+++ /dev/null
-package jalview.bin;
-
-import java.io.IOException;
-import java.net.URL;
-
-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.structure.SelectionSource;
-import jalview.structure.VamsasSource;
-
-/**
- * JAL-3369 JalviewJS API BH 2019.07.17
- *
- * @author hansonr
- *
- */
-public interface JalviewJSApi
-{
-
- // debug flag - controls output to standard out
- public static boolean debug = false;
-
- /**
- * 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 or null
- * @param pdbId
- * - the four-character PDB ID
- * @param pdbFile
- * - pdb file - either a URL or a valid PDB file or null.
- * @return true if binding was success
- */
- public boolean addPdbFile(AlignFrame alFrame, String sequenceId,
- String pdbId, String pdbFile);
-
- /**
- * The following public methods may be called externally, eg via javascript in
- * an HTML page.
- *
- * <br>
- * <em>TODO: introduce interface for jalview.appletgui.AlignFrame</em><br>
- *
- * Most function arguments are strings, which contain serialised versions of
- * lists. Lists of things are separated by a separator character - either the
- * default or a user supplied one. Ranges and positions on an alignment or
- * sequence can be specified as a list, where an item containing a single
- * number is a single position, and an item like 1-2 specifies columns 1 and 2
- * as a range.
- */
-
- // /**
- // * @author jimp
- // *
- // */
- // public interface JalviewLiteJsApi
- // {
-
- /**
- * get alignment as format (format names FASTA, BLC, CLUSTAL, MSF, PILEUP,
- * PFAM - see jalview.io.AppletFormatAdapter for full list);
- *
- * @param format
- * @return
- */
-
- public String getAlignment(String format);
-
- /**
- * get alignment as format with jalview start-end sequence suffix appended
- *
- * @param format
- * @param suffix
- * @return
- */
-
- public String getAlignment(String format, String suffix);
-
- /**
- * get alignment displayed in alf as format
- *
- * @param alf
- * @param format
- * @return
- */
- public 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 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 String getAlignmentOrder();
-
- /**
- * get a separator separated list of sequence IDs reflecting the order of the
- * alignment in alf
- *
- * @param alf
- * @return
- */
- public String[] getAlignmentOrderFrom(AlignFrame alf);
-
- /**
- * get current alignment's annotation as an annotation file
- *
- * @return
- */
-
- public String getAnnotation();
-
- /**
- * get alignment view alf's annotation as an annotation file
- *
- * @param alf
- * @return
- */
- public String getAnnotationFrom(AlignFrame alf);
-
- public Object getAppletParameter(String name, boolean asString);
-
- public URL getCodeBase();
-
- public URL getDocumentBase();
-
- /**
- *
- * @return
- * @see jalview.appletgui.AlignFrame#getFeatureGroups();
- */
-
- public String[] getFeatureGroups();
-
- /**
- * @param visible
- * @return
- * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean);
- */
-
- public String[] getFeatureGroupsOfState(boolean visible);
-
- /**
- * @param alf
- * align frame to get groups of state visible
- * @param visible
- * @return
- * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean);
- */
- public String[] getFeatureGroupsOfStateOn(AlignFrame alf,
- boolean visible);
-
- /**
- * @param alf
- * AlignFrame to get feature groups on
- * @return
- * @see jalview.appletgui.AlignFrame#getFeatureGroups();
- */
- public String[] getFeatureGroupsOn(AlignFrame alf);
-
- /**
- * get the sequence features in the given format (Jalview or GFF);
- *
- * @param format
- * @return
- */
-
- public String getFeatures(String format);
-
- /**
- * get the sequence features in alf in the given format (Jalview or GFF);
- *
- * @param alf
- * @param format
- * @return
- */
- public String getFeaturesFrom(AlignFrame alf, String format);
-
- public Object getFrameForSource(VamsasSource source);
-
- public String getParameter(String name);
-
- /**
- * @return String list of selected sequence IDs, each terminated by the
- * 'boolean not' character (""+0x00AC); or (¬);
- */
-
- public SequenceI[] getSelectedSequences();
-
- /**
- * @param sep
- * separator string or null for default
- * @return String list of selected sequence IDs, each terminated by given
- * separator string
- */
-
- public SequenceI[] 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 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 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 SequenceI[] getSelectedSequencesFrom(AlignFrame alf);
-
- // BH incompatibility here -- JalviewLite created an AlignFrame; Jalview
- // creates an AlignmentPanel
- // /**
- // * create a new view and return the AlignFrame instance
- // *
- // * @return
- // */
- //
- // public AlignFrame newView();
- //
- // /**
- // * create a new view named name and return the AlignFrame instance
- // *
- // * @param name
- // * @return
- // */
- //
- // public AlignFrame newView(String name);
- //
- // /**
- // * create a new view on alf and return the AlignFrame instance
- // *
- // * @param alf
- // * @return
- // */
- // public AlignFrame newViewFrom(AlignFrame alf);
- //
- // /**
- // * create a new view named name on alf
- // *
- // * @param alf
- // * @param name
- // * @return
- // */
- // public AlignFrame newViewFrom(AlignFrame alf, String name);
-
- /**
- * 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 SequenceI[] getSelectedSequencesFrom(AlignFrame alf, String sep);
-
- public Object[] getSelectionForListener(SequenceGroup seqsel,
- ColumnSelection colsel, HiddenColumns hidden,
- SelectionSource source, Object alignFrame);
-
- 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 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 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 AlignFrame loadAlignment(String text, String title);
-
- /**
- * add the given features or annotation to the current alignment
- *
- * @param annotation
- */
-
- public void loadAnnotation(String annotation);
-
- /**
- * add the given features or annotation to the given alignment view
- *
- * @param alf
- * @param annotation
- */
- public 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 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 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);
-
- /// 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 array of sequence IDs
- *
- * @param alf
- * @param ids
- * array of sequence IDs
- * @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.
- */
- String orderAlignmentBy(AlignFrame alf, String[] ids, String undoName);
-
- // get a string array from a list
-
- /**
- * re-order the current alignment using the given list of sequence IDs
- *
- * @param ids
- * array of sequence IDs
- * @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 String orderBy(String[] ids, String undoName);
-
- /**
- * re-order the current alignment using the given list of sequence IDs
- *
- * @param ids
- * array of sequence IDs
- * @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 String orderBy(String[] ids, String undoName, String sep);
- //
-
- // 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 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 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 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 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 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 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 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 void selectIn(AlignFrame alf, String sequenceIds, String columns,
- String sep);
-
- public 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 void setFeatureGroupStateOn(AlignFrame alf, String groups,
- boolean state);
-
- public 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 void setSelectionListener(String listener);
-
- public void updateForAnnotations();
-
- // Bob's additions:
-
- /**
- * 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);
-
- /**
- * process commandline arguments after the JavaScript application has started
- *
- * @param args
- * @return
- */
- public Object parseArguments(String[] args);
-
- public void showStructure(AlignFrame af, String pdbID, String fileType);
-
- public void showOverview();
-
-}
-package jalview.api;
+package jalview.bin;
import java.awt.EventQueue;
//import java.applet.AppletContext;
import java.util.StringTokenizer;
import java.util.Vector;
-import jalview.bin.ArgsParser;
-import jalview.bin.Jalview;
-import jalview.bin.JalviewJSApi;
+import jalview.api.JalviewJSApi;
+import jalview.api.StructureSelectionManagerProvider;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
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 netscape.javascript.JSObject;
-
/**
* Basically the JalviewLite application, but without JalviewLite
*
+ * Processing all "applet parameters" and also all "applet interface" methods.
