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
public interface JalviewJSApi
{
- void showOverview();
+ // debug flag - controls output to standard out
+ public static boolean debug = false;
/**
- * process commandline arguments after the JavaScript application has started
- *
- * @param args
- * @return
- */
- Object parseArguments(String[] args);
-
-
- /**
- * Open a new Tree panel on the desktop statically. Params are standard (not
- * set by Groovy). No dialog is opened.
+ * bind a pdb file to a sequence in the given AlignFrame.
*
- * @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
+ * @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 Object openTreePanel(AlignFrame af, String treeType,
- String modelName);
-
- /**
- * public static method for JalviewJS API to open a PCAPanel without
- * necessarily using a dialog.
- *
- * @param af
- * may be null
- * @param modelName
- * @return the PCAPanel, or the string "label.you_need_at_least_n_sequences"
- * if number of sequences selected is inappropriate
- */
- public Object openPcaPanel(AlignFrame af, String modelName);
+ public 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 abstract interface for
- * jalview.appletgui.AlignFrame</em><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
// public interface JalviewLiteJsApi
// {
- /**
- * @return String list of selected sequence IDs, each terminated by the
- * 'boolean not' character (""+0x00AC); or (¬);
- */
-
- public abstract String getSelectedSequences();
-
- /**
- * @param sep
- * separator string or null for default
- * @return String list of selected sequence IDs, each terminated by given
- * separator string
- */
-
- public abstract String getSelectedSequences(String sep);
-
- /**
- * @param alf
- * AlignFrame containing selection
- * @return String list of selected sequence IDs, each terminated by current
- * default separator sequence
- *
- */
- public abstract String getSelectedSequencesFrom(AlignFrame alf);
-
- /**
- * get list of selected sequence IDs separated by given separator
- *
- * @param alf
- * window containing selection
- * @param sep
- * separator string to use - default is 'boolean not'
- * @return String list of selected sequence IDs, each terminated by the given
- * separator
- */
- public abstract String getSelectedSequencesFrom(AlignFrame alf,
- String sep);
-
- /**
- *
- * @param sequenceId
- * id of sequence to highlight
- * @param position
- * integer position [ tobe implemented or range ] on sequence
- * @param alignedPosition
- * true/false/empty string - indicate if position is an alignment
- * column or unaligned sequence position
- */
-
- public abstract void highlight(String sequenceId, String position,
- String alignedPosition);
-
- /**
- *
- * @param sequenceId
- * id of sequence to highlight
- * @param position
- * integer position [ tobe implemented or range ] on sequence
- * @param alignedPosition
- * false, blank or something else - indicate if position is an
- * alignment column or unaligned sequence position
- */
- public abstract void highlightIn(AlignFrame alf, String sequenceId,
- String position, String alignedPosition);
-
- /**
- * select regions of the currrent alignment frame
- *
- * @param sequenceIds
- * String separated list of sequence ids or empty string
- * @param columns
- * String separated list { column range or column, ..} or empty
- * string
- */
-
- public abstract void select(String sequenceIds, String columns);
-
- /**
- * select regions of the currrent alignment frame
- *
- * @param toselect
- * String separated list { column range, seq1...seqn sequence ids }
- * @param sep
- * separator between toselect fields
- */
-
- public abstract void select(String sequenceIds, String columns,
- String sep);
-
- /**
- * select regions of the given alignment frame
- *
- * @param alf
- * @param toselect
- * String separated list { column range, seq1...seqn sequence ids }
- * @param sep
- * separator between toselect fields
- */
- public abstract void selectIn(AlignFrame alf, String sequenceIds,
- String columns);
-
- /**
- * select regions of the given alignment frame
- *
- * @param alf
- * @param toselect
- * String separated list { column range, seq1...seqn sequence ids }
- * @param sep
- * separator between toselect fields
- */
- public abstract void selectIn(AlignFrame alf, String sequenceIds,
- String columns, String sep);
-
- /**
- * get sequences selected in current AlignFrame and return their alignment in
- * format 'format' either with or without suffix
- *
- * @param alf
- * - where selection is
- * @param format
- * - format of alignment file
- * @param suffix
- * - "true" to append /start-end string to each sequence ID
- * @return selected sequences as flat file or empty string if there was no
- * current selection
- */
-
- public abstract String getSelectedSequencesAsAlignment(String format,
- String suffix);
-
- /**
- * get sequences selected in alf and return their alignment in format 'format'
- * either with or without suffix
- *
- * @param alf
- * - where selection is
- * @param format
- * - format of alignment file
- * @param suffix
- * - "true" to append /start-end string to each sequence ID
- * @return selected sequences as flat file or empty string if there was no
- * current selection
- */
- public abstract String getSelectedSequencesAsAlignmentFrom(
- AlignFrame alf,
- String format, String suffix);
-
- /**
- * get a separator separated list of sequence IDs reflecting the order of the
- * current alignment
- *
- * @return
- */
-
- public abstract String getAlignmentOrder();
-
- /**
- * get a separator separated list of sequence IDs reflecting the order of the
- * alignment in alf
- *
- * @param alf
- * @return
- */
- public abstract String getAlignmentOrderFrom(AlignFrame alf);
-
- /**
- * get a sep separated list of sequence IDs reflecting the order of the
- * alignment in alf
- *
- * @param alf
- * @param sep
- * - separator to use
- * @return
- */
- public abstract String getAlignmentOrderFrom(AlignFrame alf,
- String sep);
-
- /**
- * re-order the current alignment using the given list of sequence IDs
- *
- * @param order
- * - sep separated list
- * @param undoName
- * - string to use when referring to ordering action in undo buffer
- * @return 'true' if alignment was actually reordered. empty string if
- * alignment did not contain sequences.
