+++ /dev/null
-package jalview.api;
-
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.io.DataSourceType;
-import jalview.io.NewickFile;
-import jalview.javascript.JSFunctionExec;
-import jalview.javascript.MouseOverStructureListener;
-import jalview.structure.SelectionSource;
-import jalview.structure.VamsasSource;
-
-//import java.applet.AppletContext;
-import java.io.IOException;
-import java.net.URL;
-import java.util.Hashtable;
-import java.util.Vector;
-
-import netscape.javascript.JSObject;
-
-public interface JalviewApp
-{
- public String getParameter(String name);
-
- public boolean getDefaultParameter(String name, boolean def);
-
- public URL getDocumentBase();
-
- public URL getCodeBase();
-
- public void setAlignPdbStructures(boolean defaultParameter);
-
- public void newStructureView(PDBEntry pdb, SequenceI[] seqs,
- String[] chains, DataSourceType protocol);
-
- public void alignedStructureView(PDBEntry[] pdb, SequenceI[][] seqs,
- String[][] chains, String[] protocols);
-
- public void updateForAnnotations();
-
- public AlignViewportI getViewport();
-
- public void setFeatureGroupState(String[] groups, boolean state);
-
- public boolean parseFeaturesFile(String param, DataSourceType protocol);
-
- public void newFeatureSettings();
-
- public boolean loadScoreFile(String sScoreFile) throws IOException;
-
- public void loadTree(NewickFile fin, String treeFile) throws IOException;
-
- public Vector<Runnable> getJsExecQueue(JSFunctionExec jsFunctionExec);
-
-// deprecated public AppletContext getAppletContext();
-
- public boolean isJsfallbackEnabled();
-
- public JSObject getJSObject();
-
- public StructureSelectionManagerProvider getStructureSelectionManagerProvider();
-
- public void updateColoursFromMouseOver(Object source,
- MouseOverStructureListener mouseOverStructureListener);
-
- public Object[] getSelectionForListener(SequenceGroup seqsel, ColumnSelection colsel,
- HiddenColumns hidden, SelectionSource source, Object alignFrame);
-
- public String arrayToSeparatorList(String[] array);
-
- public Hashtable<String, int[]> getJSHashes();
-
- Hashtable<String, Hashtable<String, String[]>> getJSMessages();
-
- public Object getFrameForSource(VamsasSource source);
-
- public jalview.renderer.seqfeatures.FeatureRenderer getNewFeatureRenderer(
- AlignViewportI vp);
-
-}
-package jalview.bin;
+package jalview.api;
-import jalview.api.JalviewApp;
-import jalview.api.StructureSelectionManagerProvider;
+import java.awt.EventQueue;
+//import java.applet.AppletContext;
+import java.io.IOException;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+import jalview.bin.ArgsParser;
+import jalview.bin.Jalview;
+import jalview.bin.JalviewJSApi;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.AlignViewport;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.CalculationChooser;
import jalview.gui.Desktop;
+import jalview.gui.StructureViewer;
import jalview.io.AnnotationFile;
import jalview.io.AppletFormatAdapter;
import jalview.io.DataSourceType;
import jalview.io.JPredFile;
import jalview.io.JnetAnnotationMaker;
import jalview.io.NewickFile;
+import jalview.renderer.seqfeatures.FeatureRenderer;
+import jalview.structure.SelectionListener;
import jalview.structure.SelectionSource;
import jalview.structure.StructureSelectionManager;
+import jalview.structure.VamsasSource;
import jalview.util.HttpUtils;
import jalview.util.MessageManager;
+import jalview.util.Platform;
-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;
+//import netscape.javascript.JSObject;
/**
- * A class to load parameters for either JalviewLite or Jalview
+ * Basically the JalviewLite application, but without JalviewLite
*
* @author hansonr
*
*/
-public class JalviewAppLoader
+public class JalviewJSApp implements JalviewJSApi
{
+ private ArgsParser aparser;
- private JalviewApp app; // Jalview or JalviewJS or JalviewLite
+ private String j2sAppletID;
private boolean debug;
- String separator = "\u00AC"; // JalviewLite note: the default used to
+ private String[] ret = new String[1];
+
+ private 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)
+ public JalviewJSApp(ArgsParser aparser)
{
- this.separator = separator;
+ this.aparser = aparser;
+ this.j2sAppletID = (String) aparser.getAppletValue("j2sAppletID",
+ "Jalview", true);
+ Platform.setAppClass(this);
}
- public JalviewAppLoader(boolean debug)
- {
- this.debug = debug;
- }
- public void load(JalviewApp app)
+ public void load(AlignFrame af)
{
-
- this.app = app;
-
- String sep = app.getParameter("separator");
+ String sep = (String) getAppletParameter("separator", true);
if (sep != null)
{
if (sep.length() > 0)
}
}
- loadTree();
+ loadTree(af);
loadScoreFile();
- loadFeatures();
- loadAnnotations();
- loadJnetFile();
- loadPdbFiles();
- callInitCallback();
+ loadFeatures(af);
+ loadAnnotations(af);
+ loadJnetFile(af);
+ loadPdbFiles(af);
+ }
+
+ public String getAppID(String frameType)
+ {
+ return j2sAppletID + (frameType == null ? "" : "-" + frameType);
+ }
+
+ // 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<String, Hashtable<String, String[]>> jsmessages;
+
+ private Hashtable<String, int[]> jshashes;
+
+ @Override
+ public String getParameter(String name)
+ {
+ return (String) getAppletParameter(name, true);
+ }
+
+ @Override
+ public Object getAppletParameter(String name, boolean asString)
+ {
+ return aparser.getAppletValue(name, null, asString);
}
/**
- * Load PDBFiles if any specified by parameter(s). Returns true if loaded,
- * else false.
- *
- * @param loaderFrame
- * @return
+ * Get the applet-like code base even though this is an application.
*/
- protected boolean loadPdbFiles()
+
+ @Override
+ public URL getCodeBase()
{
- boolean result = false;
- /*
- * <param name="alignpdbfiles" value="false/true"/> Undocumented for 2.6 -
- * related to JAL-434
- */
+ return Platform.getCodeBase();
+ }
- boolean doAlign = app.getDefaultParameter("alignpdbfiles", false);
- app.setAlignPdbStructures(doAlign);
- /*
- * <param name="PDBfile" value="1gaq.txt PDB|1GAQ|1GAQ|A PDB|1GAQ|1GAQ|B
- * PDB|1GAQ|1GAQ|C">
- *
- * <param name="PDBfile2" value="1gaq.txt A=SEQA B=SEQB C=SEQB">
- *
- * <param name="PDBfile3" value="1q0o Q45135_9MICO">
- */
+ /**
+ * Get the applet-like document base even though this is an application.
+ */
- // Accumulate pdbs here if they are heading for the same view (if
- // alignPdbStructures is true)
- Vector<Object[]> 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;
+ @Override
+ public URL getDocumentBase()
+ {
+ return Platform.getDocumentBase();
+ }
- int pdbFileCount = 0;
- String param;
- do
+ @Override
+ public Object getFrameForSource(VamsasSource source)
+ {
+ if (source != null)
{
- if (pdbFileCount > 0)
- {
- param = app.getParameter("PDBFILE" + pdbFileCount);
- }
- else
+ AlignFrame af;
+ if (source instanceof jalview.gui.AlignViewport
+ && source == (af = Jalview.getCurrentAlignFrame())
+ .getViewport())
{
- param = app.getParameter("PDBFILE");
+ // 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;
+ }
- if (param != null)
- {
- PDBEntry pdb = new PDBEntry();
+ @Override
+ public Hashtable<String, int[]> getJSHashes()
+ {
+ return (jshashes == null ? (jshashes = new Hashtable<>()) : jshashes);
+ }
- String seqstring;
- SequenceI[] seqs = null;
- String[] chains = null;
+ @Override
+ public Hashtable<String, Hashtable<String, String[]>> getJSMessages()
+ {
+ return (jsmessages == null ? (jsmessages = new Hashtable<>())
+ : jsmessages);
+ }
- StringTokenizer st = new StringTokenizer(param, " ");
+ @Override
+ public Object getJSObject()
+ {
+ return Jalview.getInstance();
+ }
- 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) };
- }
+ @Override
+ public FeatureRenderer getNewFeatureRenderer(AlignViewportI vp)
+ {
+ return new jalview.gui.FeatureRenderer((AlignmentPanel) vp);
+ }
- }
- else
- {
- param = st.nextToken();
- List<SequenceI> tmp = new ArrayList<>();
- List<String> tmp2 = new ArrayList<>();
+ @Override
+ public Object[] getSelectionForListener(SequenceGroup seqsel,
+ ColumnSelection colsel, HiddenColumns hidden,
+ SelectionSource source, Object alignFrame)
+ {
+ return getSelectionForListener(null, seqsel, colsel, hidden, source,
+ alignFrame);
+ }
- 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));
- }
+ /**
+ * scorefile
+ *
+ */
- 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]);
+ @Override
+ public boolean loadScoreFile(String sScoreFile) throws IOException
+ {
+ return loadScoreFile(null, sScoreFile);
+ }
+
+ public boolean loadScoreFile(AlignFrame af, String sScoreFile) throws IOException
+ {
+ (af == null ? Jalview.getCurrentAlignFrame() : af).loadJalviewDataFile(sScoreFile, null, null, null);
+ return true;
+ }
- 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 + ")");
- }
- }
- }
+ public void loadTree(AlignFrame af, NewickFile nf, String treeFile) throws IOException
+ {
+ if (af == null)
+ af = Jalview.getCurrentAlignFrame();
+ af.getViewport()
+ .setCurrentTree(af.showNewickTree(nf, treeFile).getTree());
+ }
- if (doAlign)
- {
- pdbs.addElement(new Object[] { pdb, seqs, chains, protocol });
- }
- else
- {
- app.newStructureView(pdb, seqs, chains, protocol);
- }
- }
- }
+ @Override
+ public void newFeatureSettings()
+ {
+ System.err.println(
+ "Jalview applet interface newFeatureSettings not implemented");
+ }
- 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;
+ //
+ //
+ // public void setAlignPdbStructures(boolean defaultParameter)
+ // {
+ // alignPDBStructures = true;
+ // }
+ //
+
+ @Override
+ public void newStructureView(PDBEntry pdb, SequenceI[] seqs,
+ String[] chains, DataSourceType protocol)
+ {
+ newStructureView(null, pdb, seqs, chains, protocol);
+
}
- /**
- * Load in a Jnetfile if specified by parameter. Returns true if loaded, else
- * false.
- *
- * @param alignFrame
- * @return
- */
- protected boolean loadJnetFile()
+ public void newStructureView(AlignFrame af, PDBEntry pdb,
+ SequenceI[] seqs, String[] chains, DataSourceType protocol)
{
- 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;
+ StructureViewer.launchStructureViewer(
+ (af == null ? Jalview.getCurrentAlignFrame() : af).alignPanel,
+ pdb, seqs);
}
/**
- * Load annotations if specified by parameter. Returns true if loaded, else
- * false.
+ * features
+ * @param af
*
- * @param alignFrame
- * @return
*/
- protected boolean loadAnnotations()
+
+ @Override
+ public boolean parseFeaturesFile(String filename, DataSourceType protocol)
{
- 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;
+ return parseFeaturesFile(null, filename, protocol);
+ }
+
+ public boolean parseFeaturesFile(AlignFrame af, String filename, DataSourceType protocol)
+ {
+ return af.parseFeaturesFile(filename, protocol);
}
+ @Override
+ public void setFeatureGroupState(String[] groups, boolean state)
+ {
+ setFeatureGroupState(null, groups, state);
+ }
+
+ public void setFeatureGroupState(AlignFrame af, String[] groups, boolean state) {
+ (af == null ? Jalview.getCurrentAlignFrame() : af).setFeatureGroupState(groups, state);
+ }
/**
- * Load features file and view settings as specified by parameters. Returns
- * true if features were loaded, else false.
+ * annotations, jpredfile, jnetfile
*
- * @param alignFrame
- * @return
*/
- protected boolean loadFeatures()
+
+ @Override
+ public void updateForAnnotations()
{
- 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;
+ updateForAnnotations(null);
}
- /**
- * Load a score file if specified by parameter. Returns true if file was
- * loaded, else false.
- *
- * @param loaderFrame
- */
- protected boolean loadScoreFile()
+ public void updateForAnnotations(AlignFrame af)
{
- 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;
+ (af == null ? Jalview.getCurrentAlignFrame() : af).updateForAnnotations();
}
- 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()
+ @Override
+ public boolean addPdbFile(AlignFrame alf, String sequenceId,
+ String pdbEntryString, String pdbFile)
{
- boolean result = false;
- String treeFile = app.getParameter("tree");
- if (treeFile == null)
+ if (alf == null)
{
- treeFile = app.getParameter("treeFile");
+ alf = Jalview.getCurrentAlignFrame();
}
-
- if (treeFile != null)
+ SequenceI toaddpdb = alf.getViewport().getAlignment()
+ .findName(sequenceId);
+ boolean needtoadd = false;
+ if (toaddpdb != null)
{
- try
+ Vector<PDBEntry> pdbe = toaddpdb.getAllPDBEntries();
+ PDBEntry pdbentry = null;
+ if (pdbe != null && pdbe.size() > 0)
{
- ret[0] = treeFile;
- NewickFile fin = new NewickFile(treeFile,
- resolveFileProtocol(app, ret));
- fin.parse();
-
- if (fin.getTree() != null)
+ for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
{
- app.loadTree(fin, ret[0]);
- result = true;
- if (debug)
+ pdbentry = pdbe.elementAt(pe);
+ if (!pdbentry.getId().equals(pdbEntryString)
+ && !pdbentry.getFile().equals(pdbFile))
{
- System.out.println("Successfully imported tree.");
+ pdbentry = null;
}
- }
- else
- {
- if (debug)
+ else
{
- System.out.println(
- "Tree parameter did not resolve to a valid tree.");
+ continue;
}
}
- } catch (Exception ex)
+ }
+ if (pdbentry == null)
{
- ex.printStackTrace();
+ 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);
+ alf.alignPanel.getStructureSelectionManager()
+ .registerPDBEntry(pdbentry);
}
}
- return result;
+ return true;
}
- /**
- * 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)
+ @Override
+ public String arrayToSeparatorList(String[] array)
{
- 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;
+ return arrayToSeparatorList(array, separator);
}
/**
- * parse the string into a list
+ * concatenate the list with separator
*
* @param list
* @param separator
- * @return elements separated by separator
+ * @return concatenated string
*/
- public static String[] separatorListToArray(String list, String separator)
+ public static String arrayToSeparatorList(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<String> 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)
+ // TODO use StringUtils version
+ StringBuffer v = new StringBuffer();
+ if (list != null && list.length > 0)
{
- String[] v = new String[jv.size()];
- for (int i = 0; i < v.length; i++)
+ for (int i = 0, iSize = list.length; i < iSize; i++)
{
- v[i] = jv.elementAt(i);
+ if (list[i] != null)
+ {
+ if (i > 0)
+ {
+ v.append(separator);
+ }
+ v.append(list[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] + "'");
- // }
+ // System.err
+ // .println("Returning '" + separator + "' separated List:\n");
+ // System.err.println(v);
// }
- return v;
+ return v.toString();
}
// if (debug)
// {
// System.err.println(
- // "Empty Array from '" + separator + "' separated List");
+ // "Returning empty '" + separator + "' separated List\n");
// }
- return null;
+ return "" + separator;
}
- public static DataSourceType resolveFileProtocol(JalviewApp app,
- String[] retPath)
+ @Override
+ public String getAlignment(String format)
{
- String path = retPath[0];
- /*
- * is it paste data?