+ *
* @author hansonr
*
*/
{
private ArgsParser aparser;
- private boolean debug;
-
private String[] ret = new String[1];
+ // private boolean alignPDBStructures; From JalviewLite; not implemented
+
private String separator = "\u00AC"; // JalviewLite note: the default used to
// be '|', but many sequence IDS include
// pipes.
/**
- * We maintain a pointer to the jalview instance here, because only with that do we have a direct
- * connection from the JavaScript "applet" object to the proper instance of Jalview in case there
- * are multiple applets on a page.
+ * We maintain a pointer to the jalview instance here, because only with that
+ * do we have a direct connection from the JavaScript "applet" object to the
+ * proper instance of Jalview in case there are multiple applets on a page.
*/
private Jalview jalview;
-
- public JalviewJSApp(Jalview jalview, ArgsParser aparser)
+ public class JsSelectionListener
+ implements jalview.structure.SelectionListener
{
- this.jalview = jalview;
- this.aparser = aparser;
- Platform.setAppClass(this);
- }
+ AlignFrame _alf;
- public void load(AlignFrame af)
- {
- String sep = (String) getAppletParameter("separator", true);
- if (sep != null)
+ String _listener;
+
+ public JsSelectionListener(AlignFrame alf, String listener)
{
- if (sep.length() > 0)
- {
- separator = sep;
- }
- else
- {
- throw new Error(MessageManager
- .getString("error.invalid_separator_parameter"));
- }
+ _alf = alf;
+ _listener = listener;
}
- loadTree(af);
- loadScoreFile();
- loadFeatures(af);
- loadAnnotations(af);
- loadJnetFile(af);
- loadPdbFiles(af);
- }
-
- // 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
- //
-
- @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);
- }
-
- /**
- * Get the applet-like code base even though this is an application.
- */
-
- @Override
- public URL getCodeBase()
- {
- return Platform.getCodeBase();
- }
-
- /**
- * Get the applet-like document base even though this is an application.
- */
-
- @Override
- public URL getDocumentBase()
- {
- return Platform.getDocumentBase();
- }
+ public boolean isFor(AlignFrame alf, String listener)
+ {
+ return (_alf == null || _alf == alf) && _listener.equals(listener);
+ }
- @Override
- public Object getFrameForSource(VamsasSource source)
- {
- if (source != null)
+ @Override
+ public void selection(SequenceGroup seqsel, ColumnSelection colsel,
+ HiddenColumns hidden, SelectionSource source)
{
- AlignFrame af;
- if (source instanceof jalview.gui.AlignViewport
- && source == (af = Jalview.getCurrentAlignFrame())
- .getViewport())
+ // System.err.println("Testing selection event relay to
+ // jsfunction:"+_listener);
+ String setid = "";
+ AlignFrame srcFrame = (_alf == null ? getCurrentAlignFrame() : _alf);
+ if (source != null)
{
- // should be valid if it just generated an event!
- return af;
+ if (source instanceof AlignViewport
+ && srcFrame.getViewport() != source)
+ {
+ return;
+ }
}
- // 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 Object[] getSelectionForListener(SequenceGroup seqsel,
- ColumnSelection colsel, HiddenColumns hidden,
- SelectionSource source, Object alignFrame)
- {
- return getSelectionForListener(null, seqsel, colsel, hidden, source,
- alignFrame);
- }
-
- /**
- * scorefile
- *
- */
-
- @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;
- }
-
- 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());
- }
-
- @Override
- public void newFeatureSettings()
- {
- System.err.println(
- "Jalview applet interface newFeatureSettings not implemented");
- }
-
- //
- //
- // 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);
-
- }
-
- /**
- * @j2sAlias showStructure
- */
- @Override
- public void showStructure(AlignFrame af, String pdbID, String fileType) {
- if (af == null)
- af = Jalview.getCurrentAlignFrame();
- PDBEntry pe = null;
- SequenceI[] seqs = null;
- if (pdbID == null) {
- seqs = af.getViewport().getSequenceSelection();
- if (seqs.length == 0)
- seqs = af.getViewport().getAlignment().getSequencesArray();
- for (int i = 0; i < seqs.length; i++) {
- Vector<PDBEntry> list = seqs[i].getAllPDBEntries();
- if (list.size() > 0) {
- pe = list.get(0);
- break;
+ String[] seqs = new String[] {};
+ String[] cols = new String[] {};
+ int strt = 0, end = (srcFrame == null) ? -1
+ : srcFrame.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 (pe == null) {
- if (pdbID == null)
- return;
- pe = new PDBEntry(pdbID, null, fileType);
- List<SequenceI> list = af.getViewport().getAlignment().getSequences();
- List<SequenceI> tmp = new ArrayList<SequenceI>();
- for (int i = 0; i < list.size(); i++) {
- SequenceI seq = list.get(i);
- if (seq.getPDBEntry(pdbID) != null) {
- tmp.add(seq);
+ 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());
}
}
- seqs = tmp.toArray(new SequenceI[tmp.size()]);
- af.alignPanel.selectSequences(tmp);
+ else
+ {
+ if (seqsel != null && seqsel.getSize() > 0)
+ {
+ // send a valid range, otherwise we send the empty selection
+ cols = new String[1];
+ cols[0] = "" + (1 + strt) + "-" + (1 + end);
+ }
+ }
+ doSendCallback(_listener,
+ new Object[]
+ { Jalview.getInstance().j2sAppletID, srcFrame, source, setid,
+ seqs, cols });
}
- StructureViewer.launchStructureViewer(
- af.alignPanel,
- pe, seqs);
- }
-
- public void newStructureView(AlignFrame af, PDBEntry pdb,
- SequenceI[] seqs, String[] chains, DataSourceType protocol)
- {
- StructureViewer.launchStructureViewer(
- (af == null ? Jalview.getCurrentAlignFrame() : af).alignPanel,
- pdb, seqs);
- }
- /**
- * features
- * @param af
- *
- */
-
- @Override
- public boolean parseFeaturesFile(String filename, DataSourceType protocol)
- {
- return parseFeaturesFile(null, filename, protocol);
- }
-
- /**
- * @j2sAlias parseFeatureFile
- *
- * @param af
- * @param filename
- * @param protocol
- * @return
- */
- public boolean parseFeaturesFile(AlignFrame af, String filename, DataSourceType protocol)
- {
- return (af == null ? Jalview.getCurrentAlignFrame() : af).parseFeaturesFile(filename, protocol);
- }
-
- /**
- * annotations, jpredfile, jnetfile
- *
- */
-
- @Override
- public void updateForAnnotations()
- {
- updateForAnnotations(null);
}
- public void updateForAnnotations(AlignFrame af)
