/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$);
- * Copyright (C); $$Year-Rel$$ The Jalview Authors
+ * 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.
+ * 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
*/
package jalview.javascript;
-import jalview.api.AlignFrameI;
+import jalview.appletgui.AlignFrame;
/**
* The following public methods may be called
* externally, eg via javascript in an HTML page.
*
- * <br><em>TODO: introduce abstract interface for jalview.appletgui.AlignFrameI</em><br>
+ * <br><em>TODO: introduce abstract 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.
/**
* @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
- * AlignFrameI containing selection
+ * alignframe containing selection
* @return String list of selected sequence IDs, each terminated by current
* default separator sequence
*
*/
- public abstract String getSelectedSequencesFrom(AlignFrameI alf);
+ public abstract String getSelectedSequencesFrom(AlignFrame 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(AlignFrameI alf,
+ public abstract String getSelectedSequencesFrom(AlignFrame alf,
String sep);
/**
* false, blank or something else - indicate if position is an
* alignment column or unaligned sequence position
*/
- public abstract void highlightIn(AlignFrameI alf, String sequenceId,
+ public abstract void highlightIn(AlignFrame alf, String sequenceId,
String position, String alignedPosition);
/**
* @param sep
* separator between toselect fields
*/
- public abstract void selectIn(AlignFrameI alf, String sequenceIds,
+ public abstract void selectIn(AlignFrame alf, String sequenceIds,
String columns);
/**
* @param sep
* separator between toselect fields
*/
- public abstract void selectIn(AlignFrameI alf, String sequenceIds,
+ public abstract void selectIn(AlignFrame alf, String sequenceIds,
String columns, String sep);
/**
- * get sequences selected in current AlignFrameI and return their alignment in
+ * get sequences selected in current alignFrame and return their alignment in
* format 'format' either with or without suffix
*
* @param alf
* @return selected sequences as flat file or empty string if there was no
* current selection
*/
- public abstract String getSelectedSequencesAsAlignmentFrom(
- AlignFrameI alf,
+ public abstract String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
String format, String suffix);
/**
* @param alf
* @return
*/
- public abstract String getAlignmentOrderFrom(AlignFrameI alf);
+ public abstract String getAlignmentOrderFrom(AlignFrame alf);
/**
* get a sep separated list of sequence IDs reflecting the order of the
* - separator to use
* @return
*/
- public abstract String getAlignmentOrderFrom(AlignFrameI alf,
- String sep);
+ public abstract String getAlignmentOrderFrom(AlignFrame alf, String sep);
/**
* re-order the current alignment using the given list of sequence IDs
* @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
* @return 'true' if alignment was actually reordered. empty string if
* alignment did not contain sequences.
*/
- public abstract String orderAlignmentBy(AlignFrameI alf, String order,
+ 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);
+ * PFAM - see jalview.io.AppletFormatAdapter for full list)
*
* @param format
* @return
* @param format
* @return
*/
- public abstract String getAlignmentFrom(AlignFrameI alf, String format);
+ public abstract String getAlignmentFrom(AlignFrame alf, String format);
/**
* get alignment as format with jalview start-end sequence suffix appended
* @param suffix
* @return
*/
- public abstract String getAlignmentFrom(AlignFrameI alf, String format,
+ public abstract String getAlignmentFrom(AlignFrame alf, String format,
String suffix);
/**
* @param alf
* @param annotation
*/
- public abstract void loadAnnotationFrom(AlignFrameI alf,
+ 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 AlignFrameI
+ * optionally enable feature display on the current alignFrame
*
* @param features
* - gff or features file
/**
* parse the given string as a jalview feature or GFF annotation file and
- * optionally enable feature display on the given AlignFrameI.
+ * optionally enable feature display on the given alignFrame.
*
* @param alf
* @param features
* be parsed from the string.
* @return true if data parsed as features
*/
- public abstract boolean loadFeaturesFrom(AlignFrameI alf, String features,
+ public abstract boolean loadFeaturesFrom(AlignFrame alf, String features,
boolean autoenabledisplay);
/**
- * get the sequence features in the given format (Jalview or GFF);
+ * 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(AlignFrameI alf, String format);
+ public abstract String getFeaturesFrom(AlignFrame alf, String format);
/**
* get current alignment's annotation as an annotation file
* @param alf
* @return
*/
- public abstract String getAnnotationFrom(AlignFrameI alf);
+ public abstract String getAnnotationFrom(AlignFrame alf);
/**
- * create a new view and return the AlignFrameI instance
+ * create a new view and return the alignFrame instance
*
* @return
*/
- public abstract AlignFrameI newView();
+ public abstract AlignFrame newView();
/**
- * create a new view named name and return the AlignFrameI instance
+ * create a new view named name and return the alignFrame instance
*
* @param name
* @return
*/
- public abstract AlignFrameI newView(String name);
+ public abstract AlignFrame newView(String name);
/**
- * create a new view on alf and return the AlignFrameI instance
+ * create a new view on alf and return the alignFrame instance
*
* @param alf
* @return
*/
- public abstract AlignFrameI newViewFrom(AlignFrameI alf);
+ public abstract AlignFrame newViewFrom(AlignFrame alf);
/**
* create a new view named name on alf
* @param name
* @return
*/
- public abstract AlignFrameI newViewFrom(AlignFrameI alf, String name);
+ public abstract AlignFrame newViewFrom(AlignFrame alf, String name);
/**
*
* window title
* @return null or new alignment frame
*/
- public abstract AlignFrameI loadAlignment(String text, String title);
+ 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.AlignFrameI,String(sequence id);,String(column
- * in alignment);, String(position in sequence);]
+ * [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 AlignFrameI for which events are to be listened
- * for);
+ * (null or specific alignframe for which events are to be listened
+ * for)
* @param listener
* name of javascript function
*/
- public abstract void setMouseoverListener(AlignFrameI af,
- String listener);
+ public abstract void setMouseoverListener(AlignFrame af, String listener);
/**
* register a javascript function to handle any alignment selection events.