- */
- if (path.startsWith("PASTE"))
- {
- retPath[0] = path.substring(5);
- return DataSourceType.PASTE;
- }
+ return getAlignmentFrom(null, format, null);
+ }
- /*
- * is it a URL?
- */
- if (path.indexOf("://") >= 0)
- {
- return DataSourceType.URL;
- }
+ @Override
+ public String getAlignment(String format, String suffix)
+ {
+ return getAlignmentFrom(Jalview.getCurrentAlignFrame(), format, suffix);
+ }
- /*
- * 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;
+ @Override
+ public String getAlignmentFrom(AlignFrame alf, String format)
+ {
+ return getAlignmentFrom(alf, format, null);
+ }
+
+ @Override
+ public String getAlignmentFrom(AlignFrame alf, String format,
+ String suffix)
+ {
+ try
+ {
+ if (alf == null)
+ {
+ alf = Jalview.getCurrentAlignFrame();
+ }
+ 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;
}
+ }
- /*
- * 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))
+ @Override
+ public String getAlignmentOrder()
+ {
+ return getAlignmentFrom(Jalview.getCurrentAlignFrame(), null);
+ }
+
+ @Override
+ public String getAlignmentOrderFrom(AlignFrame alf)
+ {
+ return getAlignmentFrom(alf, null);
+ }
+
+ @Override
+ public String getAlignmentOrderFrom(AlignFrame alf, String sep)
+ {
+ if (alf == null)
{
- // if (debug)
- // {
- // System.err.println("Prepended codebase '" + codeBase
- // + "' to make: '" + withCodeBase + "'");
- // }
- retPath[0] = withCodeBase;
- return DataSourceType.URL;
+ alf = Jalview.getCurrentAlignFrame();
+ }
+ 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);
+ }
- /*
- * try locating by classloader; try this last so files in the directory
- * are resolved using document base
- */
- if (inArchive(app.getClass(), path))
+ @Override
+ public String getAnnotation()
+ {
+ return getAnnotationFrom(null);
+ }
+
+ @Override
+ public String getAnnotationFrom(AlignFrame alf)
+ {
+ if (alf == null)
{
- return DataSourceType.CLASSLOADER;
+ alf = Jalview.getCurrentAlignFrame();
+ }
+ String annotation = new AnnotationFile()
+ .printAnnotationsForView(alf.getViewport());
+ return annotation;
+ }
+
+ @Override
+ public String getFeatureGroups()
+ {
+ return getFeatureGroupsOn(null);
+ }
+
+ @Override
+ public String getFeatureGroupsOfState(boolean visible)
+ {
+ return getFeatureGroupsOfStateOn(null, visible);
+ }
+
+ @Override
+ public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)
+ {
+ if (alf == null)
+ {
+ alf = Jalview.getCurrentAlignFrame();
+ }
+ return arrayToSeparatorList(alf.getFeatureGroupsOfState(visible));
+ }
+
+ @Override
+ public String getFeatureGroupsOn(AlignFrame alf)
+ {
+ if (alf == null)
+ {
+ alf = Jalview.getCurrentAlignFrame();
+ }
+ return arrayToSeparatorList(alf.getFeatureGroups());
+ }
+
+ @Override
+ public String getFeatures(String format)
+ {
+ return getFeaturesFrom(null, format);
+ }
+
+ /**
+ * 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
+ */
+ @Override
+ public String getFeaturesFrom(AlignFrame alf, String format)
+ {
+ if (alf == null)
+ {
+ alf = Jalview.getCurrentAlignFrame();
+ }
+ 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(
+ alf.getViewport().getAlignment().getSequencesArray(),
+ alf.alignPanel.getFeatureRenderer(), nonpos, compl);
+ }
+ else
+ {
+ features = formatter.printGffFormat(
+ alf.getViewport().getAlignment().getSequencesArray(),
+ alf.alignPanel.getFeatureRenderer(), nonpos, compl);
+ }
+
+ if (features == null)
+ {
+ features = "";
}
+ return features;
+
+ }
+
+ @Override
+ public String getJsMessage(String messageclass, String viewId)
+ {
+ // TODO Auto-generated method stub
return null;
}
/**
- * Discovers whether the given file is in the Applet Archive
+ * read sequence1...sequenceN as a raw alignment
*
- * @param f
- * String
- * @return boolean
+ * @param jalviewApp
+ * @return
*/
- private static boolean inArchive(Class<?> c, String f)
+ public String getPastedSequence(JalviewJSApp jalviewApp)
{
- // This might throw a security exception in certain browsers
- // Netscape Communicator for instance.
+ StringBuffer data = new StringBuffer("PASTE");
+ int i = 1;
+ String file = null;
+ while ((file = (String) getAppletParameter("sequence" + i,
+ true)) != null)
+ {
+ data.append(file.toString() + "\n");
+ i++;
+ }
+ if (data.length() > 5)
+ {
+ file = data.toString();
+ }
+ return file;
+ }
+
+ /**
+ *
+ * @see jalview.appletgui.js.JalviewLiteJsApi#getSelectedSequences()
+ */
+ @Override
+ public String getSelectedSequences()
+ {
+ return getSelectedSequencesFrom(Jalview.getCurrentAlignFrame());
+ }
+
+ /**
+ *
+ * @see jalview.appletgui.js.JalviewLiteJsApi#getSelectedSequences(java.lang.String)
+ */
+ @Override
+ public String getSelectedSequences(String sep)
+ {
+ return getSelectedSequencesFrom(Jalview.getCurrentAlignFrame(), sep);
+ }
+
+ @Override
+ public String getSelectedSequencesAsAlignment(String format,
+ String suffix)
+ {
+ return getSelectedSequencesAsAlignmentFrom(null, format, suffix);
+ }
+
+ @Override
+ public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
+ String format, String suffix)
+ {
+
+ if (alf == null)
+ {
+ alf = Jalview.getCurrentAlignFrame();
+ }
+
+ boolean seqlimits = (suffix == null || suffix.equalsIgnoreCase("true"));
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)
+ AlignViewport vp = alf.getViewport();
+ FileFormatI theFormat = FileFormats.getInstance().forName(format);
+ 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)
{
- System.out.println("Exception checking resources: " + f + " " + ex);
- return false;
+ ex.printStackTrace();
+ return "Error retrieving alignment, possibly invalid format specifier: "
+ + format;
+ }
+ return "";
+ }
+
+ /**
+ *
+ * @see jalview.appletgui.js.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
+ * .AlignFrame)
+ */
+ @Override
+ public String getSelectedSequencesFrom(AlignFrame alf)
+ {
+ return getSelectedSequencesFrom(alf, null);
+ }
+
+ @Override
+ public String getSelectedSequencesFrom(AlignFrame alf, String sep)
+ {
+ if (alf == null)
+ {
+ alf = Jalview.getCurrentAlignFrame();
+ }
+ 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 Object[] getSelectionForListener(AlignFrame alf,
+ SequenceGroup seqsel, ColumnSelection colsel,
+ HiddenColumns hidden, SelectionSource source, Object alignFrame)
+ {
+ if (alf == null)
+ {
+ alf = Jalview.getCurrentAlignFrame();
+ }
+ // System.err.println("Testing selection event relay to
+ // jsfunction:"+_listener);
+ String setid = "";
+ AlignFrame src = (AlignFrame) alignFrame;
+ if (source != null)
+ {
+ if (source instanceof AlignViewport && alf.getViewport() == source)
+ {
+ // should be valid if it just generated an event!
+ src = alf;
+
+ }
+ }
+ 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) };
+ }
+
+ @Override
+ public String getSeparator()
+ {
+ return separator;
+ }
+
+ /**
+ *
+ * @see jalview.appletgui.js.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, final String sequenceId,
+ final String position, final String alignedPosition)
+ {
+ if (alf == null)
+ {
+ alf = Jalview.getCurrentAlignFrame();
+ }
+ // 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 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 void setMouseoverListener(String listener)
+ // {
+ // appLoader.setMouseoverListener(listener);
+ // }
+ //
+ //
+ // public void setMouseoverListener(AlignFrame af, String listener)
+ // {
+ // }
+ //
+
+ @Override
+ public AlignFrame loadAlignment(String text, String title)
+ {
+ return loadAlignment(text, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT, title);
+ }
+
+ @Override
+ public void loadAnnotation(String annotation)
+ {
+ loadAnnotationFrom(null, annotation);
+ }
+
+ @Override
+ public void loadAnnotationFrom(AlignFrame alf, String annotation)
+ {
+ if (alf == null)
+ {
+ alf = Jalview.getCurrentAlignFrame();
+ }
+ if (new AnnotationFile().annotateAlignmentView(alf.getViewport(),
+ annotation, DataSourceType.PASTE))
+ {
+ alf.alignPanel.fontChanged();
+ alf.alignPanel.setScrollValues(0, 0);
+ }
+ else
+ {
+ alf.parseFeaturesFile(annotation, DataSourceType.PASTE);
+ }
+ }
+
+ /**
+ * Load annotations if specified by parameter. Returns true if loaded, else
+ * false.
+ *
+ *
+ * @param alignFrame
+ * @return
+ */
+ protected boolean loadAnnotations(AlignFrame af)
+ {
+ boolean result = false;
+ String param = (String) getAppletParameter("annotations", true);
+ if (param != null)
+ {
+ ret[0] = param;
+ DataSourceType protocol = resolveFileProtocol(ret);
+ param = ret[0];
+ if (new AnnotationFile().annotateAlignmentView(af.getViewport(), param,
+ protocol))
+ {
+ updateForAnnotations();
+ result = true;
+ }
+ else
+ {
+ System.err
+ .println("Annotations were not added from annotation file '"
+ + param + "'");
+ }
+ }
+ return result;
+ }
+
+ //// JalviewJSApi
+
+ /**
+ * Load features file and view settings as specified by parameters. Returns
+ * true if features were loaded, else false.
+ * @param
+ *
+ * @param alignFrame
+ * @return
+ */
+ protected boolean loadFeatures(AlignFrame af)
+ {
+ 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 = (String) getAppletParameter("hidefeaturegroups", true);
+ if (param != null)
+ {
+ setFeatureGroupState(af, separatorListToArray(param, separator), false);
+ // setFeatureGroupStateOn(newAlignFrame, param, false);
+ }
+ // show specific groups
+ param = (String) getAppletParameter("showfeaturegroups", true);
+ if (param != null)
+ {
+ setFeatureGroupState(af, separatorListToArray(param, separator), true);
+ // setFeatureGroupStateOn(newAlignFrame, param, true);
+ }
+ // and now load features
+ param = (String) getAppletParameter("features", true);
+ if (param != null)
+ {
+ ret[0] = param;
+ DataSourceType protocol = resolveFileProtocol(ret);
+
+ result = parseFeaturesFile(af, ret[0], protocol);
+ }
+
+ param = (String) getAppletParameter("showFeatureSettings", true);
+ if (param != null && param.equalsIgnoreCase("true"))
+ {
+ newFeatureSettings();
+ }
+ return result;
+ }
+
+ @Override
+ public void loadFeatures(String features, boolean autoenabledisplay)
+ {
+ loadFeaturesFrom(null, features, autoenabledisplay);
+ }
+
+ @Override
+ public boolean loadFeaturesFrom(AlignFrame alf, String features,
+ boolean autoenabledisplay)
+ {
+ if (alf == null)
+ {
+ alf = Jalview.getCurrentAlignFrame();
+ }
+ 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;
+ }
+
+ /**
+ * Load in a Jnetfile if specified by parameter. Returns true if loaded, else
+ * false.
+ *
+ * @param alignFrame
+ * @return
+ */
+ protected boolean loadJnetFile(AlignFrame af)
+ {
+ boolean result = false;
+ String param = (String) getAppletParameter("jnetfile", true);
+ if (param == null)
+ {
+ // jnet became jpred around 2016
+ param = (String) getAppletParameter("jpredfile", true);
+ }
+ if (param != null)
+ {
+ try
+ {
+ ret[0] = param;
+ DataSourceType protocol = resolveFileProtocol(ret);
+ JPredFile predictions = new JPredFile(ret[0], protocol);
+ JnetAnnotationMaker.add_annotation(predictions,
+ af.getViewport().getAlignment(), 0, false);
+ // false == do not add sequence profile from concise output
+ af.getViewport().getAlignment().setupJPredAlignment();
+ updateForAnnotations();
+ result = true;
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Load PDBFiles if any specified by parameter(s). Returns true if loaded,
+ * else false.
+ *
+ * @param loaderFrame
+ * @return
+ */
+ protected boolean loadPdbFiles(AlignFrame af)
+ {
+ boolean result = false;
+ /*
+ * <param name="alignpdbfiles" value="false/true"/> Undocumented for 2.6 -
+ * related to JAL-434
+ */
+
+ // not supported (as for JalviewLite)
+ // boolean doAlign = false;//"true".equalsIgnoreCase("" +
+ // getAppletParameter("alignpdbfiles", false));
+ // setAlignPdbStructures(doAlign);
+ /*
+ * <param name="PDBfile" value="1gaq.txt PDB|1GAQ|1GAQ|A PDB|1GAQ|1GAQ|B
+ * PDB|1GAQ|1GAQ|C">
+ *
+ * <param name="PDBfile2" value="1gaq.txt A=SEQA B=SEQB C=SEQB">
+ *
+ * <param name="PDBfile3" value="1q0o Q45135_9MICO">
+ */
+
+ // Accumulate pdbs here if they are heading for the same view (if
+ // alignPdbStructures is true)
+ // ArrayList<Object[]> pdbs = new ArrayList<>();
+ // create a lazy matcher if we're asked to
+ boolean relaxed = "true".equalsIgnoreCase(
+ "" + getAppletParameter("relaxedidmatch", false));
+ jalview.analysis.SequenceIdMatcher matcher = relaxed
+ ? new jalview.analysis.SequenceIdMatcher(
+ af.getViewport().getAlignment().getSequencesArray())
+ : null;
+
+ int pdbFileCount = 0;
+ String param;
+ do
+ {
+ if (pdbFileCount > 0)
+ {
+ param = (String) getAppletParameter("PDBFILE" + pdbFileCount, true);
+ }
+ else
+ {
+ param = (String) getAppletParameter("PDBFILE", true);
+ }
+
+ 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 = (String) getAppletParameter("PDBSEQ", true);
+ if (sequence != null)
+ {
+ seqs = new SequenceI[] { matcher == null
+ ? (Sequence) af.getViewport().getAlignment()
+ .findName(sequence)
+ : matcher.findIdMatch(sequence) };
+ }
+
+ }
+ else
+ {
+ param = st.nextToken();
+ List<SequenceI> tmp = new ArrayList<>();
+ List<String> 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) af.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(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) this)
+ .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.add(new Object[] { pdb, seqs, chains, protocol });
+ // }
+ // else
+ {
+ newStructureView(af, pdb, seqs, chains, protocol);
+ }
+ }
+ }
+
+ pdbFileCount++;
+ } while (param != null || pdbFileCount < 10);
+ //
+ // if (doAlign && 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.get(pdbsi);
+ // pdb[pdbsi] = (PDBEntry) o[0];
+ // seqs[pdbsi] = (SequenceI[]) o[1];
+ // chains[pdbsi] = (String[]) o[2];
+ // protocols[pdbsi] = (String) o[3];
+ // }
+ //// alignedStructureView(pdb, seqs, chains, protocols);
+ // result = true;
+ // }
+ 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 = (String) getAppletParameter("scoreFile", true);
+ if (sScoreFile != null && !"".equals(sScoreFile))
+ {
+ try
+ {
+ if (debug)
+ {
+ System.err.println(
+ "Attempting to load T-COFFEE score file from the scoreFile parameter");
+ }
+ result = 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;
}
- public void callInitCallback()
+ /**
+ * Load a tree for the alignment if specified by parameter. Returns true if a
+ * tree was loaded, else false.