+ public JalviewJSApp(Jalview jalview, ArgsParser aparser, AlignFrame alf)
{
- (af == null ? Jalview.getCurrentAlignFrame() : af).updateForAnnotations();
+ Platform.setAppClass(this);
+ this.jalview = jalview;
+ this.aparser = aparser;
+ initFromParams(alf);
+ callInitCallback();
}
@Override
- public boolean addPdbFile(AlignFrame alf, String sequenceId, String pdbId,
- String pdbFile)
+ public boolean addPdbFile(String sequenceId, String pdbId, String pdbFile,
+ AlignFrame alf)
{
if (alf == null)
{
- alf = Jalview.getCurrentAlignFrame();
+ alf = getCurrentAlignFrame();
}
SequenceI seq = alf.getViewport().getAlignment().findName(sequenceId);
if (seq != null)
return true;
}
-// @Override
-// public String arrayToSeparatorList(String[] array)
-// {
-// return arrayToSeparatorList(array, separator);
-// }
-
-// /**
-// * concatenate the list with separator
-// *
-// * @param list
-// * @param separator
-// * @return concatenated string
-// */
-// public static String arrayToSeparatorList(String[] list, String separator)
-// {
-// // TODO use StringUtils version
-// StringBuffer v = new StringBuffer();
-// if (list != null && list.length > 0)
-// {
-// for (int i = 0, iSize = list.length; i < iSize; i++)
-// {
-// if (list[i] != null)
-// {
-// if (i > 0)
-// {
-// v.append(separator);
-// }
-// v.append(list[i]);
-// }
-// }
-// // if (debug)
-// // {
-// // System.err
-// // .println("Returning '" + separator + "' separated List:\n");
-// // System.err.println(v);
-// // }
-// return v.toString();
-// }
-// // if (debug)
-// // {
-// // System.err.println(
-// // "Returning empty '" + separator + "' separated List\n");
-// // }
-// return "" + separator;
-// }
-
- @Override
- public String getAlignment(String format)
- {
- return getAlignmentFrom(null, format, null);
- }
-
- /**
- * suffix string "true"/"false" (default true)
- * passed to AlnFile class controls whether /START-END is added to
- * sequence names
- */
- @Override
- public String getAlignment(String format, String suffix)
- {
- return getAlignmentFrom(Jalview.getCurrentAlignFrame(), format, suffix);
- }
-
- @Override
- public String getAlignmentFrom(AlignFrame alf, String format)
- {
- return getAlignmentFrom(alf, format, null);
- }
-
@Override
- public String getAlignmentFrom(AlignFrame alf, String format,
- String suffix)
+ public String getAlignment(String format, boolean addSuffix,
+ AlignFrame alf)
{
try
{
if (alf == null)
{
- alf = Jalview.getCurrentAlignFrame();
+ alf = getCurrentAlignFrame();
}
- boolean seqlimits = (suffix == null
- || suffix.equalsIgnoreCase("true"));
FileFormatI theFormat = FileFormats.getInstance().forName(format);
String reply = new AppletFormatAdapter().formatSequences(theFormat,
- alf.getViewport().getAlignment(), seqlimits);
+ alf.getViewport().getAlignment(), addSuffix);
return reply;
} catch (IllegalArgumentException ex)
{
}
@Override
- public String getAlignmentOrder()
- {
- return getAlignmentFrom(Jalview.getCurrentAlignFrame(), null);
- }
-
- @Override
- public String[] getAlignmentOrderFrom(AlignFrame alf)
+ public String[] getAlignmentOrder(AlignFrame alf)
{
if (alf == null)
{
- alf = Jalview.getCurrentAlignFrame();
+ alf = getCurrentAlignFrame();
}
AlignmentI alorder = alf.getViewport().getAlignment();
String[] order = new String[alorder.getHeight()];
{
order[i] = alorder.getSequenceAt(i).getName();
}
- return order;// arrayToSeparatorList(order, sep);
- }
-
- @Override
- public String getAnnotation()
- {
- return getAnnotationFrom(null);
+ return order;// arrayToSeparatorList(order, sep);
}
@Override
- public String getAnnotationFrom(AlignFrame alf)
+ public String getAnnotation(AlignFrame alf)
{
if (alf == null)
{
- alf = Jalview.getCurrentAlignFrame();
+ alf = getCurrentAlignFrame();
}
String annotation = new AnnotationFile()
.printAnnotationsForView(alf.getViewport());
return annotation;
}
+ /**
+ * Get the applet-like code base even though this is an application.
+ */
+
@Override
- public String[] getFeatureGroups()
+ public URL getCodeBase()
{
- return getFeatureGroupsOn(null);
+ return Platform.getCodeBase();
}
@Override
- public String[] getFeatureGroupsOfState(boolean visible)
+ public AlignFrame getCurrentAlignFrame()
{
- return getFeatureGroupsOfStateOn(null, visible);
+ // if (jalview != Jalview.getInstance() || jalview.currentAlignFrame !=
+ // Jalview.getCurrentAlignFrame()) {
+ // /** @j2sNative debugger */
+ // }
+ return jalview.currentAlignFrame;
}
+ /**
+ * Get the applet-like document base even though this is an application.
+ */
+
@Override
- public String[] getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)
+ public URL getDocumentBase()
{
- if (alf == null)
- {
- alf = Jalview.getCurrentAlignFrame();
- }
- return alf.getFeatureGroupsOfState(visible);
+ return Platform.getDocumentBase();
}
@Override
- public String[] getFeatureGroupsOn(AlignFrame alf)
+ public String[] getFeatureGroups(AlignFrame alf)
{
if (alf == null)
{
- alf = Jalview.getCurrentAlignFrame();
+ alf = getCurrentAlignFrame();
}
return alf.getFeatureGroups();
}
@Override
- public String getFeatures(String format)
+ public String[] getFeatureGroupsOfState(boolean visible, AlignFrame alf)
{
- return getFeaturesFrom(null, format);
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ return alf.getFeatureGroupsOfState(visible);
}
/**
* 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"
+ * @param alf
+ *
* @return
*/
@Override
- public String getFeaturesFrom(AlignFrame alf, String format)
+ public String getFeatures(String format, AlignFrame alf)
{
if (alf == null)
{
- alf = Jalview.getCurrentAlignFrame();
+ alf = getCurrentAlignFrame();
}
String features;
FeaturesFile formatter = new FeaturesFile();
format = format.toLowerCase();
if (format.indexOf(";") < 0)
format += ";includenonpositional";
- boolean nonpos = format.indexOf(";includenonpositional") > 0;
+ boolean nonpos = format.indexOf(";includenonpositional") >= 0;
boolean compl = format.indexOf(";includecomplement") >= 0;
if (format.startsWith("jalview"))
{
return features;
}
-
+
+ /**
+ * Get an applet parameter as a string.
+ *
+ */
+ @Override
+ public String getParameter(String name)
+ {
+ return (String) aparser.getAppletValue(name, null, true);
+ }
+
+ /**
+ * Get an applet parameter as an Object.
