Level.ALL); - logger.addHandler(consoleHandler); - } - - @SuppressWarnings("unused") - private static void setLogging() - { - - /** - * @j2sIgnore - * - */ + if (false) { - System.out.println("not in js"); + Platform.startJavaLogging(); } - // BH - for event debugging in JavaScript (Java mode only) - if (!Platform.isJS()) - /** - * Java only - * - * @j2sIgnore - */ - { - Logger.getLogger("").setLevel(Level.ALL); - logClass("java.awt.EventDispatchThread"); - logClass("java.awt.EventQueue"); - logClass("java.awt.Component"); - logClass("java.awt.focus.Component"); - logClass("java.awt.focus.DefaultKeyboardFocusManager"); - } - - } - - - + instance = new Jalview(); + instance.doMain(args); +} /** * @param args @@ -1086,4 +1100,817 @@ public class Jalview { Jalview.currentAlignFrame = currentAlignFrame; } + + /** + * Get the SwingJS applet ID and combine that with the frameType + * + * @param frameType + * "alignment", "desktop", etc., or null + * @return + */ + public static String getAppID(String frameType) + { + String id = Cache.getProperty("Info.j2sAppletID"); + if (id == null) + { + id = "jalview"; + } + return id + (frameType == null ? "" : "-" + frameType); + } + + /** + * Handle all JalviewLite applet parameters + * + * @param aparser + * @param af + */ + private void loadAppletParams(ArgsParser aparser, AlignFrame af) + { + JalviewApp app = new JalviewApp() + { + + // TODO BH 2019 + // + // These are methods that are in JalviewLite that various classes call + // but are not in JalviewLiteJsApi. Or, even if they are, other classes + // call + // them to JalviewLite directly. Some may not be necessary, but they have + // to + // be at least mentioned here, or the classes calling them should + // reference + // JalviewLite itself. + + private boolean alignPDBStructures; // From JalviewLite; not implemented + + private Hashtable> jsmessages; + + private Hashtable jshashes; + + @Override + public String getParameter(String name) + { + return aparser.getAppletValue(name, null); + } + + @Override + public boolean getDefaultParameter(String name, boolean def) + { + String stn; + return ((stn = getParameter(name)) == null ? def + : "true".equalsIgnoreCase(stn)); + } + + /** + * Get the applet-like document base even though this is an application. + */ + @Override + public URL getDocumentBase() + { + return Platform.getDocumentBase(); + } + + /** + * Get the applet-like code base even though this is an application. + */ + @Override + public URL getCodeBase() + { + return Platform.getCodeBase(); + } + + @Override + public AlignViewportI getViewport() + { + return af.getViewport(); + } + + /** + * features + * + */ + @Override + public boolean parseFeaturesFile(String filename, + DataSourceType protocol) + { + return af.parseFeaturesFile(filename, protocol); + } + + /** + * scorefile + * + */ + @Override + public boolean loadScoreFile(String sScoreFile) throws IOException + { + af.loadJalviewDataFile(sScoreFile, null, null, null); + return true; + } + + /** + * annotations, jpredfile, jnetfile + * + */ + @Override + public void updateForAnnotations() + { + af.updateForAnnotations(); + } + + @Override + public void loadTree(NewickFile fin, String treeFile) + throws IOException + { + // n/a -- already done by standard Jalview command line processing + } + + @Override + public void setAlignPdbStructures(boolean defaultParameter) + { + alignPDBStructures = true; + } + + @Override + public void newStructureView(PDBEntry pdb, SequenceI[] seqs, + String[] chains, DataSourceType protocol) + { + StructureViewer.launchStructureViewer(af.alignPanel, pdb, seqs); + } + + @Override + public void setFeatureGroupState(String[] groups, boolean state) + { + af.setFeatureGroupState(groups, state); + } + + @Override + public void alignedStructureView(PDBEntry[] pdb, SequenceI[][] seqs, + String[][] chains, String[] protocols) + { + System.err.println( + "Jalview applet interface alignedStructureView not implemented"); + } + + @Override + public void newFeatureSettings() + { + System.err.println( + "Jalview applet interface newFeatureSettings not implemented"); + } + + private Vector jsExecQueue; + + @Override + public Vector getJsExecQueue(JSFunctionExec exec) + { + jsFunctionExec = exec; + return (jsExecQueue == null ? (jsExecQueue = new Vector<>()) + : jsExecQueue); + } + + @Override + public AppletContext getAppletContext() + { + // TODO Auto-generated method stub + return null; + } + + @Override + public boolean isJsfallbackEnabled() + { + // TODO Auto-generated method stub + return false; + } + + @Override + public JSObject getJSObject() + { + // TODO Auto-generated method stub + return null; + } + + @Override + public StructureSelectionManagerProvider getStructureSelectionManagerProvider() + { + // TODO Q: what exactly is this? BH + return null; + } + + @Override + public void updateColoursFromMouseOver(Object source, + MouseOverStructureListener mouseOverStructureListener) + { + // TODO Auto-generated method stub + + } + + @Override + public Object[] getSelectionForListener(SequenceGroup seqsel, + ColumnSelection colsel, HiddenColumns hidden, + SelectionSource source, Object alignFrame) + { + return appLoader.getSelectionForListener(getCurrentAlignFrame(), + seqsel, colsel, hidden, source, alignFrame); + } + + @Override + public String arrayToSeparatorList(String[] array) + { + return appLoader.arrayToSeparatorList(array); + } + + @Override + public Hashtable getJSHashes() + { + return (jshashes == null ? (jshashes = new Hashtable<>()) + : jshashes); + } + + @Override + public Hashtable> getJSMessages() + { + return (jsmessages == null ? (jsmessages = new Hashtable<>()) + : jsmessages); + } + + @Override + public Object getFrameForSource(VamsasSource source) + { + if (source != null) + { + AlignFrame af; + if (source instanceof jalview.gui.AlignViewport + && source == (af = getCurrentAlignFrame()).getViewport()) + { + // should be valid if it just generated an event! + return af; + } + // TODO: ensure that if '_af' is specified along with a handler + // function, then only events from that alignFrame are sent to that + // function + } + return null; + } + + @Override + public FeatureRenderer getNewFeatureRenderer(AlignViewportI vp) + { + return new jalview.gui.FeatureRenderer((AlignmentPanel) vp); + } + + }; + + appLoader = new JalviewAppLoader(true); + appLoader.load(app); + } + + /** + * + * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences() + */ + @Override + public String getSelectedSequences() + { + return getSelectedSequencesFrom(getCurrentAlignFrame()); + } + + /** + * + * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences(java.lang.String) + */ + @Override + public String getSelectedSequences(String sep) + { + return getSelectedSequencesFrom(getCurrentAlignFrame(), sep); + } + + /** + * + * @see jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui + * .AlignFrame) + */ + @Override + public String getSelectedSequencesFrom(AlignFrame alf) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + return getSelectedSequencesFrom(alf, null); + } + + /** + * + * @see jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui + * .AlignFrame, java.lang.String) + */ + @Override + public String getSelectedSequencesFrom(AlignFrame alf, String sep) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + return appLoader.getSelectedSequencesFrom(alf, sep); + } + + /** + * + * @see jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui + * .AlignFrame, java.lang.String) + */ + @Override + public void highlight(String sequenceId, String position, + String alignedPosition) + { + highlightIn(null, sequenceId, position, + alignedPosition); + } + + @Override + public void highlightIn(AlignFrame alf, String sequenceId, + String position, String alignedPosition) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + appLoader.highlightIn(alf, sequenceId, position, alignedPosition); + } + + @Override + public void select(String sequenceIds, String columns) + { + selectIn(getCurrentAlignFrame(), sequenceIds, columns, null); + } + + @Override + public void select(String sequenceIds, String columns, String