+ *
+ * @return
+ */
+ protected boolean loadTree(AlignFrame af)
{
- String initjscallback = app.getParameter("oninit");
- if (initjscallback == null)
+ boolean result = false;
+ String treeFile = (String) getAppletParameter("tree", true);
+ if (treeFile == null)
{
- return;
+ treeFile = (String) getAppletParameter("treefile", true);
}
- initjscallback = initjscallback.trim();
- if (initjscallback.length() > 0)
+
+ if (treeFile != null)
{
- // TODO
+ try
+ {
+ ret[0] = treeFile;
+ NewickFile fin = new NewickFile(treeFile, resolveFileProtocol(ret));
+ fin.parse();
+
+ if (fin.getTree() != null)
+ {
+ loadTree(af, 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;
}
/**
- * read sequence1...sequenceN as a raw alignment
+ * public static method for JalviewJS API to open a PCAPanel without
+ * necessarily using a dialog.
*
- * @param jalviewApp
- * @return
+ * @param af
+ * @param modelName
+ * @return the PCAPanel, or the string "label.you_need_at_least_n_sequences"
+ * if number of sequences selected is inappropriate
*/
- public String getPastedSequence(JalviewApp jalviewApp)
+ @Override
+ public Object openPcaPanel(AlignFrame af, String modelName)
{
- StringBuffer data = new StringBuffer("PASTE");
- int i = 1;
- String file = null;
- while ((file = app.getParameter("sequence" + i)) != null)
+ if (af == null)
{
- data.append(file.toString() + "\n");
- i++;
- }
- if (data.length() > 5)
- {
- file = data.toString();
+ af = Jalview.getCurrentAlignFrame();
}
- return file;
+ return CalculationChooser.openPcaPanel(af, modelName, null);
}
/**
- * concatenate the list with separator
+ * Open a new Tree panel on the desktop statically. Params are standard (not
+ * set by Groovy). No dialog is opened.
*
- * @param list
- * @param separator
- * @return concatenated string
+ * @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
*/
- public static String arrayToSeparatorList(String[] list, String separator)
+ @Override
+ public Object openTreePanel(AlignFrame af, String treeType,
+ String modelName)
{
- // TODO use StringUtils version
- StringBuffer v = new StringBuffer();
- if (list != null && list.length > 0)
+ if (af == null)
{
- 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();
+ af = Jalview.getCurrentAlignFrame();
}
- // if (debug)
- // {
- // System.err.println(
- // "Returning empty '" + separator + "' separated List\n");
- // }
- return "" + separator;
- }
-
- public String arrayToSeparatorList(String[] array)
- {
- return arrayToSeparatorList(array, separator);
+ return CalculationChooser.openTreePanel(af, treeType, modelName, null);
}
- public String getSelectedSequencesFrom(AlignFrame alf, String sep)
+ @Override
+ public String orderAlignmentBy(AlignFrame alf, String order,
+ String undoName, String sep)
{
- StringBuffer result = new StringBuffer("");
if (sep == null || sep.length() == 0)
{
- sep = separator; // "+0x00AC;
+ sep = separator;
}
- AlignViewport v = alf.getViewport();
- if (v.getSelectionGroup() != null)
+ String[] ids = separatorListToArray(order, sep);
+ SequenceI[] sqs = null;
+ if (ids != null && ids.length > 0)
{
- SequenceI[] seqs = v.getSelectionGroup()
- .getSequencesInOrder(v.getAlignment());
-
- for (int i = 0; i < seqs.length; i++)
+ if (alf == null)
{
- result.append(seqs[i].getName());
- result.append(sep);
+ alf = Jalview.getCurrentAlignFrame();
+ }
+ 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);
- return result.toString();
+ 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 void setFeatureGroupStateOn(final AlignFrame alf,
- final String groups, boolean state)
+ @Override
+ public String orderBy(String order, String undoName)
{
- java.awt.EventQueue.invokeLater(new Runnable()
- {
- @Override
- public void run()
- {
- alf.setFeatureGroupState(
- separatorListToArray(groups, separator), state);
- }
- });
+ return orderBy(order, undoName, null);
}
- public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)
+ @Override
+ public String orderBy(String order, String undoName, String sep)
{
- return arrayToSeparatorList(
- alf.getFeatureGroupsOfState(visible));
+ return orderAlignmentBy(Jalview.getCurrentAlignFrame(), order, undoName,
+ sep);
}
- public void scrollViewToIn(final AlignFrame alf, final String topRow,
- final String leftHandColumn)
+ /**
+ * Allow an outside entity to initiate the second half of argument parsing
+ * (only).
+ *
+ * @param args
+ * @return null is good
+ */
+ @Override
+ public Object parseArguments(String[] args)
{
- // 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();
- }
- }
- });
+ try
+ {
+ Jalview.getInstance().parseArguments(new ArgsParser(args), false);
+ return null;
+ } catch (Throwable t)
+ {
+ return t;
+ }
}
- public void scrollViewToRowIn(final AlignFrame alf, final String topRow)
+ @Override
+ public void removeSelectionListener(AlignFrame af, String listener)
{
- // TODO test
- java.awt.EventQueue.invokeLater(new Runnable()
+ List<SelectionListener> listeners = Desktop
+ .getStructureSelectionManager().getListeners();
+ for (int i = listeners.size(); --i >= 0;)
{
- @Override
- public void run()
+ SelectionListener l = listeners.get(i);
+ if (l instanceof JsSelectionListener
+ && ((JsSelectionListener) l).isFor(af, listener))
{
- try
- {
- alf.scrollToRow(Integer.valueOf(topRow).intValue());
-
- } catch (Exception ex)
- {
- System.err.println("Couldn't parse integer arguments (topRow='"
- + topRow + "')");
- ex.printStackTrace();
- }
-
+ listeners.remove(i);
+ break;
}
- });
+ }
}
+ @Override
public void scrollViewToColumnIn(final AlignFrame alf,
final String leftHandColumn)
{
- // TODO test
java.awt.EventQueue.invokeLater(new Runnable()
{
{
try
{
- alf
- .scrollToColumn(Integer.valueOf(leftHandColumn).intValue());
+ (alf == null ? Jalview.getCurrentAlignFrame() : alf)
+ .scrollToColumn(
+ Integer.valueOf(leftHandColumn).intValue());
} catch (Exception ex)
{
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<PDBEntry> 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)
+ @Override
+ public void scrollViewToIn(final AlignFrame alf, final String topRow,
+ final String leftHandColumn)
{
- AlignmentI al = null;
-
- try
+ // TODO test
+ java.awt.EventQueue.invokeLater(new Runnable()
{
- FileFormatI format = new IdentifyFile().identify(text,
- DataSourceType.PASTE);
- al = new AppletFormatAdapter().readFile(text, DataSourceType.PASTE,
- format);
- if (al.getHeight() > 0)
+ @Override
+ public void run()
{
- return new AlignFrame(al, width, height, title);
+ try
+ {
+ (alf == null ? Jalview.getCurrentAlignFrame() : 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();
+ }
}
- } catch (IOException ex)
- {
- ex.printStackTrace();
- }
- return null;
+ });
}
- public String getFeatureGroupsOn(AlignFrame alf)
+ @Override
+ public void scrollViewToRowIn(final AlignFrame alf, final String topRow)
{
- return arrayToSeparatorList(
- alf.getFeatureGroups());
- }
+ // TODO test
- 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)
+ java.awt.EventQueue.invokeLater(new Runnable()
{
- 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))
+ @Override
+ public void run()
{
- java.awt.EventQueue.invokeLater(new Runnable()
+ try
{
- @Override
- public void run()
- {
- StructureSelectionManager
- .getStructureSelectionManager(Desktop.getInstance())
- .mouseOverVamsasSequence(sq, sq.findIndex(pos), null);
- }
- });
- }
- else
- {
- java.awt.EventQueue.invokeLater(new Runnable()
+ (alf == null ? Jalview.getCurrentAlignFrame() : alf)
+ .scrollToRow(Integer.valueOf(topRow).intValue());
+
+ } catch (Exception ex)
{
- @Override
- public void run()
- {
- StructureSelectionManager
- .getStructureSelectionManager(Desktop.getInstance())
- .mouseOverVamsasSequence(sq, pos, null);
- }
- });
+ System.err.println("Couldn't parse integer arguments (topRow='"
+ + topRow + "')");
+ ex.printStackTrace();
+ }
+
}
- }
+ });
+ }
+
+ @Override
+ public void select(String sequenceIds, String columns)
+ {
+ selectIn(Jalview.getCurrentAlignFrame(), sequenceIds, columns, null);
}
- public void selectIn(final AlignFrame alf, String sequenceIds,
- String columns, String sep)
+ @Override
+ public void select(String sequenceIds, String columns, String sep)
{
+ selectIn(null, sequenceIds, columns, sep);
+ }
+
+ // @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 = Jalview.getCurrentAlignFrame();
+ // }
+ // return appLoader.newViewFrom(alf, name);
+ // }
+
+ @Override
+ public void selectIn(AlignFrame alf, String sequenceIds, String columns)
+ {
+ selectIn(alf, sequenceIds, columns, null);
+ }
+
+ @Override
+ public void selectIn(AlignFrame af, String sequenceIds, String columns,
+ String sep)
+ {
+ AlignFrame alf = (af == null ? Jalview.getCurrentAlignFrame() : af);
+
if (sep == null || sep.length() == 0)
{
sep = separator;
}
}
// deparse fields
- String[] ids = JalviewAppLoader.separatorListToArray(sequenceIds, sep);
- String[] cols = JalviewAppLoader.separatorListToArray(columns, sep);
+ String[] ids = separatorListToArray(sequenceIds, sep);
+ String[] cols = 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());
+ alf.getViewport().getAlignment().getSequencesArray());
int start = 0, end = al.getWidth(), alw = al.getWidth();
boolean seqsfound = true;
if (ids != null && ids.length > 0)
@Override
public void run()
{
- alf.select(sel, csel, alf
- .getCurrentView().getAlignment().getHiddenColumns());
+ alf.select(sel, csel,
+ alf.getCurrentView().getAlignment().getHiddenColumns());
}
});
}
}
- public String getAlignmentOrderFrom(AlignFrame alf, String sep)
+ // public AlignFrame newViewFrom(AlignFrame alf, String name)
+ // {
+ // return (AlignFrame) alf.newView(name, true);
+ // }
+ //
+ @Override
+ public String[] separatorListToArray(String list)
{
- 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);
+ return separatorListToArray(list, separator);
}
- public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
- String format, String suffix)
+ @Override
+ public void setFeatureGroupState(String groups, boolean state)
+ { // JalviewLite API
+ setFeatureGroupStateOn(null, groups, state);
+ }
+
+ @Override
+ public void setFeatureGroupStateOn(final AlignFrame alf,
+ final String groups, boolean state)
{
- try
+
+ java.awt.EventQueue.invokeLater(new Runnable()
{
- AlignViewport vp = alf.getViewport();
- FileFormatI theFormat = FileFormats.getInstance().forName(format);
- boolean seqlimits = (suffix == null
- || suffix.equalsIgnoreCase("true"));
- if (vp.getSelectionGroup() != null)
+ @Override
+ public void run()
{
- // 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;
+ (alf == null ? Jalview.getCurrentAlignFrame() : alf)
+ .setFeatureGroupState(
+ separatorListToArray(groups, separator), state);
}
- } catch (IllegalArgumentException ex)
+ });
+ }
+
+ @Override
+ public void setSelectionListener(AlignFrame af, String listener)
+ {
+ Desktop.getStructureSelectionManager()
+ .addSelectionListener(new JsSelectionListener(af, listener));
+ }
+
+ @Override
+ public void setSelectionListener(String listener)
+ {
+ Desktop.getStructureSelectionManager()
+ .addSelectionListener(new JsSelectionListener(null, listener));
+ }
+
+ @Override
+ public void setSeparator(String separator)
+ {
+ this.separator = separator;
+ }
+
+ @Override
+ public void showOverview()
+ {
+ Jalview.getCurrentAlignFrame().overviewMenuItem_actionPerformed(null);
+ }
+
+ /**
+ * Allowing for a JavaScript function here.
+ */
+ public void callInitCallback()
+ {
+ Object initjscallback = getAppletParameter("oninit", false);
+ if (initjscallback != null)
{
- ex.printStackTrace();
- return "Error retrieving alignment, possibly invalid format specifier: "
- + format;
+ try
+ {
+ doSendCallback(initjscallback, new Object[0]);
+ } catch (Exception e)
+ {
+ System.err.println("Exception when executing _oninit callback '"
+ + initjscallback + "'.");
+ e.printStackTrace();
+ }
+ }
+ }
+
+ /**
+ * Pass the provided array prepended with Jalview.this
+ *
+ * Appropriated from org.jmol.appletjs.Jmol
+ *
+ * @param callback
+ * a window function or "alert"
+ * @param data
+ * @return String return from the callback method.
+ */
+ public String doSendCallback(Object callback, Object[] data)
+ {
+ Jalview me = Jalview.getInstance();
+
+ if (me != null && callback != null)
+ {
+ /**
+ * @j2sNative
+ *
+ * try{
+ *
+ * if (callback == "alert") { alert(data[0]); return ""; } var
+ * o; if (typeof callback == "function") { o = callback; } else
+ * { if (!callback)return; var tokens = callback.split("."); o
+ * = window[tokens[0]]; for (var i = 1; i < tokens.length; i++)
+ * o = o[tokens[i]]; } var a = [me]; for (var i = 0; i <
+ * data.length; i++) a.push(data[i] ? data[i].booleanValue &&
+ * (data[i] = data[i].booleanValue()) : data[i]); return
+ * o.apply(null,a) } catch (e) { System.out.println(callback +
+ * " failed " + e); }
+ */
}
return "";
}
- public String orderAlignmentBy(AlignFrame alf, String order,
- String undoName, String sep)
+ private DataSourceType resolveFileProtocol(String[] retPath)
{
- if (sep == null || sep.length() == 0)
+ String path = retPath[0];
+ /*
+ * is it paste data?
+ */
+ if (path.startsWith("PASTE"))
{
- sep = separator;
+ retPath[0] = path.substring(5);
+ return DataSourceType.PASTE;
}
- String[] ids = JalviewAppLoader.separatorListToArray(order, sep);
- SequenceI[] sqs = null;
- if (ids != null && ids.length > 0)
+
+ /*
+ * is it a URL?
