Merge branch 'bug/JAL-2589gapColour' into develop

diff --git a/RELEASE b/RELEASE
index 9bc5817..6dffc29 100644 (file)
--- a/RELEASE
+++ b/RELEASE
@@ -1,2 +1,2 @@
-jalview.release=releases/Release_2_10_1_Branch
-jalview.version=2.10.1
+jalview.release=releases/Release_2_10_2_Branch
+jalview.version=2.10.2

diff --git a/help/html/releases.html b/help/html/releases.html
index 5c8da91..97d6789 100755 (executable)
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -71,7 +71,7 @@ li:before {
       <td width="60" nowrap>
         <div align="center">
           <strong><a name="Jalview.2.10.2">2.10.2</a><br />
-            <em>30/5/2017</em></strong>
+            <em>20/6/2017</em></strong>
         </div>
       </td>
       <td><div align="left">

diff --git a/src/jalview/appletgui/AnnotationColumnChooser.java b/src/jalview/appletgui/AnnotationColumnChooser.java
index 60775d3..22978c3 100644 (file)
--- a/src/jalview/appletgui/AnnotationColumnChooser.java
+++ b/src/jalview/appletgui/AnnotationColumnChooser.java
@@ -310,6 +310,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
         }
         av.getAlignment().setHiddenColumns(oldHidden);
       }
+      av.sendSelection();
       ap.paintAlignment(true);
     }
 
@@ -428,8 +429,8 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
       }
 
       adjusting = true;
-      float range = getCurrentAnnotation().graphMax * 1000
-              - getCurrentAnnotation().graphMin * 1000;
+      // float range = getCurrentAnnotation().graphMax * 1000
+      // - getCurrentAnnotation().graphMin * 1000;
 
       slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
       slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
@@ -504,10 +505,13 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
       }
     }
 
+    // show hidden columns here, before changing the column selection in
+    // filterAnnotations, because showing hidden columns has the side effect of
+    // adding them to the selection
+    av.showAllHiddenColumns();
     av.getColumnSelection().filterAnnotations(
             getCurrentAnnotation().annotations, filterParams);
 
-    av.showAllHiddenColumns();
     if (getActionOption() == ACTION_OPTION_HIDE)
     {
       av.hideSelectedColumns();
@@ -515,6 +519,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
 
     filterParams = null;
     av.setAnnotationColumnSelectionState(this);
+    av.sendSelection();
     ap.paintAlignment(true);
   }
 

diff --git a/src/jalview/gui/AnnotationColumnChooser.java b/src/jalview/gui/AnnotationColumnChooser.java
index 9c2a1b9..f81455e 100644 (file)
--- a/src/jalview/gui/AnnotationColumnChooser.java
+++ b/src/jalview/gui/AnnotationColumnChooser.java
@@ -256,9 +256,9 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
         }
         av.getAlignment().setHiddenColumns(oldHidden);
       }
+      av.sendSelection();
       ap.paintAlignment(true);
     }
-
   }
 
   @Override
@@ -397,6 +397,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     {
       av.hideSelectedColumns();
     }
+    av.sendSelection();
 
     filterParams = null;
     av.setAnnotationColumnSelectionState(this);

diff --git a/src/jalview/urls/UrlLinkDisplay.java b/src/jalview/urls/UrlLinkDisplay.java
index 5b376a2..09566c3 100644 (file)
--- a/src/jalview/urls/UrlLinkDisplay.java
+++ b/src/jalview/urls/UrlLinkDisplay.java
@@ -177,7 +177,7 @@ public class UrlLinkDisplay
       break;
     case NAME:
       setDescription((String) value);
-      break;
+      // deliberate fall through
     case DATABASE:
       setDBName((String) value);
       break;

diff --git a/test/jalview/urls/UrlLinkDisplayTest.java b/test/jalview/urls/UrlLinkDisplayTest.java
index ff7d957..9eeac9f 100644 (file)
--- a/test/jalview/urls/UrlLinkDisplayTest.java
+++ b/test/jalview/urls/UrlLinkDisplayTest.java
@@ -131,7 +131,7 @@ public class UrlLinkDisplayTest {
 
     u.setValue(UrlLinkDisplay.NAME, "New Desc");
     Assert.assertEquals(u.getValue(UrlLinkDisplay.NAME), "New Desc");
-    Assert.assertEquals(u.getValue(UrlLinkDisplay.DATABASE), "TestDB");
+    Assert.assertEquals(u.getValue(UrlLinkDisplay.DATABASE), "New Desc");
 
     u.setValue(UrlLinkDisplay.DATABASE, "NewName");
     Assert.assertEquals(u.getValue(UrlLinkDisplay.DATABASE), "NewName");