+ */
+
+ @Override
+ public Object getParameterAsObject(String name)
+ {
+ return aparser.getAppletValue(name, null, false);
+ }
+
/**
* read sequence1...sequenceN as a raw alignment
*
StringBuffer data = new StringBuffer("PASTE");
int i = 1;
String file = null;
- while ((file = (String) getAppletParameter("sequence" + i,
- true)) != null)
+ while ((file = getParameter("sequence" + i)) != null)
{
data.append(file.toString() + "\n");
i++;
}
/**
+ * @j2sAlias getSelectedSequences
*
- * @see jalview.appletgui.js.JalviewLiteJsApi#getSelectedSequences()
+ * @see jalview.appletgui.js.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
+ * .AlignFrame)
*/
@Override
- public SequenceI[] getSelectedSequences()
+ public SequenceI[] getSelectedSequences(AlignFrame alf)
{
- return getSelectedSequencesFrom(Jalview.getCurrentAlignFrame());
- }
-
- /**
- *
- * @see jalview.appletgui.js.JalviewLiteJsApi#getSelectedSequences(java.lang.String)
- */
- @Override
- public SequenceI[] getSelectedSequences(String sep)
- {
- return getSelectedSequencesFrom(Jalview.getCurrentAlignFrame(), sep);
+ // return getSelectedSequencesFrom(alf, null);
+ // }
+ //
+ // @Override
+ // public SequenceI[] getSelectedSequencesFrom(AlignFrame alf, String sep)
+ // {
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ AlignViewport v = alf.getViewport();
+ if (v.getSelectionGroup() != null)
+ {
+ return v.getSelectionGroup().getSequencesInOrder(v.getAlignment());
+ }
+ return null;
}
+ // /**
+ // *
+ // * @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);
+ // }
+ /**
+ * @j2sAlias getSelectedSequencesAsAlignment
+ */
@Override
public String getSelectedSequencesAsAlignment(String format,
- String suffix)
- {
- return getSelectedSequencesAsAlignmentFrom(null, format, suffix);
- }
-
- @Override
- public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
- String format, String suffix)
+ boolean addSuffix, AlignFrame alf)
{
if (alf == null)
{
- alf = Jalview.getCurrentAlignFrame();
+ alf = getCurrentAlignFrame();
}
-
- boolean seqlimits = (suffix == null || suffix.equalsIgnoreCase("true"));
try
{
AlignViewport vp = alf.getViewport();
// 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);
+ new Alignment(vp.getSelectionAsNewSequence()), addSuffix);
return reply;
}
} catch (IllegalArgumentException ex)
return "";
}
- /**
- *
- * @see jalview.appletgui.js.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
- * .AlignFrame)
- */
- @Override
- public SequenceI[] getSelectedSequencesFrom(AlignFrame alf)
- {
- return getSelectedSequencesFrom(alf, null);
- }
-
- @Override
- public SequenceI[] getSelectedSequencesFrom(AlignFrame alf, String sep)
- {
- if (alf == null)
- {
- alf = Jalview.getCurrentAlignFrame();
- }
- AlignViewport v = alf.getViewport();
- if (v.getSelectionGroup() != null)
- {
- return v.getSelectionGroup()
- .getSequencesInOrder(v.getAlignment());
- }
-
- return null;
- }
-
- 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, seqs, cols };
- }
-
- /**
- *
- * @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)
+ String alignedPosition, AlignFrame alf)
{
if (alf == null)
{
- alf = Jalview.getCurrentAlignFrame();
+ alf = getCurrentAlignFrame();
}
// TODO: could try to highlight in all alignments if alf==null
jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
}
}
- public AlignFrame loadAlignment(String text, int width, int height,
- String title)
+ @Override
+ public AlignFrame loadAlignment(String text, String title, int width,
+ int height)
{
AlignmentI al = null;
format);
if (al.getHeight() > 0)
{
- return new AlignFrame(al, width, height, title);
+ return new AlignFrame(al,
+ width > 0 ? width : AlignFrame.DEFAULT_WIDTH,
+ height > 0 ? height : AlignFrame.DEFAULT_HEIGHT, title);
}
} catch (IOException ex)
{
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)
+ public void loadAnnotation(String annotation, AlignFrame alf)
{
if (alf == null)
{
- alf = Jalview.getCurrentAlignFrame();
+ alf = getCurrentAlignFrame();
}
if (new AnnotationFile().annotateAlignmentView(alf.getViewport(),
annotation, DataSourceType.PASTE))
}
}
- /**
- * Load annotations if specified by parameter. Returns true if loaded, else
- * false.
- *
- *
- * @param alignFrame
- * @return
- */
- protected boolean loadAnnotations(AlignFrame af)
+ @Override
+ public boolean loadFeatures(String features, boolean autoenabledisplay,
+ AlignFrame alf)
{
- boolean result = false;
- String param = (String) getAppletParameter("annotations", true);
- if (param != null)
+ if (alf == 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 + "'");
- }
+ alf = getCurrentAlignFrame();
}
- 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)
+ boolean ret = alf.parseFeaturesFile(features, DataSourceType.PASTE);
+ if (!ret)
{
- setFeatureGroupState(af, separatorListToArray(param, separator), false);
- // setFeatureGroupStateOn(newAlignFrame, param, false);
+ return false;
}
- // show specific groups
- param = (String) getAppletParameter("showfeaturegroups", true);
- if (param != null)
+ if (autoenabledisplay)
{
- setFeatureGroupState(af, separatorListToArray(param, separator), true);
- // setFeatureGroupStateOn(newAlignFrame, param, true);
+ alf.getViewport().setShowSequenceFeatures(true);
+ // this next was for a checkbox in JalviewLite
+ // ((AlignFrame) alf).getViewport().sequenceFeatures.setState(true);
}
- // and now load features
- param = (String) getAppletParameter("features", true);
- if (param != null)
- {
- ret[0] = param;
- DataSourceType protocol = resolveFileProtocol(ret);
+ return true;
+ }
- result = parseFeaturesFile(af, ret[0], protocol);
+ @Override
+ public boolean loadScoreFile(String fileName, AlignFrame alf)
+ {
+ try
+ {
+ (alf == null ? getCurrentAlignFrame() : alf)
+ .loadJalviewDataFile(fileName, null, null, null);
+ return true;
+ } catch (Throwable t)
+ {
+ return false;
}
+ }
- param = (String) getAppletParameter("showFeatureSettings", true);
- if (param != null && param.equalsIgnoreCase("true"))
+ /**
+ * @j2sAlias openPcaPanel
+ *
+ * public static method for JalviewJS API to open a PCAPanel without
+ * necessarily using a dialog.
+ * @param modelName
+ * @param alf
+ *
+ * @return the PCAPanel, or the string "label.you_need_at_least_n_sequences"
+ * if number of sequences selected is inappropriate
+ */
+ @Override
+ public Object openPcaPanel(String modelName, AlignFrame alf)
+ {
+ if (alf == null)
{
- newFeatureSettings();
+ alf = getCurrentAlignFrame();
}
- return result;
+ return CalculationChooser.openPcaPanel(alf, modelName, null);
}
+ /**
+ * @j2sAlias openTreePanel
+ *
+ * Open a new Tree panel on the desktop statically. Params are
+ * standard (not set by Groovy). No dialog is opened.