+ */
+ if (path.indexOf("://") >= 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;
- }
+ return DataSourceType.URL;
}
- if (sqs == null)
+
+ /*
+ * 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 + "'");
+ // }
+ retPath[0] = withDocBase;
+ return DataSourceType.URL;
+ }
+
+ /*
+ * try relative to codebase (if different to document base)
+ */
+ URL codeBase = getCodeBase();
+ String withCodeBase = resolveUrlForLocalOrAbsolute(path, codeBase);
+ if (!withCodeBase.equals(withDocBase)
+ && HttpUtils.isValidUrl(withCodeBase))
{
- return "";
+ // if (debug)
+ // {
+ // System.err.println("Prepended codebase '" + codeBase
+ // + "' to make: '" + withCodeBase + "'");
+ // }
+ retPath[0] = withCodeBase;
+ return DataSourceType.URL;
}
- ;
- final AlignmentOrder aorder = new AlignmentOrder(sqs);
- if (undoName != null && undoName.trim().length() == 0)
+ /*
+ * try locating by classloader; try this last so files in the directory
+ * are resolved using document base
+ */
+ if (inArchive(getClass(), path))
{
- undoName = null;
+ return DataSourceType.CLASSLOADER;
}
- final String _undoName = undoName;
- // TODO: deal with synchronization here: cannot raise any events until after
- // this has returned.
- return alf.sortBy(aorder, _undoName) ? "true" : "";
+ return null;
}
- public String getAlignmentFrom(AlignFrame alf, String format,
- String suffix)
+ /**
+ * 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 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)
+ boolean rtn = (c.getResourceAsStream("/" + f) != null);
+ return rtn;
+ } catch (Exception ex)
{
- ex.printStackTrace();
- return "Error retrieving alignment, possibly invalid format specifier: "
- + format;
+ System.out.println("Exception checking resources: " + f + " " + ex);
+ return false;
}
}
- public void loadAnnotationFrom(AlignFrame alf, String annotation)
+ /**
+ * 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)
{
- if (new AnnotationFile().annotateAlignmentView(
- alf.getViewport(), annotation,
- DataSourceType.PASTE))
+ String resolvedPath = "";
+ if (targetPath.startsWith("/"))
{
- alf.alignPanel.fontChanged();
- alf.alignPanel.setScrollValues(0, 0);
+ String codebase = localref.toString();
+ String localfile = localref.getFile();
+ resolvedPath = codebase.substring(0,
+ codebase.length() - localfile.length()) + targetPath;
+ return resolvedPath;
}
- else
+
+ /*
+ * 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)
{
- alf.parseFeaturesFile(annotation,
- DataSourceType.PASTE);
+ directoryPath = directoryPath.substring(0, lastSeparator + 1);
}
- }
- public boolean loadFeaturesFrom(AlignFrame alf, String features,
- boolean autoenabledisplay)
- {
- boolean ret = alf.parseFeaturesFile(features,
- DataSourceType.PASTE);
- if (!ret)
+ if (targetPath.startsWith("/"))
{
- return false;
+ /*
+ * 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);
}
- if (autoenabledisplay)
+ else
{
- alf.getViewport().setShowSequenceFeatures(true);
- // this next was for a checkbox in JalviewLite
- // ((AlignFrame) alf).getViewport().sequenceFeatures.setState(true);
+ resolvedPath = directoryPath + targetPath;
}
- return true;
+ // if (debug)
+ // {
+ // System.err.println(
+ // "resolveUrlForLocalOrAbsolute returning " + resolvedPath);
+ // }
+ return resolvedPath;
}
/**
- * JavaScript interface to print the alignment frame
+ * parse the string into a list
*
- * @param alf
- * @param format
- * "jalview" or "gff" with or without ";includeComplement" or
- * ";includeNonpositional"; default with no ";" is
- * ";includeNonpositional"
- * @return
+ * @param list
+ * @param separator
+ * @return elements separated by separator
*/
- public String getFeaturesFrom(AlignFrame alf, String format)
+ public static String[] separatorListToArray(String list, String separator)
{
- 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"))
+ // TODO use StringUtils version (slightly different...)
+ int seplen = separator.length();
+ if (list == null || list.equals("") || list.equals(separator))
{
- features = formatter.printJalviewFormat(
- f.getViewport().getAlignment().getSequencesArray(),
- f.alignPanel.getFeatureRenderer(), nonpos, compl);
+ return null;
}
- else
+ Vector<String> jv = new Vector<>();
+ int cp = 0, pos;
+ while ((pos = list.indexOf(separator, cp)) > cp)
{
- features = formatter.printGffFormat(
- f.getViewport().getAlignment().getSequencesArray(),
- f.alignPanel.getFeatureRenderer(), nonpos, compl);
+ jv.addElement(list.substring(cp, pos));
+ cp = pos + seplen;
}
-
- if (features == null)
+ if (cp < list.length())
{
- features = "";
+ String c = list.substring(cp);
+ if (!c.equals(separator))
+ {
+ jv.addElement(c);
+ }
}
- return features;
-
+ 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();
+ return v;
+ }
+ return null;
}
- public String getAnnotationFrom(AlignFrame alf)
+ public class JsSelectionListener
+ implements jalview.structure.SelectionListener
{
- 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);
- }
+ AlignFrame _af;
- 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 _listener;
- }
+ public JsSelectionListener(AlignFrame af, String listener)
+ {
+ _af = af;
+ _listener = listener;
}
- 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)
+
+ @Override
+ public void selection(SequenceGroup seqsel, ColumnSelection colsel,
+ HiddenColumns hidden, SelectionSource source)
{
- seqs = new String[seqsel.getSize()];
- for (int i = 0; i < seqs.length; i++)
+ // System.err.println("Testing selection event relay to
+ // jsfunction:"+_listener);
+ String setid = "";
+ AlignFrame src = _af;
+ if (source != null)
{
- seqs[i] = seqsel.getSequenceAt(i).getName();
- }
- if (strt < seqsel.getStartRes())
- {
- strt = seqsel.getStartRes();
+ if (source instanceof AlignViewport
+ && Jalview.getCurrentAlignFrame().getViewport() == source)
+ {
+ src = Jalview.getCurrentAlignFrame();
+ if (src != _af)
+ return;
+ }
}
- if (end == -1 || end > seqsel.getEndRes())
+ 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)
{
- end = seqsel.getEndRes();
+ 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)
+ if (colsel != null && !colsel.isEmpty())
{
- end = colsel.getMax() + 1;
+ 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());
+ }
}
- cols = new String[colsel.getSelected().size()];
- for (int i = 0; i < cols.length; i++)
+ else
{
- cols[i] = "" + (1 + colsel.getSelected().get(i).intValue());
+ 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);
+ }
+ ;
+
}
+
+ Jalview jalview = Jalview.getInstance();
+ jalview.doSendCallback(_listener,
+ new Object[]
+ { src, setid, jalview.arrayToSeparatorList(seqs),
+ jalview.arrayToSeparatorList(cols) });
}
- else
+
+ public boolean isFor(AlignFrame af, String listener)
{
- 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 _af == af && _listener.contentEquals(listener);
}
- return new Object[] { src, setid, arrayToSeparatorList(seqs),
- arrayToSeparatorList(cols) };
+
+ }
+
+ @Override
+ public AlignViewportI getViewport()
+ {
+ return Jalview.getCurrentAlignFrame().getViewport();
}
-}
\ No newline at end of file
+}
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-package jalview.javascript;
+package jalview.appletgui.js;
import jalview.bin.JalviewLite;
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-package jalview.javascript;
+package jalview.appletgui.js;
import jalview.appletgui.AlignFrame;
* - separator separated list of PDB file URIs that this viewer is
* handling. These files must be in the same order they appear in
* Jmol (e.g. first one is frame 1, second is frame 2, etc).
- * @see jalview.javascript.MouseOverStructureListener
+ * @see jalview.appletgui.js.MouseOverStructureListener
*/
public abstract void setStructureListener(String listener,
String modelSet);
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-package jalview.javascript;
+package jalview.appletgui.js;
public interface JsCallBack
{
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-package jalview.javascript;
+package jalview.appletgui.js;
import jalview.appletgui.AlignFrame;
import jalview.bin.JalviewLite;
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-package jalview.javascript;
+package jalview.appletgui.js;
import jalview.appletgui.AlignFrame;
import jalview.bin.JalviewLite;
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-package jalview.javascript;
+package jalview.appletgui.js;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.appletgui.AlignFrame;
+import jalview.appletgui.js.JsCallBack;
import jalview.bin.JalviewLite;
import jalview.datamodel.SequenceI;
import jalview.ext.jmol.JmolCommands;
-package jalview.bin;
-import jalview.gui.Preferences;
+package jalview.bin;
import java.util.HashMap;
+import java.util.List;
import java.util.Map;
-import java.util.Vector;
+
+import jalview.gui.Preferences;
/**
* Collection of all known applet tags from JalviewLite
*
*/
@SuppressWarnings("serial")
-public class AppletParams extends HashMap<String, String>
+public class AppletParams extends HashMap<String, Object>
{
private final static String[] params = { "alignpdbfiles",
"userDefinedColour", "widthScale", "windowHeight", "windowWidth",
"wrap", };
- public AppletParams(Map<String, String> info)
- {
- for (int i = params.length; --i >= 0;)
- {
- put(params[i], info.get(params[i]));
- }
- }
-
public String getParam(String param, String def)
{
- String val = get(param);
- return (val != null ? val : def);
+ Object val = get(param);
+ return (val != null ? val.toString() : def);
}
// <applet
public AppletParams()
{
- // TODO Auto-generated constructor stub
+ }
+
+ public static AppletParams getAppletParams(Map<String, Object> map,
+ List<String> vargs)
+ {
+ AppletParams appletParams = new AppletParams();
+ String resourcePath = getString(map, "resourcePath");
+ if (resourcePath == null)
+ resourcePath = "";
+ if (resourcePath.length() > 0 && !resourcePath.endsWith("/"))
+ {
+ resourcePath += "/";
+ }
+ for (int i = params.length; --i >= 0;)
+ {
+ String prefName = params[i];
+ Object value = map.get(prefName);
+ if (value != null)
+ addParam(vargs, prefName, value, appletParams, resourcePath);
+ }
+ return appletParams;
+ }
+
+ private static String getString(Map<String, Object> map, String key)
+ {
+ Object o = map.get(key);
+ return (o == null ? null : o.toString());
}
public static AppletParams getAppletParams(String[] args,
- Vector<String> vargs)
+ List<String> vargs)
{
AppletParams appletParams = new AppletParams();
- String resourcePath = null;
+ String resourcePath = "";
for (int i = args.length; --i > 0;) // > 0 is correct, not >=0
{
if (args[i].startsWith("name=\"Info.resourcePath\""))
if (arg.startsWith("name="))
{
String prefName = getAttr(arg, "name");
- String appletName = prefName.toLowerCase();
- String argName = prefName;
String value = getAttr(arg, "value");
+ addParam(vargs, prefName, value, appletParams, resourcePath);
+ }
+ }
+ return appletParams;
+ }
- // note that Application arguments ARE case-sensitive, but
- // Applet.getParameter() is not.
+ private static void addParam(List<String> vargs, String prefName,
+ Object value, AppletParams appletParams, String resourcePath)
+ {
- switch (appletName)
- {
+ // note that Application arguments ARE case-sensitive, but
+ // Applet.getParameter() is not.
- case "file":
- argName = "open";
- appletName = null;
- value = resourcePath + value;
- break;
- case "file2":
- argName = "open2";
- prefName = null;
- value = resourcePath + value;
- break;
- case "features":
- case "jnetfile":
- case "jpredfile":
- case "pdbfile":
- case "scorefile":
- case "sequence":
- // setting argName to null indicates that we want
- // JalviewAppLoader to take care of this.
- prefName = argName = null;
- value = resourcePath + value;
- break;
- case "tree":
- case "treefile":
- // setting appletName to null indicates that we want
- // Jalview.doMain to taken care of this as Jalview args
- argName = "tree";
- appletName = null;
- value = resourcePath + value;
- break;
+ String appletName = prefName.toLowerCase();
+ String argName = prefName;
+ switch (appletName)
+ {
- // non-loading preferences
+ case "file":
+ argName = "open";
+ appletName = null;
+ value = resourcePath + value;
+ break;
+ case "file2":
+ argName = "open2";
+ prefName = null;
+ value = resourcePath + value;
+ break;
+ case "features":
+ case "jnetfile":
+ case "jpredfile":
+ case "pdbfile":
+ case "scorefile":
+ case "sequence":
+ // setting argName to null indicates that we want
+ // JalviewAppLoader to take care of this.
+ prefName = argName = null;
+ value = resourcePath + value;
+ break;
+ case "tree":
+ case "treefile":
+ // setting appletName to null indicates that we want
+ // Jalview.doMain to taken care of this as Jalview args
+ argName = "tree";
+ appletName = null;
+ value = resourcePath + value;
+ break;
- case "defaultcolour":
- prefName = Preferences.DEFAULT_COLOUR;
- break;
- case "defaultcolournuc":
- prefName = Preferences.DEFAULT_COLOUR_NUC;
- break;
- case "defaultcolourprot":
- prefName = Preferences.DEFAULT_COLOUR_PROT;
- break;
- case "annotationcolour_max":
- prefName = Preferences.ANNOTATIONCOLOUR_MAX;
- break;
- case "annotationcolour_min":
- prefName = Preferences.ANNOTATIONCOLOUR_MIN;
- break;
- case "enablesplitframe":
- prefName = Preferences.ENABLE_SPLIT_FRAME;
- break;
- case "centrecolumnlabels":
- prefName = Preferences.CENTRE_COLUMN_LABELS;
- break;
- case "sortby":
- prefName = Preferences.SORT_ALIGNMENT; // id, etc.
- break;
- case "normalisesequencelogo":
- prefName = Preferences.NORMALISE_CONSENSUS_LOGO;
- break;
- case "relaxedidmatch":
- prefName = Preferences.RELAXEDSEQIDMATCHING;
- break;
- case "scaleproteinascdna":
- prefName = Preferences.SCALE_PROTEIN_TO_CDNA;
- break;
- case "userdefinedcolour":
- argName = "colour";
- prefName = Preferences.USER_DEFINED_COLOURS;
- break;
- case "wrap":
- prefName = Preferences.WRAP_ALIGNMENT;
- break;
+ // non-loading preferences
- // implemented; not tested:
+ case "defaultcolour":
+ prefName = Preferences.DEFAULT_COLOUR;
+ break;
+ case "defaultcolournuc":
+ prefName = Preferences.DEFAULT_COLOUR_NUC;
+ break;
+ case "defaultcolourprot":
+ prefName = Preferences.DEFAULT_COLOUR_PROT;
+ break;
+ case "annotationcolour_max":
+ prefName = Preferences.ANNOTATIONCOLOUR_MAX;
+ break;
+ case "annotationcolour_min":
+ prefName = Preferences.ANNOTATIONCOLOUR_MIN;
+ break;
+ case "enablesplitframe":
+ prefName = Preferences.ENABLE_SPLIT_FRAME;
+ break;
+ case "centrecolumnlabels":
+ prefName = Preferences.CENTRE_COLUMN_LABELS;
+ break;
+ case "sortby":
+ prefName = Preferences.SORT_ALIGNMENT; // id, etc.
