+/*
+ * 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.schemes;
import jalview.binding.JalviewUserColours;
{
InputStreamReader in = new InputStreamReader(
new FileInputStream(file), "UTF-8");
-
+
jalview.schemabinding.version2.JalviewUserColours jucs = new jalview.schemabinding.version2.JalviewUserColours();
-
+
org.exolab.castor.xml.Unmarshaller unmar = new org.exolab.castor.xml.Unmarshaller(
jucs);
jucs = (jalview.schemabinding.version2.JalviewUserColours) unmar
.unmarshal(in);
-
+
/*
* non-case-sensitive colours are for 20 amino acid codes,
* B, Z, X and Gap
newColours = new Color[24];
Color[] lowerCase = new Color[23];
boolean caseSensitive = false;
-
+
String name;
int index;
for (int i = 0; i < jucs.getColourCount(); i++)
{
continue;
}
-
- Color color = new Color(Integer.parseInt(jucs.getColour(i)
- .getRGB(), 16));
+
+ Color color = new Color(
+ Integer.parseInt(jucs.getColour(i).getRGB(), 16));
if (name.toLowerCase().equals(name))
{
caseSensitive = true;
newColours[index] = color;
}
}
-
+
/*
* instantiate the colour scheme
*/
// Could be old Jalview Archive format
try
{
- InputStreamReader in = new InputStreamReader(new FileInputStream(
- file), "UTF-8");
-
+ InputStreamReader in = new InputStreamReader(
+ new FileInputStream(file), "UTF-8");
+
jalview.binding.JalviewUserColours jucs = new jalview.binding.JalviewUserColours();
-
+
jucs = JalviewUserColours.unmarshal(in);
-
+
newColours = new Color[jucs.getColourCount()];
-
+
for (int i = 0; i < 24; i++)
{
- newColours[i] = new Color(Integer.parseInt(jucs.getColour(i)
- .getRGB(), 16));
+ newColours[i] = new Color(
+ Integer.parseInt(jucs.getColour(i).getRGB(), 16));
}
ucs = new UserColourScheme(newColours);
ucs.setName(jucs.getSchemeName());
{
ex2.printStackTrace();
}
-
+
if (newColours == null)
{
System.out.println("Error loading User ColourFile\n" + ex);
}
}
-
+
return ucs;
}