boolean seqlimits = suffix.equalsIgnoreCase("true");\r
if (alf.viewport.getSelectionGroup() != null)\r
{\r
- // JBPNote: getSelectionAsNewSequence behaviour has changed - this method now returns a full copy of sequence data\r
+ // JBPNote: getSelectionAsNewSequence behaviour has changed - this\r
+ // method now returns a full copy of sequence data\r
// TODO consider using getSequenceSelection instead here\r
String reply = new AppletFormatAdapter().formatSequences(format,\r
new Alignment(alf.viewport.getSelectionAsNewSequence()),\r
* jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame\r
* , java.lang.String)\r
*/\r
- public boolean loadFeaturesFrom(AlignFrame alf, String features, boolean autoenabledisplay)\r
+ public boolean loadFeaturesFrom(AlignFrame alf, String features,\r
+ boolean autoenabledisplay)\r
{\r
- return alf.parseFeaturesFile(features, AppletFormatAdapter.PASTE, autoenabledisplay);\r
+ return alf.parseFeaturesFile(features, AppletFormatAdapter.PASTE,\r
+ autoenabledisplay);\r
}\r
\r
-\r
/*\r
* (non-Javadoc)\r
* \r
\r
if (protocol == jalview.io.AppletFormatAdapter.PASTE)\r
{\r
- newAlignFrame.setTitle("Sequences from " + applet.getDocumentBase());\r
+ newAlignFrame.setTitle("Sequences from "\r
+ + applet.getDocumentBase());\r
}\r
\r
newAlignFrame.statusBar.setText("Successfully loaded file " + file);\r
}\r
}\r
\r
-\r
/*\r
* Try to load T-Coffee score file\r
*/\r
String sScoreFile = applet.getParameter("scoreFile");\r
- if( sScoreFile != null && !"".equals(sScoreFile) ) {\r
- try {\r
- if (debug) {\r
- System.err.println("Attempting to load T-COFFEE score file from the scoreFile parameter");\r
- }\r
- if (!newAlignFrame.loadScoreFile(sScoreFile)) {\r
- System.err.println("Failed to parse T-COFFEE parameter as a valid score file ('"+sScoreFile+"')");\r
- }\r
- }catch( Exception e ) {\r
- System.err.printf("Cannot read score file: '%s'. Cause: %s \n", sScoreFile, e.getMessage());\r
+ if (sScoreFile != null && !"".equals(sScoreFile))\r
+ {\r
+ try\r
+ {\r
+ if (debug)\r
+ {\r
+ System.err\r
+ .println("Attempting to load T-COFFEE score file from the scoreFile parameter");\r
+ }\r
+ if (!newAlignFrame.loadScoreFile(sScoreFile))\r
+ {\r
+ System.err\r
+ .println("Failed to parse T-COFFEE parameter as a valid score file ('"\r
+ + sScoreFile + "')");\r
}\r
+ } catch (Exception e)\r
+ {\r
+ System.err.printf("Cannot read score file: '%s'. Cause: %s \n",\r
+ sScoreFile, e.getMessage());\r
+ }\r
}\r
- \r
\r
// ///////////////////////////\r
// modify display of features\r
- // we do this before any features have been loaded, ensuring any hidden groups are hidden when features first displayed\r
+ // we do this before any features have been loaded, ensuring any hidden\r
+ // groups are hidden when features first displayed\r
//\r
// hide specific groups\r
- // \r
+ //\r
String param = applet.getParameter("hidefeaturegroups");\r
if (param != null)\r
{\r
- newAlignFrame.setFeatureGroupState(separatorListToArray(param), false); \r
-// applet.setFeatureGroupStateOn(newAlignFrame, param, false);\r
+ newAlignFrame.setFeatureGroupState(separatorListToArray(param),\r
+ false);\r
+ // applet.setFeatureGroupStateOn(newAlignFrame, param, false);\r
}\r
// show specific groups\r
param = applet.getParameter("showfeaturegroups");\r
if (param != null)\r
{\r
- newAlignFrame.setFeatureGroupState(separatorListToArray(param), true); \r
-// applet.setFeatureGroupStateOn(newAlignFrame, param, true);\r
+ newAlignFrame.setFeatureGroupState(separatorListToArray(param),\r
+ true);\r
+ // applet.setFeatureGroupStateOn(newAlignFrame, param, true);\r
}\r
// and now load features\r
param = applet.getParameter("features");\r