/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
String externalsviewer = getParameter("externalstructureviewer");
if (externalsviewer != null)
{
- useXtrnalSviewer = externalsviewer.trim().toLowerCase()
- .equals(TRUE);
+ useXtrnalSviewer = externalsviewer.trim().toLowerCase().equals(TRUE);
}
/**
* if true disable the check for jmol
}
else
{
- throw new Error(MessageManager.getString("error.invalid_separator_parameter"));
+ throw new Error(
+ MessageManager
+ .getString("error.invalid_separator_parameter"));
}
}
int r = 255;
AlignmentI al = null;
try
{
- al = new AppletFormatAdapter().readFile(resolvedFile, protocol, format);
+ al = new AppletFormatAdapter().readFile(resolvedFile, protocol,
+ format);
if ((al != null) && (al.getHeight() > 0))
{
dbgMsg("Successfully loaded file.");
if (protocol == AppletFormatAdapter.PASTE)
{
newAlignFrame.setTitle(MessageManager.formatMessage(
- "label.sequences_from", new Object[]
- { applet.getDocumentBase().toString() }));
+ "label.sequences_from", new Object[] { applet
+ .getDocumentBase().toString() }));
}
newAlignFrame.statusBar.setText(MessageManager.formatMessage(
- "label.successfully_loaded_file", new Object[]
- { resolvedFile }));
+ "label.successfully_loaded_file",
+ new Object[] { resolvedFile }));
return newAlignFrame;
}
String sequence = applet.getParameter("PDBSEQ");
if (sequence != null)
{
- seqs = new SequenceI[]
- { matcher == null ? (Sequence) alignFrame.getAlignViewport()
- .getAlignment().findName(sequence) : matcher
- .findIdMatch(sequence) };
+ seqs = new SequenceI[] { matcher == null ? (Sequence) alignFrame
+ .getAlignViewport().getAlignment().findName(sequence)
+ : matcher.findIdMatch(sequence) };
}
}
}
else
{
- pdbs.addElement(new Object[]
- { pdb, seqs, chains, new String(protocol) });
+ pdbs.addElement(new Object[] { pdb, seqs, chains,
+ new String(protocol) });
}
}
}
if (debug)
{
System.err.println("Prepended document base '" + documentBase
- + "' to make: '" + url
- + "'");
+ + "' to make: '" + url + "'");
}
return url;
}
if (url.indexOf("/") == 0)
{
String localfile = localref.getFile();
- url = codebase.substring(0, codebase.length()
- - localfile.length())
+ url = codebase.substring(0, codebase.length() - localfile.length())
+ url;
}
else