X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FAlignmentViewport.java;h=7cea5a325f06815796aec184406d62307cf1a038;hb=e7b6c76c3b028aeeef7770c99c87d895c1b46172;hp=07cb689a891a5e84af44cb865e68cf6b95df4a7d;hpb=a73dfac0f8c2280f13651bcd804cd7bb2420e8d5;p=jalview.git

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 07cb689..7cea5a3 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -49,6 +49,7 @@ import jalview.structure.CommandListener;
 import jalview.structure.StructureSelectionManager;
 import jalview.structure.VamsasSource;
 import jalview.util.Comparison;
+import jalview.util.MapList;
 import jalview.util.MappingUtils;
 import jalview.viewmodel.styles.ViewStyle;
 import jalview.workers.AlignCalcManager;
@@ -848,7 +849,9 @@ public abstract class AlignmentViewport implements AlignViewportI,
        */
       AlignedCodonFrame mapping = al.getCodonFrames().iterator().next();
       // TODO hold mapping type e.g. dna-to-protein in AlignedCodonFrame?
-      if (mapping.getdnaToProt()[0].getFromRatio() == 3)
+      MapList[] mapLists = mapping.getdnaToProt();
+      // mapLists can be empty if project load has not finished resolving seqs
+      if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3)
       {
         if (calculator
                 .getRegisteredWorkersOfClass(ComplementConsensusThread.class) == null)
@@ -1075,6 +1078,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
     {
       updateHiddenColumns();
     }
+    isColSelChanged(true);
   }
 
   /**
@@ -1203,8 +1207,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    */
   public boolean isColSelChanged(boolean b)
   {
-    int hc = (colSel == null || colSel.isEmpty()) ? -1 : colSel
-            .hashCode();
+    int hc = (colSel == null || colSel.isEmpty()) ? -1 : colSel.hashCode();
     if (hc != -1 && hc != colselhash)
     {
       if (b)
@@ -1305,7 +1308,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
     colSel.hideSelectedColumns();
     setSelectionGroup(null);
-
+    isColSelChanged(true);
   }
 
   public void hideColumns(int start, int end)
@@ -1318,17 +1321,19 @@ public abstract class AlignmentViewport implements AlignViewportI,
     {
       colSel.hideColumns(start, end);
     }
+    isColSelChanged(true);
   }
 
   public void showColumn(int col)
   {
     colSel.revealHiddenColumns(col);
-
+    isColSelChanged(true);
   }
 
   public void showAllHiddenColumns()
   {
     colSel.revealAllHiddenColumns();
+    isColSelChanged(true);
   }
 
   // common hide/show seq stuff
@@ -1460,13 +1465,42 @@ public abstract class AlignmentViewport implements AlignViewportI,
 
   }
 
+  /**
+   * 
+   * @return null or the current reference sequence
+   */
+  public SequenceI getReferenceSeq()
+  {
+    return alignment.getSeqrep();
+  }
+
+  /**
+   * @param seq
+   * @return true iff seq is the reference for the alignment
+   */
+  public boolean isReferenceSeq(SequenceI seq)
+  {
+    return alignment.getSeqrep() == seq;
+  }
+
+  /**
+   * 
+   * @param seq
+   * @return true if there are sequences represented by this sequence that are
+   *         currently hidden
+   */
   public boolean isHiddenRepSequence(SequenceI seq)
   {
-    return alignment.getSeqrep() == seq
-            || (hiddenRepSequences != null && hiddenRepSequences
+    return (hiddenRepSequences != null && hiddenRepSequences
                     .containsKey(seq));
   }
 
+  /**
+   * 
+   * @param seq
+   * @return null or a sequence group containing the sequences that seq
+   *         represents
+   */
   public SequenceGroup getRepresentedSequences(SequenceI seq)
   {
     return (SequenceGroup) (hiddenRepSequences == null ? null
@@ -1554,6 +1588,13 @@ public abstract class AlignmentViewport implements AlignViewportI,
   @Override
   public String[] getViewAsString(boolean selectedRegionOnly)
   {
+    return getViewAsString(selectedRegionOnly, true);
+  }
+
+  @Override
+  public String[] getViewAsString(boolean selectedRegionOnly,
+          boolean isExportHiddenSeqs)
+  {
     String[] selection = null;
     SequenceI[] seqs = null;
     int i, iSize;
@@ -1567,7 +1608,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
     }
     else
     {
-      if (hasHiddenRows())
+      if (hasHiddenRows() && isExportHiddenSeqs)
       {
         iSize = alignment.getHiddenSequences().getFullAlignment()
                 .getHeight();
@@ -1797,7 +1838,9 @@ public abstract class AlignmentViewport implements AlignViewportI,
         // fudge: check mappings are not protein-to-protein
         // TODO: nicer
         AlignedCodonFrame mapping = codonMappings.iterator().next();
-        if (mapping.getdnaToProt()[0].getFromRatio() == 3)
+        MapList[] mapLists = mapping.getdnaToProt();
+        // mapLists can be empty if project load has not finished resolving seqs
+        if (mapLists.length > 0 && mapLists[0].getFromRatio() == 3)
         {
           complementConsensus = new AlignmentAnnotation("cDNA Consensus",
                   "PID for cDNA", new Annotation[1], 0f, 100f,
@@ -2650,4 +2693,39 @@ public abstract class AlignmentViewport implements AlignViewportI,
             sequence.findPosition(middleColumn), mappings);
     return seqOffset;
   }
+
+  /**
+   * synthesize a column selection if none exists so it covers the given
+   * selection group. if wholewidth is false, no column selection is made if the
+   * selection group covers the whole alignment width.
+   * 
+   * @param sg
+   * @param wholewidth
+   */
+  public void expandColSelection(SequenceGroup sg, boolean wholewidth)
+  {
+    int sgs, sge;
+    if (sg != null
+            && (sgs = sg.getStartRes()) >= 0
+            && sg.getStartRes() <= (sge = sg.getEndRes())
+            && (colSel == null || colSel.getSelected() == null || colSel
+                    .getSelected().size() == 0))
+    {
+      if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
+      {
+        // do nothing
+        return;
+      }
+      if (colSel == null)
+      {
+        colSel = new ColumnSelection();
+      }
+      for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++)
+      {
+        colSel.addElement(cspos);
+      }
+    }
+  }
+
+
 }