sep) + { + selectIn(null, sequenceIds, columns, sep); + } + + @Override + public void selectIn(AlignFrame alf, String sequenceIds, String columns) + { + selectIn(alf, sequenceIds, columns, null); + } + + @Override + public void selectIn(AlignFrame alf, String sequenceIds, String columns, + String sep) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + appLoader.selectIn(alf, sequenceIds, columns, sep); + } + + @Override + public String getSelectedSequencesAsAlignment(String format, + String suffix) + { + return getSelectedSequencesAsAlignmentFrom(null, + format, suffix); + } + + @Override + public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf, + String format, String sep) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + return appLoader.getSelectedSequencesAsAlignmentFrom(alf, format, sep); + } + + @Override + public String getAlignmentOrder() + { + return getAlignmentFrom(getCurrentAlignFrame(), null); + } + + @Override + public String getAlignmentOrderFrom(AlignFrame alf) + { + return getAlignmentFrom(alf, null); + } + + @Override + public String getAlignmentOrderFrom(AlignFrame alf, String sep) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + return appLoader.getAlignmentOrderFrom(alf, sep); + } + + @Override + public String orderBy(String order, String undoName) + { + return orderBy(order, undoName, null); + } + + @Override + public String orderBy(String order, String undoName, String sep) + { + return orderAlignmentBy(getCurrentAlignFrame(), order, undoName, sep); + } + + @Override + public String orderAlignmentBy(AlignFrame alf, String order, + String undoName, String sep) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + return appLoader.orderAlignmentBy(alf, order, undoName, sep); + } + + @Override + public String getAlignment(String format) + { + return getAlignmentFrom(null, format, null); + } + + @Override + public String getAlignmentFrom(AlignFrame alf, String format) + { + return getAlignmentFrom(alf, format, null); + } + + @Override + public String getAlignment(String format, String suffix) + { + return getAlignmentFrom(getCurrentAlignFrame(), format, suffix); + } + + @Override + public String getAlignmentFrom(AlignFrame alf, String format, + String suffix) + { + return appLoader.getAlignmentFrom(alf, format, suffix); + } + + @Override + public void loadAnnotation(String annotation) + { + loadAnnotationFrom(getCurrentAlignFrame(), annotation); + } + + @Override + public void loadAnnotationFrom(AlignFrame alf, String annotation) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + appLoader.loadAnnotationFrom(alf, annotation); + } + + @Override + public void loadFeatures(String features, boolean autoenabledisplay) + { + loadFeaturesFrom(currentAlignFrame, features, autoenabledisplay); + } + + @Override + public boolean loadFeaturesFrom(AlignFrame alf, String features, + boolean autoenabledisplay) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + return appLoader.loadFeaturesFrom(alf, features, autoenabledisplay); + } + + @Override + public String getFeatures(String format) + { + return getFeaturesFrom(null, format); + } + + @Override + public String getFeaturesFrom(AlignFrame alf, String format) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + return appLoader.getFeaturesFrom(alf, format); + } + + @Override + public String getAnnotation() + { + return getAnnotationFrom(null); + } + + @Override + public String getAnnotationFrom(AlignFrame alf) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + return appLoader.getAnnotationFrom(alf); + } + +// @Override +// public AlignFrame newView() +// { +// return newViewFrom(null, null); +// } +// +// @Override +// public AlignFrame newView(String name) +// { +// return newViewFrom(null, name); +// } +// +// @Override +// public AlignFrame newViewFrom(AlignFrame alf) +// { +// return newViewFrom(alf, null); +// } +// +// @Override +// public AlignFrame newViewFrom(AlignFrame alf, String name) +// { +// if (alf == null) +// { +// alf = getCurrentAlignFrame(); +// } +// return appLoader.newViewFrom(alf, name); +// } + + @Override + public AlignFrame loadAlignment(String text, String title) + { + return appLoader.loadAlignment(text, AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT, title); + } + + @Override + public boolean addPdbFile(AlignFrame alFrame, String sequenceId, + String pdbEntryString, String pdbFile) + { + if (alFrame == null) + { + alFrame = getCurrentAlignFrame(); + } + return appLoader.addPdbFile(alFrame, sequenceId, pdbEntryString, + pdbFile); + } + + @Override + public void scrollViewToIn(AlignFrame alf, String topRow, + String leftHandColumn) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + appLoader.scrollViewToIn(alf, topRow, leftHandColumn); + } + + @Override + public void scrollViewToRowIn(AlignFrame alf, String topRow) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + appLoader.scrollViewToRowIn(alf, topRow); + } + + @Override + public void scrollViewToColumnIn(AlignFrame alf, String leftHandColumn) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + appLoader.scrollViewToColumnIn(alf, leftHandColumn); + } + + @Override + public String getFeatureGroups() + { + return getFeatureGroupsOn(null); + } + + @Override + public String getFeatureGroupsOn(AlignFrame alf) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + return appLoader.getFeatureGroupsOn(alf); + } + + @Override + public String getFeatureGroupsOfState(boolean visible) + { + return getFeatureGroupsOfStateOn(null, visible); + } + + @Override + public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + return appLoader.getFeatureGroupsOfStateOn(alf, visible); + } + + @Override + public void setFeatureGroupState(String groups, boolean state) + { // JalviewLite API + setFeatureGroupStateOn(null, groups, state); + } + + @Override + public void setFeatureGroupStateOn(AlignFrame alf, String groups, + boolean state) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + appLoader.setFeatureGroupStateOn(alf, groups, state); + } + + @Override + public String getSeparator() + { + return appLoader.getSeparator(); + } + + @Override + public void setSeparator(String separator) + { + appLoader.setSeparator(separator); + } + + @Override + public String getJsMessage(String messageclass, String viewId) + { + // see http://www.jalview.org/examples/jalviewLiteJs.html + return null; + } + + /** + * Open a new Tree panel on the desktop statically. Params are standard (not + * set by Groovy). No dialog is opened. + * + * @param af + * @param treeType + * @param modelName + * @return null, or the string "label.you_need_at_least_n_sequences" if number + * of sequences selected is inappropriate + */ + @Override + public Object openTreePanel(AlignFrame af, String treeType, + String modelName) + { // JalviewJS api + if (af == null) + { + af = getCurrentAlignFrame(); + } + return CalculationChooser.openTreePanel(af, treeType, modelName, null); + } + + /** + * public static method for JalviewJS API to open a PCAPanel without + * necessarily using a dialog. + * + * @param af + * @param modelName + * @return the PCAPanel, or the string "label.you_need_at_least_n_sequences" + * if number of sequences selected is inappropriate + */ + @Override + public Object openPcaPanel(AlignFrame af, String modelName) + { + if (af == null) + { + af = getCurrentAlignFrame(); + } + return CalculationChooser.openPcaPanel(af, modelName, null); + } + + @Override + public String getSelectedSequencesAsAlignment(String format, + boolean suffix) + { + return getSelectedSequencesAsAlignmentFrom(null, + format, suffix); + } + + @Override + public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf, + String format, boolean suffix) + { + if (alf == null) + { + alf = getCurrentAlignFrame(); + } + return appLoader.getSelectedSequencesAsAlignmentFrom(alf, format, + "" + suffix); + } + + @Override + public String arrayToSeparatorList(String[] array) + { + return appLoader.arrayToSeparatorList(array); + } + + @Override + public String[] separatorListToArray(String list) + { + return appLoader.separatorListToArray(list); + } + + //// probably not needed in JalviewJS -- From when Jmol and Jalview did not + //// have a direct connection? + + @Override + public void setMouseoverListener(String listener) + { + // TODO Auto-generated method stub + + } + + @Override + public void setMouseoverListener(AlignFrame af, String listener) + { + // TODO Auto-generated method stub + + } + + @Override + public void setSelectionListener(String listener) + { + // TODO Auto-generated method stub + + } + + @Override + public void setSelectionListener(AlignFrame af, String listener) + { + // TODO Auto-generated method stub + + } + + @Override + public void setStructureListener(String listener, String modelSet) + { + // TODO Auto-generated method stub + + } + + @Override + public void removeJavascriptListener(AlignFrame af, String listener) + { + // TODO Auto-generated method stub + + } + + @Override + public void mouseOverStructure(String pdbResNum, String chain, + String pdbfile) + { + // TODO Auto-generated method stub + + } + + @Override + public void showOverview() + { + currentAlignFrame.overviewMenuItem_actionPerformed(null); + } + + public void notifyWorker(AlignCalcWorkerI worker, String status) + { + // System.out.println("Jalview worker " + worker.getClass().getSimpleName() + // + " " + status); + } + + @Override + public Object parseArguments(String[] args) + { + // TODO Auto-generated method stub + return null; + } + + + + } diff --git a/src/jalview/bin/JalviewAppLoader.java b/src/jalview/bin/JalviewAppLoader.java new file mode 100644 index 0000000..1cdeaec --- /dev/null +++ b/src/jalview/bin/JalviewAppLoader.java @@ -0,0 +1,1500 @@ +package jalview.bin; + +import jalview.api.JalviewApp; +import jalview.api.StructureSelectionManagerProvider; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.AlignmentOrder; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.gui.AlignFrame; +import jalview.gui.AlignViewport; +import jalview.gui.Desktop; +import jalview.io.AnnotationFile; +import jalview.io.AppletFormatAdapter; +import jalview.io.DataSourceType; +import jalview.io.FeaturesFile; +import jalview.io.FileFormat; +import jalview.io.FileFormatI; +import jalview.io.FileFormats; +import jalview.io.IdentifyFile; +import jalview.io.JPredFile; +import jalview.io.JnetAnnotationMaker; +import jalview.io.NewickFile; +import jalview.structure.SelectionSource; +import jalview.structure.StructureSelectionManager; +import jalview.util.HttpUtils; +import jalview.util.MessageManager; + +import java.awt.EventQueue; +import java.io.IOException; +import java.net.URL; +import java.util.ArrayList; +import java.util.List; +import java.util.StringTokenizer; +import java.util.Vector; + +/** + * A class to load parameters for either JalviewLite or Jalview + * + * @author hansonr + * + */ +public class JalviewAppLoader +{ + + private JalviewApp app; // Jalview or JalviewJS or JalviewLite + + private boolean debug; + + String separator = "\u00AC"; // JalviewLite note: the default used to + // be '|', but many sequence IDS include + // pipes. + + public String getSeparator() + { + return separator; + } + + public void setSeparator(String separator) + { + this.separator = separator; + } + + public JalviewAppLoader(boolean debug) + { + this.debug = debug; + } + + public void load(JalviewApp app) + { + + this.app = app; + + String sep = app.getParameter("separator"); + if (sep != null) + { + if (sep.length() > 0) + { + separator = sep; + } + else + { + throw new Error(MessageManager + .getString("error.invalid_separator_parameter")); + } + } + + loadTree(); + loadScoreFile(); + loadFeatures(); + loadAnnotations(); + loadJnetFile(); + loadPdbFiles(); + callInitCallback(); + } + + /** + * Load PDBFiles if any specified by parameter(s). Returns true if loaded, + * else false. + * + * @param loaderFrame + * @return + */ + protected boolean loadPdbFiles() + { + boolean result = false; + /* + * Undocumented for 2.6 - + * related to JAL-434 + */ + + boolean doAlign = app.getDefaultParameter("alignpdbfiles", false); + app.setAlignPdbStructures(doAlign); + /* + * + * + * + * + * + */ + + // Accumulate pdbs here if they are heading for the same view (if + // alignPdbStructures is true) + Vector pdbs = new Vector<>(); + // create a lazy matcher if we're asked to + jalview.analysis.SequenceIdMatcher matcher = (app + .getDefaultParameter("relaxedidmatch", false)) + ? new jalview.analysis.SequenceIdMatcher( + app.getViewport().getAlignment() + .getSequencesArray()) + : null; + + int pdbFileCount = 0; + String param; + do + { + if (pdbFileCount > 0) + { + param = app.getParameter("PDBFILE" + pdbFileCount); + } + else + { + param = app.getParameter("PDBFILE"); + } + + if (param != null) + { + PDBEntry pdb = new PDBEntry(); + + String seqstring; + SequenceI[] seqs = null; + String[] chains = null; + + StringTokenizer st = new StringTokenizer(param, " "); + + if (st.countTokens() < 2) + { + String sequence = app.getParameter("PDBSEQ"); + if (sequence != null) + { + seqs = new SequenceI[] { matcher == null + ? (Sequence) app.getViewport().getAlignment() + .findName(sequence) + : matcher.findIdMatch(sequence) }; + } + + } + else + { + param = st.nextToken(); + List tmp = new ArrayList<>(); + List tmp2 = new ArrayList<>(); + + while (st.hasMoreTokens()) + { + seqstring = st.nextToken(); + StringTokenizer st2 = new StringTokenizer(seqstring, "="); + if (st2.countTokens() > 1) + { + // This is the chain + tmp2.add(st2.nextToken()); + seqstring = st2.nextToken(); + } + tmp.add(matcher == null + ? (Sequence) app.getViewport().getAlignment() + .findName(seqstring) + : matcher.findIdMatch(seqstring)); + } + + seqs = tmp.toArray(new SequenceI[tmp.size()]); + if (tmp2.size() == tmp.size()) + { + chains = tmp2.toArray(new String[tmp2.size()]); + } + } + pdb.setId(param); + ret[0] = param; + DataSourceType protocol = resolveFileProtocol(app, ret); + // TODO check JAL-357 for files in a jar (CLASSLOADER) + pdb.setFile(ret[0]); + + if (seqs != null) + { + for (int i = 0; i < seqs.length; i++) + { + if (seqs[i] != null) + { + ((Sequence) seqs[i]).addPDBId(pdb); + StructureSelectionManager + .getStructureSelectionManager( + (StructureSelectionManagerProvider) app) + .registerPDBEntry(pdb); + } + else + { + if (debug) + { + // 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 " + + i + ")"); + } + } + } + + if (doAlign) + { + pdbs.addElement(new Object[] { pdb, seqs, chains, protocol }); + } + else + { + app.newStructureView(pdb, seqs, chains, protocol); + } + } + } + + pdbFileCount++; + } while (param != null || pdbFileCount < 10); + if (pdbs.size() > 0) + { + SequenceI[][] seqs = new SequenceI[pdbs.size()][]; + 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++) + { + Object[] o = pdbs.elementAt(pdbsi); + pdb[pdbsi] = (PDBEntry) o[0]; + seqs[pdbsi] = (SequenceI[]) o[1]; + chains[pdbsi] = (String[]) o[2]; + protocols[pdbsi] = (String) o[3]; + } + app.alignedStructureView(pdb, seqs, chains, protocols); + result = true; + } + return result; + } + + /** + * Load in a Jnetfile if specified by parameter. Returns true if loaded, else + * false. + * + * @param alignFrame + * @return + */ + protected boolean loadJnetFile() + { + boolean result = false; + String param = app.getParameter("jnetfile"); + if (param == null) + { + // jnet became jpred around 2016 + param = app.getParameter("jpredfile"); + } + if (param != null) + { + try + { + ret[0] = param; + DataSourceType protocol = resolveFileProtocol(app, ret); + JPredFile predictions = new JPredFile(ret[0], protocol); + JnetAnnotationMaker.add_annotation(predictions, + app.getViewport().getAlignment(), 0, false); + // false == do not add sequence profile from concise output + app.getViewport().getAlignment().setupJPredAlignment(); + app.updateForAnnotations(); + result = true; + } catch (Exception ex) + { + ex.printStackTrace(); + } + } + return result; + } + + /** + * Load annotations if specified by parameter. Returns true if loaded, else + * false. + * + * @param alignFrame + * @return + */ + protected boolean loadAnnotations() + { + boolean result = false; + String param = app.getParameter("annotations"); + if (param != null) + { + ret[0] = param; + DataSourceType