+ break;
+ case "normalisesequencelogo":
+ prefName = Preferences.NORMALISE_CONSENSUS_LOGO;
+ break;
+ case "relaxedidmatch":
+ prefName = Preferences.RELAXEDSEQIDMATCHING;
+ break;
+ case "scaleproteinascdna":
+ prefName = Preferences.SCALE_PROTEIN_TO_CDNA;
+ break;
+ case "userdefinedcolour":
+ argName = "colour";
+ prefName = Preferences.USER_DEFINED_COLOURS;
+ break;
+ case "wrap":
+ prefName = Preferences.WRAP_ALIGNMENT;
+ break;
- case "oninit":
- prefName = null;
- break;
- case "annotations":
- value = resourcePath + value;
- argName = null;
- break;
- case "hidefeaturegroups":
- // TODO
- break;
- case "pdbseq":
- argName = prefName = null;
- break;
- case "sortbytree":
- prefName = Preferences.SORT_BY_TREE;
- value = checkTF(value);
- appletName = null; // taken care of by Jalview
- break;
- case "format":
- break;
- case "alignpdbfiles":
- argName = prefName = null;
- break;
- case "separator":
- break;
+ // implemented; not tested:
- // TODO: probably not relevant?
+ case "oninit":
+ prefName = null;
+ break;
+ case "annotations":
+ value = resourcePath + value;
+ argName = null;
+ break;
+ case "hidefeaturegroups":
+ // TODO
+ break;
+ case "pdbseq":
+ argName = prefName = null;
+ break;
+ case "sortbytree":
+ prefName = Preferences.SORT_BY_TREE;
+ value = checkTF(value);
+ appletName = null; // taken care of by Jalview
+ break;
+ case "format":
+ break;
+ case "alignpdbfiles":
+ argName = prefName = null;
+ break;
+ case "separator":
+ break;
- case "rgb":
- prefName = null; // TODO no background for application?
- break;
- case "externalstructureviewer":
- break;
- case "application_url":
- break;
- case "automaticscrolling":
- break;
- case "heightscale":
- break;
- case "jalviewhelpurl":
- break;
- case "label":
- break;
- case "linklabel_":
- prefName = "linkLabel_";
- break;
- case "linklabel_1":
- prefName = "linkLabel_1";
- break;
- case "linkurl_":
- prefName = "linkURL_";
- break;
+ // TODO: probably not relevant?
- // unknown:
+ case "rgb":
+ prefName = null; // TODO no background for application?
+ break;
+ case "externalstructureviewer":
+ break;
+ case "application_url":
+ break;
+ case "automaticscrolling":
+ break;
+ case "heightscale":
+ break;
+ case "jalviewhelpurl":
+ break;
+ case "label":
+ break;
+ case "linklabel_":
+ prefName = "linkLabel_";
+ break;
+ case "linklabel_1":
+ prefName = "linkLabel_1";
+ break;
+ case "linkurl_":
+ prefName = "linkURL_";
+ break;
- case "nojmol":
- case "normaliselogo":
- case "resolvetocodebase":
- case "uppercase":
- case "widthscale":
- case "windowheight":
- case "windowwidth":
- argName = prefName = null;
- break;
+ // unknown:
- // TRUE/FALSE
+ case "nojmol":
+ case "normaliselogo":
+ case "resolvetocodebase":
+ case "uppercase":
+ case "widthscale":
+ case "windowheight":
+ case "windowwidth":
+ argName = prefName = null;
+ break;
- case "debug":
- value = checkTF(value);
- break;
- case "embedded":
- value = checkTF(value);
- break;
- case "showbutton":
- value = checkTF(value);
- break;
- case "showannotation":
- prefName = Preferences.SHOW_ANNOTATIONS;
- value = checkTF(value);
- break;
- case "showconsensus":
- prefName = Preferences.SHOW_CONSENSUS_LOGO;
- value = checkTF(value);
- break;
- case "showconsensushistogram":
- prefName = Preferences.SHOW_CONSENSUS_HISTOGRAM;
- value = checkTF(value);
- break;
- case "showconservation":
- prefName = Preferences.SHOW_CONSERVATION;
- value = checkTF(value);
- break;
- case "showgroupconsensus":
- prefName = Preferences.SHOW_GROUP_CONSENSUS;
- value = checkTF(value);
- break;
- case "showgroupconservation":
- prefName = Preferences.SHOW_GROUP_CONSERVATION;
- value = checkTF(value);
- break;
- case "showoccupancy":
- prefName = Preferences.SHOW_OCCUPANCY;
- value = checkTF(value);
- break;
- case "showquality":
- prefName = Preferences.SHOW_QUALITY;
- value = checkTF(value);
- break;
- case "showsequencelogo":
- prefName = Preferences.SHOW_CONSENSUS_LOGO;
- value = checkTF(value);
- break;
- case "showfeaturegroups":
- value = checkTF(value);
- break;
- case "showfeaturesettings":
- value = checkTF(value);
- break;
- case "showfullid":
- value = checkTF(value);
- break;
- case "showtreebootstraps":
- value = checkTF(value);
- break;
- case "showtreedistances":
- value = checkTF(value);
- break;
- case "showunconserved":
- prefName = Preferences.SHOW_UNCONSERVED;
- value = checkTF(value);
- break;
- case "showunlinkedtreenodes":
- value = checkTF(value);
- break;
- default:
- if (appletName.startsWith("pdbfile")
- || appletName.startsWith("sequence") && Character.isDigit(
- appletName.charAt(appletName.length() - 1)))
- {
- // could be pdbFile2, for example
- prefName = argName = null;
- value = resourcePath + value;
- break;
- }
- // or one of the app preference names
- break;
- }
- // put name and value into application args
- if (value != null && argName != null)
- {
- vargs.add(argName);
- if (value != "true")
- {
- vargs.add(value);
- }
- }
- if (value == null)
- {
- value = "false";
- }
- System.out.println("AppletParams propName=" + prefName + " argName="
- + argName + " appletName="
- + appletName + " value=" + value);
- if (appletName != null)
- {
- appletParams.put(appletName, value);
- }
- if (prefName != null)
- {
- Cache.setPropertyNoSave(prefName, value);
- }
+ // TRUE/FALSE
+
+ case "debug":
+ value = checkTF(value);
+ break;
+ case "embedded":
+ value = checkTF(value);
+ break;
+ case "showbutton":
+ value = checkTF(value);
+ break;
+ case "showannotation":
+ prefName = Preferences.SHOW_ANNOTATIONS;
+ value = checkTF(value);
+ break;
+ case "showconsensus":
+ prefName = Preferences.SHOW_CONSENSUS_LOGO;
+ value = checkTF(value);
+ break;
+ case "showconsensushistogram":
+ prefName = Preferences.SHOW_CONSENSUS_HISTOGRAM;
+ value = checkTF(value);
+ break;
+ case "showconservation":
+ prefName = Preferences.SHOW_CONSERVATION;
+ value = checkTF(value);
+ break;
+ case "showgroupconsensus":
+ prefName = Preferences.SHOW_GROUP_CONSENSUS;
+ value = checkTF(value);
+ break;
+ case "showgroupconservation":
+ prefName = Preferences.SHOW_GROUP_CONSERVATION;
+ value = checkTF(value);
+ break;
+ case "showoccupancy":
+ prefName = Preferences.SHOW_OCCUPANCY;
+ value = checkTF(value);
+ break;
+ case "showquality":
+ prefName = Preferences.SHOW_QUALITY;
+ value = checkTF(value);
+ break;
+ case "showsequencelogo":
+ prefName = Preferences.SHOW_CONSENSUS_LOGO;
+ value = checkTF(value);
+ break;
+ case "showfeaturegroups":
+ value = checkTF(value);
+ break;
+ case "showfeaturesettings":
+ value = checkTF(value);
+ break;
+ case "showfullid":
+ value = checkTF(value);
+ break;
+ case "showtreebootstraps":
+ value = checkTF(value);
+ break;
+ case "showtreedistances":
+ value = checkTF(value);
+ break;
+ case "showunconserved":
+ prefName = Preferences.SHOW_UNCONSERVED;
+ value = checkTF(value);
+ break;
+ case "showunlinkedtreenodes":
+ value = checkTF(value);
+ break;
+ default:
+ if (appletName.startsWith("pdbfile")
+ || appletName.startsWith("sequence") && Character
+ .isDigit(appletName.charAt(appletName.length() - 1)))
+ {
+ // could be pdbFile2, for example
+ prefName = argName = null;
+ value = resourcePath + value;
+ break;
}
+ // or one of the app preference names
+ break;
+ }
+
+ // put name and value into application args
+ if (value != null && argName != null)
+ {
+ vargs.add(argName);
+ if (value != "true")
+ {
+ vargs.add(value.toString());
+ }
+ }
+ if (value == null)
+ {
+ value = "false";
+ }
+ System.out.println("AppletParams propName=" + prefName + " argName="
+ + argName + " appletName=" + appletName + " value=" + value);
+ if (appletName != null)
+ {
+ appletParams.put(appletName, value);
+ }
+ if (prefName != null)
+ {
+ Cache.setPropertyNoSave(prefName, value.toString());
}
- return appletParams;
}
/**
* @param value
* @return "true" or null
*/
- private static String checkTF(String value)
+ private static String checkTF(Object value)
{
- return (value.toLowerCase() == "true" ? "true" : null);
+ return (("" + value).toLowerCase() == "true" ? "true" : null);
}
/**
*/
package jalview.bin;
+import jalview.util.Platform;
+
import java.net.URLDecoder;
-import java.util.Vector;
+import java.util.ArrayList;
+import java.util.List;
/**
* Notes: this argParser does not distinguish between parameter switches,
public static final String VSESS = "vsess";
- private Vector<String> vargs = null;
+ private List<String> vargs = null;
private boolean isApplet;
public ArgsParser(String[] args)
{
- vargs = new Vector<>();
+ vargs = new ArrayList<>();
isApplet = (args.length > 0 && args[0].startsWith("<applet"));
if (isApplet)
{
appletParams = AppletParams.getAppletParams(args, vargs);
}
+ else if (Platform.isJS() && args.length == 0)
+ {
+ isApplet = true;
+ appletParams = AppletParams
+ .getAppletParams(Platform.getAppletInfoAsMap(), vargs);
+ }
else
{
for (int i = 0; i < args.length; i++)
{
arg = arg.substring(1);
}
- vargs.addElement(arg);
+ vargs.add(arg);
}
}
}
String dc = null, ret = null;
if (index != -1)
{
- ret = vargs.elementAt(index + 1).toString();
- vargs.removeElementAt(index);
- vargs.removeElementAt(index);
+ ret = vargs.get(index + 1).toString();
+ vargs.remove(index);
+ vargs.remove(index);
if (utf8decode && ret != null)
{
try
{
if (vargs.contains(arg))
{
- vargs.removeElement(arg);
+ vargs.remove(arg);
return true;
}
else
return vargs.size();
}
- public String getAppletValue(String key, String def)
+ public Object getAppletValue(String key, String def, boolean asString)
{
- String value;
+ Object value;
return (appletParams == null ? null
- : (value = appletParams.get(key.toLowerCase())) != null ? value
- : def);
+ : (value = appletParams.get(key.toLowerCase())) == null
+ ? def : asString ? value.toString()
+ : value);
}
}
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 groovy.lang.Binding;
import groovy.util.GroovyScriptEngine;
import jalview.api.AlignCalcWorkerI;
-import jalview.api.AlignViewportI;
-import jalview.api.JalviewApp;
-import jalview.api.StructureSelectionManagerProvider;
+import jalview.api.JalviewJSApp;
import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
-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.AlignViewport;
-import jalview.gui.AlignmentPanel;
-import jalview.gui.CalculationChooser;
import jalview.gui.Desktop;
import jalview.gui.Preferences;
import jalview.gui.PromptUserConfig;
-import jalview.gui.StructureViewer;
import jalview.io.AppletFormatAdapter;
import jalview.io.BioJsHTMLOutput;
import jalview.io.DataSourceType;
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 netscape.javascript.JSObject;
/**
* Main class for Jalview Application <br>
* @author $author$
* @version $Revision$
*/
-public class Jalview implements ApplicationSingletonI, JalviewJSApi
+public class Jalview implements ApplicationSingletonI
{
// for testing those nasty messages you cannot ever find.
private Desktop desktop;
- public static AlignFrame currentAlignFrame;
-
- public boolean isJavaAppletTag;
+ public AlignFrame currentAlignFrame;
public String appletResourcePath;
- JalviewAppLoader appLoader;
-
- protected JSFunctionExec jsFunctionExec;
-
+ JalviewJSApp app; // JalviewJS-specific JavaScript interface
+
private boolean noCalculation, noMenuBar, noStatus;
private boolean noAnnotation;
{
boolean isJS = Platform.isJS();
- if (isJS)
- {
- Platform.setAppClass(this);
- }
- else
+ if (!isJS)
{
System.setSecurityManager(null);
}
if (isJS)
{
- isJavaAppletTag = aparser.isApplet();
- if (isJavaAppletTag)
- {
+ app = new JalviewJSApp(aparser);
Preferences.setAppletDefaults();
Cache.loadProperties(usrPropsFile); // again, because we
// might be changing defaults here?
- }
- System.out.println(
- "<Applet> found: " + aparser.getValue("Info.j2sAppletID"));
- appletResourcePath = aparser.getValue("Info.resourcePath");
+ appletResourcePath = (String) aparser.getAppletValue("resourcepath", null, true);
}
else
/**
}
parseArguments(aparser, true);
- }
-
- /**
- * Allow an outside entity to initiate the second half of argument parsing
- * (only).
- *
- * @param args
- * @return null is good
- */
- @Override
- public Object parseArguments(String[] args)
- {
-
- try
- {
- parseArguments(new ArgsParser(args), false);
- return null;
- } catch (Throwable t)
- {
- return t;
- }
+
}
/**
* @param aparser
* @param isStartup
*/
- private void parseArguments(ArgsParser aparser, boolean isStartup)
+ public void parseArguments(ArgsParser aparser, boolean isStartup)
{
String groovyscript = null; // script to execute after all loading is
}
}
}
- String fileFormat = (isJavaAppletTag
- ? aparser.getAppletValue("format", null)
+ String fileFormat = (isJS ? (String) aparser.getAppletValue("format", null, true)
: null);
protocol = AppletFormatAdapter.checkProtocol(file);
try
{
- format = (isJavaAppletTag && fileFormat != null
+ format = (fileFormat != null
? FileFormats.getInstance().forName(fileFormat)
: null);
if (format == null)
{
format = new IdentifyFile().identify(file, protocol);
}
- format = new IdentifyFile().identify(file, protocol);
} catch (FileFormatException e1)
{
// TODO ?
