- /**
- *
- * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences(java.lang.String)
- */
- @Override
- public String getSelectedSequences(String sep)
- {
- return getSelectedSequencesFrom(getCurrentAlignFrame(), sep);
- }
-
- /**
- *
- * @see jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
- * .AlignFrame)
- */
- @Override
- public String getSelectedSequencesFrom(AlignFrame alf)
- {
- if (alf == null)
- {
- alf = getCurrentAlignFrame();
- }
- return getSelectedSequencesFrom(alf, null);
- }
-
- /**
- *
- * @see jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
- * .AlignFrame, java.lang.String)
- */
- @Override
- public String getSelectedSequencesFrom(AlignFrame alf, String sep)
- {
- if (alf == null)
- {
- alf = getCurrentAlignFrame();
- }
- return appLoader.getSelectedSequencesFrom(alf, sep);
- }
-
- /**
- *
- * @see jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
- * .AlignFrame, java.lang.String)
- */
- @Override
- public void highlight(String sequenceId, String position,
- String alignedPosition)
- {
- highlightIn(null, sequenceId, position, alignedPosition);
- }
-
- @Override
- public void highlightIn(AlignFrame alf, String sequenceId,
- String position, String alignedPosition)
- {
- if (alf == null)
- {
- alf = getCurrentAlignFrame();
- }
- appLoader.highlightIn(alf, sequenceId, position, alignedPosition);
- }
-
- @Override
- public void select(String sequenceIds, String columns)
- {
- selectIn(getCurrentAlignFrame(), sequenceIds, columns, null);
- }
-
- @Override
- public void select(String sequenceIds, String columns, String sep)
- {
- selectIn(null, sequenceIds, columns, sep);
- }
-
- @Override
- public void selectIn(AlignFrame alf, String sequenceIds, String columns)
- {
- selectIn(alf, sequenceIds, columns, null);
- }
-
- @Override
- public void selectIn(AlignFrame alf, String sequenceIds, String columns,
- String sep)
- {
- if (alf == null)
- {
- alf = getCurrentAlignFrame();
- }
- appLoader.selectIn(alf, sequenceIds, columns, sep);
- }
-
- @Override
- public String getSelectedSequencesAsAlignment(String format,
- String suffix)
- {
- return getSelectedSequencesAsAlignmentFrom(null, format, suffix);
- }
-
- @Override
- public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
- String format, String sep)
- {
- if (alf == null)
- {
- alf = getCurrentAlignFrame();
- }
- return appLoader.getSelectedSequencesAsAlignmentFrom(alf, format, sep);
- }
-
- @Override
- public String getAlignmentOrder()
- {
- return getAlignmentFrom(getCurrentAlignFrame(), null);
- }
-
- @Override
- public String getAlignmentOrderFrom(AlignFrame alf)
- {
- return getAlignmentFrom(alf, null);
- }
-
- @Override
- public String getAlignmentOrderFrom(AlignFrame alf, String sep)
- {
- if (alf == null)
- {
- alf = getCurrentAlignFrame();
- }
- return appLoader.getAlignmentOrderFrom(alf, sep);
- }
-
- @Override
- public String orderBy(String order, String undoName)
- {
- return orderBy(order, undoName, null);
- }
-
- @Override
- public String orderBy(String order, String undoName, String sep)
- {
- return orderAlignmentBy(getCurrentAlignFrame(), order, undoName, sep);
- }
-
- @Override
- public String orderAlignmentBy(AlignFrame alf, String order,
- String undoName, String sep)
- {
- if (alf == null)
- {
- alf = getCurrentAlignFrame();
- }
- return appLoader.orderAlignmentBy(alf, order, undoName, sep);
- }
-
- @Override
- public String getAlignment(String format)
- {
- return getAlignmentFrom(null, format, null);
- }
-
- @Override
- public String getAlignmentFrom(AlignFrame alf, String format)
- {
- return getAlignmentFrom(alf, format, null);
- }
-
- @Override
- public String getAlignment(String format, String suffix)
- {
- return getAlignmentFrom(getCurrentAlignFrame(), format, suffix);
- }
-
- @Override
- public String getAlignmentFrom(AlignFrame alf, String format,
- String suffix)
- {
- return appLoader.getAlignmentFrom(alf, format, suffix);
- }
-
- @Override
- public void loadAnnotation(String annotation)
- {
- loadAnnotationFrom(getCurrentAlignFrame(), annotation);
- }
-
- @Override
- public void loadAnnotationFrom(AlignFrame alf, String annotation)
- {
- if (alf == null)
- {
- alf = getCurrentAlignFrame();
- }
- appLoader.loadAnnotationFrom(alf, annotation);
- }
-
- @Override
- public void loadFeatures(String features, boolean autoenabledisplay)
- {
- loadFeaturesFrom(currentAlignFrame, features, autoenabledisplay);
- }
-
- @Override
- public boolean loadFeaturesFrom(AlignFrame alf, String features,
- boolean autoenabledisplay)
- {
- if (alf == null)
- {
- alf = getCurrentAlignFrame();
- }
- return appLoader.loadFeaturesFrom(alf, features, autoenabledisplay);
- }
-
- @Override
- public String getFeatures(String format)
- {
- return getFeaturesFrom(null, format);
- }
-
- @Override
- public String getFeaturesFrom(AlignFrame alf, String format)
- {
- if (alf == null)
- {
- alf = getCurrentAlignFrame();
- }
- return appLoader.getFeaturesFrom(alf, format);
- }
-
- @Override
- public String getAnnotation()
- {
- return getAnnotationFrom(null);
- }
-
- @Override
- public String getAnnotationFrom(AlignFrame alf)
- {
- if (alf == null)
- {
- alf = getCurrentAlignFrame();
- }
- return appLoader.getAnnotationFrom(alf);
- }
-
- // @Override
- // public AlignFrame newView()
- // {
- // return newViewFrom(null, null);
- // }
- //
- // @Override
