+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$);
+ * Copyright (C); $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option); any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.javascript;
-import jalview.appletgui.AlignFrame;
+import jalview.api.AlignFrameI;
/**
* 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>
+ * <br><em>TODO: introduce abstract interface for jalview.appletgui.AlignFrameI</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.
/**
* @author jimp
- *
+ *
*/
public interface JalviewLiteJsApi
{
/**
* @return String list of selected sequence IDs, each terminated by the
- * 'boolean not' character (""+0x00AC) or (¬)
+ * 'boolean not' character (""+0x00AC); or (¬);
*/
public abstract String getSelectedSequences();
/**
* @param alf
- * alignframe containing selection
+ * AlignFrameI containing selection
* @return String list of selected sequence IDs, each terminated by current
* default separator sequence
*
*/
- public abstract String getSelectedSequencesFrom(AlignFrame alf);
+ public abstract String getSelectedSequencesFrom(AlignFrameI alf);
/**
* get list of selected sequence IDs separated by given separator
* @return String list of selected sequence IDs, each terminated by the given
* separator
*/
- public abstract String getSelectedSequencesFrom(AlignFrame alf, String sep);
+ public abstract String getSelectedSequencesFrom(AlignFrameI alf,
+ String sep);
/**
*
* false, blank or something else - indicate if position is an
* alignment column or unaligned sequence position
*/
- public abstract void highlightIn(AlignFrame alf, String sequenceId,
+ public abstract void highlightIn(AlignFrameI alf, String sequenceId,
String position, String alignedPosition);
/**
* @param sep
* separator between toselect fields
*/
- public abstract void select(String sequenceIds, String columns, String sep);
+ public abstract void select(String sequenceIds, String columns,
+ String sep);
/**
* select regions of the given alignment frame
* @param sep
* separator between toselect fields
*/
- public abstract void selectIn(AlignFrame alf, String sequenceIds,
+ public abstract void selectIn(AlignFrameI alf, String sequenceIds,
String columns);
/**
* @param sep
* separator between toselect fields
*/
- public abstract void selectIn(AlignFrame alf, String sequenceIds,
+ public abstract void selectIn(AlignFrameI alf, String sequenceIds,
String columns, String sep);
/**
- * get sequences selected in current alignFrame and return their alignment in
+ * get sequences selected in current AlignFrameI and return their alignment in
* format 'format' either with or without suffix
*
* @param alf
* current selection
*/
public abstract String getSelectedSequencesAsAlignmentFrom(
- AlignFrame alf, String format, String suffix);
+ AlignFrameI alf,
+ String format, String suffix);
/**
- * get a separator separated list of sequence IDs reflecting the order of the current alignment
+ * 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
- *
+ * 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);
+ public abstract String getAlignmentOrderFrom(AlignFrameI alf);
/**
- * get a sep separated list of sequence IDs reflecting the order of the alignment in alf
+ * get a sep separated list of sequence IDs reflecting the order of the
+ * alignment in alf
*
* @param alf
- * @param sep - separator to use
+ * @param sep
+ * - separator to use
* @return
*/
- public abstract String getAlignmentOrderFrom(AlignFrame alf, String sep);
+ public abstract String getAlignmentOrderFrom(AlignFrameI 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.
+ *
+ * @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);
* @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.
+ * @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);
+ 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
+ * re-order the given alignment using the given list of sequence IDs separated
+ * by sep
*
* @param alf
* @param order
* @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.
+ * @return 'true' if alignment was actually reordered. empty string if
+ * alignment did not contain sequences.
*/
- public abstract String orderAlignmentBy(AlignFrame alf, String order,
+ public abstract String orderAlignmentBy(AlignFrameI 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)
+ * get alignment as format (format names FASTA, BLC, CLUSTAL, MSF, PILEUP,
+ * PFAM - see jalview.io.AppletFormatAdapter for full list);
+ *
* @param format
* @return
*/
/**
* get alignment displayed in alf as format
+ *
* @param alf
* @param format
* @return
*/
- public abstract String getAlignmentFrom(AlignFrame alf, String format);
+ public abstract String getAlignmentFrom(AlignFrameI 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
+ * 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,
+ public abstract String getAlignmentFrom(AlignFrameI 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);
+ public abstract void loadAnnotationFrom(AlignFrameI alf,
+ String annotation);
/**
- * get the sequence features in the given format (Jalview or GFF)
+ * parse the given string as a jalview feature or GFF annotation file and
+ * optionally enable feature display on the current AlignFrameI
+ *
+ * @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 AlignFrameI.