{
try
{
- System.out.println(
- "CMD [-tree " + data + "] executed successfully!");
NewickFile nf = new NewickFile(data,
AppletFormatAdapter.checkProtocol(data));
af.getViewport()
.setCurrentTree(af.showNewickTree(nf, data).getTree());
+ System.out.println(
+ "CMD [-tree " + data + "] executed successfully!");
} catch (IOException ex)
{
System.err.println("Couldn't add tree " + data);
// TODO - load PDB structure(s) to alignment JAL-629
// (associate with identical sequence in alignment, or a specified
// sequence)
- if (isJavaAppletTag)
+
+ if (isJS)
{
- loadAppletParams(aparser, af);
+ app.load(af);
}
- else if (!isJS)
+ else
/**
* Java only
*
+ "] executed successfully!");
groovyscript = null;
}
- }
- createOutputFiles(aparser, af, format);
- while (aparser.getSize() > 0)
- {
- System.out.println("Unknown arg: " + aparser.nextValue());
+ createOutputFiles(aparser, af, format);
}
}
}
}
desktop.setInBatchMode(false);
}
+
+ if (isJS && isStartup)
+ {
+ app.callInitCallback();
+ }
}
+
/**
* Writes an output file for each format (if any) specified in the
private void createOutputFiles(ArgsParser aparser, AlignFrame af,
FileFormatI format)
{
- String imageName = "unnamed.png";
- while (aparser.getSize() > 1)
+ while (aparser.getSize() >= 2)
{
String outputFormat = aparser.nextValue();
- String file = aparser.nextValue();
-
- if (outputFormat.equalsIgnoreCase("png"))
+ File imageFile;
+ String fname;
+ switch (outputFormat.toLowerCase())
{
- af.createPNG(new File(file));
- imageName = (new File(file)).getName();
- System.out.println("Creating PNG image: " + file);
+ case "png":
+ imageFile = new File(aparser.nextValue());
+ af.createPNG(imageFile);
+ System.out.println(
+ "Creating PNG image: " + imageFile.getAbsolutePath());
continue;
- }
- else if (outputFormat.equalsIgnoreCase("svg"))
- {
- File imageFile = new File(file);
- imageName = imageFile.getName();
+ case "svg":
+ imageFile = new File(aparser.nextValue());
af.createSVG(imageFile);
- System.out.println("Creating SVG image: " + file);
+ System.out.println(
+ "Creating SVG image: " + imageFile.getAbsolutePath());
continue;
- }
- else if (outputFormat.equalsIgnoreCase("html"))
- {
- File imageFile = new File(file);
- imageName = imageFile.getName();
- HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
- htmlSVG.exportHTML(file);
- System.out.println("Creating HTML image: " + file);
+ case "eps":
+ imageFile = new File(aparser.nextValue());
+ System.out.println(
+ "Creating EPS file: " + imageFile.getAbsolutePath());
+ af.createEPS(imageFile);
continue;
- }
- else if (outputFormat.equalsIgnoreCase("biojsmsa"))
- {
- if (file == null)
- {
- System.err.println("The output html file must not be null");
- return;
- }
+ case "biojsmsa":
+ fname = new File(aparser.nextValue()).getAbsolutePath();
try
{
BioJsHTMLOutput.refreshVersionInfo(
e.printStackTrace();
}
BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
- bjs.exportHTML(file);
- System.out.println("Creating BioJS MSA Viwer HTML file: " + file);
+ bjs.exportHTML(fname);
+ System.out.println("Creating BioJS MSA Viwer HTML file: " + fname);
continue;
- }
- else if (outputFormat.equalsIgnoreCase("imgMap"))
- {
- af.createImageMap(new File(file), imageName);
- System.out.println("Creating image map: " + file);
+ case "html":
+ fname = new File(aparser.nextValue()).getAbsolutePath();
+ HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
+ htmlSVG.exportHTML(fname);
+ System.out.println("Creating HTML image: " + fname);
continue;
- }
- else if (outputFormat.equalsIgnoreCase("eps"))
- {
- File outputFile = new File(file);
+ case "imgmap":
+ imageFile = new File(aparser.nextValue());
+ af.alignPanel.makePNGImageMap(imageFile, "unnamed.png");
System.out.println(
- "Creating EPS file: " + outputFile.getAbsolutePath());
- af.createEPS(outputFile);
+ "Creating image map: " + imageFile.getAbsolutePath());
continue;
}
-
- af.saveAlignment(file, format);
- if (af.isSaveAlignmentSuccessful())
+ if (!Platform.isJS())
{
- System.out.println(
- "Written alignment in " + format + " format to " + file);
+ // skipping outputFormat?
+ System.out.println("Unknown arg: " + outputFormat);
+ fname = new File(aparser.nextValue()).getAbsolutePath();
+ af.saveAlignment(fname, format);
+ if (af.isSaveAlignmentSuccessful())
+ {
+ System.out.println(
+ "Written alignment in " + format + " format to " + fname);
+ }
+ else
+ {
+ System.out.println("Error writing file " + fname + " in " + format
+ + " format!!");
+ }
}
- else
+ while (aparser.getSize() > 0)
{
- System.out.println("Error writing file " + file + " in " + format
- + " format!!");
+ System.out.println("Unknown arg: " + aparser.nextValue());
}
-
+ break;
}
}
public static AlignFrame getCurrentAlignFrame()
{
- return Jalview.currentAlignFrame;
+ return Jalview.getInstance().currentAlignFrame;
}
public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
{
- Jalview.currentAlignFrame = currentAlignFrame;
+ Jalview.getInstance().currentAlignFrame = currentAlignFrame;
}
+
/**
* Get the SwingJS applet ID and combine that with the frameType
*
*/
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<String, Hashtable<String, String[]>> jsmessages;
-
- private Hashtable<String, int[]> 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<Runnable> jsExecQueue;
-
- @Override
- public Vector<Runnable> getJsExecQueue(JSFunctionExec exec)
- {
- jsFunctionExec = exec;
- return (jsExecQueue == null ? (jsExecQueue = new Vector<>())
- : jsExecQueue);
- }
-
- // AppletContext deprecated
- //
- // @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<String, int[]> getJSHashes()
- {
- return (jshashes == null ? (jshashes = new Hashtable<>())
- : jshashes);
- }
-
- @Override
- public Hashtable<String, Hashtable<String, String[]>> 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());
+ return (Platform.isJS() ? getInstance().app.getAppID(frameType) : null);
}
- /**
- *
- * @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 String doSendCallback(Object callback, Object[] data) {
+ return (Platform.isJS() ? app.doSendCallback(callback, data) : null);
}
public void notifyWorker(AlignCalcWorkerI worker, String status)
// + " " + status);
}
+ public Object arrayToSeparatorList(String[] seqs)
+ {
+ return (Platform.isJS() ? app.arrayToSeparatorList(seqs) : null);
+ }
+
+
}
static {
/**
- * @j2sNative
+ * @ could do it this way:
*
- * J2S.thisApplet.__Info.args =
- * ["open","examples/uniref50.fa","features",
- * "examples/exampleFeatures.txt"];
+ * j2sNative
+ *
+ * J2S.thisApplet.__Info.args = [ "open","examples/uniref50.fa",
+ * "features","examples/exampleFeatures.txt", "noannotation" ];
*/
}
public static void main(String[] args) throws Exception
{
+ if (args.length == 0)
+ {
+ args = new String[] {
+ // "headless",
+ "open", "examples/uniref50.fa",
+ "features",
+ "examples/exampleFeatures.txt"
+ , "noannotation"
+ //, "showoverview"
+ //, "png", "test-bh.png"
+ };
+ }
+
+ // String cmds = "nodisplay -open examples/uniref50.fa -sortbytree -props
+ // test/jalview/io/testProps.jvprops -colour zappo "
+ // + "-jabaws http://www.compbio.dundee.ac.uk/jabaws -nosortbytree "
+ // + "-features examples/testdata/plantfdx.features -annotations
+ // examples/testdata/plantfdx.annotations -tree
+ // examples/testdata/uniref50_test_tree";
+ // args = cmds.split(" ");
Jalview.main(args);
//showFocusTimer();
}
package jalview.bin;
+import java.io.IOException;
+import java.net.URL;
+import java.util.Hashtable;
+
+import jalview.api.AlignViewportI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
+import jalview.io.DataSourceType;
+import jalview.io.NewickFile;
+import jalview.structure.SelectionSource;
+import jalview.structure.VamsasSource;
/**
* JAL-3369 JalviewJS API BH 2019.07.17
public interface JalviewJSApi
{
- void showOverview();
+ // debug flag - controls output to standard out
+ public static boolean debug = false;
/**
- * process commandline arguments after the JavaScript application has started
+ * bind a pdb file to a sequence in the given AlignFrame.
*
- * @param args
- * @return
+ * @param alFrame
+ * - null or specific AlignFrame. This specifies the dataset that
+ * will be searched for a seuqence called sequenceId
+ * @param sequenceId
+ * - sequenceId within the dataset.
+ * @param pdbEntryString
+ * - the short name for the PDB file
+ * @param pdbFile
+ * - pdb file - either a URL or a valid PDB file.
+ * @return true if binding was as success TODO: consider making an exception
+ * structure for indicating when PDB parsing or sequenceId location
+ * fails.
*/
- Object parseArguments(String[] args);
-
-
- /**
- * Open a new Tree panel on the desktop statically. Params are standard (not
- * set by Groovy). No dialog is opened.
- *
- * @param af
- * may be null
- * @param treeType
- * @param modelName
- * @return null, or the string "label.you_need_at_least_n_sequences" if number
- * of sequences selected is inappropriate
- */
- public Object openTreePanel(AlignFrame af, String treeType,
- String modelName);
+ public abstract boolean addPdbFile(AlignFrame alFrame, String sequenceId,
+ String pdbEntryString, String pdbFile);
- /**
- * public static method for JalviewJS API to open a PCAPanel without
- * necessarily using a dialog.
- *
- * @param af
- * may be null
- * @param modelName
- * @return the PCAPanel, or the string "label.you_need_at_least_n_sequences"
- * if number of sequences selected is inappropriate
- */
- public Object openPcaPanel(AlignFrame af, String modelName);
+ public String arrayToSeparatorList(String[] array);
/**
* The following public methods may be called externally, eg via javascript in
// public interface JalviewLiteJsApi
// {
- /**
- * @return String list of selected sequence IDs, each terminated by the
- * 'boolean not' character (""+0x00AC); or (¬);
- */
-
- public abstract String getSelectedSequences();
-
- /**
- * @param sep
- * separator string or null for default
- * @return String list of selected sequence IDs, each terminated by given
- * separator string
- */
-
- public abstract String getSelectedSequences(String sep);
-
- /**
- * @param alf
- * AlignFrame containing selection
- * @return String list of selected sequence IDs, each terminated by current
- * default separator sequence
- *
- */
- public abstract String getSelectedSequencesFrom(AlignFrame alf);
-
- /**
- * get list of selected sequence IDs separated by given separator
- *
- * @param alf
- * window containing selection
- * @param sep
- * separator string to use - default is 'boolean not'
- * @return String list of selected sequence IDs, each terminated by the given
- * separator
- */
- public abstract String getSelectedSequencesFrom(AlignFrame alf,
- String sep);
-
- /**
- *
- * @param sequenceId
- * id of sequence to highlight
- * @param position
- * integer position [ tobe implemented or range ] on sequence
- * @param alignedPosition
- * true/false/empty string - indicate if position is an alignment
- * column or unaligned sequence position
- */
-
- public abstract void highlight(String sequenceId, String position,
- String alignedPosition);
-
- /**
- *
- * @param sequenceId
- * id of sequence to highlight
- * @param position
- * integer position [ tobe implemented or range ] on sequence
- * @param alignedPosition
- * false, blank or something else - indicate if position is an
- * alignment column or unaligned sequence position
- */
- public abstract void highlightIn(AlignFrame alf, String sequenceId,
- String position, String alignedPosition);
-
- /**
- * select regions of the currrent alignment frame
- *
- * @param sequenceIds
- * String separated list of sequence ids or empty string
- * @param columns
- * String separated list { column range or column, ..} or empty
- * string
- */
-
- public abstract void select(String sequenceIds, String columns);
-
- /**
- * select regions of the currrent alignment frame
- *
- * @param toselect
- * String separated list { column range, seq1...seqn sequence ids }
- * @param sep
- * separator between toselect fields
- */
-
- public abstract void select(String sequenceIds, String columns,
- String sep);
-
- /**
- * select regions of the given alignment frame
- *
- * @param alf
- * @param toselect
- * String separated list { column range, seq1...seqn sequence ids }
- * @param sep
- * separator between toselect fields
- */
- public abstract void selectIn(AlignFrame alf, String sequenceIds,
- String columns);
-
- /**
- * select regions of the given alignment frame
- *
- * @param alf
- * @param toselect
- * String separated list { column range, seq1...seqn sequence ids }
- * @param sep
- * separator between toselect fields
- */
- public abstract void selectIn(AlignFrame alf, String sequenceIds,
- String columns, String sep);
-
- /**
- * get sequences selected in current AlignFrame and return their alignment in
- * format 'format' either with or without suffix
- *
- * @param alf
- * - where selection is
- * @param format
- * - format of alignment file
- * @param suffix
- * - "true" to append /start-end string to each sequence ID
- * @return selected sequences as flat file or empty string if there was no
- * current selection
- */
-
- public abstract String getSelectedSequencesAsAlignment(String format,
- String suffix);
-
- /**
- * get sequences selected in alf and return their alignment in format 'format'
- * either with or without suffix
- *
- * @param alf
- * - where selection is
- * @param format
- * - format of alignment file
- * @param suffix
- * - "true" to append /start-end string to each sequence ID
- * @return selected sequences as flat file or empty string if there was no
- * current selection
- */
- public abstract String getSelectedSequencesAsAlignmentFrom(
- AlignFrame alf,
- String format, String suffix);
-
- /**
- * get a separator separated list of sequence IDs reflecting the order of the
- * current alignment
- *
- * @return
- */
-
- public abstract String getAlignmentOrder();
-
- /**
- * get a separator separated list of sequence IDs reflecting the order of the
- * alignment in alf
- *
- * @param alf
- * @return
- */
- public abstract String getAlignmentOrderFrom(AlignFrame alf);
-
- /**
- * get a sep separated list of sequence IDs reflecting the order of the
- * alignment in alf
- *
- * @param alf
- * @param sep
- * - separator to use
- * @return
- */
- public abstract String getAlignmentOrderFrom(AlignFrame alf,
- String sep);
-
- /**
- * re-order the current alignment using the given list of sequence IDs
- *
- * @param order
- * - sep separated list
- * @param undoName
- * - string to use when referring to ordering action in undo buffer
- * @return 'true' if alignment was actually reordered. empty string if
- * alignment did not contain sequences.
- */
-
- public abstract String orderBy(String order, String undoName);
-
- /**
- * re-order the current alignment using the given list of sequence IDs
- * separated by sep
- *
- * @param order
- * - sep separated list
- * @param undoName
- * - string to use when referring to ordering action in undo buffer
- * @param sep
- * @return 'true' if alignment was actually reordered. empty string if
- * alignment did not contain sequences.
- */
-
- public abstract String orderBy(String order, String undoName,
- String sep);
-
- /**
- * re-order the given alignment using the given list of sequence IDs separated
- * by sep
- *
- * @param alf
- * @param order
- * - sep separated list
- * @param undoName
- * - string to use when referring to ordering action in undo buffer
- * @param sep
- * @return 'true' if alignment was actually reordered. empty string if
- * alignment did not contain sequences.
