+ 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);
+ }