+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.io;
import jalview.api.AlignExportSettingI;
};
}
AlignmentExportData exportData = jalview.gui.AlignFrame
- .getAlignmentForExport(FileFormat.Json,
- ap.getAlignViewport(), exportSettings);
+ .getAlignmentForExport(FileFormat.Json, ap.getAlignViewport(),
+ exportSettings);
String bioJSON = new FormatAdapter(ap, exportData.getSettings())
.formatSequences(FileFormat.Json, exportData.getAlignment(),
- exportData.getOmitHidden(), exportData
- .getStartEndPostions(), ap.getAlignViewport()
- .getColumnSelection());
+ exportData.getOmitHidden(),
+ exportData.getStartEndPostions(), ap.getAlignViewport()
+ .getAlignment().getHiddenColumns());
return bioJSON;
}
{
sb.append(line).append(lineSeparator);
}
-
+
} catch (Exception ex)
{
ex.printStackTrace();
{
isReader.close();
}
-
+
if (buffReader != null)
{
buffReader.close();
public static String getImageMapHTML()
{
- return new String(
- "<html>\n"
- + "<head>\n"
- + "<script language=\"JavaScript\">\n"
- + "var ns4 = document.layers;\n"
- + "var ns6 = document.getElementById && !document.all;\n"
- + "var ie4 = document.all;\n"
- + "offsetX = 0;\n"
- + "offsetY = 20;\n"
- + "var toolTipSTYLE=\"\";\n"
- + "function initToolTips()\n"
- + "{\n"
- + " if(ns4||ns6||ie4)\n"
- + " {\n"
- + " if(ns4) toolTipSTYLE = document.toolTipLayer;\n"
- + " else if(ns6) toolTipSTYLE = document.getElementById(\"toolTipLayer\").style;\n"
- + " else if(ie4) toolTipSTYLE = document.all.toolTipLayer.style;\n"
- + " if(ns4) document.captureEvents(Event.MOUSEMOVE);\n"
- + " else\n"
- + " {\n"
- + " toolTipSTYLE.visibility = \"visible\";\n"
- + " toolTipSTYLE.display = \"none\";\n"
- + " }\n"
- + " document.onmousemove = moveToMouseLoc;\n"
- + " }\n"
- + "}\n"
- + "function toolTip(msg, fg, bg)\n"
- + "{\n"
- + " if(toolTip.arguments.length < 1) // hide\n"
- + " {\n"
- + " if(ns4) toolTipSTYLE.visibility = \"hidden\";\n"
- + " else toolTipSTYLE.display = \"none\";\n"
- + " }\n"
- + " else // show\n"
- + " {\n"
- + " if(!fg) fg = \"#555555\";\n"
- + " if(!bg) bg = \"#FFFFFF\";\n"
- + " var content =\n"
- + " '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + fg + '\"><td>' +\n"
- + " '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + bg + \n"
- + " '\"><td align=\"center\"><font face=\"sans-serif\" color=\"' + fg +\n"
- + " '\" size=\"-2\"> ' + msg +\n"
- + " ' </font></td></table></td></table>';\n"
- + " if(ns4)\n"
- + " {\n"
- + " toolTipSTYLE.document.write(content);\n"
- + " toolTipSTYLE.document.close();\n"
- + " toolTipSTYLE.visibility = \"visible\";\n"
- + " }\n"
- + " if(ns6)\n"
- + " {\n"
- + " document.getElementById(\"toolTipLayer\").innerHTML = content;\n"
- + " toolTipSTYLE.display='block'\n"
- + " }\n"
- + " if(ie4)\n"
- + " {\n"
- + " document.all(\"toolTipLayer\").innerHTML=content;\n"
- + " toolTipSTYLE.display='block'\n"
- + " }\n"
- + " }\n"
- + "}\n"
- + "function moveToMouseLoc(e)\n"
- + "{\n"
- + " if(ns4||ns6)\n"
- + " {\n"
- + " x = e.pageX;\n"
- + " y = e.pageY;\n"
- + " }\n"
- + " else\n"
- + " {\n"
- + " x = event.x + document.body.scrollLeft;\n"
- + " y = event.y + document.body.scrollTop;\n"
- + " }\n"
- + " toolTipSTYLE.left = x + offsetX;\n"
- + " toolTipSTYLE.top = y + offsetY;\n"
- + " return true;\n"
- + "}\n"
- + "</script>\n"
- + "</head>\n"
- + "<body>\n"
- + "<div id=\"toolTipLayer\" style=\"position:absolute; visibility: hidden\"></div>\n"
- + "<script language=\"JavaScript\"><!--\n"