- */
- public abstract String orderAlignmentBy(AlignFrame alf, String order,
- String undoName, String sep);
-
- /**
- * get alignment as format (format names FASTA, BLC, CLUSTAL, MSF, PILEUP,
- * PFAM - see jalview.io.AppletFormatAdapter for full list);
- *
- * @param format
- * @return
- */
-
- public abstract String getAlignment(String format);
-
- /**
- * get alignment displayed in alf as format
- *
- * @param alf
- * @param format
- * @return
- */
- public abstract String getAlignmentFrom(AlignFrame alf, String format);
-
- /**
- * get alignment as format with jalview start-end sequence suffix appended
- *
- * @param format
- * @param suffix
- * @return
- */
-
- public abstract String getAlignment(String format, String suffix);
-
- /**
- * get alignment displayed in alf as format with or without the jalview
- * start-end sequence suffix appended
- *
- * @param alf
- * @param format
- * @param suffix
- * @return
- */
- public abstract String getAlignmentFrom(AlignFrame alf, String format,
- String suffix);
-
- /**
- * add the given features or annotation to the current alignment
- *
- * @param annotation
- */
-
- public abstract void loadAnnotation(String annotation);
-
- /**
- * add the given features or annotation to the given alignment view
- *
- * @param alf
- * @param annotation
- */
- public abstract void loadAnnotationFrom(AlignFrame alf,
- String annotation);
-
- /**
- * parse the given string as a jalview feature or GFF annotation file and
- * optionally enable feature display on the current AlignFrame
- *
- * @param features
- * - gff or features file
- * @param autoenabledisplay
- * - when true, feature display will be enabled if any features can
- * be parsed from the string.
- */
-
- public abstract void loadFeatures(String features,
- boolean autoenabledisplay);
-
- /**
- * parse the given string as a jalview feature or GFF annotation file and
- * optionally enable feature display on the given AlignFrame.
- *
- * @param alf
- * @param features
- * - gff or features file
- * @param autoenabledisplay
- * - when true, feature display will be enabled if any features can
- * be parsed from the string.
- * @return true if data parsed as features
- */
- public abstract boolean loadFeaturesFrom(AlignFrame alf, String features,
- boolean autoenabledisplay);
-
- /**
- * get the sequence features in the given format (Jalview or GFF);
- *
- * @param format
- * @return
- */
-
- public abstract String getFeatures(String format);
-
- /**
- * get the sequence features in alf in the given format (Jalview or GFF);
- *
- * @param alf
- * @param format
- * @return
- */
- public abstract String getFeaturesFrom(AlignFrame alf, String format);
-
- /**
- * get current alignment's annotation as an annotation file
- *
- * @return
- */
-
- public abstract String getAnnotation();
-
- /**
- * get alignment view alf's annotation as an annotation file
- *
- * @param alf
- * @return
- */
- public abstract String getAnnotationFrom(AlignFrame alf);
+ /**
+ * get alignment as format (format names FASTA, BLC, CLUSTAL, MSF, PILEUP,
+ * PFAM - see jalview.io.AppletFormatAdapter for full list);
+ *
+ * @param format
+ * @return
+ */
+
+ public abstract String getAlignment(String format);
+
+ /**
+ * get alignment as format with jalview start-end sequence suffix appended
+ *
+ * @param format
+ * @param suffix
+ * @return
+ */
+
+ public abstract String getAlignment(String format, String suffix);
+
+ /**
+ * get alignment displayed in alf as format
+ *
+ * @param alf
+ * @param format
+ * @return
+ */
+ public abstract String getAlignmentFrom(AlignFrame alf, String format);
+
+ /**
+ * get alignment displayed in alf as format with or without the jalview
+ * start-end sequence suffix appended
+ *
+ * @param alf
+ * @param format
+ * @param suffix
+ * @return
+ */
+ public abstract String getAlignmentFrom(AlignFrame alf, String format,
+ String suffix);
+
+ /**
+ * get a separator separated list of sequence IDs reflecting the order of the
+ * current alignment
+ *
+ * @return
+ */
+
+ public abstract String getAlignmentOrder();
+
+ /**
+ * get a separator separated list of sequence IDs reflecting the order of the
+ * alignment in alf
+ *
+ * @param alf
+ * @return
+ */
+ public abstract String getAlignmentOrderFrom(AlignFrame alf);
+
+ /**
+ * get a sep separated list of sequence IDs reflecting the order of the
+ * alignment in alf
+ *
+ * @param alf
+ * @param sep
+ * - separator to use
+ * @return
+ */
+ public abstract String getAlignmentOrderFrom(AlignFrame alf, String sep);
+
+ /**
+ * get current alignment's annotation as an annotation file
+ *
+ * @return
+ */
+
+ public abstract String getAnnotation();
+
+ /**
+ * get alignment view alf's annotation as an annotation file
+ *
+ * @param alf
+ * @return
+ */
+ public abstract String getAnnotationFrom(AlignFrame alf);
+
+ public Object getAppletParameter(String name, boolean asString);
+
+ public URL getCodeBase();
+
+ public URL getDocumentBase();
+
+ /**
+ *
+ * @return
+ * @see jalview.appletgui.AlignFrame#getFeatureGroups();
+ */
+
+ public abstract String getFeatureGroups();
+
+ /**
+ * @param visible
+ * @return
+ * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean);
+ */
+
+ public abstract String getFeatureGroupsOfState(boolean visible);
+
+ /**
+ * @param alf
+ * align frame to get groups of state visible
+ * @param visible
+ * @return
+ * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean);
+ */
+ public abstract String getFeatureGroupsOfStateOn(AlignFrame alf,
+ boolean visible);
+
+ /**
+ * @param alf
+ * AlignFrame to get feature groups on
+ * @return
+ * @see jalview.appletgui.AlignFrame#getFeatureGroups();
+ */
+ public abstract String getFeatureGroupsOn(AlignFrame alf);
+
+ /**
+ * get the sequence features in the given format (Jalview or GFF);
+ *
+ * @param format
+ * @return
+ */
+
+ public abstract String getFeatures(String format);
+
+ /**
+ * get the sequence features in alf in the given format (Jalview or GFF);
+ *
+ * @param alf
+ * @param format
+ * @return
+ */
+ public abstract String getFeaturesFrom(AlignFrame alf, String format);
+
+ public Object getFrameForSource(VamsasSource source);
+
+ public Hashtable<String, int[]> getJSHashes();
+
+ /**
+ * Retrieve fragments of a large packet of data made available by JalviewLite.
+ *
+ * @param messageclass
+ * @param viewId
+ * @return next chunk of message
+ */
+
+ public abstract String getJsMessage(String messageclass, String viewId);
+
+ Hashtable<String, Hashtable<String, String[]>> getJSMessages();
+
+ public Object getJSObject();
+
+ public jalview.renderer.seqfeatures.FeatureRenderer getNewFeatureRenderer(
+ AlignViewportI vp);
+
+ public String getParameter(String name);
+
+ /**
+ * @return String list of selected sequence IDs, each terminated by the
+ * 'boolean not' character (""+0x00AC); or (¬);
+ */
+
+ public abstract String getSelectedSequences();
+
+ /**
+ * @param sep
+ * separator string or null for default
+ * @return String list of selected sequence IDs, each terminated by given
+ * separator string
+ */
+
+ public abstract String getSelectedSequences(String sep);
+
+ /**
+ * get sequences selected in current AlignFrame and return their alignment in
+ * format 'format' either with or without suffix
+ *
+ * @param alf
+ * - where selection is
+ * @param format
+ * - format of alignment file
+ * @param suffix
+ * - "true" to append /start-end string to each sequence ID
+ * @return selected sequences as flat file or empty string if there was no
+ * current selection
+ */
+
+ public abstract String getSelectedSequencesAsAlignment(String format,
+ String suffix);
+
+ /**
+ * get sequences selected in alf and return their alignment in format 'format'
+ * either with or without suffix
+ *
+ * @param alf
+ * - where selection is
+ * @param format
+ * - format of alignment file
+ * @param suffix
+ * - "true" to append /start-end string to each sequence ID
+ * @return selected sequences as flat file or empty string if there was no
+ * current selection
+ */
+ public abstract String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
+ String format, String suffix);
+
+ /**
+ * @param alf
+ * AlignFrame containing selection
+ * @return String list of selected sequence IDs, each terminated by current
+ * default separator sequence
+ *
+ */
+ public abstract String getSelectedSequencesFrom(AlignFrame alf);
// BH incompatibility here -- JalviewLite created an AlignFrame; Jalview
// creates an AlignmentPanel
// */
// public abstract AlignFrame newViewFrom(AlignFrame alf, String name);
- /**
- *
- * @param text
- * alignment file as a string
- * @param title
- * window title
- * @return null or new alignment frame
- */
-
- public abstract AlignFrame loadAlignment(String text, String title);
-
- /**
- * register a javascript function to handle any alignment mouseover events
- *
- * @param listener
- * name of javascript function (called with arguments
- * [jalview.appletgui.AlignFrame,String(sequence id);,String(column
- * in alignment);, String(position in sequence);]
- */
-
- public abstract void setMouseoverListener(String listener);
-
- /**
- * register a javascript function to handle mouseover events
- *
- * @param af
- * (null or specific AlignFrame for which events are to be listened
- * for);
- * @param listener
- * name of javascript function
- */
- public abstract void setMouseoverListener(AlignFrame af,
- String listener);
-
- /**
- * register a javascript function to handle any alignment selection events.
- * Events are generated when the user completes a selection event, or when the
- * user deselects all selected regions.
- *
- * @param listener
- * name of javascript function (called with arguments
- * [jalview.appletgui.AlignFrame, String(sequence set id);,
- * String(separator separated list of sequences which were
- * selected);, String(separator separated list of column ranges (i.e.
- * single number or hyphenated range); that were selected);]
- */
-
- public abstract void setSelectionListener(String listener);
-
- public abstract void setSelectionListener(AlignFrame af,
- String listener);
-
- /**
- * register a javascript function to handle events normally routed to a Jmol
- * structure viewer.
- *
- * @param listener
- * - javascript function (arguments are variable, see
- * jalview.javascript.MouseOverStructureListener for full details);
- * @param modelSet
- * - separator separated list of PDB file URIs that this viewer is
- * handling. These files must be in the same order they appear in
- * Jmol (e.g. first one is frame 1, second is frame 2, etc);.
- * @see jalview.javascript.MouseOverStructureListener
- */
-
- public abstract void setStructureListener(String listener,
- String modelSet);
-
- /**
- * remove any callback using the given listener function and associated with
- * the given AlignFrame (or null for all callbacks);
- *
- * @param af
- * (may be null);
- * @param listener
- * (may be null);
- */
- public abstract void removeJavascriptListener(AlignFrame af,
- String listener);
-
- /**
- * send a mouseover message to all the alignment windows associated with the
- * given residue in the pdbfile
- *
- * @param pdbResNum
- * @param chain
- * @param pdbfile
- */
-
- public abstract void mouseOverStructure(String pdbResNum, String chain,
- String pdbfile);
-
- /**
- * bind a pdb file to a sequence in the given AlignFrame.
- *
- * @param alFrame
- * - null or specific AlignFrame. This specifies the dataset that
- * will be searched for a seuqence called sequenceId
- * @param sequenceId
- * - sequenceId within the dataset.
- * @param pdbEntryString
- * - the short name for the PDB file
- * @param pdbFile
- * - pdb file - either a URL or a valid PDB file.
- * @return true if binding was as success TODO: consider making an exception
- * structure for indicating when PDB parsing or sequenceId location
- * fails.
- */
- public abstract boolean addPdbFile(AlignFrame alFrame, String sequenceId,
- String pdbEntryString, String pdbFile);
-
- /**
- * adjust horizontal/vertical scroll to make the given location the top left
- * hand corner for the given view
- *
- * @param alf
- * @param topRow
- * @param leftHandColumn
- */
- public abstract void scrollViewToIn(AlignFrame alf, String topRow,
- String leftHandColumn);
-
- /**
- * adjust vertical scroll to make the given row the top one for given view
- *
- * @param alf
- * @param topRow
- */
- public abstract void scrollViewToRowIn(AlignFrame alf, String topRow);
-
- /**
- * adjust horizontal scroll to make the given column the left one in the given
- * view
- *
- * @param alf
- * @param leftHandColumn
- */
- public abstract void scrollViewToColumnIn(AlignFrame alf,
- String leftHandColumn);
-
- /**
- *
- * @return
- * @see jalview.appletgui.AlignFrame#getFeatureGroups();
- */
-
- public abstract String getFeatureGroups();
-
- /**
- * @param alf
- * AlignFrame to get feature groups on
- * @return
- * @see jalview.appletgui.AlignFrame#getFeatureGroups();
- */
- public abstract String getFeatureGroupsOn(AlignFrame alf);
-
- /**
- * @param visible
- * @return
- * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean);
- */
-
- public abstract String getFeatureGroupsOfState(boolean visible);
-
- /**
- * @param alf
- * align frame to get groups of state visible
- * @param visible
- * @return
- * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean);
- */
- public abstract String getFeatureGroupsOfStateOn(AlignFrame alf,
- boolean visible);
-
- /**
- * @param groups
- * tab separated list of group names
- * @param state
- * true or false
- * @see jalview.appletgui.AlignFrame#setFeatureGroupState(java.lang.String[],
- * boolean);
- */
- public abstract void setFeatureGroupStateOn(AlignFrame alf,
- String groups,
- boolean state);
-
-
- public abstract void setFeatureGroupState(String groups, boolean state);
-
- /**
- * List separator string
- *
- * @return the separator
- */
-
- public abstract String getSeparator();
-
- /**
- * List separator string
- *
- * @param separator
- * the separator to set. empty string will reset separator to default
- */
-
- public abstract void setSeparator(String separator);
-
- /**
- * Retrieve fragments of a large packet of data made available by JalviewLite.
- *
- * @param messageclass
- * @param viewId
- * @return next chunk of message
- */
-
- public abstract String getJsMessage(String messageclass, String viewId);
-
- /// in http://www.jalview.org/examples/jalviewLiteJs.html but missing here
-
- // get selected sequences as alignment as format with or without start-end
- // suffix
-
- public String getSelectedSequencesAsAlignment(String format,
- boolean suffix);
-
- // get selected sequences as alignment from given view as format with or
- // without start-end suffix
- public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
- String format, boolean suffix);
-
-
- public String arrayToSeparatorList(String[] array);
-
- // get a string array from a list
-
- public String[] separatorListToArray(String list);
-
- // debug flag - controls output to standard out
- public static boolean debug = false;
+ /**
+ * get list of selected sequence IDs separated by given separator
+ *
+ * @param alf
+ * window containing selection
+ * @param sep
+ * separator string to use - default is 'boolean not'
+ * @return String list of selected sequence IDs, each terminated by the given
+ * separator
+ */
+ public abstract String getSelectedSequencesFrom(AlignFrame alf,
+ String sep);
+
+ public Object[] getSelectionForListener(SequenceGroup seqsel,
+ ColumnSelection colsel, HiddenColumns hidden,
+ SelectionSource source, Object alignFrame);
+
+ /**
+ * List separator string
+ *
+ * @return the separator
+ */
+
+ public abstract String getSeparator();
+
+ public AlignViewportI getViewport();
+
+ /**
+ *
+ * @param sequenceId
+ * id of sequence to highlight
+ * @param position
+ * integer position [ tobe implemented or range ] on sequence
+ * @param alignedPosition
+ * true/false/empty string - indicate if position is an alignment
+ * column or unaligned sequence position
+ */
+
+ public abstract void highlight(String sequenceId, String position,
+ String alignedPosition);
+
+ /**
+ *
+ * @param sequenceId
+ * id of sequence to highlight
+ * @param position
+ * integer position [ tobe implemented or range ] on sequence
+ * @param alignedPosition
+ * false, blank or something else - indicate if position is an
+ * alignment column or unaligned sequence position
+ */
+ public abstract void highlightIn(AlignFrame alf, String sequenceId,
+ String position, String alignedPosition);
+
+ /**
+ *
+ * @param text
+ * alignment file as a string
+ * @param title
+ * window title
+ * @return null or new alignment frame
+ */
+
+ public abstract AlignFrame loadAlignment(String text, String title);
+
+ /**
+ * add the given features or annotation to the current alignment
+ *
+ * @param annotation
+ */
+
+ public abstract void loadAnnotation(String annotation);
+
+ /**
+ * add the given features or annotation to the given alignment view
+ *
+ * @param alf
+ * @param annotation
+ */
+ public abstract void loadAnnotationFrom(AlignFrame alf,
+ String annotation);
+
+ /**
+ * parse the given string as a jalview feature or GFF annotation file and
+ * optionally enable feature display on the current AlignFrame
+ *
+ * @param features
+ * - gff or features file
+ * @param autoenabledisplay
+ * - when true, feature display will be enabled if any features can
+ * be parsed from the string.