+ * @param treeType
+ * @param modelName
+ * @param alf
+ *
+ * @return null, or the string "label.you_need_at_least_n_sequences" if number
+ * of sequences selected is inappropriate
+ */
@Override
- public void loadFeatures(String features, boolean autoenabledisplay)
+ public Object openTreePanel(String treeType, String modelName,
+ AlignFrame alf)
{
- loadFeaturesFrom(null, features, autoenabledisplay);
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ return CalculationChooser.openTreePanel(alf, treeType, modelName, null);
}
@Override
- public boolean loadFeaturesFrom(AlignFrame alf, String features,
- boolean autoenabledisplay)
+ public boolean orderAlignment(String[] ids, String undoName,
+ AlignFrame alf)
{
if (alf == null)
+ alf = getCurrentAlignFrame();
+ SequenceI[] sqs = null;
+ if (ids != null && ids.length > 0)
{
- 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;
+ }
}
- boolean ret = alf.parseFeaturesFile(features, DataSourceType.PASTE);
- if (!ret)
+ if (sqs == null)
{
return false;
}
- if (autoenabledisplay)
+ ;
+ final AlignmentOrder aorder = new AlignmentOrder(sqs);
+
+ if (undoName != null && undoName.trim().length() == 0)
{
- alf.getViewport().setShowSequenceFeatures(true);
- // this next was for a checkbox in JalviewLite
- // ((AlignFrame) alf).getViewport().sequenceFeatures.setState(true);
+ undoName = null;
}
- return true;
+ final String _undoName = undoName;
+ // TODO: deal with synchronization here: cannot raise any events until
+ // alfter
+ // this has returned.
+ return alf.sortBy(aorder, _undoName);
}
/**
- * Load in a Jnetfile if specified by parameter. Returns true if loaded, else
- * false.
+ * Allow an outside entity to initiate the second half of argument parsing
+ * (only).
*
- * @param alignFrame
- * @return
+ * @param args
+ * @return null is good
*/
- protected boolean loadJnetFile(AlignFrame af)
+ @Override
+ public Object parseArguments(String[] args)
{
- boolean result = false;
- String param = (String) getAppletParameter("jnetfile", true);
- if (param == null)
+
+ try
{
- // jnet became jpred around 2016
- param = (String) getAppletParameter("jpredfile", true);
- }
- if (param != null)
+ jalview.parseArguments(new ArgsParser(args), false);
+ return null;
+ } catch (Throwable t)
{
- 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 t;
}
- return result;
}
/**
- * Load PDBFiles if any specified by parameter(s). Returns true if loaded,
- * else false.
+ * @j2sAlias parseFeatureFile
*
- * @param loaderFrame
+ * @param filename
+ * @param alf
* @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()
+ @Override
+ public boolean parseFeaturesFile(String filename, AlignFrame alf)
{
- 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;
+ ret[0] = filename;
+ DataSourceType protocol = resolveFileProtocol(ret);
+ if (protocol == null)
+ return false;
+ return (alf == null ? getCurrentAlignFrame() : alf)
+ .parseFeaturesFile(ret[0], protocol);
}
- /**
- * 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)
+ @Override
+ public void removeSelectionListener(String listener, AlignFrame alf)
{
- boolean result = false;
- String treeFile = (String) getAppletParameter("tree", true);
- if (treeFile == null)
- {
- treeFile = (String) getAppletParameter("treefile", true);
- }
- if (treeFile != null)
+ List<SelectionListener> listeners = Desktop
+ .getStructureSelectionManager().getListeners();
+ for (int i = listeners.size(); --i >= 0;)
{
- 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)
+ SelectionListener l = listeners.get(i);
+ if (l instanceof JsSelectionListener
+ && ((JsSelectionListener) l).isFor(alf, listener))
{
- ex.printStackTrace();
+ listeners.remove(i);
+ break;
}
}
- return result;
- }
-
- /**
- * @j2sAlias openPcaPanel
- *
- * 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 = Jalview.getCurrentAlignFrame();
- }
- return CalculationChooser.openPcaPanel(af, modelName, null);
}
- /**
- * @j2sAlias openTreePanel
- *
- * 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)
+ private DataSourceType resolveFileProtocol(String[] retPath)
{
- if (af == null)
+ String path = retPath[0];
+ /*
+ * is it paste data?
+ */
+ if (path.startsWith("PASTE"))
{
- af = Jalview.getCurrentAlignFrame();
+ retPath[0] = path.substring(5);
+ return DataSourceType.PASTE;
}
- return CalculationChooser.openTreePanel(af, treeType, modelName, null);
- }
-
-
- @Override
- public String orderBy(String[] ids, String undoName)
- {
- return orderAlignmentBy(null, ids, undoName);
- }
- @Override
- public String orderAlignmentBy(AlignFrame alf, String[] ids,
- String undoName)
- {
- if (alf == null)
- alf = Jalview.getCurrentAlignFrame();
- SequenceI[] sqs = null;
- if (ids != null && ids.length > 0)
- {
- jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
- alf.getViewport().getAlignment().getSequencesArray());
- int s = 0;
- sqs = new SequenceI[ids.length];
- for (int i = 0; i < ids.length; i++)
- {
- if (ids[i].trim().length() == 0)
- {
- continue;
- }
- SequenceI sq = matcher.findIdMatch(ids[i]);
- if (sq != null)
- {
- sqs[s++] = sq;
- }
- }
- if (s > 0)
- {
- SequenceI[] sqq = new SequenceI[s];
- System.arraycopy(sqs, 0, sqq, 0, s);
- sqs = sqq;
- }
- else
- {
- sqs = null;
- }
- }
- if (sqs == null)
+ /*
+ * is it a URL?
+ */
+ if (path.indexOf("://") >= 0)
{
- return "";
+ return DataSourceType.URL;
}
- ;
- final AlignmentOrder aorder = new AlignmentOrder(sqs);
- if (undoName != null && undoName.trim().length() == 0)
+ /*
+ * try relative to document root
+ */
+ URL documentBase = getDocumentBase();
+ String withDocBase = resolveUrlForLocalOrAbsolute(path, documentBase);
+ if (HttpUtils.isValidUrl(withDocBase))
{
- undoName = null;
+ // if (debug)
+ // {
+ // System.err.println("Prepended document base '" + documentBase
+ // + "' to make: '" + withDocBase + "'");
+ // }
+ retPath[0] = withDocBase;
+ return DataSourceType.URL;
}
- final String _undoName = undoName;
- // TODO: deal with synchronization here: cannot raise any events until after
- // this has returned.
