Merge branch 'develop' into bug/JAL-2346annotationChoice

[jalview.git] / src / jalview / schemes / ColourSchemes.java

diff --git a/src/jalview/schemes/ColourSchemes.java b/src/jalview/schemes/ColourSchemes.java
index 817fb01..dc7e403 100644 (file)
--- a/src/jalview/schemes/ColourSchemes.java
+++ b/src/jalview/schemes/ColourSchemes.java
@@ -1,14 +1,9 @@
 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;
 
@@ -177,114 +172,4 @@ public class ColourSchemes
     }
     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;
-  }
 }