import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.io.DataSourceType;
-import jalview.io.NewickFile;
import jalview.structure.SelectionSource;
import jalview.structure.VamsasSource;
* structure for indicating when PDB parsing or sequenceId location
* fails.
*/
- public abstract boolean addPdbFile(AlignFrame alFrame, String sequenceId,
- String pdbEntryString, String pdbFile);
+ public boolean addPdbFile(AlignFrame alFrame, String sequenceId, String pdbEntryString, String pdbFile);
public String arrayToSeparatorList(String[] array);
* an HTML page.
*
* <br>
- * <em>TODO: introduce abstract interface for
+ * <em>TODO: introduce interface for
* jalview.appletgui.AlignFrame</em><br>
*
* Most function arguments are strings, which contain serialised versions of
* @return
*/
- public abstract String getAlignment(String format);
+ public String getAlignment(String format);
/**
* get alignment as format with jalview start-end sequence suffix appended
* @return
*/
- public abstract String getAlignment(String format, String suffix);
+ public String getAlignment(String format, String suffix);
/**
* get alignment displayed in alf as format
* @param format
* @return
*/
- public abstract String getAlignmentFrom(AlignFrame alf, String format);
+ public String getAlignmentFrom(AlignFrame alf, String format);
/**
* get alignment displayed in alf as format with or without the jalview
* @param suffix
* @return
*/
- public abstract String getAlignmentFrom(AlignFrame alf, String format,
- String suffix);
+ public String getAlignmentFrom(AlignFrame alf, String format, String suffix);
/**
* get a separator separated list of sequence IDs reflecting the order of the
* @return
*/
- public abstract String getAlignmentOrder();
+ public String getAlignmentOrder();
/**
* get a separator separated list of sequence IDs reflecting the order of the
* @param alf
* @return
*/
- public abstract String getAlignmentOrderFrom(AlignFrame alf);
+ public 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(AlignFrame alf, String sep);
+ public String getAlignmentOrderFrom(AlignFrame alf, String sep);
/**
* get current alignment's annotation as an annotation file
* @return
*/
- public abstract String getAnnotation();
+ public String getAnnotation();
/**
* get alignment view alf's annotation as an annotation file
* @param alf
* @return
*/
- public abstract String getAnnotationFrom(AlignFrame alf);
+ public String getAnnotationFrom(AlignFrame alf);
public Object getAppletParameter(String name, boolean asString);
* @see jalview.appletgui.AlignFrame#getFeatureGroups();
*/
- public abstract String getFeatureGroups();
+ public String getFeatureGroups();
/**
* @param visible
* @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean);
*/
- public abstract String getFeatureGroupsOfState(boolean visible);
+ public String getFeatureGroupsOfState(boolean visible);
/**
* @param alf
* @return
* @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean);
*/
- public abstract String getFeatureGroupsOfStateOn(AlignFrame alf,
- boolean visible);
+ public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible);
/**
* @param alf
* @return
* @see jalview.appletgui.AlignFrame#getFeatureGroups();
*/
- public abstract String getFeatureGroupsOn(AlignFrame alf);
+ public String getFeatureGroupsOn(AlignFrame alf);
/**
* get the sequence features in the given format (Jalview or GFF);
* @return
*/
- public abstract String getFeatures(String format);
+ public String getFeatures(String format);
/**
* get the sequence features in alf in the given format (Jalview or GFF);
* @param format
* @return
*/
- public abstract String getFeaturesFrom(AlignFrame alf, String format);
+ public String getFeaturesFrom(AlignFrame alf, String format);
public Object getFrameForSource(VamsasSource source);
- public Hashtable<String, int[]> getJSHashes();
-
- /**
- * 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);
-
- Hashtable<String, Hashtable<String, String[]>> getJSMessages();
-
- public Object getJSObject();
-
- public jalview.renderer.seqfeatures.FeatureRenderer getNewFeatureRenderer(
- AlignViewportI vp);
+ public jalview.renderer.seqfeatures.FeatureRenderer getNewFeatureRenderer(AlignViewportI vp);
public String getParameter(String name);
* 'boolean not' character (""+0x00AC); or (¬);
*/
- public abstract String getSelectedSequences();
+ public SequenceI[] getSelectedSequences();
/**
* @param sep
* separator string
*/
- public abstract String getSelectedSequences(String sep);
+ public SequenceI[] getSelectedSequences(String sep);
/**
* get sequences selected in current AlignFrame and return their alignment in
* current selection
*/
- public abstract String getSelectedSequencesAsAlignment(String format,
- String suffix);
+ public String getSelectedSequencesAsAlignment(String format, String suffix);
/**
* get sequences selected in alf and return their alignment in format 'format'
* @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);
+ public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf, String format, String suffix);
/**
* @param alf
* default separator sequence
*
*/
- public abstract String getSelectedSequencesFrom(AlignFrame alf);
+ 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);
+ // public AlignFrame newViewFrom(AlignFrame alf, String name);
/**
* 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 SequenceI[] getSelectedSequencesFrom(AlignFrame alf, String sep);
- public Object[] getSelectionForListener(SequenceGroup seqsel,
- ColumnSelection colsel, HiddenColumns hidden,
- SelectionSource source, Object alignFrame);
+ public Object[] getSelectionForListener(SequenceGroup seqsel, ColumnSelection colsel, HiddenColumns hidden, SelectionSource source, Object alignFrame);
/**
* List separator string
* @return the separator
*/
- public abstract String getSeparator();
+ public String getSeparator();
public AlignViewportI getViewport();
* column or unaligned sequence position
*/
- public abstract void highlight(String sequenceId, String position,
- String alignedPosition);
+ public void highlight(String sequenceId, String position, String 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);
+ public void highlightIn(AlignFrame alf, String sequenceId, String position, String alignedPosition);
/**
*
* @return null or new alignment frame
*/
- public abstract AlignFrame loadAlignment(String text, String title);
+ public AlignFrame loadAlignment(String text, String title);
/**
* add the given features or annotation to the current alignment
* @param annotation
*/
- public abstract void loadAnnotation(String annotation);
+ public 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 void loadAnnotationFrom(AlignFrame alf, String annotation);
/**
* parse the given string as a jalview feature or GFF annotation file and
* be parsed from the string.
