merge

diff --git a/help/html/features/uniprotsequencefetcher.html b/help/html/features/uniprotsequencefetcher.html
index 55b4d71..9b2e3fa 100644 (file)
--- a/help/html/features/uniprotsequencefetcher.html
+++ b/help/html/features/uniprotsequencefetcher.html
@@ -64,7 +64,7 @@
 
                <li><strong>Bulk Uniprot retrieval</strong><br>
       Firstly, switch the search target to Uniprot Id, then enter multiple IDs by separating them with a semi-colon.
-      e.g. fila_human; mnt_human; mnt_mouse<br />Hitting Return or OK will automatically
+      e.g. fila_human; mnt_human; mnt_mouse.<br />Hitting Return or OK will automatically
       fetch those IDs, like the default Sequence Fetcher interface.</li>
       
             <li><strong>Advanced / Custom querying</strong>  
@@ -141,7 +141,7 @@
     <strong>Result pagination</strong>
   </p>
   The query results returned from the Uniprot server are paginated for performance optimisation. 
-  The button labelled <strong>' << '</strong> and <strong>' >> '</strong> can be used to navigate to the next or previous result page respectively. 
+  The button labelled <strong>'&nbsp;&lt;&lt;&nbsp;'</strong> and <strong>'&nbsp;&gt;&gt;&nbsp;'</strong> can be used to navigate to the next or previous result page respectively. 
   The page range is shown on the title bar of the Free Text Search interface. Jalview's pagination implementation supports multiple selection of entries across multiple pages. 
   
   

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 45e77ba..f40b73b 100644 (file)
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -376,5 +376,20 @@ public interface AlignViewportI extends ViewStyleI
    */
   void setFollowHighlight(boolean b);
 
+  /**
+   * Set whether hidden Sequences should be trimmed off during an export
+   * operation.
+   * 
+   * @param isExportHiddenSeqs
+   */
+  public void setExportHiddenSeqs(boolean isExportHiddenSeqs);
+
+  /**
+   * If true hidden Sequences are exported otherwise they aren't
+   * 
+   * @return
+   */
+  public boolean isExportHiddenSeqs();
+
   public void applyFeaturesStyle(FeatureSettingsModelI featureSettings);
 }

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index d548695..818c150 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1313,6 +1313,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
     {
+      viewport.setExportHiddenSeqs(settings.isExportHiddenSequences());
       omitHidden = viewport.getViewAsString(false);
     }
 

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index c16fdce..6581bef 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -1601,7 +1601,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
     }
     else
     {
-      if (hasHiddenRows())
+      if (hasHiddenRows() && isExportHiddenSeqs)
       {
         iSize = alignment.getHiddenSequences().getFullAlignment()
                 .getHeight();
@@ -2719,4 +2719,18 @@ public abstract class AlignmentViewport implements AlignViewportI,
       }
     }
   }
+
+  private boolean isExportHiddenSeqs = true;
+
+  @Override
+  public void setExportHiddenSeqs(boolean isExportHiddenSeqs)
+  {
+    this.isExportHiddenSeqs = isExportHiddenSeqs;
+  }
+
+  @Override
+  public boolean isExportHiddenSeqs()
+  {
+    return isExportHiddenSeqs;
+  }
 }