import java.io.IOException;
import java.net.URL;
-import java.util.Hashtable;
import jalview.api.AlignViewportI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.io.DataSourceType;
-import jalview.io.NewickFile;
import jalview.structure.SelectionSource;
import jalview.structure.VamsasSource;
* - 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
+ * - 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.
- * @return true if binding was as success TODO: consider making an exception
- * structure for indicating when PDB parsing or sequenceId location
- * fails.
+ * - pdb file - either a URL or a valid PDB file or null.
+ * @return true if binding was success
*/
- public abstract boolean addPdbFile(AlignFrame alFrame, String sequenceId,
- String pdbEntryString, String pdbFile);
-
- public String arrayToSeparatorList(String[] array);
+ 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
* @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,
+ public String getAlignmentFrom(AlignFrame alf, String format,
String suffix);
/**
* @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);
-
- /**
- * 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);
+ public String[] getAlignmentOrderFrom(AlignFrame alf);
/**
* 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,
+ public String[] getFeatureGroupsOfStateOn(AlignFrame alf,
boolean visible);
/**
* @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 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,
+ public String getSelectedSequencesAsAlignment(String format,
String suffix);
/**
* @return selected sequences as flat file or empty string if there was no
* current selection
*/
- public abstract String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
+ public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
String format, String suffix);
/**
* 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);
- /**
- * List separator string
- *
- * @return the separator
- */
-
- public abstract String getSeparator();
-
public AlignViewportI getViewport();
/**
* column or unaligned sequence position
*/
- public abstract void highlight(String sequenceId, String position,
+ 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,
+ 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,
+ public boolean loadFeaturesFrom(AlignFrame alf, String features,
boolean autoenabledisplay);
public boolean loadScoreFile(String sScoreFile) throws IOException;
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
+ * re-order the given alignment using the given array of sequence IDs
*
* @param alf
- * @param order
- * - sep separated list
+ * @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 abstract String orderAlignmentBy(AlignFrame alf, String order,
- String undoName, String sep);
+ 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 order
- * - sep separated list
+ * @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 abstract String orderBy(String order, String undoName);
+ public String orderBy(String[] ids, String undoName);
/**
* re-order the current alignment using the given list of sequence IDs
- * separated by sep
*
- * @param order
- * - sep separated list
+ * @param ids
+ * array of sequence IDs
* @param undoName
* - string to use when referring to ordering action in undo buffer
* @param sep
* alignment did not contain sequences.
*/
- public abstract 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 String orderBy(String[] ids, String undoName, String sep);
+ //
// 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,
+ public void scrollViewToIn(AlignFrame alf, String topRow,
String leftHandColumn);
/**
* @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 String[] separatorListToArray(String list);
+ public void selectIn(AlignFrame alf, String sequenceIds, String columns,
+ String sep);
- 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,
+ 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);
+
+ public void updateForAnnotations();
+
+ // Bob's additions:
/**
- * List separator string
+ * public static method for JalviewJS API to open a PCAPanel without
+ * necessarily using a dialog.
*
- * @param separator
- * the separator to set. empty string will reset separator to default
+ * @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 abstract void setSeparator(String separator);
+ /**
+ * 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);
- void showOverview();
+ /**
+ * process commandline arguments after the JavaScript application has started
+ *
+ * @param args
+ * @return
+ */
+ public Object parseArguments(String[] args);
- public void updateForAnnotations();
+ public void showStructure(AlignFrame af, String pdbID, String fileType);
+
+ public void showOverview();
}
git://source.jalview.org / jalview.git / blobdiff