- // 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;
+ // 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);
+
+ /**
+ * List separator string
+ *
+ * @return the separator
+ */
+
+ public 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 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);
+
+ /**
+ * 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 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 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 String orderBy(String order, String undoName, String sep);
+
+ /**
+ * process commandline arguments after the JavaScript application has started
+ *
+ * @param args
+ * @return
+ */
+ public 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 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 String[] separatorListToArray(String list);
+
+ 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);
+
+ /**
+ * List separator string
+ *
+ * @param separator
+ * the separator to set. empty string will reset separator to default
+ */
+
+ public void setSeparator(String separator);
+
+ public void showOverview();
+
+ public void updateForAnnotations();