From 0f649b7bf0e7ba6b62198d7bdcfece9413f9408d Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 25 May 2005 16:36:40 +0000
Subject: [PATCH] saves usercolours

---
 src/jalview/gui/Jalview2XML.java |   87 +++++++++++++++++++++++++++++++++-----
 1 file changed, 77 insertions(+), 10 deletions(-)

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 6b6bd86..3eebf5c 100755
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -80,6 +80,7 @@ public class Jalview2XML
   {
 
     Vector seqids = new Vector();
+    Vector userColours = new Vector();
 
     AlignViewport av = af.viewport;
 
@@ -185,11 +186,15 @@ public class Jalview2XML
 
         if (sg.cs instanceof ResidueColourScheme)
           groups[i].setPidThreshold( ( (ResidueColourScheme) sg.cs).getThreshold());
-       else if (sg.cs instanceof ScoreColourScheme)
-         groups[i].setPidThreshold( ( (ScoreColourScheme) sg.cs).getThreshold());
+        else if (sg.cs instanceof ScoreColourScheme)
+          groups[i].setPidThreshold( ( (ScoreColourScheme) sg.cs).getThreshold());
 
 
-        groups[i].setColour( ColourSchemeProperty.getColourName(sg.cs) );
+        if (sg.cs instanceof jalview.schemes.UserColourScheme)
+          groups[i].setColour(SetUserColourScheme(sg.cs, userColours, jms));
+        else
+          groups[i].setColour(ColourSchemeProperty.getColourName(sg.cs));
+
         groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
         groups[i].setDisplayBoxes(sg.getDisplayBoxes());
         groups[i].setDisplayText(sg.getDisplayText());
@@ -203,7 +208,6 @@ public class Jalview2XML
         }
 
       }
-
       jms.setJGroup(groups);
 
     }
@@ -217,6 +221,12 @@ public class Jalview2XML
    view.setHeight(af.getHeight());
    view.setStartRes(av.startRes);
    view.setStartSeq(av.startSeq);
+
+
+ if( av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
+   view.setBgColour( SetUserColourScheme(av.getGlobalColourScheme(),
+                                         userColours, jms) );
+ else
    view.setBgColour( ColourSchemeProperty.getColourName
                      ( av.getGlobalColourScheme()));
 
@@ -269,6 +279,52 @@ public class Jalview2XML
     }
   }
 
+  static String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
+                                    Vector userColours,
+                                    JalviewModelSequence jms)
+  {
+    String id=null;
+    jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme)cs;
+    if (!userColours.contains(ucs))
+    {
+      userColours.add(ucs);
+      java.awt.Color [] colours = ucs.getColours();
+      jalview.binding.UserColours uc = new jalview.binding.UserColours();
+      jalview.binding.UserColourScheme jbucs = new jalview.binding.UserColourScheme();
+      for(int i=0; i<colours.length; i++)
+      {
+             jalview.binding.Colour col = new jalview.binding.Colour();
+             col.setRGB( jalview.util.Format.getHexString(colours[i]) );
+             jbucs.addColour(col);
+      }
+      id = "ucs"+userColours.indexOf(ucs);
+      uc.setId(id);
+      uc.setUserColourScheme(jbucs);
+      jms.addUserColours(uc);
+    }
+    return id;
+  }
+
+  static jalview.schemes.UserColourScheme GetUserColourScheme(JalviewModelSequence jms, String id)
+  {
+    UserColours [] uc = jms.getUserColours();
+    UserColours colours=null;
+    for(int i=0; i<uc.length; i++)
+    {
+       if(uc[i].getId().equals(id))
+       {  colours = uc[i]; break;  }
+    }
+    int csize = colours.getUserColourScheme().getColourCount();
+    java.awt.Color [] newColours = new java.awt.Color[csize];
+
+    for(int i=0; i<csize;i++)
+      newColours[i] = new java.awt.Color(
+        Integer.parseInt( colours.getUserColourScheme().getColour(i).getRGB(), 16) );
+
+    return  new jalview.schemes.UserColourScheme(newColours);
+
+  }
+
 
   public static void LoadJalviewAlign(String file)
   {
@@ -374,7 +430,12 @@ public class Jalview2XML
       JGroup[] groups = jms.getJGroup();
       for (int i = 0; i < groups.length; i++)
       {
-       ColourSchemeI cs = ColourSchemeProperty.getColour(al, groups[i].getColour() );
+       ColourSchemeI cs=null;
+       if(groups[i].getColour().startsWith("ucs"))
+         cs = GetUserColourScheme(jms,groups[i].getColour());
+       else
+         cs = ColourSchemeProperty.getColour(al, groups[i].getColour() );
+
        if (cs instanceof ResidueColourScheme)
          ( (ResidueColourScheme) cs).setThreshold(groups[i].getPidThreshold());
        else if (cs instanceof ScoreColourScheme)
@@ -442,12 +503,13 @@ public class Jalview2XML
     af.viewport.setShowBoxes( view.getShowBoxes() );
     af.viewport.setShowText( view.getShowText() );
 
-    af.viewport.setGlobalColourScheme( ColourSchemeProperty.getColour(al, view.getBgColour()));
-    af.viewport.setColourAppliesToAllGroups(false);
-    af.changeColour( af.viewport.getGlobalColourScheme() );
-    af.viewport.setColourAppliesToAllGroups(true);
+    ColourSchemeI cs=null;
+    if (view.getBgColour().startsWith("ucs"))
+      cs = GetUserColourScheme(jms, view.getBgColour());
+    else
+      cs = ColourSchemeProperty.getColour(al, view.getBgColour());
+    af.viewport.setGlobalColourScheme( cs );
 
-    ColourSchemeI cs = af.viewport.getGlobalColourScheme();
     if(cs instanceof ConservationColourScheme)
       ( (ConservationColourScheme) cs).inc = view.getConsThreshold();
 
@@ -456,6 +518,11 @@ public class Jalview2XML
     else if (cs instanceof ScoreColourScheme)
       ( (ScoreColourScheme) cs).setThreshold(view.getPidThreshold());
 
+    af.viewport.setColourAppliesToAllGroups(false);
+    af.changeColour(af.viewport.getGlobalColourScheme());
+    af.viewport.setColourAppliesToAllGroups(true);
+
+
     //LOAD TREES - THIS RELEASE ONLY ALLOWS 1 TREE
     if(object.getVamsasModel().getTreeCount()>0)
     {
-- 
1.7.10.2