- return alf.sortBy(aorder, _undoName) ? "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
- {
- jalview.parseArguments(new ArgsParser(args), false);
- return null;
- } catch (Throwable t)
+ /*
+ * 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 t;
+ // if (debug)
+ // {
+ // System.err.println("Prepended codebase '" + codeBase
+ // + "' to make: '" + withCodeBase + "'");
+ // }
+ retPath[0] = withCodeBase;
+ return DataSourceType.URL;
}
- }
- @Override
- public void removeSelectionListener(AlignFrame af, String listener)
- {
-
- List<SelectionListener> listeners = Desktop
- .getStructureSelectionManager().getListeners();
- for (int i = listeners.size(); --i >= 0;)
+ /*
+ * try locating by classloader; try this last so files in the directory
+ * are resolved using document base
+ */
+ if (inArchive(getClass(), path))
{
- SelectionListener l = listeners.get(i);
- if (l instanceof JsSelectionListener
- && ((JsSelectionListener) l).isFor(af, listener))
- {
- listeners.remove(i);
- break;
- }
+ return DataSourceType.CLASSLOADER;
}
+ return null;
}
@Override
- public void scrollViewToColumnIn(final AlignFrame alf,
- final String leftHandColumn)
- {
- java.awt.EventQueue.invokeLater(new Runnable()
- {
-
- @Override
- public void run()
- {
- try
- {
- (alf == null ? Jalview.getCurrentAlignFrame() : alf)
- .scrollToColumn(
- Integer.valueOf(leftHandColumn).intValue());
-
- } catch (Exception ex)
- {
- System.err.println(
- "Couldn't parse integer arguments (leftHandColumn='"
- + leftHandColumn + "')");
- ex.printStackTrace();
- }
- }
- });
-
- }
-
- @Override
- public void scrollViewToIn(final AlignFrame alf, final String topRow,
- final String leftHandColumn)
+ public void scrollViewTo(int topRow, int leftHandColumn, AlignFrame alf)
{
// TODO test
java.awt.EventQueue.invokeLater(new Runnable()
{
try
{
- (alf == null ? Jalview.getCurrentAlignFrame() : alf).scrollTo(
- Integer.valueOf(topRow).intValue(),
- Integer.valueOf(leftHandColumn).intValue());
-
+ (alf == null ? getCurrentAlignFrame() : alf).scrollTo(topRow,
+ leftHandColumn);
} catch (Exception ex)
{
System.err.println("Couldn't parse integer arguments (topRow='"
}
@Override
- public void scrollViewToRowIn(final AlignFrame alf, final String topRow)
- {
- // TODO test
-
- java.awt.EventQueue.invokeLater(new Runnable()
- {
- @Override
- public void run()
- {
- try
- {
- (alf == null ? Jalview.getCurrentAlignFrame() : alf)
- .scrollToRow(Integer.valueOf(topRow).intValue());
-
- } catch (Exception ex)
- {
- 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);
- }
-
- @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)
+ public void select(String ids[], String cols[], AlignFrame alf)
{
- AlignFrame alf = (af == null ? Jalview.getCurrentAlignFrame() : af);
-
- if (sep == null || sep.length() == 0)
- {
- sep = separator;
- }
- else
- {
- if (debug)
- {
- System.err.println("Selecting region using separator string '"
- + separator + "'");
- }
- }
- // deparse fields
- String[] ids = separatorListToArray(sequenceIds, sep);
- String[] cols = separatorListToArray(columns, sep);
+ if (alf == null)
+ alf = getCurrentAlignFrame();
final SequenceGroup sel = new SequenceGroup();
final ColumnSelection csel = new ColumnSelection();
AlignmentI al = alf.getViewport().getAlignment();
csel.addElement(r);
}
}
- if (debug)
- {
- System.err.println("Range '" + cl + "' deparsed as [" + from
- + "," + to + "]");
- }
}
else
{
}
}
csel.addElement(r);
- if (debug)
- {
- System.err.println("Point selection '" + cl
- + "' deparsed as [" + r + "]");
- }
}
else
{
}
sel.setStartRes(start);
sel.setEndRes(end);
+ AlignFrame af = alf;
EventQueue.invokeLater(new Runnable()
{
@Override
public void run()
{
- alf.select(sel, csel,
- alf.getCurrentView().getAlignment().getHiddenColumns());
+ af.select(sel, csel,
+ af.getCurrentView().getAlignment().getHiddenColumns());
}
});
}
}
+ //
+ // @Override
+ // public void setFeatureGroupState(String[] groups, boolean state)
+ // {
+ // setFeatureGroupState(null, groups, state);
+ // }
+ //
+ // @Override
+ // public void setFeatureGroupState(String[] groups, boolean state)
+ // { // JalviewLite API
+ // setFeatureGroupStateOn(null, groups, state);
+ // }
+ //
+ @Override
+ public void setFeatureGroupState(final String[] groups,
+ boolean state, AlignFrame alf)
+ {
+ // setFeatureGroupState(alf, groups, state);
+ // java.awt.EventQueue.invokeLater(new Runnable()
+ // {
+ // @Override
+ // public void run()
+ // {
+ // (alf == null ? getCurrentAlignFrame() : alf)
+ // .setFeatureGroupState(
+ // separatorListToArray(groups, separator), state);
+ // }
+ // });
+ // }
+ //
+ // public void setFeatureGroupState(AlignFrame alf, String[] groups, boolean
+ // state) {
+ (alf == null ? getCurrentAlignFrame() : alf)
+ .setFeatureGroupState(groups, state);
+ }
+
@Override
- public void setFeatureGroupState(String[] groups, boolean state)
+ public void setSelectionListener(String listener, AlignFrame alf)
{
- setFeatureGroupState(null, groups, state);
+ Desktop.getStructureSelectionManager()
+ .addSelectionListener(new JsSelectionListener(alf, listener));
}
@Override
- public void setFeatureGroupState(String groups, boolean state)
- { // JalviewLite API
- setFeatureGroupStateOn(null, groups, state);
+ public void showOverview()
+ {
+ getCurrentAlignFrame().overviewMenuItem_actionPerformed(null);
}
+ /**
+ * @j2sAlias showStructure
+ */
@Override
- public void setFeatureGroupStateOn(final AlignFrame alf,
- final String groups, boolean state)
+ public void showStructure(String pdbID, String fileType, AlignFrame alf)
{
- setFeatureGroupState(alf, separatorListToArray(groups, separator), state);
-// java.awt.EventQueue.invokeLater(new Runnable()
-// {
-// @Override
-// public void run()
-// {
-// (alf == null ? Jalview.getCurrentAlignFrame() : alf)
-// .setFeatureGroupState(
-// separatorListToArray(groups, separator), state);
-// }
-// });
- }
-
- public void setFeatureGroupState(AlignFrame af, String[] groups, boolean state) {
- (af == null ? Jalview.getCurrentAlignFrame() : af).setFeatureGroupState(groups, state);
+ if (alf == null)
+ alf = getCurrentAlignFrame();
+ PDBEntry pe = null;
+ SequenceI[] seqs = null;
+ if (pdbID == null)
+ {
+ seqs = alf.getViewport().getSequenceSelection();
+ if (seqs.length == 0)
+ seqs = alf.getViewport().getAlignment().getSequencesArray();
+ for (int i = 0; i < seqs.length; i++)
+ {
+ Vector<PDBEntry> list = seqs[i].getAllPDBEntries();
+ if (list.size() > 0)
+ {
+ pe = list.get(0);
+ break;
+ }
+ }
+ }
+ if (pe == null)
+ {
+ if (pdbID == null)
+ return;
+ pe = new PDBEntry(pdbID, null, fileType);
+ List<SequenceI> list = alf.getViewport().getAlignment()
+ .getSequences();
+ List<SequenceI> tmp = new ArrayList<SequenceI>();
+ for (int i = 0; i < list.size(); i++)
+ {
+ SequenceI seq = list.get(i);
+ if (seq.getPDBEntry(pdbID) != null)
+ {
+ tmp.add(seq);
+ }
+ }
+ seqs = tmp.toArray(new SequenceI[tmp.size()]);
+ alf.alignPanel.selectSequences(tmp);
+ }
+ StructureViewer.launchStructureViewer(alf.alignPanel, pe, seqs);
}
+ // private or package-private methods
- @Override
- public void setSelectionListener(AlignFrame af, String listener)
+ /**
+ * 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
+ */
+ private static String resolveUrlForLocalOrAbsolute(String targetPath,
+ URL localref)
{
- Desktop.getStructureSelectionManager()
- .addSelectionListener(new JsSelectionListener(af, listener));
+ 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;
}
- @Override
- public void setSelectionListener(String listener)
+ /**
+ * parse the string into a list
+ *
+ * @param list
+ * @param separator
+ * @return elements separated by separator
+ */
+ private static String[] separatorListToArray(String list,
+ String separator)
{
- Desktop.getStructureSelectionManager()
- .addSelectionListener(new JsSelectionListener(null, listener));
+ // 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)
+ {
+ 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;
}
- @Override
- public void showOverview()
+ /**
+ * Discovers whether the given file is in the Applet Archive
+ *
+ * @param f
+ * String
+ * @return boolean
+ */
+ private static boolean inArchive(Class<?> c, String f)
{
- Jalview.getCurrentAlignFrame().overviewMenuItem_actionPerformed(null);
+ // This might throw a security exception in certain browsers
+ // Netscape Communicator for instance.
