X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FHTMLOutput.java;h=bebfd280c90be0cb5a8ae3efca3303222f80beb8;hb=0cbe9f1b595a51355953a932961a0256857d230e;hp=77006db33573e9bd5b0eecdf62c319dc6fcc8c55;hpb=136c0793b90b72b928c4d77dc109dd5c644e00d3;p=jalview.git
diff --git a/src/jalview/io/HTMLOutput.java b/src/jalview/io/HTMLOutput.java
old mode 100755
new mode 100644
index 77006db..bebfd28
--- a/src/jalview/io/HTMLOutput.java
+++ b/src/jalview/io/HTMLOutput.java
@@ -1,3 +1,23 @@
+/*
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.io;
import jalview.api.AlignExportSettingI;
@@ -86,12 +106,12 @@ public abstract class HTMLOutput implements Runnable
};
}
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()
+ exportData.getOmitHidden(),
+ exportData.getStartEndPostions(), ap.getAlignViewport()
.getAlignment().getHiddenColumns());
return bioJSON;
}
@@ -124,7 +144,7 @@ public abstract class HTMLOutput implements Runnable
{
sb.append(line).append(lineSeparator);
}
-
+
} catch (Exception ex)
{
ex.printStackTrace();
@@ -134,7 +154,7 @@ public abstract class HTMLOutput implements Runnable
{
isReader.close();
}
-
+
if (buffReader != null)
{
buffReader.close();
@@ -146,89 +166,55 @@ public abstract class HTMLOutput implements Runnable
public static String getImageMapHTML()
{
- return new String(
- "\n"
- + "\n"
- + "\n"
- + "\n"
- + "\n"
- + "\n"
- + "\n");
+ return new String("\n" + "\n"
+ + "\n" + "\n" + "\n"
+ + "\n"
+ + "\n");
}
@@ -246,15 +232,15 @@ public abstract class HTMLOutput implements Runnable
"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