*/
- public abstract void loadFeatures(String features,
- boolean autoenabledisplay);
+ public void loadFeatures(String features, boolean autoenabledisplay);
/**
* parse the given string as a jalview feature or GFF annotation file and
* be parsed from the string.
* @return true if data parsed as features
*/
- public abstract boolean loadFeaturesFrom(AlignFrame alf, String features,
- boolean autoenabledisplay);
+ 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 void newStructureView(PDBEntry pdb, SequenceI[] seqs, String[] chains, DataSourceType protocol);
/**
* public static method for JalviewJS API to open a PCAPanel without
* @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);
+ public Object openTreePanel(AlignFrame af, String treeType, String modelName);
/// in http://www.jalview.org/examples/jalviewLiteJs.html but missing here
* @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);
+ public String orderAlignmentBy(AlignFrame alf, String order, String undoName, String sep);
// get a string array from a list
* alignment did not contain sequences.
*/
- public abstract String orderBy(String order, String undoName);
+ public String orderBy(String order, String undoName);
/**
* re-order the current alignment using the given list of sequence IDs
* alignment did not contain sequences.
*/
- public abstract String orderBy(String order, String undoName, String sep);
+ public String orderBy(String order, String undoName, String sep);
/**
* process commandline arguments after the JavaScript application has started
* @param args
* @return
*/
- Object parseArguments(String[] args);
+ public Object parseArguments(String[] args);
// public boolean getDefaultParameter(String name, boolean def);
* @param listener
* (may be null);
*/
- public abstract void removeSelectionListener(AlignFrame af,
- String listener);
+ public void removeSelectionListener(AlignFrame af, String listener);
// public void setAlignPdbStructures(boolean defaultParameter);
* @param alf
* @param leftHandColumn
*/
- public abstract void scrollViewToColumnIn(AlignFrame alf,
- String leftHandColumn);
+ public void scrollViewToColumnIn(AlignFrame alf, String leftHandColumn);
/**
* adjust horizontal/vertical scroll to make the given location the top left
* @param topRow
* @param leftHandColumn
*/
- public abstract void scrollViewToIn(AlignFrame alf, String topRow,
- String 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 abstract void scrollViewToRowIn(AlignFrame alf, String topRow);
+ public void scrollViewToRowIn(AlignFrame alf, String topRow);
/**
* select regions of the currrent alignment frame
* string
*/
- public abstract void select(String sequenceIds, String columns);
+ public void select(String sequenceIds, String columns);
/**
* select regions of the currrent alignment frame
* separator between toselect fields
*/
- public abstract void select(String sequenceIds, String columns,
- String sep);
+ public 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,
- String columns);
+ public void selectIn(AlignFrame alf, String sequenceIds, String columns);
/**
* select regions of the given alignment frame
* @param sep
* separator between toselect fields
*/
- public abstract void selectIn(AlignFrame alf, String sequenceIds,
- String columns, String sep);
+ public void selectIn(AlignFrame alf, String sequenceIds, String columns, String sep);
public String[] separatorListToArray(String list);
- public abstract void setFeatureGroupState(String groups, boolean state);
+ public void setFeatureGroupState(String groups, boolean state);
public void setFeatureGroupState(String[] groups, boolean state);
* @see jalview.appletgui.AlignFrame#setFeatureGroupState(java.lang.String[],
* boolean);
*/
- public abstract void setFeatureGroupStateOn(AlignFrame alf, String groups,
- boolean state);
+ public void setFeatureGroupStateOn(AlignFrame alf, String groups, boolean state);
- public abstract void setSelectionListener(AlignFrame af, String listener);
+ public void setSelectionListener(AlignFrame af, String listener);
/**
* register a javascript function to handle any alignment selection events.
* single number or hyphenated range); that were selected);]
*/
- public abstract void setSelectionListener(String listener);
+ public void setSelectionListener(String listener);
/**
* List separator string
* the separator to set. empty string will reset separator to default
*/
- public abstract void setSeparator(String separator);
+ public void setSeparator(String separator);
- void showOverview();
+ public void showOverview();
public void updateForAnnotations();