JAL-2360 fix applet build by separating castor XML dependency from jalview.schemes...

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 48c1ee9..da3cb92 100755 (executable)
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -22,6 +22,7 @@ package jalview.bin;
 
 import jalview.datamodel.PDBEntry;
 import jalview.gui.UserDefinedColours;
+import jalview.schemes.ColourSchemeLoader;
 import jalview.schemes.ColourSchemes;
 import jalview.schemes.UserColourScheme;
 import jalview.structure.StructureImportSettings;
@@ -1037,7 +1038,7 @@ public class Cache
       String file = st.nextToken();
       try
       {
-        UserColourScheme ucs = ColourSchemes.loadColourScheme(file);
+        UserColourScheme ucs = ColourSchemeLoader.loadColourScheme(file);
         if (ucs != null)
         {
           if (coloursFound.length() > 0)

diff --git a/src/jalview/gui/ColourMenuHelper.java b/src/jalview/gui/ColourMenuHelper.java
index 31780d6..19ad939 100644 (file)
--- a/src/jalview/gui/ColourMenuHelper.java
+++ b/src/jalview/gui/ColourMenuHelper.java
@@ -3,6 +3,7 @@ package jalview.gui;
 import jalview.bin.Cache;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeLoader;
 import jalview.schemes.ColourSchemes;
 import jalview.schemes.ResidueColourScheme;
 import jalview.schemes.UserColourScheme;
@@ -258,7 +259,7 @@ public class ColourMenuHelper
     {
       try
       {
-        UserColourScheme ucs = ColourSchemes.loadColourScheme(file);
+        UserColourScheme ucs = ColourSchemeLoader.loadColourScheme(file);
         if (ucs != null
                 && ColourSchemes.getInstance().nameExists(ucs.getName()))
         {

diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index 83a8d24..463d8cd 100755 (executable)
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -29,6 +29,7 @@ import jalview.jbgui.GUserDefinedColours;
 import jalview.schemabinding.version2.Colour;
 import jalview.schemabinding.version2.JalviewUserColours;
 import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeLoader;
 import jalview.schemes.ColourSchemes;
 import jalview.schemes.ResidueProperties;
 import jalview.schemes.UserColourScheme;
@@ -625,7 +626,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
     File choice = chooser.getSelectedFile();
     Cache.setProperty(LAST_DIRECTORY, choice.getParent());
 
-    UserColourScheme ucs = ColourSchemes.loadColourScheme(choice
+    UserColourScheme ucs = ColourSchemeLoader.loadColourScheme(choice
             .getAbsolutePath());
     Color[] colors = ucs.getColours();
     schemeName.setText(ucs.getSchemeName());
@@ -674,7 +675,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
       {
         colours = colours.substring(0, colours.indexOf("|"));
       }
-      ret = ColourSchemes.loadColourScheme(colours);
+      ret = ColourSchemeLoader.loadColourScheme(colours);
     }
 
     if (ret == null)

diff --git a/src/jalview/schemes/ColourSchemeLoader.java b/src/jalview/schemes/ColourSchemeLoader.java
new file mode 100644 (file)
index 0000000..8660f3e
--- /dev/null
+++ b/src/jalview/schemes/ColourSchemeLoader.java
@@ -0,0 +1,125 @@
+package jalview.schemes;
+
+import jalview.binding.JalviewUserColours;
+
+import java.awt.Color;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.InputStreamReader;
+
+import org.exolab.castor.xml.Unmarshaller;
+
+public class ColourSchemeLoader
+{
+
+  /**
+   * 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;
+  }
+
+}

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;
-  }
 }