- // public AlignFrame newView(String name)
- // {
- // return newViewFrom(null, name);
- // }
- //
- // @Override
- // public AlignFrame newViewFrom(AlignFrame alf)
- // {
- // return newViewFrom(alf, null);
- // }
- //
- // @Override
- // public AlignFrame newViewFrom(AlignFrame alf, String name)
- // {
- // if (alf == null)
- // {
- // alf = getCurrentAlignFrame();
- // }
- // return appLoader.newViewFrom(alf, name);
- // }
-
- @Override
- public AlignFrame loadAlignment(String text, String title)
- {
- return appLoader.loadAlignment(text, AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT, title);
- }
-
- @Override
- public boolean addPdbFile(AlignFrame alFrame, String sequenceId,
- String pdbEntryString, String pdbFile)
- {
- if (alFrame == null)
- {
- alFrame = getCurrentAlignFrame();
- }
- return appLoader.addPdbFile(alFrame, sequenceId, pdbEntryString,
- pdbFile);
- }
-
- @Override
- public void scrollViewToIn(AlignFrame alf, String topRow,
- String leftHandColumn)
- {
- if (alf == null)
- {
- alf = getCurrentAlignFrame();
- }
- appLoader.scrollViewToIn(alf, topRow, leftHandColumn);
- }
-
- @Override
- public void scrollViewToRowIn(AlignFrame alf, String topRow)
- {
- if (alf == null)
- {
- alf = getCurrentAlignFrame();
- }
- appLoader.scrollViewToRowIn(alf, topRow);
- }
-
- @Override
- public void scrollViewToColumnIn(AlignFrame alf, String leftHandColumn)
- {
- if (alf == null)
- {
- alf = getCurrentAlignFrame();
- }
- appLoader.scrollViewToColumnIn(alf, leftHandColumn);
- }
-
- @Override
- public String getFeatureGroups()
- {
- return getFeatureGroupsOn(null);
- }
-
- @Override
- public String getFeatureGroupsOn(AlignFrame alf)
- {
- if (alf == null)
- {
- alf = getCurrentAlignFrame();
- }
- return appLoader.getFeatureGroupsOn(alf);
- }
-
- @Override
- public String getFeatureGroupsOfState(boolean visible)
- {
- return getFeatureGroupsOfStateOn(null, visible);
- }
-
- @Override
- public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)
- {
- if (alf == null)
- {
- alf = getCurrentAlignFrame();
- }
- return appLoader.getFeatureGroupsOfStateOn(alf, visible);
- }
-
- @Override
- public void setFeatureGroupState(String groups, boolean state)
- { // JalviewLite API
- setFeatureGroupStateOn(null, groups, state);
- }
-
- @Override
- public void setFeatureGroupStateOn(AlignFrame alf, String groups,
- boolean state)
- {
- if (alf == null)
- {
- alf = getCurrentAlignFrame();
- }
- appLoader.setFeatureGroupStateOn(alf, groups, state);
- }
-
- @Override
- public String getSeparator()
- {
- return appLoader.getSeparator();
- }
-
- @Override
- public void setSeparator(String separator)
- {
- appLoader.setSeparator(separator);
- }
-
- @Override
- public String getJsMessage(String messageclass, String viewId)
- {
- // see http://www.jalview.org/examples/jalviewLiteJs.html
- return null;
- }
-
- /**
- * Open a new Tree panel on the desktop statically. Params are standard (not
- * set by Groovy). No dialog is opened.
- *
- * @param af
- * @param treeType
- * @param modelName
- * @return null, or the string "label.you_need_at_least_n_sequences" if number
- * of sequences selected is inappropriate
- */
- @Override
- public Object openTreePanel(AlignFrame af, String treeType,
- String modelName)
- { // JalviewJS api
- if (af == null)
- {
- af = getCurrentAlignFrame();
- }
- return CalculationChooser.openTreePanel(af, treeType, modelName, null);
- }
-
- /**
- * public static method for JalviewJS API to open a PCAPanel without
- * necessarily using a dialog.
- *
- * @param af
- * @param modelName
- * @return the PCAPanel, or the string "label.you_need_at_least_n_sequences"
- * if number of sequences selected is inappropriate
- */
- @Override
- public Object openPcaPanel(AlignFrame af, String modelName)
- {
- if (af == null)
- {
- af = getCurrentAlignFrame();
- }
- return CalculationChooser.openPcaPanel(af, modelName, null);
- }
-
- @Override
- public String getSelectedSequencesAsAlignment(String format,
- boolean suffix)
- {
- return getSelectedSequencesAsAlignmentFrom(null, format, suffix);
- }
-
- @Override
- public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
- String format, boolean suffix)
- {
- if (alf == null)
- {
- alf = getCurrentAlignFrame();
- }
- return appLoader.getSelectedSequencesAsAlignmentFrom(alf, format,
- "" + suffix);
- }
-
- @Override
- public String arrayToSeparatorList(String[] array)
- {
- return appLoader.arrayToSeparatorList(array);
- }
-
- @Override
- public String[] separatorListToArray(String list)
- {
- return appLoader.separatorListToArray(list);
- }
-
- //// probably not needed in JalviewJS -- From when Jmol and Jalview did not
- //// have a direct connection?
-
- @Override
- public void setMouseoverListener(String listener)
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public void setMouseoverListener(AlignFrame af, String listener)
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public void setSelectionListener(String listener)
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public void setSelectionListener(AlignFrame af, String listener)
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public void setStructureListener(String listener, String modelSet)
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public void removeJavascriptListener(AlignFrame af, String listener)