patch re JAL-554

[jalview.git] / src / jalview / gui / Jalview2XML.java

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 7a403a0..260f603 100755 (executable)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -2169,7 +2169,7 @@ public class Jalview2XML
           // newer files have an 'autoCalculated' flag and store calculation
           // state in viewport properties
           jaa.autoCalculated = true; // means annotation will be marked for
-                                     // update at end of load.
+          // update at end of load.
         }
         al.addAnnotation(jaa);
       }
@@ -2698,85 +2698,91 @@ public class Jalview2XML
       else if (view.getBgColour().startsWith("Annotation"))
       {
         // int find annotation
-        for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
+        if (af.viewport.alignment.getAlignmentAnnotation() != null)
         {
-          if (af.viewport.alignment.getAlignmentAnnotation()[i].label
-                  .equals(view.getAnnotationColours().getAnnotation()))
+          for (int i = 0; i < af.viewport.alignment
+                  .getAlignmentAnnotation().length; i++)
           {
-            if (af.viewport.alignment.getAlignmentAnnotation()[i]
-                    .getThreshold() == null)
+            if (af.viewport.alignment.getAlignmentAnnotation()[i].label
+                    .equals(view.getAnnotationColours().getAnnotation()))
             {
-              af.viewport.alignment.getAlignmentAnnotation()[i]
-                      .setThreshold(new jalview.datamodel.GraphLine(view
-                              .getAnnotationColours().getThreshold(),
-                              "Threshold", java.awt.Color.black)
-
-                      );
-            }
+              if (af.viewport.alignment.getAlignmentAnnotation()[i]
+                      .getThreshold() == null)
+              {
+                af.viewport.alignment.getAlignmentAnnotation()[i]
+                        .setThreshold(new jalview.datamodel.GraphLine(view
+                                .getAnnotationColours().getThreshold(),
+                                "Threshold", java.awt.Color.black)
 
-            if (view.getAnnotationColours().getColourScheme()
-                    .equals("None"))
-            {
-              cs = new AnnotationColourGradient(af.viewport.alignment
-                      .getAlignmentAnnotation()[i], new java.awt.Color(view
-                      .getAnnotationColours().getMinColour()),
-                      new java.awt.Color(view.getAnnotationColours()
-                              .getMaxColour()), view.getAnnotationColours()
-                              .getAboveThreshold());
-            }
-            else if (view.getAnnotationColours().getColourScheme()
-                    .startsWith("ucs"))
-            {
-              cs = new AnnotationColourGradient(af.viewport.alignment
-                      .getAlignmentAnnotation()[i], GetUserColourScheme(
-                      jms, view.getAnnotationColours().getColourScheme()),
-                      view.getAnnotationColours().getAboveThreshold());
-            }
-            else
-            {
-              cs = new AnnotationColourGradient(af.viewport.alignment
-                      .getAlignmentAnnotation()[i], ColourSchemeProperty
-                      .getColour(al, view.getAnnotationColours()
-                              .getColourScheme()), view
-                      .getAnnotationColours().getAboveThreshold());
-            }
+                        );
+              }
 
-            // Also use these settings for all the groups
-            if (al.getGroups() != null)
-            {
-              for (int g = 0; g < al.getGroups().size(); g++)
+              if (view.getAnnotationColours().getColourScheme().equals(
+                      "None"))
+              {
+                cs = new AnnotationColourGradient(af.viewport.alignment
+                        .getAlignmentAnnotation()[i], new java.awt.Color(
+                        view.getAnnotationColours().getMinColour()),
+                        new java.awt.Color(view.getAnnotationColours()
+                                .getMaxColour()), view
+                                .getAnnotationColours().getAboveThreshold());
+              }
+              else if (view.getAnnotationColours().getColourScheme()
+                      .startsWith("ucs"))
+              {
+                cs = new AnnotationColourGradient(af.viewport.alignment
+                        .getAlignmentAnnotation()[i],
+                        GetUserColourScheme(jms, view
+                                .getAnnotationColours().getColourScheme()),
+                        view.getAnnotationColours().getAboveThreshold());
+              }
+              else
               {
-                jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) al
-                        .getGroups().elementAt(g);
+                cs = new AnnotationColourGradient(af.viewport.alignment
+                        .getAlignmentAnnotation()[i], ColourSchemeProperty
+                        .getColour(al, view.getAnnotationColours()
+                                .getColourScheme()), view
+                        .getAnnotationColours().getAboveThreshold());
+              }
 
-                if (sg.cs == null)
+              // Also use these settings for all the groups
+              if (al.getGroups() != null)
+              {
+                for (int g = 0; g < al.getGroups().size(); g++)
                 {
-                  continue;
-                }
+                  jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) al
+                          .getGroups().elementAt(g);
 
-                /*
-                 * if
-                 * (view.getAnnotationColours().getColourScheme().equals("None"
-                 * )) { sg.cs = new AnnotationColourGradient(
-                 * af.viewport.alignment.getAlignmentAnnotation()[i], new
-                 * java.awt.Color(view.getAnnotationColours(). getMinColour()),
-                 * new java.awt.Color(view.getAnnotationColours().
-                 * getMaxColour()),
-                 * view.getAnnotationColours().getAboveThreshold()); } else
-                 */
-                {
-                  sg.cs = new AnnotationColourGradient(
-                          af.viewport.alignment.getAlignmentAnnotation()[i],
-                          sg.cs, view.getAnnotationColours()
-                                  .getAboveThreshold());
-                }
+                  if (sg.cs == null)
+                  {
+                    continue;
+                  }
+
+                  /*
+                   * if
+                   * (view.getAnnotationColours().getColourScheme().equals("None"
+                   * )) { sg.cs = new AnnotationColourGradient(
+                   * af.viewport.alignment.getAlignmentAnnotation()[i], new
+                   * java.awt.Color(view.getAnnotationColours().
+                   * getMinColour()), new
+                   * java.awt.Color(view.getAnnotationColours().
+                   * getMaxColour()),
+                   * view.getAnnotationColours().getAboveThreshold()); } else
+                   */
+                  {
+                    sg.cs = new AnnotationColourGradient(
+                            af.viewport.alignment.getAlignmentAnnotation()[i],
+                            sg.cs, view.getAnnotationColours()
+                                    .getAboveThreshold());
+                  }
 
+                }
               }
+
+              break;
             }
 
-            break;
           }
-
         }
       }
       else