JAL-2346 save annotation id instead of label with annotation colouring,

resolve either on load

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 35db33f..bebdff6 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -20,6 +20,39 @@
  */
 package jalview.gui;
 
+import java.awt.Color;
+import java.awt.Rectangle;
+import java.io.BufferedReader;
+import java.io.DataInputStream;
+import java.io.DataOutputStream;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.OutputStreamWriter;
+import java.io.PrintWriter;
+import java.lang.reflect.InvocationTargetException;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Enumeration;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Hashtable;
+import java.util.IdentityHashMap;
+import java.util.Iterator;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+import java.util.Vector;
+import java.util.jar.JarEntry;
+import java.util.jar.JarInputStream;
+import java.util.jar.JarOutputStream;
+
 import jalview.analysis.Conservation;
 import jalview.api.FeatureColourI;
 import jalview.api.ViewStyleI;
@@ -29,6 +62,7 @@ import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.GraphLine;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.RnaViewerModel;
 import jalview.datamodel.SequenceGroup;
@@ -95,41 +129,7 @@ import jalview.ws.params.ArgumentI;
 import jalview.ws.params.AutoCalcSetting;
 import jalview.ws.params.WsParamSetI;
 
-import java.awt.Color;
-import java.awt.Rectangle;
-import java.io.BufferedReader;
-import java.io.DataInputStream;
-import java.io.DataOutputStream;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.io.OutputStreamWriter;
-import java.io.PrintWriter;
-import java.lang.reflect.InvocationTargetException;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Enumeration;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Hashtable;
-import java.util.IdentityHashMap;
-import java.util.Iterator;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Set;
-import java.util.Vector;
-import java.util.jar.JarEntry;
-import java.util.jar.JarInputStream;
-import java.util.jar.JarOutputStream;
-
 import javax.swing.JInternalFrame;
-import javax.swing.JOptionPane;
 import javax.swing.SwingUtilities;
 
 import org.exolab.castor.xml.Marshaller;
@@ -1716,7 +1716,8 @@ public class Jalview2XML
     AnnotationColours ac = new AnnotationColours();
     ac.setAboveThreshold(acg.getAboveThreshold());
     ac.setThreshold(acg.getAnnotationThreshold());
-    ac.setAnnotation(acg.getAnnotation());
+    // 2.10.2 save annotationId (unique) not annotation label
+    ac.setAnnotation(acg.getAnnotation().annotationId);
     if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
     {
       ac.setColourScheme(setUserColourScheme(acg.getBaseColour(),
@@ -2638,10 +2639,12 @@ public class Jalview2XML
           @Override
           public void run()
           {
-            JvOptionPane.showInternalMessageDialog(Desktop.desktop,
-                    finalErrorMessage, "Error "
-                            + (saving ? "saving" : "loading")
-                            + " Jalview file", JvOptionPane.WARNING_MESSAGE);
+            JvOptionPane
+                    .showInternalMessageDialog(Desktop.desktop,
+                            finalErrorMessage, "Error "
+                                    + (saving ? "saving" : "loading")
+                                    + " Jalview file",
+                            JvOptionPane.WARNING_MESSAGE);
           }
         });
       }
@@ -4696,7 +4699,7 @@ public class Jalview2XML
           JalviewModelSequence jms, boolean checkGroupAnnColour)
   {
     boolean propagateAnnColour = false;
-    ColourSchemeI cs = null;
+    AnnotationColourGradient cs = null;
     AlignmentI annAlignment = af != null ? af.viewport.getAlignment() : al;
     if (checkGroupAnnColour && al.getGroups() != null
             && al.getGroups().size() > 0)
@@ -4704,7 +4707,7 @@ public class Jalview2XML
       // pre 2.8.1 behaviour
       // check to see if we should transfer annotation colours
       propagateAnnColour = true;
-      for (jalview.datamodel.SequenceGroup sg : al.getGroups())
+      for (SequenceGroup sg : al.getGroups())
       {
         if (sg.cs instanceof AnnotationColourGradient)
         {
@@ -4712,105 +4715,100 @@ public class Jalview2XML
         }
       }
     }
-    // int find annotation
-    if (annAlignment.getAlignmentAnnotation() != null)
+
+    /*
+     * pre 2.10.2: annotationId is AlignmentAnnotation.label
+     * 2.10.2- : annotationId is AlignmentAnnotation.annotationId
+     */
+    String annotationId = viewAnnColour.getAnnotation();
+    AlignmentAnnotation annotation = annotationIds.get(annotationId);
+
+    if (annotation == null && annAlignment.getAlignmentAnnotation() != null)
     {
       for (int i = 0; i < annAlignment.getAlignmentAnnotation().length; i++)
       {
-        if (annAlignment.getAlignmentAnnotation()[i].label
-                .equals(viewAnnColour.getAnnotation()))
+        if (annotationId
+                .equals(annAlignment.getAlignmentAnnotation()[i].label))
         {
-          if (annAlignment.getAlignmentAnnotation()[i].getThreshold() == null)
-          {
-            annAlignment.getAlignmentAnnotation()[i]
-                    .setThreshold(new jalview.datamodel.GraphLine(
-                            viewAnnColour.getThreshold(), "Threshold",
-                            java.awt.Color.black)
+          annotation = annAlignment.getAlignmentAnnotation()[i];
+          break;
+        }
+      }
+    }
+    if (annotation == null)
+    {
+      System.err.println("Failed to match annotation colour scheme for "
+              + annotationId);
+      return null;
+    }
+    if (annotation.getThreshold() == null)
+    {
+      annotation.setThreshold(new GraphLine(viewAnnColour.getThreshold(),
+              "Threshold", Color.black));
+    }
 
