From c8ce35475df2851ea907283d3ec6b841b7fd05fa Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Fri, 14 Sep 2018 12:31:24 +0100
Subject: [PATCH] =?utf8?q?JAL-345=20view=20controller=20method=20to=20select?=
 =?utf8?q?=20highlighted=20sequences=20(note=20-=20doesn=E2=80=99t=20select=20?=
 =?utf8?q?sequences=20which=20contain=20search=20results,=20just=20ID=20high?=
 =?utf8?q?lights)?=
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Content-Type: text/plain; charset=utf8
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---
 src/jalview/controller/AlignViewController.java |   83 +++++++++++++++++++++++
 1 file changed, 83 insertions(+)

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index d992e4e..13b84ef 100644
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -38,6 +38,7 @@ import jalview.io.FeaturesFile;
 import jalview.util.MessageManager;
 
 import java.awt.Color;
+import java.util.ArrayList;
 import java.util.BitSet;
 import java.util.List;
 
@@ -383,6 +384,88 @@ public class AlignViewController implements AlignViewControllerI
 
   }
 
+  /**
+   * 
+   * Add highlighted sequences to selected rows. Exclude highlighted sequences
+   * from selected rows. toggle inclusion or exclusion of highlighted sequences.
+   * or add/exclude/toggle for sequences not highlighted.
+   * 
+   * @param invert
+   *          - when true, sequences that are not highlighted are used to modify
+   *          selection
+   * @param extendCurrent
+   *          - normally true , the current selected group is modified.
+   * @param toggle
+   *          - if a select
+   * @return
+   */
+  public boolean selectHighlightedSequences(boolean invert,
+          boolean extendCurrent, boolean toggle)
+  {
+    List<SequenceI> results = alignPanel.getAlignViewport()
+            .getHighlightedSeqs();
+
+    SequenceGroup sq = (extendCurrent
+            && viewport.getSelectionGroup() != null)
+                    ? viewport.getSelectionGroup()
+                    : new SequenceGroup();
+
+    if (invert)
+    {
+      List<SequenceI> nothighlighted = new ArrayList();
+      for (SequenceI seq : alignPanel.getAlignViewport().getAlignment()
+              .getSequences())
+      {
+        if (!results.contains(seq))
+        {
+          nothighlighted.add(seq);
+        }
+      }
+      results = nothighlighted;
+    }
+
+    if (results == null || results.size() == 0)
+    {
+      // do nothing if no selection exists
+      // unless toggle ??
+      return false;
+    }
+
+    boolean changed = false;
+
+    for (SequenceI seq : results)
+    {
+      int size = sq.getSize();
+      if (toggle)
+      {
+        sq.addOrRemove(seq, false);
+      }
+      else
+      {
+        sq.addSequence(seq, false);
+      }
+      changed |= size != sq.getSize();
+    }
+
+    if (sq.getSize() == 0)
+    {
+      viewport.setSelectionGroup(null);
+    }
+    else
+    {
+      if (sq != viewport.getSelectionGroup())
+    {
+      sq.setStartRes(0);
+      sq.setEndRes(viewport.getRanges().getAbsoluteAlignmentWidth());
+    }
+      viewport.setSelectionGroup(sq);
+    }
+
+    alignPanel.paintAlignment(false, false);
+
+    return changed;
+  }
+
   @Override
   public boolean markHighlightedColumns(boolean invert,
           boolean extendCurrent, boolean toggle)
-- 
1.7.10.2