protocol = resolveFileProtocol(app, ret); + param = ret[0]; + if (new AnnotationFile().annotateAlignmentView(app.getViewport(), + param, protocol)) + { + app.updateForAnnotations(); + result = true; + } + else + { + System.err + .println("Annotations were not added from annotation file '" + + param + "'"); + } + } + return result; + } + + /** + * Load features file and view settings as specified by parameters. Returns + * true if features were loaded, else false. + * + * @param alignFrame + * @return + */ + protected boolean loadFeatures() + { + boolean result = false; + // /////////////////////////// + // modify display of features + // we do this before any features have been loaded, ensuring any hidden + // groups are hidden when features first displayed + // + // hide specific groups + // + String param = app.getParameter("hidefeaturegroups"); + if (param != null) + { + app.setFeatureGroupState(separatorListToArray(param, separator), + false); + // app.setFeatureGroupStateOn(newAlignFrame, param, false); + } + // show specific groups + param = app.getParameter("showfeaturegroups"); + if (param != null) + { + app.setFeatureGroupState(separatorListToArray(param, separator), + true); + // app.setFeatureGroupStateOn(newAlignFrame, param, true); + } + // and now load features + param = app.getParameter("features"); + if (param != null) + { + ret[0] = param; + DataSourceType protocol = resolveFileProtocol(app, ret); + + result = app.parseFeaturesFile(ret[0], protocol); + } + + param = app.getParameter("showFeatureSettings"); + if (param != null && param.equalsIgnoreCase("true")) + { + app.newFeatureSettings(); + } + return result; + } + + /** + * Load a score file if specified by parameter. Returns true if file was + * loaded, else false. + * + * @param loaderFrame + */ + protected boolean loadScoreFile() + { + boolean result = false; + String sScoreFile = app.getParameter("scoreFile"); + if (sScoreFile != null && !"".equals(sScoreFile)) + { + try + { + if (debug) + { + System.err.println( + "Attempting to load T-COFFEE score file from the scoreFile parameter"); + } + result = app.loadScoreFile(sScoreFile); + if (!result) + { + System.err.println( + "Failed to parse T-COFFEE parameter as a valid score file ('" + + sScoreFile + "')"); + } + } catch (Exception e) + { + System.err.printf("Cannot read score file: '%s'. Cause: %s \n", + sScoreFile, e.getMessage()); + } + } + return result; + } + + String[] ret = new String[1]; + + /** + * Load a tree for the alignment if specified by parameter. Returns true if a + * tree was loaded, else false. + * + * @param loaderFrame + * @return + */ + protected boolean loadTree() + { + boolean result = false; + String treeFile = app.getParameter("tree"); + if (treeFile == null) + { + treeFile = app.getParameter("treeFile"); + } + + if (treeFile != null) + { + try + { + ret[0] = treeFile; + NewickFile fin = new NewickFile(treeFile, + resolveFileProtocol(app, ret)); + fin.parse(); + + if (fin.getTree() != null) + { + app.loadTree(fin, ret[0]); + result = true; + if (debug) + { + System.out.println("Successfully imported tree."); + } + } + else + { + if (debug) + { + System.out.println( + "Tree parameter did not resolve to a valid tree."); + } + } + } catch (Exception ex) + { + ex.printStackTrace(); + } + } + return result; + } + + /** + * form a complete URL given a path to a resource and a reference location on + * the same server + * + * @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 + */ + public static String resolveUrlForLocalOrAbsolute(String targetPath, + 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. + * 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 + { + resolvedPath = directoryPath + targetPath; + } + // if (debug) + // { + // System.err.println( + // "resolveUrlForLocalOrAbsolute returning " + resolvedPath); + // } + return resolvedPath; + } + + /** + * parse the string into a list + * + * @param list + * @param separator + * @return elements separated by separator + */ + public static String[] separatorListToArray(String list, String separator) + { + // TODO use StringUtils version (slightly different...) + int seplen = separator.length(); + if (list == null || list.equals("") || list.equals(separator)) + { + return null; + } + Vector jv = new Vector<>(); + int cp = 0, pos; + while ((pos = list.indexOf(separator, cp)) > cp) + { + jv.addElement(list.substring(cp, pos)); + cp = pos + seplen; + } + if (cp < list.length()) + { + String c = list.substring(cp); + if (!c.equals(separator)) + { + jv.addElement(c); + } + } + if (jv.size() > 0) + { + String[] v = new String[jv.size()]; + for (int i = 0; i < v.length; i++) + { + v[i] = jv.elementAt(i); + } + jv.removeAllElements(); + // if (debug) + // { + // System.err.println("Array from '" + separator + // + "' separated List:\n" + v.length); + // for (int i = 0; i < v.length; i++) + // { + // System.err.println("item " + i + " '" + v[i] + "'"); + // } + // } + return v; + } + // if (debug) + // { + // System.err.println( + // "Empty Array from '" + separator + "' separated List"); + // } + return null; + } + + public static DataSourceType resolveFileProtocol(JalviewApp app, + String[] retPath) + { + String path = retPath[0]; + /* + * is it paste data? + */ + if (path.startsWith("PASTE")) + { + retPath[0] = path.substring(5); + return DataSourceType.PASTE; + } + + /* + * is it a URL? + */ + if (path.indexOf("://") >= 0) + { + return DataSourceType.URL; + } + + /* + * try relative to document root + */ + URL documentBase = app.getDocumentBase(); + String withDocBase = resolveUrlForLocalOrAbsolute(path, documentBase); + if (HttpUtils.isValidUrl(withDocBase)) + { + // if (debug) + // { + // System.err.println("Prepended document base '" + documentBase + // + "' to make: '" + withDocBase + "'"); + // } + retPath[0] = withDocBase; + return DataSourceType.URL; + } + + /* + * try relative to codebase (if different to document base) + */ + URL codeBase = app.getCodeBase(); + String withCodeBase = resolveUrlForLocalOrAbsolute(path, codeBase); + if (!withCodeBase.equals(withDocBase) + && HttpUtils.isValidUrl(withCodeBase)) + { + // if (debug) + // { + // System.err.println("Prepended codebase '" + codeBase + // + "' to make: '" + withCodeBase + "'"); + // } + retPath[0] = withCodeBase; + return DataSourceType.URL; + } + + /* + * try locating by classloader; try this last so files in the directory + * are resolved using document base + */ + if (inArchive(app.getClass(), path)) + { + return DataSourceType.CLASSLOADER; + } + return null; + } + + /** + * Discovers whether the given file is in the Applet Archive + * + * @param f + * String + * @return boolean + */ + private static boolean inArchive(Class c, String f) + { + // This might throw a security exception in certain browsers + // Netscape Communicator for instance. + try + { + boolean rtn = (c.getResourceAsStream("/" + f) != null); + // if (debug) + // { + // System.err.println("Resource '" + f + "' was " + // + (rtn ? "" : "not ") + "located by classloader."); + // } + return rtn; + } catch (Exception ex) + { + System.out.println("Exception checking resources: " + f + " " + ex); + return false; + } + } + + public void callInitCallback() + { + String initjscallback = app.getParameter("oninit"); + if (initjscallback == null) + { + return; + } + initjscallback = initjscallback.trim(); + if (initjscallback.length() > 0) + { + // TODO + } + } + + /** + * read sequence1...sequenceN as a raw alignment + * + * @param jalviewApp + * @return + */ + public String getPastedSequence(JalviewApp jalviewApp) + { + StringBuffer data = new StringBuffer("PASTE"); + int i = 1; + String file = null; + while ((file = app.getParameter("sequence" + i)) != null) + { + data.append(file.toString() + "\n"); + i++; + } + if (data.length() > 5) + { + file = data.toString(); + } + return file; + } + + /** + * concatenate the list with separator + * + * @param list + * @param separator + * @return concatenated string + */ + public static String arrayToSeparatorList(String[] list, String separator) + { + // TODO use StringUtils version + StringBuffer v = new StringBuffer(); + if (list != null && list.length > 0) + { + for (int i = 0, iSize = list.length; i < iSize; i++) + { + if (list[i] != null) + { + if (i > 0) + { + v.append(separator); + } + v.append(list[i]); + } + } + // if (debug) + // { + // 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"); + // } + return "" + separator; + } + + public String arrayToSeparatorList(String[] array) + { + return arrayToSeparatorList(array, separator); + } + + public String getSelectedSequencesFrom(AlignFrame alf, String sep) + { + StringBuffer result = new StringBuffer(""); + if (sep == null || sep.length() == 0) + { + sep = separator; // "+0x00AC; + } + AlignViewport v = alf.getViewport(); + if (v.getSelectionGroup() != null) + { + SequenceI[] seqs = v.getSelectionGroup() + .getSequencesInOrder(v.getAlignment()); + + for (int i = 0; i < seqs.length; i++) + { + result.append(seqs[i].getName()); + result.append(sep); + } + } + + return result.toString(); + } + + public void setFeatureGroupStateOn(final AlignFrame alf, + final String groups, boolean state) + { + java.awt.EventQueue.invokeLater(new Runnable() + { + @Override + public void run() + { + alf.setFeatureGroupState( + separatorListToArray(groups, separator), state); + } + }); + } + + public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible) + { + return arrayToSeparatorList( + alf.getFeatureGroupsOfState(visible)); + } + + public void scrollViewToIn(final AlignFrame alf, final String topRow, + final String leftHandColumn) + { + // TODO test + java.awt.EventQueue.invokeLater(new Runnable() + { + @Override + public void run() + { + try + { + alf.scrollTo(Integer.valueOf(topRow).intValue(), + Integer.valueOf(leftHandColumn).intValue()); + + } catch (Exception ex) + { + System.err.println("Couldn't parse integer arguments (topRow='" + + topRow + "' and leftHandColumn='" + leftHandColumn + + "')"); + ex.printStackTrace(); + } + } + }); + } + + public void scrollViewToRowIn(final AlignFrame alf, final String topRow) + { + // TODO test + + java.awt.EventQueue.invokeLater(new Runnable() + { + @Override + public void run() + { + try + { + alf.scrollToRow(Integer.valueOf(topRow).intValue()); + + } catch (Exception ex) + { + System.err.println("Couldn't parse integer arguments (topRow='" + + topRow + "')"); + ex.printStackTrace(); + } + + } + }); + } + + public void scrollViewToColumnIn(final AlignFrame alf, + final String leftHandColumn) + { + // TODO test + java.awt.EventQueue.invokeLater(new Runnable() + { + + @Override + public void run() + { + try + { + alf + .scrollToColumn(Integer.valueOf(leftHandColumn).intValue()); + + } catch (Exception ex) + { + System.err.println( + "Couldn't parse integer arguments (leftHandColumn='" + + leftHandColumn + "')"); + ex.printStackTrace(); + } + } + }); + + } + + public boolean addPdbFile(AlignFrame alf, String sequenceId, + String pdbEntryString, String pdbFile) + { + AlignFrame alFrame = alf; + SequenceI toaddpdb = alFrame.getViewport().getAlignment() + .findName(sequenceId); + boolean needtoadd = false; + if (toaddpdb != null) + { + Vector pdbe = toaddpdb.getAllPDBEntries(); + PDBEntry pdbentry = null; + if (pdbe != null && pdbe.size() > 0) + { + for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++) + { + pdbentry = pdbe.elementAt(pe); + if (!pdbentry.getId().equals(pdbEntryString) + && !pdbentry.getFile().equals(pdbFile)) + { + pdbentry = null; + } + else + { + continue; + } + } + } + if (pdbentry == null) + { + pdbentry = new PDBEntry(); + pdbentry.setId(pdbEntryString); + pdbentry.setFile(pdbFile); + needtoadd = true; // add this new entry to sequence. + } + // resolve data source + // TODO: this code should be a refactored to an io package + DataSourceType protocol = AppletFormatAdapter.resolveProtocol(pdbFile, + FileFormat.PDB); + if (protocol == null) + { + return false; + } + if (needtoadd) + { + pdbentry.setProperty("protocol", protocol); + toaddpdb.addPDBId(pdbentry); + alFrame.alignPanel.getStructureSelectionManager() + .registerPDBEntry(pdbentry); + } + } + return true; + } + + public AlignFrame loadAlignment(String text, int width, int height, + String title) + { + AlignmentI al = null; + + try + { + FileFormatI format = new IdentifyFile().identify(text, + DataSourceType.PASTE); + al = new AppletFormatAdapter().readFile(text, DataSourceType.PASTE, + format); + if (al.getHeight() > 0) + { + return new AlignFrame(al, width, height, title); + } + } catch (IOException ex) + { + ex.printStackTrace(); + } + return null; + } + + public String getFeatureGroupsOn(AlignFrame alf) + { + return arrayToSeparatorList( + alf.getFeatureGroups()); + } + + public void highlightIn(final AlignFrame alf, final String sequenceId, + final String position, final String alignedPosition) + { + // TODO: could try to highlight in all alignments if alf==null + jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher( + alf.getViewport().getAlignment() + .getSequencesArray()); + final SequenceI sq = matcher.findIdMatch(sequenceId); + if (sq != null) + { + int apos = -1; + try + { + apos = Integer.valueOf(position).intValue(); + apos--; + } catch (NumberFormatException ex) + { + return; + } + 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)) + { + java.awt.EventQueue.invokeLater(new Runnable() + { + @Override + public void run() + { + StructureSelectionManager + .getStructureSelectionManager(Desktop.getInstance()) + .mouseOverVamsasSequence(sq, sq.findIndex(pos), null); + } + }); + } + else + { + java.awt.EventQueue.invokeLater(new Runnable() + { + @Override + public void run() + { + StructureSelectionManager + .getStructureSelectionManager(Desktop.getInstance()) + .mouseOverVamsasSequence(sq, pos, null); + } + }); + } + } + } + + public void selectIn(final AlignFrame alf, String sequenceIds, + String columns, String sep) + { + if (sep == null || sep.length() == 0) + { + sep = separator; + } + else + { + if (debug) + { + System.err.println("Selecting region using separator string '" + + separator + "'"); + } + } + // deparse fields + String[] ids = JalviewAppLoader.separatorListToArray(sequenceIds, sep); + String[] cols = JalviewAppLoader.separatorListToArray(columns, sep); + final SequenceGroup sel = new SequenceGroup(); + final ColumnSelection csel = new ColumnSelection(); + AlignmentI al = alf.getViewport().getAlignment(); + jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher( + alf.getViewport().getAlignment() + .getSequencesArray()); + int start = 0, end = al.getWidth(), alw = al.getWidth(); + boolean seqsfound = true; + if (ids != null && ids.length > 0) + { + seqsfound = false; + for (int i = 0; i < ids.length; i++) + { + if (ids[i].trim().length() == 0) + { + continue; + } + SequenceI sq = matcher.findIdMatch(ids[i]); + if (sq != null) + { + seqsfound = true; + sel.addSequence(sq, false); + } + } + } + boolean inseqpos = false; + if (cols != null && cols.length > 0) + { + boolean seset = false; + for (int i = 0; i < cols.length; i++) + { + String cl = cols[i].trim(); + if (cl.length() == 0) + { + continue; + } + int p; + if ((p = cl.indexOf("-")) > -1) + { + int from = -1, to = -1; + try + { + 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 '" + + cl + "' - format is 'from-to'"); + return; + } + try + { + 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 '" + + cl + "' - format is 'from-to'"); + return; + } + if (from >= 0 && to >= 0) + { + // valid range + if (from < to) + { + int t = to; + to = from; + to = t; + } + if (!seset) + { + start = from; + end = to; + seset = true; + } + else + { + // comment to prevent range extension + if (start > from) + { + start = from; + } + if (end < to) + { + end = to; + } + } + for (int r = from; r <= to; r++) + { + if (r >= 0 && r < alw) + { + csel.addElement(r); + } + } + if (debug) + { + System.err.println("Range '" + cl + "' deparsed as [" + from + + "," + to + "]"); + } + } + else + { + System.err.println("ERROR: Invalid Range '" + cl + + "' deparsed as [" + from + "," + to + "]"); + } + } + else + { + int r = -1; + try + { + r = Integer.valueOf(cl).intValue(); + r--; + } catch (NumberFormatException ex) + { + if (cl.toLowerCase().equals("sequence")) + { + // we