/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.bin;
callInitCallback();
}
}
+
private void initLiveConnect()
{
// try really hard to get the liveConnect thing working
- boolean notFailed=false;
- int tries=0;
- while (!notFailed && tries<10) {
- if (tries>0)
+ boolean notFailed = false;
+ int tries = 0;
+ while (!notFailed && tries < 10)
+ {
+ if (tries > 0)
{
System.err.println("LiveConnect request thread going to sleep.");
}
- try {
- Thread.sleep(700*(1+tries));
+ try
+ {
+ Thread.sleep(700 * (1 + tries));
+ } catch (InterruptedException q)
+ {
}
- catch (InterruptedException q) {};
- if (tries++>0)
+ ;
+ if (tries++ > 0)
{
System.err.println("LiveConnect request thread woken up.");
}
- try {
+ try
+ {
JSObject scriptObject = JSObject.getWindow(this);
- if (scriptObject.eval("navigator")!=null)
+ if (scriptObject.eval("navigator") != null)
{
- notFailed=true;
+ notFailed = true;
}
} catch (JSException jsex)
{
- System.err.println("Attempt "+tries+" to access LiveConnect javascript failed.");
+ System.err.println("Attempt " + tries
+ + " to access LiveConnect javascript failed.");
}
}
}
+
private void callInitCallback()
{
String initjscallback = getParameter("oninit");
{
}
;
- // try really hard to let the browser plugin know we want liveconnect
+ // try really hard to let the browser plugin know we want liveconnect
initLiveConnect();
if (scriptObject != null)
g.setColor(Color.cyan);
g.fillRect(0, 0, getSize().width, getSize().height);
g.setColor(Color.red);
- g.drawString(MessageManager.getString("label.jalview_cannot_open_file"), 5, 15);
+ g.drawString(
+ MessageManager.getString("label.jalview_cannot_open_file"),
+ 5, 15);
g.drawString("\"" + file + "\"", 5, 30);
}
else if (embedded)
{
g.setColor(Color.black);
g.setFont(new Font("Arial", Font.BOLD, 24));
- g.drawString(MessageManager.getString("label.jalview_applet"), 50, getSize().height / 2 - 30);
- g.drawString(MessageManager.getString("label.loading_data") + "...", 50, getSize().height / 2);
+ g.drawString(MessageManager.getString("label.jalview_applet"), 50,
+ getSize().height / 2 - 30);
+ g.drawString(MessageManager.getString("label.loading_data") + "...",
+ 50, getSize().height / 2);
}
}
if (protocol == jalview.io.AppletFormatAdapter.PASTE)
{
- newAlignFrame.setTitle(MessageManager.formatMessage("label.sequences_from", new String[]{applet.getDocumentBase().toString()}));
+ newAlignFrame.setTitle(MessageManager.formatMessage(
+ "label.sequences_from", new String[]
+ { applet.getDocumentBase().toString() }));
}
- newAlignFrame.statusBar.setText(MessageManager.formatMessage("label.successfully_loaded_file", new String []{file}));
+ newAlignFrame.statusBar.setText(MessageManager.formatMessage(
+ "label.successfully_loaded_file", new String[]
+ { file }));
String treeFile = applet.getParameter("tree");
if (treeFile == null)
param = applet.getParameter("showFeatureSettings");
if (param != null && param.equalsIgnoreCase("true"))
{
- newAlignFrame.viewport.showSequenceFeatures(true);
+ newAlignFrame.viewport.setShowSequenceFeatures(true);
new FeatureSettings(newAlignFrame.alignPanel);
}