*
* @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);]
+ * [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(AlignFrameI af,
- String listener);
+ public abstract void setSelectionListener(AlignFrame af, String listener);
/**
* register a javascript function to handle events normally routed to a Jmol
*
* @param listener
* - javascript function (arguments are variable, see
- * jalview.javascript.MouseOverStructureListener for full details);
+ * 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);.
+ * Jmol (e.g. first one is frame 1, second is frame 2, etc).
* @see jalview.javascript.MouseOverStructureListener
*/
public abstract void setStructureListener(String listener,
/**
* remove any callback using the given listener function and associated with
- * the given AlignFrameI (or null for all callbacks);
+ * the given alignFrame (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(AlignFrameI af,
+ public abstract void removeJavascriptListener(AlignFrame af,
String listener);
/**
String pdbfile);
/**
- * bind a pdb file to a sequence in the given AlignFrameI.
+ * bind a pdb file to a sequence in the given alignFrame.
*
* @param alFrame
- * - null or specific AlignFrameI. This specifies the dataset that
+ * - null or specific alignFrame. 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(AlignFrameI alFrame, String sequenceId,
+ public abstract boolean addPdbFile(AlignFrame alFrame, String sequenceId,
String pdbEntryString, String pdbFile);
/**
* @param topRow
* @param leftHandColumn
*/
- public abstract void scrollViewToIn(AlignFrameI alf, String topRow,
+ public abstract void scrollViewToIn(AlignFrame alf, String topRow,
String leftHandColumn);
/**
* @param alf
* @param topRow
*/
- public abstract void scrollViewToRowIn(AlignFrameI alf, String topRow);
+ public abstract void scrollViewToRowIn(AlignFrame alf, String topRow);
/**
* adjust horizontal scroll to make the given column the left one in the given
* @param alf
* @param leftHandColumn
*/
- public abstract void scrollViewToColumnIn(AlignFrameI alf,
+ public abstract void scrollViewToColumnIn(AlignFrame alf,
String leftHandColumn);
/**
*
* @return
- * @see jalview.appletgui.AlignFrameI#getFeatureGroups();
+ * @see jalview.appletgui.AlignFrame#getFeatureGroups()
*/
public abstract String getFeatureGroups();
/**
* @param alf
- * AlignFrameI to get feature groups on
+ * alignframe to get feature groups on
* @return
- * @see jalview.appletgui.AlignFrameI#getFeatureGroups();
+ * @see jalview.appletgui.AlignFrame#getFeatureGroups()
*/
- public abstract String getFeatureGroupsOn(AlignFrameI alf);
+ public abstract String getFeatureGroupsOn(AlignFrame alf);
/**
* @param visible
* @return
- * @see jalview.appletgui.AlignFrameI#getFeatureGroupsOfState(boolean);
+ * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean)
*/
public abstract String getFeatureGroupsOfState(boolean visible);
* align frame to get groups of state visible
* @param visible
* @return
- * @see jalview.appletgui.AlignFrameI#getFeatureGroupsOfState(boolean);
+ * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean)
*/
- public abstract String getFeatureGroupsOfStateOn(AlignFrameI alf,
+ public abstract String getFeatureGroupsOfStateOn(AlignFrame alf,
boolean visible);
/**
* tab separated list of group names
* @param state
* true or false
- * @see jalview.appletgui.AlignFrameI#setFeatureGroupState(java.lang.String[],
- * boolean);
+ * @see jalview.appletgui.AlignFrame#setFeatureGroupState(java.lang.String[],
+ * boolean)
*/
- public abstract void setFeatureGroupStateOn(AlignFrameI alf,
- String groups,
+ public abstract void setFeatureGroupStateOn(AlignFrame alf, String groups,
boolean state);
public abstract void setFeatureGroupState(String groups, boolean state);
*/
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(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