X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemes.java;h=817fb0136767e4106fd656db2d554faea0e0c58a;hb=09d9063e70931a6cb75d16b230f5cd0665f0f340;hp=21faa2a43e8165817df5be5d1468c530931eadc3;hpb=94379c810f9115b8564ee7bac46ed119218d5fd2;p=jalview.git

diff --git a/src/jalview/schemes/ColourSchemes.java b/src/jalview/schemes/ColourSchemes.java
index 21faa2a..817fb01 100644
--- a/src/jalview/schemes/ColourSchemes.java
+++ b/src/jalview/schemes/ColourSchemes.java
@@ -1,8 +1,14 @@
 package jalview.schemes;
 
-import jalview.api.AlignViewportI;
+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;
 
@@ -102,33 +108,39 @@ public class ColourSchemes
    * 
    * @param name
    *          name of the colour scheme
-   * @param viewport
+   * @param forData
+   *          the data to be coloured
+   * @param optional
+   *          map from hidden representative sequences to the sequences they
+   *          represent
    * @return
    */
-  public ColourSchemeI getColourScheme(String name, AlignViewportI viewport)
+  public ColourSchemeI getColourScheme(String name,
+          AnnotatedCollectionI forData,
+          Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
   {
     if (name == null)
     {
       return null;
     }
     ColourSchemeI cs = schemes.get(name.toLowerCase());
-    return cs == null ? null : cs.getInstance(viewport.getAlignment(),
-            viewport.getHiddenRepSequences());
+    return cs == null ? null : cs.getInstance(forData, hiddenRepSequences);
   }
 
   /**
-   * Returns an instance of the colour scheme with which the given data may be
+   * Returns an instance of the colour scheme with which the given view may be
    * coloured
    * 
    * @param name
+   *          name of the colour scheme
    * @param forData
+   *          the data to be coloured
    * @return
    */
   public ColourSchemeI getColourScheme(String name,
           AnnotatedCollectionI forData)
   {
-    ColourSchemeI cs = schemes.get(name.toLowerCase());
-    return cs == null ? null : cs.getInstance(forData, null);
+    return getColourScheme(name, forData, null);
   }
 
   /**
@@ -141,4 +153,138 @@ public class ColourSchemes
   {
     return schemes.values();
   }
+
+  /**
+   * Answers true if there is a scheme with the given name, else false. The test
+   * is not case-sensitive.
+   * 
+   * @param name
+   * @return
+   */
+  public boolean nameExists(String name)
+  {
+    if (name == null)
+    {
+      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;
+  }
 }