X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=2c4eb7aceb922e904ef1fa2f1825af2558a776a7;hb=58962a97c9819d186ce347072e8750dbcae16f0f;hp=38f409f8591be137da9b0bd18b11a0efcdc1e1a8;hpb=d1707d4c26db76cfeb640f0dbeb3e3427fd40eb7;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 38f409f..2c4eb7a 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -55,7 +55,9 @@ import jalview.util.UrlLink;
 import java.awt.Color;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
+import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.BitSet;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.Hashtable;
@@ -450,7 +452,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
         buildGroupURLMenu(sg, groupLinks);
       }
       // Add a 'show all structures' for the current selection
-      Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>(), reppdb = new Hashtable<String, PDBEntry>();
+      Hashtable<String, PDBEntry> pdbe = new Hashtable<>(), reppdb = new Hashtable<>();
       SequenceI sqass = null;
       for (SequenceI sq : ap.av.getSequenceSelection())
       {
@@ -517,7 +519,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
   void addFeatureLinks(final SequenceI seq, List<String> links)
   {
     JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
-    Map<String, List<String>> linkset = new LinkedHashMap<String, List<String>>();
+    Map<String, List<String>> linkset = new LinkedHashMap<>();
 
     for (String link : links)
     {
@@ -601,8 +603,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
      * the insertion order, which is the order of the annotations on the
      * alignment.
      */
-    Map<String, List<List<String>>> shownTypes = new LinkedHashMap<String, List<List<String>>>();
-    Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<String, List<List<String>>>();
+    Map<String, List<List<String>>> shownTypes = new LinkedHashMap<>();
+    Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<>();
     AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
             AlignmentAnnotationUtils.asList(annotations), forSequences);
 
@@ -708,7 +710,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
 
     SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
     String[][] idandseqs = GroupUrlLink.formStrings(seqs);
-    Hashtable<String, Object[]> commonDbrefs = new Hashtable<String, Object[]>();
+    Hashtable<String, Object[]> commonDbrefs = new Hashtable<>();
     for (int sq = 0; sq < seqs.length; sq++)
     {
 
@@ -1367,8 +1369,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
      * Temporary store to hold distinct calcId / type pairs for the tooltip.
      * Using TreeMap means calcIds are shown in alphabetical order.
      */
-    SortedMap<String, String> tipEntries = new TreeMap<String, String>();
-    final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<SequenceI, List<AlignmentAnnotation>>();
+    SortedMap<String, String> tipEntries = new TreeMap<>();
+    final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>();
     AlignmentI al = this.ap.av.getAlignment();
     AlignmentUtils.findAddableReferenceAnnotations(forSequences,
             tipEntries, candidates, al);
@@ -1443,24 +1445,59 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
 
   protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
   {
-    if (sequence != null)
+
+    HiddenColumns hidden = new HiddenColumns();
+    BitSet inserts = new BitSet(), mask = new BitSet();
+
+    // set mask to preserve existing hidden columns outside selected group
+    if (ap.av.hasHiddenColumns())
     {
-      /* ColumnSelection cs = ap.av.getColumnSelection();
-       if (cs == null)
-       {
-         cs = new ColumnSelection();
-       }
-       cs.hideInsertionsFor(sequence);
-       ap.av.setColumnSelection(cs);*/
+      ap.av.getAlignment().getHiddenColumns().markHiddenRegions(mask);
+    }
+
+    boolean markedPopup = false;
+    // mark inserts in current selection
+    if (ap.av.getSelectionGroup() != null)
+    {
+      // mark just the columns in the selection group to be hidden
+      inserts.set(ap.av.getSelectionGroup().getStartRes(), ap.av
+              .getSelectionGroup().getEndRes() + 1);
+
+      // and clear that part of the mask
+      mask.andNot(inserts);
 
-      HiddenColumns hidden = ap.av.getAlignment().getHiddenColumns();
-      if (hidden == null)
+      // now clear columns without gaps
+      for (SequenceI sq : ap.av.getSelectionGroup().getSequences())
       {
-        hidden = new HiddenColumns();
+        if (sq == sequence)
+        {
+          markedPopup = true;
+        }
+        inserts.and(sq.getInsertionsAsBits());
       }
-      hidden.hideInsertionsFor(sequence);
-      ap.av.getAlignment().setHiddenColumns(hidden);
     }
+    else
+    {
+      // initially, mark all columns to be hidden
+      inserts.set(0, ap.av.getAlignment().getWidth());
+
+      // and clear out old hidden regions completely
+      mask.clear();
+    }
+
+    // now mark for sequence under popup if we haven't already done it
+    if (!markedPopup && sequence != null)
+    {
+      inserts.and(sequence.getInsertionsAsBits());
+    }
+
+    // finally, preserve hidden regions outside selection
+    inserts.or(mask);
+
+    // and set hidden columns accordingly
+    hidden.hideMarkedBits(inserts);
+
+    ap.av.getAlignment().setHiddenColumns(hidden);
     refresh();
   }
 
@@ -1519,7 +1556,9 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
   void refresh()
   {
     ap.updateAnnotation();
-    ap.paintAlignment(true);
+    // removed paintAlignment(true) here:
+    // updateAnnotation calls paintAlignment already, so don't need to call
+    // again
 
     PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
   }
@@ -1888,33 +1927,36 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       return;
     }
 
-    int rsize = 0, gSize = sg.getSize();
-    SequenceI[] rseqs, seqs = new SequenceI[gSize];
-    SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
+    List<SequenceI> seqs = new ArrayList<>();
+    List<SequenceFeature> features = new ArrayList<>();
 
+    /*
+     * assemble dataset sequences, and template new sequence features,
+     * for the amend features dialog
+     */
+    int gSize = sg.getSize();
     for (int i = 0; i < gSize; i++)
     {
       int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
       int end = sg.findEndRes(sg.getSequenceAt(i));
       if (start <= end)
       {
-        seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
-        features[rsize] = new SequenceFeature(null, null, null, start, end,
-                "Jalview");
-        rsize++;
+        seqs.add(sg.getSequenceAt(i).getDatasetSequence());
+        features.add(new SequenceFeature(null, null, null, start, end, null));
       }
     }
-    rseqs = new SequenceI[rsize];
-    tfeatures = new SequenceFeature[rsize];
-    System.arraycopy(seqs, 0, rseqs, 0, rsize);
-    System.arraycopy(features, 0, tfeatures, 0, rsize);
-    features = tfeatures;
-    seqs = rseqs;
-    if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
-            features, true, ap))
-    {
-      ap.alignFrame.setShowSeqFeatures(true);
-      ap.highlightSearchResults(null);
+
+    /*
+     * an entirely gapped region will generate empty lists of sequence / features
+     */
+    if (!seqs.isEmpty())
+    {
+      if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(
+              seqs, features, true, ap))
+      {
+        ap.alignFrame.setShowSeqFeatures(true);
+        ap.highlightSearchResults(null);
+      }
     }
   }