are in the dataset sequence's coordinate frame. + inseqpos = true; + } + else + { + System.err.println( + "ERROR: Couldn't parse integer from point selection element of column selection string '" + + cl + "'"); + return; + } + } + if (r >= 0 && r <= alw) + { + if (!seset) + { + start = r; + end = r; + seset = true; + } + else + { + // comment to prevent range extension + if (start > r) + { + start = r; + } + if (end < r) + { + end = r; + } + } + csel.addElement(r); + if (debug) + { + System.err.println("Point selection '" + cl + + "' deparsed as [" + r + "]"); + } + } + else + { + System.err.println("ERROR: Invalid Point selection '" + cl + + "' deparsed as [" + r + "]"); + } + } + } + } + if (seqsfound) + { + // we only propagate the selection when it was the null selection, or the + // given sequences were found in the alignment. + if (inseqpos && sel.getSize() > 0) + { + // assume first sequence provides reference frame ? + SequenceI rs = sel.getSequenceAt(0); + start = rs.findIndex(start); + end = rs.findIndex(end); + List cs = new ArrayList<>(csel.getSelected()); + csel.clear(); + for (Integer selectedCol : cs) + { + csel.addElement(rs.findIndex(selectedCol)); + } + } + sel.setStartRes(start); + sel.setEndRes(end); + EventQueue.invokeLater(new Runnable() + { + @Override + public void run() + { + alf.select(sel, csel, alf + .getCurrentView().getAlignment().getHiddenColumns()); + } + }); + } + } + + public String getAlignmentOrderFrom(AlignFrame alf, String sep) + { + AlignmentI alorder = alf.getViewport().getAlignment(); + String[] order = new String[alorder.getHeight()]; + for (int i = 0; i < order.length; i++) + { + order[i] = alorder.getSequenceAt(i).getName(); + } + return arrayToSeparatorList(order, sep); + } + + public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf, + String format, String suffix) + { + try + { + AlignViewport vp = alf.getViewport(); + FileFormatI theFormat = FileFormats.getInstance().forName(format); + boolean seqlimits = (suffix == null + || suffix.equalsIgnoreCase("true")); + if (vp.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(theFormat, + new Alignment(vp.getSelectionAsNewSequence()), + seqlimits); + return reply; + } + } catch (IllegalArgumentException ex) + { + ex.printStackTrace(); + return "Error retrieving alignment, possibly invalid format specifier: " + + format; + } + return ""; + } + + public String orderAlignmentBy(AlignFrame alf, String order, + String undoName, String sep) + { + if (sep == null || sep.length() == 0) + { + sep = separator; + } + String[] ids = JalviewAppLoader.separatorListToArray(order, sep); + SequenceI[] sqs = null; + if (ids != null && ids.length > 0) + { + jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher( + alf.getViewport().getAlignment() + .getSequencesArray()); + int s = 0; + sqs = new SequenceI[ids.length]; + for (int i = 0; i < ids.length; i++) + { + if (ids[i].trim().length() == 0) + { + continue; + } + SequenceI sq = matcher.findIdMatch(ids[i]); + if (sq != null) + { + sqs[s++] = sq; + } + } + if (s > 0) + { + SequenceI[] sqq = new SequenceI[s]; + System.arraycopy(sqs, 0, sqq, 0, s); + sqs = sqq; + } + else + { + sqs = null; + } + } + if (sqs == null) + { + return ""; + } + ; + final AlignmentOrder aorder = new AlignmentOrder(sqs); + + if (undoName != null && undoName.trim().length() == 0) + { + undoName = null; + } + final String _undoName = undoName; + // TODO: deal with synchronization here: cannot raise any events until after + // this has returned. + return alf.sortBy(aorder, _undoName) ? "true" : ""; + } + + public String getAlignmentFrom(AlignFrame alf, String format, + String suffix) + { + try + { + boolean seqlimits = (suffix == null + || suffix.equalsIgnoreCase("true")); + + FileFormatI theFormat = FileFormats.getInstance().forName(format); + String reply = new AppletFormatAdapter().formatSequences(theFormat, + alf.getViewport().getAlignment(), seqlimits); + return reply; + } catch (IllegalArgumentException ex) + { + ex.printStackTrace(); + return "Error retrieving alignment, possibly invalid format specifier: " + + format; + } + } + + public void loadAnnotationFrom(AlignFrame alf, String annotation) + { + if (new AnnotationFile().annotateAlignmentView( + alf.getViewport(), annotation, + DataSourceType.PASTE)) + { + alf.alignPanel.fontChanged(); + alf.alignPanel.setScrollValues(0, 0); + } + else + { + alf.parseFeaturesFile(annotation, + DataSourceType.PASTE); + } + } + + public boolean loadFeaturesFrom(AlignFrame alf, String features, + boolean autoenabledisplay) + { + boolean ret = alf.parseFeaturesFile(features, + DataSourceType.PASTE); + if (!ret) + { + return false; + } + if (autoenabledisplay) + { + alf.getViewport().setShowSequenceFeatures(true); + // this next was for a checkbox in JalviewLite + // ((AlignFrame) alf).getViewport().sequenceFeatures.setState(true); + } + return true; + } + + /** + * JavaScript interface to print the alignment frame + * + * @param alf + * @param format + * "jalview" or "gff" with or without ";includeComplement" or + * ";includeNonpositional"; default with no ";" is + * ";includeNonpositional" + * @return + */ + public String getFeaturesFrom(AlignFrame alf, String format) + { + AlignFrame f = (alf); + + String features; + FeaturesFile formatter = new FeaturesFile(); + format = format.toLowerCase(); + if (format.indexOf(";") < 0) + format += ";includenonpositional"; + boolean nonpos = format.indexOf(";includenonpositional") > 0; + boolean compl = format.indexOf(";includecomplement") >= 0; + if (format.startsWith("jalview")) + { + features = formatter.printJalviewFormat( + f.getViewport().getAlignment().getSequencesArray(), + f.alignPanel.getFeatureRenderer(), nonpos, compl); + } + else + { + features = formatter.printGffFormat( + f.getViewport().getAlignment().getSequencesArray(), + f.alignPanel.getFeatureRenderer(), nonpos, compl); + } + + if (features == null) + { + features = ""; + } + return features; + + } + + public String getAnnotationFrom(AlignFrame alf) + { + AlignFrame f = alf; + String annotation = new AnnotationFile() + .printAnnotationsForView(f.getViewport()); + return annotation; + } + + // public AlignFrame newViewFrom(AlignFrame alf, String name) + // { + // return (AlignFrame) alf.newView(name, true); + // } + // + public String[] separatorListToArray(String list) + { + return separatorListToArray(list, separator); + } + + public Object[] getSelectionForListener(AlignFrame currentFrame, + SequenceGroup seqsel, ColumnSelection colsel, + HiddenColumns hidden, SelectionSource source, Object alignFrame) + { + // System.err.println("Testing selection event relay to + // jsfunction:"+_listener); + String setid = ""; + AlignFrame src = (AlignFrame) alignFrame; + if (source != null) + { + if (source instanceof AlignViewport + && currentFrame.getViewport() == source) + { + // should be valid if it just generated an event! + src = currentFrame; + + } + } + String[] seqs = new String[] {}; + String[] cols = new String[] {}; + int strt = 0, end = (src == null) ? -1 + : src.alignPanel.av.getAlignment().getWidth(); + if (seqsel != null && seqsel.getSize() > 0) + { + seqs = new String[seqsel.getSize()]; + for (int i = 0; i < seqs.length; i++) + { + seqs[i] = seqsel.getSequenceAt(i).getName(); + } + if (strt < seqsel.getStartRes()) + { + strt = seqsel.getStartRes(); + } + if (end == -1 || end > seqsel.getEndRes()) + { + end = seqsel.getEndRes(); + } + } + if (colsel != null && !colsel.isEmpty()) + { + if (end == -1) + { + end = colsel.getMax() + 1; + } + cols = new String[colsel.getSelected().size()]; + for (int i = 0; i < cols.length; i++) + { + cols[i] = "" + (1 + colsel.getSelected().get(i).intValue()); + } + } + else + { + if (seqsel != null && seqsel.getSize() > 0) + { + // send a valid range, otherwise we send the empty selection + cols = new String[2]; + cols[0] = "" + (1 + strt) + "-" + (1 + end); + } + } + return new Object[] { src, setid, arrayToSeparatorList(seqs), + arrayToSeparatorList(cols) }; + } + +} \ No newline at end of file diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index ec00647..ba2c1d3 