+ try
+ {
+ boolean rtn = (c.getResourceAsStream("/" + f) != null);
+ return rtn;
+ } catch (Exception ex)
+ {
+ System.out.println("Exception checking resources: " + f + " " + ex);
+ return false;
+ }
}
/**
* Allowing for a JavaScript function here.
*/
- public void callInitCallback()
+ void callInitCallback()
{
- Object initjscallback = getAppletParameter("oninit", false);
+ Object initjscallback = getParameterAsObject("oninit");
if (initjscallback != null)
{
try
* @param data
* @return String return from the callback method.
*/
- public String doSendCallback(Object callback, Object[] data)
+ String doSendCallback(Object callback, Object[] data)
{
Jalview me = jalview;
return "";
}
- private DataSourceType resolveFileProtocol(String[] retPath)
+ /**
+ * Initialize from Info.key/value pairs that match the old JalviewLite applet
+ * parameters.
+ *
+ * See http://www.jalview.org/old/v2_8/examples/appletParameters.html
+ *
+ * Note that some of these parameters are handled as command-line arguments,
+ * as determined in ArgsParser.
+ *
+ * @param alf
+ */
+ private void initFromParams(AlignFrame alf)
{
- String path = retPath[0];
- /*
- * is it paste data?
- */
- if (path.startsWith("PASTE"))
- {
- retPath[0] = path.substring(5);
- return DataSourceType.PASTE;
- }
-
- /*
- * is it a URL?
- */
- if (path.indexOf("://") >= 0)
- {
- return DataSourceType.URL;
- }
-
- /*
- * try relative to document root
- */
- URL documentBase = 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))
- {
- // if (debug)
- // {
- // System.err.println("Prepended codebase '" + codeBase
- // + "' to make: '" + withCodeBase + "'");
- // }
- retPath[0] = withCodeBase;
- return DataSourceType.URL;
- }
-
- /*
- * try locating by classloader; try this last so files in the directory
- * are resolved using document base
- */
- if (inArchive(getClass(), path))
+ String sep = getParameter("separator");
+ if (sep != null && sep.length() > 0)
{
- return DataSourceType.CLASSLOADER;
+ separator = sep;
}
- return null;
+ initTree(alf);
+ initScoreFile(alf);
+ initFeatures(alf);
+ initAnnotations(alf);
+ initJnetFile(alf);
+ initPdbFiles(alf);
}
/**
- * Discovers whether the given file is in the Applet Archive
+ * Load annotations if specified by parameter. Returns true if loaded, else
+ * false.
*
- * @param f
- * String
- * @return boolean
+ *
+ * @param alignFrame
+ * @return
*/
- private static boolean inArchive(Class<?> c, String f)
+ private boolean initAnnotations(AlignFrame alf)
{
- // This might throw a security exception in certain browsers
- // Netscape Communicator for instance.
- try
- {
- boolean rtn = (c.getResourceAsStream("/" + f) != null);
- return rtn;
- } catch (Exception ex)
- {
- System.out.println("Exception checking resources: " + f + " " + ex);
+
+ String param = getParameter("annotations");
+ if (param == null)
+ return false;
+ ret[0] = param;
+ DataSourceType protocol = resolveFileProtocol(ret);
+ param = ret[0];
+ if (!new AnnotationFile().annotateAlignmentView(alf.getViewport(),
+ param, protocol))
+ {
+ System.err.println("Annotations were not added from annotation file '"
+ + param + "'");
return false;
}
+ updateForAnnotations();
+ 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
+ * Load features file and view settings as specified by parameters. Returns
+ * true if features were loaded, else false.
+ *
+ * @param
+ *
+ * @param alignFrame
+ * @return
*/
- public static String resolveUrlForLocalOrAbsolute(String targetPath,
- URL localref)
+ private boolean initFeatures(AlignFrame alf)
{
- String resolvedPath = "";
- if (targetPath.startsWith("/"))
+
+ // ///////////////////////////
+ // 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 = getParameter("hidefeaturegroups");
+ if (param != null)
{
- String codebase = localref.toString();
- String localfile = localref.getFile();
- resolvedPath = codebase.substring(0,
- codebase.length() - localfile.length()) + targetPath;
- return resolvedPath;
+ setFeatureGroupState(separatorListToArray(param, separator),
+ false, alf);
+ // setFeatureGroupStateOn(newAlignFrame, param, false);
}
-
- /*
- * 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)
+ // show specific groups
+ param = getParameter("showfeaturegroups");
+ if (param != null)
{
- directoryPath = directoryPath.substring(0, lastSeparator + 1);
+ setFeatureGroupState(separatorListToArray(param, separator),
+ true, alf);
+ // setFeatureGroupStateOn(newAlignFrame, param, true);
}
-
- if (targetPath.startsWith("/"))
+ // and now load features
+ param = getParameter("features");
+ if (param == null)
{
- /*
- * 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);
+ return false;
}
- else
+ if (!parseFeaturesFile(param, alf))
+ return false;
+ param = getParameter("showFeatureSettings");
+ if (param != null && param.equalsIgnoreCase("true"))
{
- resolvedPath = directoryPath + targetPath;
+ alf.showFeatureSettingsUI();
}
- // if (debug)
- // {
- // System.err.println(
- // "resolveUrlForLocalOrAbsolute returning " + resolvedPath);
- // }
- return resolvedPath;
+ return true;
}
/**
- * parse the string into a list
+ * Load in a Jnetfile if specified by parameter. Returns true if loaded, else
+ * false.