+ *
+ * @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(AlignFrameI 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)
+ * get the sequence features in alf in the given format (Jalview or GFF);
+ *
* @param alf
* @param format
* @return
*/
- public abstract String getFeaturesFrom(AlignFrame alf, String format);
+ public abstract String getFeaturesFrom(AlignFrameI 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);
+ public abstract String getAnnotationFrom(AlignFrameI alf);
/**
- * create a new view and return the alignFrame instance
+ * create a new view and return the AlignFrameI instance
+ *
* @return
*/
- public abstract AlignFrame newView();
+ public abstract AlignFrameI newView();
/**
- * create a new view named name and return the alignFrame instance
+ * create a new view named name and return the AlignFrameI instance
+ *
* @param name
* @return
*/
- public abstract AlignFrame newView(String name);
+ public abstract AlignFrameI newView(String name);
/**
- * create a new view on alf and return the alignFrame instance
+ * create a new view on alf and return the AlignFrameI instance
+ *
* @param alf
* @return
*/
- public abstract AlignFrame newViewFrom(AlignFrame alf);
+ public abstract AlignFrameI newViewFrom(AlignFrameI alf);
/**
* create a new view named name on alf
+ *
* @param alf
* @param name
* @return
*/
- public abstract AlignFrame newViewFrom(AlignFrame alf, String name);
+ public abstract AlignFrameI newViewFrom(AlignFrameI alf, String name);
/**
*
* window title
* @return null or new alignment frame
*/
- public abstract AlignFrame loadAlignment(String text, String title);
+ public abstract AlignFrameI 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)]
+ *
+ * @param listener
+ * name of javascript function (called with arguments
+ * [jalview.appletgui.AlignFrameI,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
+ *
+ * @param af
+ * (null or specific AlignFrameI for which events are to be listened
+ * for);
+ * @param listener
+ * name of javascript function
*/
- public abstract void setMouseoverListener(AlignFrame af, String listener);
+ public abstract void setMouseoverListener(AlignFrameI 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)]
+ * 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.AlignFrameI, 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);
+ public abstract void setSelectionListener(AlignFrameI 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.
- @see jalview.javascript.MouseOverStructureListener
+ * 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);
+ 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)
+ * the given AlignFrameI (or null for all callbacks);
*
* @param af
- * (may be null)
+ * (may be null);
* @param listener
- * (may be null)
+ * (may be null);
*/
- public abstract void removeJavascriptListener(AlignFrame af,
+ public abstract void removeJavascriptListener(AlignFrameI af,
String listener);
/**
String pdbfile);
/**
- * bind a pdb file to a sequence in the given alignFrame.
+ * bind a pdb file to a sequence in the given AlignFrameI.
*
* @param alFrame
- * - null or specific alignFrame. This specifies the dataset that
+ * - null or specific AlignFrameI. This specifies the dataset that
* will be searched for a seuqence called sequenceId
* @param sequenceId
* - sequenceId within the dataset.
* structure for indicating when PDB parsing or sequenceId location
* fails.
*/
- public abstract boolean addPdbFile(AlignFrame alFrame, String sequenceId,
+ public abstract boolean addPdbFile(AlignFrameI alFrame, String sequenceId,
String pdbEntryString, String pdbFile);
/**
- * adjust horizontal/vertical scroll to the make the given location the top left hand corner for given current view
+ * 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,
+ public abstract void scrollViewToIn(AlignFrameI 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(AlignFrameI 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(AlignFrameI alf,
String leftHandColumn);
/**
*
* @return
- * @see jalview.appletgui.AlignFrame#getFeatureGroups()
+ * @see jalview.appletgui.AlignFrameI#getFeatureGroups();
*/
public abstract String getFeatureGroups();
/**
* @param alf
- * alignframe to get feature groups on
+ * AlignFrameI to get feature groups on
* @return
- * @see jalview.appletgui.AlignFrame#getFeatureGroups()
+ * @see jalview.appletgui.AlignFrameI#getFeatureGroups();
*/
- public abstract String getFeatureGroupsOn(AlignFrame alf);
+ public abstract String getFeatureGroupsOn(AlignFrameI alf);
/**
* @param visible
* @return
- * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean)
+ * @see jalview.appletgui.AlignFrameI#getFeatureGroupsOfState(boolean);
*/
public abstract String getFeatureGroupsOfState(boolean visible);
* align frame to get groups of state visible
* @param visible
* @return
- * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean)
+ * @see jalview.appletgui.AlignFrameI#getFeatureGroupsOfState(boolean);
*/
- public abstract String getFeatureGroupsOfStateOn(AlignFrame alf,
+ public abstract String getFeatureGroupsOfStateOn(AlignFrameI alf,
boolean visible);
/**
* tab separated list of group names
* @param state
* true or false
- * @see jalview.appletgui.AlignFrame#setFeatureGroupState(java.lang.String[],
- * boolean)
+ * @see jalview.appletgui.AlignFrameI#setFeatureGroupState(java.lang.String[],
+ * boolean);
*/
- public abstract void setFeatureGroupStateOn(AlignFrame alf,
- String groups, boolean state);
+ public abstract void setFeatureGroupStateOn(AlignFrameI alf,
+ String groups,
+ boolean state);
public abstract void setFeatureGroupState(String groups, boolean state);
/**
* 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);
-}
\ No newline at end of file
+ /// 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(AlignFrameI 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;
+
+}
git://source.jalview.org / jalview.git / blobdiff