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -23,6 +23,7 @@ package jalview.gui; import java.awt.BorderLayout; import java.awt.Color; import java.awt.Component; +import java.awt.Dimension; import java.awt.Rectangle; import java.awt.Toolkit; import java.awt.datatransfer.Clipboard; @@ -3368,12 +3369,38 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } JInternalFrame frame = new JInternalFrame(); - final OverviewPanel overview = new OverviewPanel(alignPanel); + + + + // BH 2019.07.26 we allow for an embedded + // undecorated overview with defined size + frame.setName(Jalview.getAppID("overview")); + // + Dimension dim = Platform.getDimIfEmbedded(frame, -1, -1); + if (dim != null && dim.width == 0) + { + dim = null; // hidden, not embedded + } + OverviewPanel overview = new OverviewPanel(alignPanel, dim); + frame.setContentPane(overview); + if (dim == null) + { + dim = new Dimension(); + // was frame.getSize(), but that is 0,0 at this point; + } + else + { + // we are imbedding, and so we have an undecorated frame + // and we can set the the frame dimensions accordingly. + } + // allowing for unresizable option using, style="resize:none" + boolean resizable = (Platform.getEmbeddedAttribute(frame, + "resize") != "none"); Desktop.addInternalFrame(frame, MessageManager .formatMessage("label.overview_params", new Object[] - { this.getTitle() }), true, frame.getWidth(), frame.getHeight(), - true, true); + { this.getTitle() }), true, dim.width, dim.height, resizable, + true); frame.pack(); frame.setLayer(JLayeredPane.PALETTE_LAYER); frame.addInternalFrameListener( @@ -3732,7 +3759,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, frameTitle += this.title; - Desktop.addInternalFrame(tp, frameTitle, 600, 500); + Dimension dim = Platform.getDimIfEmbedded(tp, 600, 500); + Desktop.addInternalFrame(tp, frameTitle, dim.width, dim.height); } /** @@ -4084,15 +4112,24 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (nf.getTree() != null) { tp = new TreePanel(alignPanel, nf, treeTitle, input); - - tp.setSize(w, h); + Dimension dim = Platform.getDimIfEmbedded(tp, -1, -1); + if (dim == null) + { + dim = new Dimension(w, h); + } + else + { + // no offset, either + x = 0; + } + tp.setSize(dim.width, dim.height); if (x > 0 && y > 0) { tp.setLocation(x, y); } - Desktop.addInternalFrame(tp, treeTitle, w, h); + Desktop.addInternalFrame(tp, treeTitle, dim.width, dim.height); } } catch (Exception ex) { diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index eaf99be..1b85dd5 100644 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -209,7 +209,7 @@ public class Desktop extends jalview.jbgui.GDesktop * * @return */ - public static Object getInstance() + public static Desktop getInstance() { return instance; } @@ -881,8 +881,8 @@ public class Desktop extends jalview.jbgui.GDesktop frame.setMaximizable(resizable); frame.setIconifiable(resizable); frame.setOpaque(Platform.isJS()); - - if (frame.getX() < 1 && frame.getY() < 1) + boolean isEmbedded = (Platform.getDimIfEmbedded(frame, -1, -1) != null); + if (!isEmbedded && frame.getX() < 1 && frame.getY() < 1) { frame.setLocation(xOffset * openFrameCount, yOffset * ((openFrameCount - 1) % 10) + yOffset); diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java index a5aaf7c..cf15aa1 100755 --- a/src/jalview/gui/OverviewPanel.java +++ b/src/jalview/gui/OverviewPanel.java @@ -73,34 +73,41 @@ public class OverviewPanel extends JPanel protected boolean draggingBox = false; + private Dimension dim; + + private boolean showProgress = !Platform.isJS(); + protected ProgressPanel progressPanel; + /** - * Creates a new OverviewPanel object. - * - * @param alPanel - * The alignment panel which is shown in the overview panel + * Creates the appropriate type of OverviewDimensions, with the desired size */ - public OverviewPanel(AlignmentPanel alPanel) + private void createOverviewDimensions() { - this.av = alPanel.av; - this.ap = alPanel; - - showHidden = Cache.getDefault(Preferences.SHOW_OV_HIDDEN_AT_START, - false); + boolean showAnnotation = (av.isShowAnnotation() + && av.getAlignmentConservationAnnotation() != null); if (showHidden) { - od = new OverviewDimensionsShowHidden(av.getRanges(), - (av.isShowAnnotation() - && av.getAlignmentConservationAnnotation() != null)); + od = new OverviewDimensionsShowHidden(av.getRanges(), showAnnotation, + dim); } else { - od = new OverviewDimensionsHideHidden(av.getRanges(), - (av.isShowAnnotation() - && av.getAlignmentConservationAnnotation() != null)); + od = new OverviewDimensionsHideHidden(av.getRanges(), showAnnotation, + dim); } + } + public OverviewPanel(AlignmentPanel alPanel, Dimension dim) + { + this.av = alPanel.av; + this.ap = alPanel; + this.dim = dim; + + showHidden = Cache.getDefault(Preferences.SHOW_OV_HIDDEN_AT_START, + false); + createOverviewDimensions(); setLayout(new BorderLayout()); progressPanel = new ProgressPanel(OverviewRenderer.UPDATE, MessageManager.getString("label.oview_calc"), getWidth()); @@ -285,20 +292,8 @@ public class OverviewPanel extends JPanel */ protected void toggleHiddenColumns() { - if (showHidden) - { - showHidden = false; - od = new OverviewDimensionsHideHidden(av.getRanges(), - (av.isShowAnnotation() - && av.getAlignmentConservationAnnotation() != null)); - } - else - { - showHidden = true; - od = new OverviewDimensionsShowHidden(av.getRanges(), - (av.isShowAnnotation() - && av.getAlignmentConservationAnnotation() != null)); - } + showHidden = !showHidden; + createOverviewDimensions(); oviewCanvas.resetOviewDims(od); updateOverviewImage(); setBoxPosition(); diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java index 96a8b0d..5eca00f 100644 --- a/src/jalview/gui/PCAPanel.java +++ b/src/jalview/gui/PCAPanel.java @@ -36,6 +36,7 @@ import jalview.jbgui.GPCAPanel; import jalview.math.RotatableMatrix.Axis; import jalview.util.ImageMaker; import jalview.util.MessageManager; +import jalview.util.Platform; import jalview.viewmodel.AlignmentViewport; import jalview.viewmodel.PCAModel; @@ -200,10 +201,7 @@ public class PCAPanel extends GPCAPanel repaint(); if (getParent() == null) { - Desktop.addInternalFrame(this, - MessageManager.formatMessage("label.calc_title", "PCA", - getPcaModel().getScoreModelName()), - 475, 450); + addToDesktop(this, getPcaModel().getScoreModelName()); this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT)); } working = false; @@ -762,4 +760,12 @@ public class PCAPanel extends GPCAPanel getRotatableCanvas().ap = panel; PaintRefresher.Register(PCAPanel.this, panel.av.getSequenceSetId()); } + + public static void addToDesktop(PCAPanel panel, String modelName) + { + Dimension dim = Platform.getDimIfEmbedded(panel, 475, 450); + Desktop.addInternalFrame(panel, MessageManager.formatMessage( + "label.calc_title", "PCA", modelName), dim.width, + dim.height); + } } diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index 3aa433e..ac55911 100755 --- a/src/jalview/io/FileLoader.java +++ b/src/jalview/io/FileLoader.java @@ -20,6 +20,7 @@ */ package jalview.io; +import java.awt.Dimension; import java.io.File; import java.io.IOException; import java.util.StringTokenizer; @@ -46,6 +47,7 @@ import jalview.project.Jalview2XML; import jalview.schemes.ColourSchemeI; import jalview.structure.StructureSelectionManager; import jalview.util.MessageManager; +import jalview.util.Platform; import jalview.ws.utils.UrlDownloadClient; public class FileLoader implements Runnable @@ -480,8 +482,12 @@ public class FileLoader implements Runnable // status in Jalview 3 // TODO: define 'virtual desktop' for benefit of headless scripts // that perform queries to find the 'current working alignment' - Desktop.addInternalFrame(alignFrame, title, + + Dimension dim = Platform.getDimIfEmbedded(alignFrame, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); + alignFrame.setSize(dim); + Desktop.addInternalFrame(alignFrame, title, dim.width, + dim.height); } try diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index 6685c67..1eb0fb9 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -25,6 +25,7 @@ import jalview.analysis.GeneticCodeI; import jalview.analysis.GeneticCodes; import