- + "initToolTips(); //--></script>\n");
+ return new String("<html>\n" + "<head>\n"
+ + "<script language=\"JavaScript\">\n"
+ + "var ns4 = document.layers;\n"
+ + "var ns6 = document.getElementById && !document.all;\n"
+ + "var ie4 = document.all;\n" + "offsetX = 0;\n"
+ + "offsetY = 20;\n" + "var toolTipSTYLE=\"\";\n"
+ + "function initToolTips()\n" + "{\n" + " if(ns4||ns6||ie4)\n"
+ + " {\n"
+ + " if(ns4) toolTipSTYLE = document.toolTipLayer;\n"
+ + " else if(ns6) toolTipSTYLE = document.getElementById(\"toolTipLayer\").style;\n"
+ + " else if(ie4) toolTipSTYLE = document.all.toolTipLayer.style;\n"
+ + " if(ns4) document.captureEvents(Event.MOUSEMOVE);\n"
+ + " else\n" + " {\n"
+ + " toolTipSTYLE.visibility = \"visible\";\n"
+ + " toolTipSTYLE.display = \"none\";\n" + " }\n"
+ + " document.onmousemove = moveToMouseLoc;\n" + " }\n"
+ + "}\n" + "function toolTip(msg, fg, bg)\n" + "{\n"
+ + " if(toolTip.arguments.length < 1) // hide\n" + " {\n"
+ + " if(ns4) toolTipSTYLE.visibility = \"hidden\";\n"
+ + " else toolTipSTYLE.display = \"none\";\n" + " }\n"
+ + " else // show\n" + " {\n"
+ + " if(!fg) fg = \"#555555\";\n"
+ + " if(!bg) bg = \"#FFFFFF\";\n" + " var content =\n"
+ + " '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + fg + '\"><td>' +\n"
+ + " '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + bg + \n"
+ + " '\"><td align=\"center\"><font face=\"sans-serif\" color=\"' + fg +\n"
+ + " '\" size=\"-2\"> ' + msg +\n"
+ + " ' </font></td></table></td></table>';\n"
+ + " if(ns4)\n" + " {\n"
+ + " toolTipSTYLE.document.write(content);\n"
+ + " toolTipSTYLE.document.close();\n"
+ + " toolTipSTYLE.visibility = \"visible\";\n" + " }\n"
+ + " if(ns6)\n" + " {\n"
+ + " document.getElementById(\"toolTipLayer\").innerHTML = content;\n"
+ + " toolTipSTYLE.display='block'\n" + " }\n"
+ + " if(ie4)\n" + " {\n"
+ + " document.all(\"toolTipLayer\").innerHTML=content;\n"
+ + " toolTipSTYLE.display='block'\n" + " }\n" + " }\n"
+ + "}\n" + "function moveToMouseLoc(e)\n" + "{\n"
+ + " if(ns4||ns6)\n" + " {\n" + " x = e.pageX;\n"
+ + " y = e.pageY;\n" + " }\n" + " else\n" + " {\n"
+ + " x = event.x + document.body.scrollLeft;\n"
+ + " y = event.y + document.body.scrollTop;\n" + " }\n"
+ + " toolTipSTYLE.left = x + offsetX;\n"
+ + " toolTipSTYLE.top = y + offsetY;\n" + " return true;\n"
+ + "}\n" + "</script>\n" + "</head>\n" + "<body>\n"
+ + "<div id=\"toolTipLayer\" style=\"position:absolute; visibility: hidden\"></div>\n"
+ + "<script language=\"JavaScript\"><!--\n"
+ + "initToolTips(); //--></script>\n");
}
pSessionId);
}
- JalviewFileChooser jvFileChooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
- new String[] { "html" }, new String[] { "HTML files" },
+ JalviewFileChooser jvFileChooser = new JalviewFileChooser("html",
"HTML files");
jvFileChooser.setFileView(new JalviewFileView());
- jvFileChooser.setDialogTitle(MessageManager
- .getString("label.save_as_html"));
+ jvFileChooser
+ .setDialogTitle(MessageManager.getString("label.save_as_html"));
jvFileChooser.setToolTipText(MessageManager.getString("action.save"));
int fileChooserOpt = jvFileChooser.showSaveDialog(null);
if (fileChooserOpt == JalviewFileChooser.APPROVE_OPTION)
{
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", jvFileChooser
- .getSelectedFile().getParent());
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+ jvFileChooser.getSelectedFile().getParent());
selectedFile = jvFileChooser.getSelectedFile().getPath();
}
else