- */
-
- public abstract String orderBy(String order, String undoName);
-
- /**
- * re-order the current alignment using the given list of sequence IDs
- * separated by sep
- *
- * @param order
- * - sep separated list
- * @param undoName
- * - string to use when referring to ordering action in undo buffer
- * @param sep
- * @return 'true' if alignment was actually reordered. empty string if
- * alignment did not contain sequences.
- */
-
- public abstract String orderBy(String order, String undoName,
- String sep);
-
- /**
- * re-order the given alignment using the given list of sequence IDs separated
- * by sep
- *
- * @param alf
- * @param order
- * - sep separated list
- * @param undoName
- * - string to use when referring to ordering action in undo buffer
- * @param sep
- * @return 'true' if alignment was actually reordered. empty string if
- * alignment did not contain sequences.
- */
- public abstract String orderAlignmentBy(AlignFrame alf, String order,
- String undoName, String sep);
-
- /**
- * get alignment as format (format names FASTA, BLC, CLUSTAL, MSF, PILEUP,
- * PFAM - see jalview.io.AppletFormatAdapter for full list);
- *
- * @param format
- * @return
- */
-
- public abstract String getAlignment(String format);
-
- /**
- * get alignment displayed in alf as format
- *
- * @param alf
- * @param format
- * @return
- */
- public abstract String getAlignmentFrom(AlignFrame alf, String format);
-
- /**
- * get alignment as format with jalview start-end sequence suffix appended
- *
- * @param format
- * @param suffix
- * @return
- */
-
- public abstract String getAlignment(String format, String suffix);
-
- /**
- * get alignment displayed in alf as format with or without the jalview
- * start-end sequence suffix appended
- *
- * @param alf
- * @param format
- * @param suffix
- * @return
- */
- public abstract String getAlignmentFrom(AlignFrame alf, String format,
- String suffix);
-
- /**
- * add the given features or annotation to the current alignment
- *
- * @param annotation
- */
-
- public abstract void loadAnnotation(String annotation);
-
- /**
- * add the given features or annotation to the given alignment view
- *
- * @param alf
- * @param annotation
- */
- public abstract void loadAnnotationFrom(AlignFrame alf,
- String annotation);
-
- /**
- * parse the given string as a jalview feature or GFF annotation file and
- * optionally enable feature display on the current AlignFrame
- *
- * @param features
- * - gff or features file
- * @param autoenabledisplay
- * - when true, feature display will be enabled if any features can
- * be parsed from the string.
- */
-
- public abstract void loadFeatures(String features,
- boolean autoenabledisplay);
-
- /**
- * parse the given string as a jalview feature or GFF annotation file and
- * optionally enable feature display on the given AlignFrame.
- *
- * @param alf
- * @param features
- * - gff or features file
- * @param autoenabledisplay
- * - when true, feature display will be enabled if any features can
- * be parsed from the string.
- * @return true if data parsed as features
- */
- public abstract boolean loadFeaturesFrom(AlignFrame alf, String features,
- boolean autoenabledisplay);
-
- /**
- * get the sequence features in the given format (Jalview or GFF);
- *
- * @param format
- * @return
- */
-
- public abstract String getFeatures(String format);
-
- /**
- * get the sequence features in alf in the given format (Jalview or GFF);
- *
- * @param alf
- * @param format
- * @return
- */
- public abstract String getFeaturesFrom(AlignFrame alf, String format);
-
- /**
- * get current alignment's annotation as an annotation file
- *
- * @return
- */
-
- public abstract String getAnnotation();
-
- /**
- * get alignment view alf's annotation as an annotation file
- *
- * @param alf
- * @return
- */
- public abstract String getAnnotationFrom(AlignFrame alf);
+ /**
+ * get alignment as format (format names FASTA, BLC, CLUSTAL, MSF, PILEUP,
+ * PFAM - see jalview.io.AppletFormatAdapter for full list);
+ *
+ * @param format
+ * @return
+ */
+
+ public 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
// * @return
// */
//
- // public abstract AlignFrame newView();
+ // public AlignFrame newView();
//
// /**
// * create a new view named name and return the AlignFrame instance
// * @return
// */
//
- // public abstract AlignFrame newView(String name);
+ // public AlignFrame newView(String name);
//
// /**
// * create a new view on alf and return the AlignFrame instance
// * @param alf
// * @return
// */
- // public abstract AlignFrame newViewFrom(AlignFrame alf);
+ // public AlignFrame newViewFrom(AlignFrame alf);
//
// /**
// * create a new view named name on alf
// * @param name
// * @return
// */
- // 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);
+
+ 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();
}
git://source.jalview.org / jalview.git / blobdiff