+ /**
+ *
+ * @see jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
+ * .AlignFrame, java.lang.String)
+ */
+ @Override
+ public String getSelectedSequencesFrom(AlignFrameI 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(AlignFrameI 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(AlignFrameI alf, String sequenceIds, String columns)
+ {
+ selectIn(alf, sequenceIds, columns, null);
+ }
+
+ @Override
+ public void selectIn(AlignFrameI 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(AlignFrameI 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(AlignFrameI alf)
+ {
+ return getAlignmentFrom(alf, null);
+ }
+
+ @Override
+ public String getAlignmentOrderFrom(AlignFrameI 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(AlignFrameI 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(AlignFrameI 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(AlignFrameI alf, String format,
+ String suffix)
+ {
+ return appLoader.getAlignmentFrom(alf, format, suffix);
+ }
+
+ @Override
+ public void loadAnnotation(String annotation)
+ {
+ loadAnnotationFrom(getCurrentAlignFrame(), annotation);
+ }
+
+ @Override
+ public void loadAnnotationFrom(AlignFrameI 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(AlignFrameI 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(AlignFrameI alf, String format)
+ {
+ if (alf == null)
+ {
+ alf = getCurrentAlignFrame();
+ }
+ return appLoader.getFeaturesFrom(alf, format, true, false);
+ }