*
- * @param list
- * @param separator
- * @return elements separated by separator
+ * @param alignFrame
+ * @return
*/
- public static String[] separatorListToArray(String list, String separator)
+ private boolean initJnetFile(AlignFrame alf)
{
- // 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)
+
+ String param = getParameter("jnetfile");
+ if (param == null)
{
- jv.addElement(list.substring(cp, pos));
- cp = pos + seplen;
+ // jnet became jpred around 2016
+ param = getParameter("jpredfile");
}
- if (cp < list.length())
+ if (param != null)
{
- String c = list.substring(cp);
- if (!c.equals(separator))
+ try
{
- jv.addElement(c);
- }
- }
- if (jv.size() > 0)
- {
- String[] v = new String[jv.size()];
- for (int i = 0; i < v.length; i++)
+ ret[0] = param;
+ DataSourceType protocol = resolveFileProtocol(ret);
+ JPredFile predictions = new JPredFile(ret[0], protocol);
+ JnetAnnotationMaker.add_annotation(predictions,
+ alf.getViewport().getAlignment(), 0, false);
+ // false == do not add sequence profile from concise output
+ alf.getViewport().getAlignment().setupJPredAlignment();
+ updateForAnnotations();
+ } catch (Exception ex)
{
- v[i] = jv.elementAt(i);
+ ex.printStackTrace();
+ return false;
}
- jv.removeAllElements();
- return v;
}
- return null;
+ return true;
}
- public class JsSelectionListener
- implements jalview.structure.SelectionListener
+ /**
+ * Load PDBFiles if any specified by parameter(s). Returns true if loaded,
+ * else false.
+ *
+ * @param loaderFrame
+ * @return
+ */
+ private boolean initPdbFiles(AlignFrame alf)
{
- AlignFrame _af;
+ /*
+ * <param name="alignpdbfiles" value="false/true"/> Undocumented for 2.6 -
+ * related to JAL-434
+ */
- String _listener;
+ // 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<>();
+ // init a lazy matcher if we're asked to
+ boolean relaxed = "true"
+ .equalsIgnoreCase(getParameter("relaxedidmatch"));
+ jalview.analysis.SequenceIdMatcher matcher = relaxed
+ ? new jalview.analysis.SequenceIdMatcher(
+ alf.getViewport().getAlignment().getSequencesArray())
+ : null;
- public JsSelectionListener(AlignFrame af, String listener)
+ String param = getParameter("PDBFILE");
+ int plast = (param == null ? 9 : 1);
+ if (param == null && (param = getParameter("PDBFILE1")) == null)
{
- _af = af;
- _listener = listener;
+ return false;
}
-
- @Override
- public void selection(SequenceGroup seqsel, ColumnSelection colsel,
- HiddenColumns hidden, SelectionSource source)
+ for (int p = 1; p <= plast; p++)
{
- // System.err.println("Testing selection event relay to
- // jsfunction:"+_listener);
- String setid = "";
- AlignFrame src = _af;
- if (source != null)
+ if (p > 1)
{
- if (source instanceof AlignViewport
- && Jalview.getCurrentAlignFrame().getViewport() == source)
- {
- src = Jalview.getCurrentAlignFrame();
- if (src != _af)
- return;
- }
+ param = getParameter("PDBFILE" + p);
+ if (param == null)
+ break;
}
- 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)
+ PDBEntry pdb = new PDBEntry();
+
+ String seqstring;
+ SequenceI[] seqs = null;
+ String[] chains = null;
+
+ StringTokenizer st = new StringTokenizer(param, " ");
+
+ if (st.countTokens() < 2)
{
- seqs = new String[seqsel.getSize()];
- for (int i = 0; i < seqs.length; i++)
+ String sequence = getParameter("PDBSEQ");
+ if (sequence != null)
{
- seqs[i] = seqsel.getSequenceAt(i).getName();
+ seqs = new SequenceI[] { matcher == null
+ ? (Sequence) alf.getViewport().getAlignment()
+ .findName(sequence)
+ : matcher.findIdMatch(sequence) };
}
- if (strt < seqsel.getStartRes())
+
+ }
+ else
+ {
+ param = st.nextToken();
+ List<SequenceI> tmp = new ArrayList<>();
+ List<String> tmp2 = new ArrayList<>();
+
+ while (st.hasMoreTokens())
{
- strt = seqsel.getStartRes();
+ 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) alf.getViewport().getAlignment()
+ .findName(seqstring)
+ : matcher.findIdMatch(seqstring));
}
- if (end == -1 || end > seqsel.getEndRes())
+
+ seqs = tmp.toArray(new SequenceI[tmp.size()]);
+ if (tmp2.size() == tmp.size())
{
- end = seqsel.getEndRes();
+ chains = tmp2.toArray(new String[tmp2.size()]);
}
}
- if (colsel != null && !colsel.isEmpty())
+ 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)
{
- if (end == -1)
+ for (int i = 0; i < seqs.length; i++)
{
- end = colsel.getMax() + 1;
+ if (seqs[i] != null)
+ {
+ ((Sequence) seqs[i]).addPDBId(pdb);
+ StructureSelectionManager
+ .getStructureSelectionManager(
+ (StructureSelectionManagerProvider) this)
+ .registerPDBEntry(pdb);
+ }
}
- cols = new String[colsel.getSelected().size()];
- for (int i = 0; i < cols.length; i++)
+
+ // if (doAlign)
+ // {
+ // pdbs.add(new Object[] { pdb, seqs, chains, protocol });
+ // }
+ // else
{
- cols[i] = "" + (1 + colsel.getSelected().get(i).intValue());
+ StructureViewer.launchStructureViewer(
+ (alf == null ? getCurrentAlignFrame() : alf).alignPanel,
+ pdb, seqs);
}
}
- else
+ }
+ //
+ // 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 true;
+ }
+
+ /**
+ * Load a score file if specified by parameter. Returns true if file was
+ * loaded, else false.
+ *
+ * @param loaderFrame
+ */
+ private boolean initScoreFile(AlignFrame alf)
+ {
+
+ String sScoreFile = getParameter("scoreFile");
+ if (sScoreFile != null && !"".equals(sScoreFile))
+ {
+ try
{
- if (seqsel != null && seqsel.getSize() > 0)
+ if (loadScoreFile(sScoreFile, alf))
{
- // send a valid range, otherwise we send the empty selection
- cols = new String[1];
- cols[0] = "" + (1 + strt) + "-" + (1 + end);
+ return true;
}
- ;
-
+ 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());
}
-
- doSendCallback(_listener,
- new Object[]
- { src, setid, seqs, cols });
}
+ return false;
+ }
- public boolean isFor(AlignFrame af, String listener)
+ /**
+ * Load a tree for the alignment if specified by parameter. Returns true if a
+ * tree was loaded, else false.
+ *
+ * @return
+ */
+ private boolean initTree(AlignFrame alf)
+ {
+ String treeFile;
+ if ((treeFile = getParameter("tree")) == null
+ && (treeFile = getParameter("treefile")) == null)
+ return false;
+ if (alf == null)
+ alf = getCurrentAlignFrame();
+ try
{
- return _af == af && _listener.contentEquals(listener);
+ ret[0] = treeFile;
+ NewickFile nf = new NewickFile(treeFile, resolveFileProtocol(ret));
+ nf.parse();
+ if (nf.getTree() != null)
+ {
+ treeFile = ret[0];
+ alf.getViewport()
+ .setCurrentTree(alf.showNewickTree(nf, treeFile).getTree());
+ return true;
+ }
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
}
-
+ return false;
}
- @Override
- public AlignViewportI getViewport()
+ private void updateForAnnotations()
{
- return Jalview.getCurrentAlignFrame().getViewport();
+ getCurrentAlignFrame().updateForAnnotations();
}
-
}
git://source.jalview.org / jalview.git / commitdiff