+ */
+
+ public abstract void loadFeatures(String features,
+ boolean autoenabledisplay);
+
+ /**
+ * parse the given string as a jalview feature or GFF annotation file and
+ * optionally enable feature display on the given AlignFrame.
+ *
+ * @param alf
+ * @param features
+ * - gff or features file
+ * @param autoenabledisplay
+ * - when true, feature display will be enabled if any features can
+ * be parsed from the string.
+ * @return true if data parsed as features
+ */
+ public abstract boolean loadFeaturesFrom(AlignFrame alf, String features,
+ boolean autoenabledisplay);
+
+ public boolean loadScoreFile(String sScoreFile) throws IOException;
+
+ public void newFeatureSettings();
+
+ public void newStructureView(PDBEntry pdb, SequenceI[] seqs,
+ String[] chains, DataSourceType protocol);
+
+ /**
+ * public static method for JalviewJS API to open a PCAPanel without
+ * necessarily using a dialog.
+ *
+ * @param af
+ * may be null
+ * @param modelName
+ * @return the PCAPanel, or the string "label.you_need_at_least_n_sequences"
+ * if number of sequences selected is inappropriate
+ */
+ public Object openPcaPanel(AlignFrame af, String modelName);
+
+ /**
+ * Open a new Tree panel on the desktop statically. Params are standard (not
+ * set by Groovy). No dialog is opened.
+ *
+ * @param af
+ * may be null
+ * @param treeType
+ * @param modelName
+ * @return null, or the string "label.you_need_at_least_n_sequences" if number
+ * of sequences selected is inappropriate
+ */
+ public Object openTreePanel(AlignFrame af, String treeType,
+ String modelName);
+
+ /// in http://www.jalview.org/examples/jalviewLiteJs.html but missing here
+
+ // get selected sequences as alignment as format with or without start-end
+ // suffix
+
+ /**
+ * re-order the given alignment using the given list of sequence IDs separated
+ * by sep
+ *
+ * @param alf
+ * @param order
+ * - sep separated list
+ * @param undoName
+ * - string to use when referring to ordering action in undo buffer
+ * @param sep
+ * @return 'true' if alignment was actually reordered. empty string if
+ * alignment did not contain sequences.
+ */
+ public abstract String orderAlignmentBy(AlignFrame alf, String order,
+ String undoName, String sep);
+
+ // get a string array from a list
+
+ /**
+ * re-order the current alignment using the given list of sequence IDs
+ *
+ * @param order
+ * - sep separated list
+ * @param undoName
+ * - string to use when referring to ordering action in undo buffer
+ * @return 'true' if alignment was actually reordered. empty string if
+ * alignment did not contain sequences.
+ */
+
+ public abstract String orderBy(String order, String undoName);
+
+ /**
+ * re-order the current alignment using the given list of sequence IDs
+ * separated by sep
+ *
+ * @param order
+ * - sep separated list
+ * @param undoName
+ * - string to use when referring to ordering action in undo buffer
+ * @param sep
+ * @return 'true' if alignment was actually reordered. empty string if
+ * alignment did not contain sequences.
+ */
+
+ public abstract String orderBy(String order, String undoName, String sep);
+
+ /**
+ * process commandline arguments after the JavaScript application has started
+ *
+ * @param args
+ * @return
+ */
+ Object parseArguments(String[] args);
+
+ // public boolean getDefaultParameter(String name, boolean def);
+
+ public boolean parseFeaturesFile(String param, DataSourceType protocol);
+
+ /**
+ * remove any callback using the given listener function and associated with
+ * the given AlignFrame (or null for all callbacks);
+ *
+ * @param af
+ * (may be null);
+ * @param listener
+ * (may be null);
+ */
+ public abstract void removeSelectionListener(AlignFrame af,
+ String listener);
+
+ // public void setAlignPdbStructures(boolean defaultParameter);
+
+ /**
+ * adjust horizontal scroll to make the given column the left one in the given
+ * view
+ *
+ * @param alf
+ * @param leftHandColumn
+ */
+ public abstract void scrollViewToColumnIn(AlignFrame alf,
+ String leftHandColumn);
+
+ /**
+ * adjust horizontal/vertical scroll to make the given location the top left
+ * hand corner for the given view
+ *
+ * @param alf
+ * @param topRow
+ * @param leftHandColumn
+ */
+ public abstract void scrollViewToIn(AlignFrame alf, String topRow,
+ String leftHandColumn);
+
+ /**
+ * adjust vertical scroll to make the given row the top one for given view
+ *
+ * @param alf
+ * @param topRow
+ */
+ public abstract void scrollViewToRowIn(AlignFrame alf, String topRow);
+
+ /**
+ * select regions of the currrent alignment frame
+ *
+ * @param sequenceIds
+ * String separated list of sequence ids or empty string
+ * @param columns
+ * String separated list { column range or column, ..} or empty
+ * string
+ */
+
+ public abstract void select(String sequenceIds, String columns);
+
+ /**
+ * select regions of the currrent alignment frame
+ *
+ * @param toselect
+ * String separated list { column range, seq1...seqn sequence ids }
+ * @param sep
+ * separator between toselect fields
+ */
+
+ public abstract void select(String sequenceIds, String columns,
+ String sep);
+
+ /**
+ * select regions of the given alignment frame
+ *
+ * @param alf
+ * @param toselect
+ * String separated list { column range, seq1...seqn sequence ids }
+ * @param sep
+ * separator between toselect fields
+ */
+ public abstract void selectIn(AlignFrame alf, String sequenceIds,
+ String columns);
+
+ /**
+ * select regions of the given alignment frame
+ *
+ * @param alf
+ * @param toselect
+ * String separated list { column range, seq1...seqn sequence ids }
+ * @param sep
+ * separator between toselect fields
+ */
+ public abstract void selectIn(AlignFrame alf, String sequenceIds,
+ String columns, String sep);
+
+ public String[] separatorListToArray(String list);
+
+ public abstract void setFeatureGroupState(String groups, boolean state);
+
+ public void setFeatureGroupState(String[] groups, boolean state);
+
+ // public StructureSelectionManagerProvider
+ // getStructureSelectionManagerProvider();
+
+ /**
+ * @param groups
+ * tab separated list of group names
+ * @param state
+ * true or false
+ * @see jalview.appletgui.AlignFrame#setFeatureGroupState(java.lang.String[],
+ * boolean);
+ */
+ public abstract void setFeatureGroupStateOn(AlignFrame alf, String groups,
+ boolean state);
+
+ public abstract void setSelectionListener(AlignFrame af, String listener);
+
+ /**
+ * register a javascript function to handle any alignment selection events.
+ * Events are generated when the user completes a selection event, or when the
+ * user deselects all selected regions.
+ *
+ * @param listener
+ * name of javascript function (called with arguments
+ * [jalview.appletgui.AlignFrame, String(sequence set id);,
+ * String(separator separated list of sequences which were
+ * selected);, String(separator separated list of column ranges (i.e.
+ * single number or hyphenated range); that were selected);]
+ */
+
+ public abstract void setSelectionListener(String listener);
+
+ /**
+ * List separator string
+ *
+ * @param separator
+ * the separator to set. empty string will reset separator to default
+ */
+
+ public abstract void setSeparator(String separator);
+
+ void showOverview();
+
+ public void updateForAnnotations();
}
import jalview.io.JPredFile;
import jalview.io.JnetAnnotationMaker;
import jalview.io.NewickFile;
-import jalview.javascript.JSFunctionExec;
-import jalview.javascript.JalviewLiteJsApi;
-import jalview.javascript.JsCallBack;
-import jalview.javascript.MouseOverStructureListener;
+import jalview.appletgui.js.JSFunctionExec;
+import jalview.appletgui.js.JalviewLiteJsApi;
+import jalview.appletgui.js.JsCallBack;
+import jalview.appletgui.js.JsSelectionSender;
+import jalview.appletgui.js.MouseOverListener;
+import jalview.appletgui.js.MouseOverStructureListener;
import jalview.structure.SelectionListener;
import jalview.structure.StructureSelectionManager;
import jalview.util.ColorUtils;
setMouseoverListener(currentAlignFrame, listener);
}
- private Vector<jalview.javascript.JSFunctionExec> javascriptListeners = new Vector<>();
+ private Vector<JSFunctionExec> javascriptListeners = new Vector<>();
/*
* (non-Javadoc)
return;
}
}
- jalview.javascript.MouseOverListener mol = new jalview.javascript.MouseOverListener(
+ MouseOverListener mol = new MouseOverListener(
this, af, listener);
javascriptListeners.addElement(mol);
StructureSelectionManager.getStructureSelectionManager(this)
return;
}
}
- jalview.javascript.JsSelectionSender mol = new jalview.javascript.JsSelectionSender(
+ JsSelectionSender mol = new JsSelectionSender(
this, af, listener);
javascriptListeners.addElement(mol);
StructureSelectionManager.getStructureSelectionManager(this)
{
while (javascriptListeners.size() > 0)
{
- jalview.javascript.JSFunctionExec mol = javascriptListeners
+ JSFunctionExec mol = javascriptListeners
.elementAt(0);
javascriptListeners.removeElement(mol);
if (mol instanceof SelectionListener)
StructureSelectionManager.release(this);
}
- private jalview.javascript.JSFunctionExec jsFunctionExec;
+ private JSFunctionExec jsFunctionExec;
/*
* (non-Javadoc)
* (non-Javadoc)
*
* @see
- * jalview.javascript.JalviewLiteJsApi#scrollViewToRowIn(jalview.appletgui
+ * JalviewLiteJsApi#scrollViewToRowIn(jalview.appletgui
* .AlignFrame, java.lang.String)
*/
@Override
* (non-Javadoc)
*
* @see
- * jalview.javascript.JalviewLiteJsApi#scrollViewToColumnIn(jalview.appletgui
+ * JalviewLiteJsApi#scrollViewToColumnIn(jalview.appletgui
* .AlignFrame, java.lang.String)
*/
@Override
htmlName + ((Object) this).toString(), documentBase, codeBase,
commandOptions, this);
- viewer.setJmolStatusListener(this); // extends JmolCallbackListener
+ viewer.setJmolStatusListener(this);
+
+ // BH how about extending Jmol's status listener?
try
{
bjs.exportHTML(null);
}
- public void createImageMap(File file, String image)
- {
- alignPanel.makePNGImageMap(file, image);
- }
-
/**
* Creates a PNG image of the alignment and writes it to the given file. If
* the file is null, the user is prompted to choose a file.
{
if (Jalview.isHeadlessMode())
{
- return new AlignFrame[] { Jalview.currentAlignFrame };
+ return new AlignFrame[] { Jalview.getInstance().currentAlignFrame };
}
JInternalFrame[] frames = getDesktopPane().getAllFrames();
tree.getTitle(), safeInt(tree.getWidth()),
safeInt(tree.getHeight()), safeInt(tree.getXpos()),
safeInt(tree.getYpos()));
+ if (tp == null)
+ {
+ warn("There was a problem recovering stored Newick tree: \n"
+ + tree.getNewick());
+ continue;
+ }
if (tree.getId() != null)
{
// perhaps bind the tree id to something ?
tp.getTreeCanvas().setAssociatedPanel(ap); // af.alignPanel;
}
tp.getTreeCanvas().setApplyToAllViews(tree.isLinkToAllViews());
- if (tp == null)
- {
- warn("There was a problem recovering stored Newick tree: \n"
- + tree.getNewick());
- continue;
- }
-
tp.fitToWindow.setState(safeBoolean(tree.isFitToWindow()));
tp.fitToWindow_actionPerformed(null);
}
}
- public void addSelectionListener(SelectionListener selecter)
+ public List<SelectionListener> getListeners() {
+ return sel_listeners;
+ }
+
+ public void addSelectionListener(SelectionListener selecter)
{
if (!sel_listeners.contains(selecter))
{
import java.nio.file.Path;
import java.nio.file.attribute.BasicFileAttributes;
import java.util.Date;
+import java.util.Map;
import java.util.Properties;
import java.util.logging.ConsoleHandler;
import java.util.logging.Level;
return failValue;
}
+ public static Map<String, Object> getAppletInfoAsMap()
+ {
+ return (isJS ? jsutil.getAppletInfoAsMap() : null);
+ }
}
import java.io.OutputStream;
import java.net.URL;
import java.util.HashMap;
+import java.util.Map;
import java.util.Properties;
import java.util.function.Function;
import java.util.zip.ZipEntry;
/**
- * Get an attribute of applet's Info map for the applet found using
- * getApplet(null). That is, applet.__Info[InfoKey].
+ * Get the applet's __Info map or an attribute of that map for the applet found using
+ * getApplet(null). That is, applet.__Info or applet.__Info[InfoKey].
*
- * @param infoKey
+ * @param infoKey if null, return the full __Info map
*/
Object getAppletInfo(String infoKey);
*/
void setUIEnabled(JComponent jc, boolean enabled);
+
+ /**
+ * Play an audio
+ * @param buffer
+ * @param format a javax.sound.sampled.AudioFormat
+ * @throws Exception
+ */
+ void playAudio(byte[] buffer, Object format) throws Exception;
+
+ /**
+ * For either an applet or an application, get the ORIGINAL __Info as a Map that
+ * has a full set up lower-case keys along with whatever non-all-lower-case keys
+ * provided at start-up.
+ *
+ * @return
+ */
+ Map<String, Object> getAppletInfoAsMap();
+
}
--- /dev/null
+package jalview.bin;
+
+import java.io.File;
+import java.net.URISyntaxException;
+
+import jalview.gui.AlignFrame;
+import jalview.io.BioJsHTMLOutput;
+import jalview.io.FileFormatI;
+import jalview.io.HtmlSvgOutput;
+import jalview.util.Platform;
+
+/**
+ * Abandoned -- see JalviewApp
+ *
+ * A class to load parameters for either JalviewLite or Jalview
+ *
+ * @author hansonr
+ *
+ */
+public class JalviewAppLoader
+{
+
+ public JalviewAppLoader()
+ {
+ }
+
+}
\ No newline at end of file
--- /dev/null
+package jalview.bin;
+
+import java.util.List;
+
+import jalview.appletgui.js.JSFunctionExec;
+
+public interface JalviewJSApp
+{
+
+
+
+}
git://source.jalview.org / jalview.git / commitdiff