jalview.api.SplitContainerI; import jalview.bin.Cache; +import jalview.bin.Jalview; import jalview.gui.JvSwingUtils; import jalview.gui.Preferences; import jalview.io.FileFormats; @@ -220,7 +221,8 @@ public class GAlignFrame extends JInternalFrame { // for Web-page embedding using id=align-frame-div - setName("jalview-alignment"); + setName(Jalview.getAppID("alignment")); + jbInit(); setJMenuBar(alignFrameMenuBar); diff --git a/src/jalview/jbgui/GDesktop.java b/src/jalview/jbgui/GDesktop.java index e4a5905..6793663 100755 --- a/src/jalview/jbgui/GDesktop.java +++ b/src/jalview/jbgui/GDesktop.java @@ -21,6 +21,7 @@ package jalview.jbgui; import jalview.api.AlignmentViewPanel; +import jalview.bin.Jalview; import jalview.io.FileFormatException; import jalview.util.MessageManager; import jalview.util.Platform; @@ -139,7 +140,8 @@ public class GDesktop extends JFrame */ private void jbInit() throws Exception { - setName("jalview-desktop"); + + setName(Jalview.getAppID("desktop")); FileMenu.setText(MessageManager.getString("action.file")); HelpMenu.setText(MessageManager.getString("action.help")); inputLocalFileMenuItem diff --git a/src/jalview/jbgui/GPCAPanel.java b/src/jalview/jbgui/GPCAPanel.java index a6498d2..74b5afd 100755 --- a/src/jalview/jbgui/GPCAPanel.java +++ b/src/jalview/jbgui/GPCAPanel.java @@ -20,6 +20,7 @@ */ package jalview.jbgui; +import jalview.bin.Jalview; import jalview.util.ImageMaker.TYPE; import jalview.util.MessageManager; @@ -88,7 +89,7 @@ public class GPCAPanel extends JInternalFrame private void jbInit() throws Exception { - setName("jalview-pca"); + setName(Jalview.getAppID("pca")); this.getContentPane().setLayout(new BorderLayout()); JPanel jPanel2 = new JPanel(); jPanel2.setLayout(new FlowLayout()); diff --git a/src/jalview/jbgui/GStructureViewer.java b/src/jalview/jbgui/GStructureViewer.java index dfee3e2..e16d63a 100644 --- a/src/jalview/jbgui/GStructureViewer.java +++ b/src/jalview/jbgui/GStructureViewer.java @@ -21,6 +21,7 @@ package jalview.jbgui; import jalview.api.structures.JalviewStructureDisplayI; +import jalview.bin.Jalview; import jalview.gui.ColourMenuHelper.ColourChangeListener; import jalview.util.ImageMaker.TYPE; import jalview.util.MessageManager; @@ -89,7 +90,7 @@ public abstract class GStructureViewer extends JInternalFrame private void jbInit() throws Exception { - setName("jalview-structureviewer"); + setName(Jalview.getAppID("structureviewer")); JMenuBar menuBar = new JMenuBar(); this.setJMenuBar(menuBar); diff --git a/src/jalview/jbgui/GTreePanel.java b/src/jalview/jbgui/GTreePanel.java index d184e76..0f9c2a2 100755 --- a/src/jalview/jbgui/GTreePanel.java +++ b/src/jalview/jbgui/GTreePanel.java @@ -20,6 +20,7 @@ */ package jalview.jbgui; +import jalview.bin.Jalview; import jalview.util.ImageMaker.TYPE; import jalview.util.MessageManager; @@ -92,7 +93,7 @@ public class GTreePanel extends JInternalFrame private void jbInit() throws Exception { - setName("jalview-tree"); + setName(Jalview.getAppID("tree")); this.getContentPane().setLayout(borderLayout1); this.setBackground(Color.white); this.setFont(new java.awt.Font("Verdana", 0, 12)); diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java index 6340e64..751b297 100644 --- a/src/jalview/project/Jalview2XML.java +++ b/src/jalview/project/Jalview2XML.java @@ -151,6 +151,7 @@ import jalview.xml.binding.jalview.ThresholdType; import jalview.xml.binding.jalview.VAMSAS; import java.awt.Color; +import java.awt.Dimension; import java.awt.Font; import java.awt.Rectangle; import java.io.BufferedReader; @@ -5215,8 +5216,9 @@ public class Jalview2XML String complementaryViewId = view.getComplementId(); if (complementaryViewId == null) { - Desktop.addInternalFrame(af, view.getTitle(), + Dimension dim = Platform.getDimIfEmbedded(af, safeInt(view.getWidth()), safeInt(view.getHeight())); + Desktop.addInternalFrame(af, view.getTitle(), dim.width, dim.height); // recompute any autoannotation af.alignPanel.updateAnnotation(false, true); reorderAutoannotation(af, al, autoAlan); @@ -6349,9 +6351,7 @@ public class Jalview2XML panel.getRotatableCanvas().getAxisEndPoints()[i] = new Point( axis.getXPos(), axis.getYPos(), axis.getZPos()); } - - Desktop.addInternalFrame(panel, MessageManager.formatMessage( - "label.calc_title", "PCA", modelName), 475, 450); + PCAPanel.addToDesktop(panel, modelName); } } catch (Exception ex) { diff --git a/src/jalview/viewmodel/OverviewDimensions.java b/src/jalview/viewmodel/OverviewDimensions.java index 0235081..c153dc1 100644 --- a/src/jalview/viewmodel/OverviewDimensions.java +++ b/src/jalview/viewmodel/OverviewDimensions.java @@ -26,6 +26,7 @@ import jalview.datamodel.AlignmentI; import jalview.datamodel.HiddenColumns; import jalview.datamodel.HiddenSequences; +import java.awt.Dimension; import java.awt.Graphics; public abstract class OverviewDimensions @@ -71,15 +72,22 @@ public abstract class OverviewDimensions * true if the annotation panel is to be shown, false otherwise */ public OverviewDimensions(ViewportRanges ranges, - boolean showAnnotationPanel) + boolean showAnnotationPanel, Dimension dim) { + if (!showAnnotationPanel) + { + graphHeight = 0; + } + // scale the initial size of overviewpanel to shape of alignment float initialScale = (float) ranges.getAbsoluteAlignmentWidth() / (float) ranges.getAbsoluteAlignmentHeight(); - if (!showAnnotationPanel) + if (dim != null) { - graphHeight = 0; + width = dim.width; + sequencesHeight = dim.height; + return; } if (ranges.getAbsoluteAlignmentWidth() > ranges diff --git a/src/jalview/viewmodel/OverviewDimensionsHideHidden.java b/src/jalview/viewmodel/OverviewDimensionsHideHidden.java index de90a21..598b989 100644 --- a/src/jalview/viewmodel/OverviewDimensionsHideHidden.java +++ b/src/jalview/viewmodel/OverviewDimensionsHideHidden.java @@ -20,6 +20,8 @@ */ package jalview.viewmodel; +import java.awt.Dimension; + import jalview.api.AlignmentColsCollectionI; import jalview.api.AlignmentRowsCollectionI; import jalview.datamodel.AlignmentI; @@ -38,10 +40,21 @@ public class OverviewDimensionsHideHidden extends OverviewDimensions private int ydiff; // when dragging, difference in alignment units between // start sequence and original mouse click position + /** + * for testng only + * + * @param vpranges + * @param showAnnotationPanel + */ + @Deprecated + public OverviewDimensionsHideHidden(ViewportRanges vpranges, boolean showAnnotationPanel) { + this(vpranges, showAnnotationPanel, null); + } + public OverviewDimensionsHideHidden(ViewportRanges vpranges, - boolean showAnnotationPanel) + boolean showAnnotationPanel, Dimension dim) { - super(vpranges, showAnnotationPanel); + super(vpranges, showAnnotationPanel, dim); ranges = vpranges; resetAlignmentDims(); } diff --git a/src/jalview/viewmodel/OverviewDimensionsShowHidden.java b/src/jalview/viewmodel/OverviewDimensionsShowHidden.java index 3aa6e1b..a4f21f0 100644 --- a/src/jalview/viewmodel/OverviewDimensionsShowHidden.java +++ b/src/jalview/viewmodel/OverviewDimensionsShowHidden.java @@ -20,6 +20,8 @@ */ package jalview.viewmodel; +import java.awt.Dimension; + import jalview.api.AlignmentColsCollectionI; import jalview.api.AlignmentRowsCollectionI; import jalview.datamodel.AlignmentI; @@ -38,6 +40,18 @@ public class OverviewDimensionsShowHidden extends OverviewDimensions private int ydiff; // when dragging, difference in alignment units between // start sequence and original mouse click position + + /** + * for testng only + * + * @param vpranges + * @param showAnnotationPanel + */ + @Deprecated + public OverviewDimensionsShowHidden(ViewportRanges vpranges, boolean showAnnotationPanel) { + this(vpranges, showAnnotationPanel, null); + } + /** * Create an OverviewDimensions object * @@ -47,9 +61,9 @@ public class OverviewDimensionsShowHidden extends OverviewDimensions * true if the annotation panel is to be shown, false otherwise */ public OverviewDimensionsShowHidden(ViewportRanges vpranges, - boolean showAnnotationPanel) + boolean showAnnotationPanel, Dimension dim) { - super(vpranges, showAnnotationPanel); + super(vpranges, showAnnotationPanel, dim); ranges = vpranges; resetAlignmentDims(); }