-                    );
-          }
+    if (viewAnnColour.getColourScheme().equals("None"))
+    {
+      cs = new AnnotationColourGradient(annotation, new Color(
+              viewAnnColour.getMinColour()), new Color(
+              viewAnnColour.getMaxColour()),
+              viewAnnColour.getAboveThreshold());
+    }
+    else if (viewAnnColour.getColourScheme().startsWith("ucs"))
+    {
+      cs = new AnnotationColourGradient(annotation, getUserColourScheme(
+              jms, viewAnnColour.getColourScheme()),
+              viewAnnColour.getAboveThreshold());
+    }
+    else
+    {
+      cs = new AnnotationColourGradient(annotation,
+              ColourSchemeProperty.getColour(al,
+                      viewAnnColour.getColourScheme()),
+              viewAnnColour.getAboveThreshold());
+    }
+    if (viewAnnColour.hasPerSequence())
+    {
+      cs.setSeqAssociated(viewAnnColour.isPerSequence());
+    }
+    if (viewAnnColour.hasPredefinedColours())
+    {
+      cs.setPredefinedColours(viewAnnColour.isPredefinedColours());
+    }
+    if (propagateAnnColour && al.getGroups() != null)
+    {
+      // Also use these settings for all the groups
+      for (int g = 0; g < al.getGroups().size(); g++)
+      {
+        SequenceGroup sg = al.getGroups().get(g);
 
-          if (viewAnnColour.getColourScheme().equals("None"))
-          {
-            cs = new AnnotationColourGradient(
-                    annAlignment.getAlignmentAnnotation()[i],
-                    new java.awt.Color(viewAnnColour.getMinColour()),
-                    new java.awt.Color(viewAnnColour.getMaxColour()),
-                    viewAnnColour.getAboveThreshold());
-          }
-          else if (viewAnnColour.getColourScheme().startsWith("ucs"))
-          {
-            cs = new AnnotationColourGradient(
-                    annAlignment.getAlignmentAnnotation()[i],
-                    getUserColourScheme(jms,
-                            viewAnnColour.getColourScheme()),
-                    viewAnnColour.getAboveThreshold());
-          }
-          else
-          {
-            cs = new AnnotationColourGradient(
-                    annAlignment.getAlignmentAnnotation()[i],
-                    ColourSchemeProperty.getColour(al,
-                            viewAnnColour.getColourScheme()),
-                    viewAnnColour.getAboveThreshold());
-          }
+        if (sg.cs == null)
+        {
+          continue;
+        }
+
+        /*
+         * if (viewAnnColour.getColourScheme().equals("None" )) { sg.cs =
+         * new AnnotationColourGradient(
+         * annAlignment.getAlignmentAnnotation()[i], new
+         * java.awt.Color(viewAnnColour. getMinColour()), new
+         * java.awt.Color(viewAnnColour. getMaxColour()),
+         * viewAnnColour.getAboveThreshold()); } else
+         *
+        {*/
+        sg.cs = new AnnotationColourGradient(annotation, sg.cs,
+                viewAnnColour.getAboveThreshold());
+        if (cs instanceof AnnotationColourGradient)
+        {
           if (viewAnnColour.hasPerSequence())
           {
-            ((AnnotationColourGradient) cs).setSeqAssociated(viewAnnColour
-                    .isPerSequence());
+            cs.setSeqAssociated(viewAnnColour.isPerSequence());
           }
           if (viewAnnColour.hasPredefinedColours())
           {
-            ((AnnotationColourGradient) cs)
-                    .setPredefinedColours(viewAnnColour
-                            .isPredefinedColours());
+            cs.setPredefinedColours(viewAnnColour.isPredefinedColours());
           }
-          if (propagateAnnColour && al.getGroups() != null)
-          {
-            // Also use these settings for all the groups
-            for (int g = 0; g < al.getGroups().size(); g++)
-            {
-              jalview.datamodel.SequenceGroup sg = al.getGroups().get(g);
-
-              if (sg.cs == null)
-              {
-                continue;
-              }
-
-              /*
-               * if (viewAnnColour.getColourScheme().equals("None" )) { sg.cs =
-               * new AnnotationColourGradient(
-               * annAlignment.getAlignmentAnnotation()[i], new
-               * java.awt.Color(viewAnnColour. getMinColour()), new
-               * java.awt.Color(viewAnnColour. getMaxColour()),
-               * viewAnnColour.getAboveThreshold()); } else
-               */
-              {
-                sg.cs = new AnnotationColourGradient(
-                        annAlignment.getAlignmentAnnotation()[i], sg.cs,
-                        viewAnnColour.getAboveThreshold());
-                if (cs instanceof AnnotationColourGradient)
-                {
-                  if (viewAnnColour.hasPerSequence())
-                  {
-                    ((AnnotationColourGradient) cs)
-                            .setSeqAssociated(viewAnnColour.isPerSequence());
-                  }
-                  if (viewAnnColour.hasPredefinedColours())
-                  {
-                    ((AnnotationColourGradient) cs)
-                            .setPredefinedColours(viewAnnColour
-                                    .isPredefinedColours());
-                  }
-                }
-              }
-
-            }
-          }
-
-          break;
         }
-
       }
     }
     return cs;