X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemes.java;h=99e97592c55bb2c8f52de2a32c1f9ad908825391;hb=7047b076a62df177047ceb16c3611efe020bdd76;hp=817fb0136767e4106fd656db2d554faea0e0c58a;hpb=8b55eedb9d76a8c65b80f756c4412bf029906bf7;p=jalview.git
diff --git a/src/jalview/schemes/ColourSchemes.java b/src/jalview/schemes/ColourSchemes.java
index 817fb01..99e9759 100644
--- a/src/jalview/schemes/ColourSchemes.java
+++ b/src/jalview/schemes/ColourSchemes.java
@@ -1,14 +1,29 @@
+/*
+ * 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.schemes;
-import jalview.binding.JalviewUserColours;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
-import java.awt.Color;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.InputStreamReader;
import java.util.LinkedHashMap;
import java.util.Map;
@@ -20,7 +35,7 @@ public class ColourSchemes
private static ColourSchemes instance = new ColourSchemes();
/*
- * a map from scheme name to an instance of it
+ * a map from scheme name (lower-cased) to an instance of it
*/
private Map schemes;
@@ -99,9 +114,12 @@ public class ColourSchemes
*/
public void removeColourScheme(String name)
{
- schemes.remove(name);
+ if (name != null)
+ {
+ schemes.remove(name.toLowerCase());
+ }
}
-
+
/**
* Returns an instance of the colour scheme with which the given view may be
* coloured
@@ -167,124 +185,6 @@ public class ColourSchemes
{
return false;
}
- name = name.toLowerCase();
- for (ColourSchemeI scheme : getColourSchemes())
- {
- if (name.equals(scheme.getSchemeName().toLowerCase()))
- {
- return true;
- }
- }
- return false;
- }
-
- /**
- * Loads a user defined colour scheme from file. The file should contain a
- * definition of residue colours in XML format as defined in
- * JalviewUserColours.xsd.
- *
- * @param filePath
- *
- * @return
- */
- public static UserColourScheme loadColourScheme(String filePath)
- {
- UserColourScheme ucs = null;
- Color[] newColours = null;
- File file = new File(filePath);
- try
- {
- 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
- * optionally, lower-case alternatives for all except 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++)
- {
- name = jucs.getColour(i).getName();
- if (ResidueProperties.aa3Hash.containsKey(name))
- {
- index = ResidueProperties.aa3Hash.get(name).intValue();
- }
- else
- {
- index = ResidueProperties.aaIndex[name.charAt(0)];
- }
- if (index == -1)
- {
- continue;
- }
-
- Color color = new Color(Integer.parseInt(jucs.getColour(i)
- .getRGB(), 16));
- if (name.toLowerCase().equals(name))
- {
- caseSensitive = true;
- lowerCase[index] = color;
- }
- else
- {
- newColours[index] = color;
- }
- }
-
- /*
- * instantiate the colour scheme
- */
- ucs = new UserColourScheme(newColours);
- ucs.setName(jucs.getSchemeName());
- if (caseSensitive)
- {
- ucs.setLowerCaseColours(lowerCase);
- }
- } catch (Exception ex)
- {
- // Could be old Jalview Archive format
- try
- {
- 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));
- }
- ucs = new UserColourScheme(newColours);
- ucs.setName(jucs.getSchemeName());
- } catch (Exception ex2)
- {
- ex2.printStackTrace();
- }
-
- if (newColours == null)
- {
- System.out.println("Error loading User ColourFile\n" + ex);
- }
- }
-
- return ucs;
+ return schemes.containsKey(name.toLowerCase());
}
}