Merge branch 'bug/JAL-2742' into develop

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 9e6d1c0..3cb06c1 100644 (file)
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -24,7 +24,6 @@ import jalview.analysis.Conservation;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
-import jalview.datamodel.CigarArray;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.ProfilesI;
 import jalview.datamodel.SearchResultsI;
@@ -243,16 +242,6 @@ public interface AlignViewportI extends ViewStyleI
   void clearSequenceColours();
 
   /**
-   * This method returns the visible alignment as text, as seen on the GUI, ie
-   * if columns are hidden they will not be returned in the result. Use this for
-   * calculating trees, PCA, redundancy etc on views which contain hidden
-   * columns.
-   * 
-   * @return String[]
-   */
-  CigarArray getViewAsCigars(boolean selectedRegionOnly);
-
-  /**
    * return a compact representation of the current alignment selection to pass
    * to an analysis function
    * 
@@ -486,6 +475,7 @@ public interface AlignViewportI extends ViewStyleI
    * 
    * @return
    */
+  @Override
   boolean isProteinFontAsCdna();
 
   /**
@@ -493,5 +483,6 @@ public interface AlignViewportI extends ViewStyleI
    * 
    * @return
    */
+  @Override
   void setProteinFontAsCdna(boolean b);
 }

diff --git a/src/jalview/datamodel/CigarArray.java b/src/jalview/datamodel/CigarArray.java
index b6224c2..1723f1d 100644 (file)
--- a/src/jalview/datamodel/CigarArray.java
+++ b/src/jalview/datamodel/CigarArray.java
@@ -170,32 +170,30 @@ public class CigarArray extends CigarBase
         hideStart = region[0];
         hideEnd = region[1];
         // edit hidden regions to selection range
-        if (hideStart < last)
+
+        // just move on if hideEnd is before last
+        if (hideEnd < last)
         {
-          if (hideEnd > last)
-          {
-            hideStart = last;
-          }
-          else
-          {
-            continue;
-          }
+          continue;
         }
-
+        // exit if next region is after end
         if (hideStart > end)
         {
           break;
         }
 
-        if (hideEnd > end)
+        // truncate region at start if last falls in region
+        if ((hideStart < last) && (hideEnd >= last))
         {
-          hideEnd = end;
+          hideStart = last;
         }
 
-        if (hideStart > hideEnd)
+        // truncate region at end if end falls in region
+        if (hideEnd > end) // already checked that hideStart<=end
         {
-          break;
+          hideEnd = end;
         }
+
         /**
          * form operations...
          */
@@ -207,7 +205,7 @@ public class CigarArray extends CigarBase
         last = hideEnd + 1;
       }
       // Final match if necessary.
-      if (last < end)
+      if (last <= end)
       {
         addOperation(CigarArray.M, end - last + 1);
       }

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 3702cd0..b260cab 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -33,7 +33,6 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.Annotation;
-import jalview.datamodel.CigarArray;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.HiddenSequences;
@@ -1673,13 +1672,6 @@ public abstract class AlignmentViewport
   }
 
   @Override
-  public CigarArray getViewAsCigars(boolean selectedRegionOnly)
-  {
-    return new CigarArray(alignment, alignment.getHiddenColumns(),
-            (selectedRegionOnly ? selectionGroup : null));
-  }
-
-  @Override
   public jalview.datamodel.AlignmentView getAlignmentView(
           boolean selectedOnly)
   {

diff --git a/test/jalview/datamodel/CigarArrayTest.java b/test/jalview/datamodel/CigarArrayTest.java
new file mode 100644 (file)
index 0000000..7bee423
--- /dev/null
+++ b/test/jalview/datamodel/CigarArrayTest.java
@@ -0,0 +1,141 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.datamodel;
+
+import static org.testng.Assert.assertEquals;
+
+import jalview.gui.JvOptionPane;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+public class CigarArrayTest
+{
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
+  @Test(groups = "Functional")
+  public void testConstructor()
+  {
+    SequenceI seq1 = new Sequence("sq1",
+            "ASFDDABACBACBACBACBACBACBABCABCBACBABCAB");
+    Sequence seq2 = new Sequence("sq2",
+            "TTTTTTACBCBABCABCABCABCBACBACBABCABCABCBA");
+
+    // construct alignment
+    AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
+
+    // hide columns
+    HiddenColumns hc = new HiddenColumns();
+    hc.hideColumns(3, 6);
+    hc.hideColumns(16, 20);
+
+    // select group
+    SequenceGroup sg1 = new SequenceGroup();
+    sg1.addSequence(seq1, false);
+    sg1.setStartRes(2);
+    sg1.setEndRes(23);
+
+    // Cigar array meanings:
+    // M = match
+    // D = deletion
+    // I = insertion
+    // number preceding M/D/I is the number of residues which
+    // match/are deleted/are inserted
+    // In the CigarArray constructor only matches or deletions are created, as
+    // we are comparing a sequence to its own subsequence (the group) + hidden
+    // columns.
+
+    // no hidden columns case
+    CigarArray cig = new CigarArray(al, null, sg1);
+    String result = cig.getCigarstring();
+    assertEquals(result, "22M");
+
+    cig = new CigarArray(al, hc, sg1);
+    result = cig.getCigarstring();
+    assertEquals(result, "1M4D9M5D3M");
+
+    // group starts at hidden cols
+    sg1.setStartRes(3);
+    cig = new CigarArray(al, hc, sg1);
+    result = cig.getCigarstring();
+    assertEquals(result, "4D9M5D3M");
+
+    // group starts at last but 1 hidden col
+    sg1.setStartRes(5);
+    cig = new CigarArray(al, hc, sg1);
+    result = cig.getCigarstring();
+    assertEquals(result, "2D9M5D3M");
+
+    // group starts at last hidden col
+    sg1.setStartRes(6);
+    cig = new CigarArray(al, hc, sg1);
+    result = cig.getCigarstring();
+    assertEquals(result, "1D9M5D3M");
+
+    // group starts just after hidden region
+    sg1.setStartRes(7);
+    cig = new CigarArray(al, hc, sg1);
+    result = cig.getCigarstring();
+    assertEquals(result, "9M5D3M");
+
+    // group ends just before start of hidden region
+    sg1.setStartRes(5);
+    sg1.setEndRes(15);
+    cig = new CigarArray(al, hc, sg1);
+    result = cig.getCigarstring();
+    assertEquals(result, "2D9M");
+
+    // group ends at start of hidden region
+    sg1.setEndRes(16);
+    cig = new CigarArray(al, hc, sg1);
+    result = cig.getCigarstring();
+    assertEquals(result, "2D9M1D");
+
+    // group ends 1 after start of hidden region
+    sg1.setEndRes(17);
+    cig = new CigarArray(al, hc, sg1);
+    result = cig.getCigarstring();
+    assertEquals(result, "2D9M2D");
+
+    // group ends at end of hidden region
+    sg1.setEndRes(20);
+    cig = new CigarArray(al, hc, sg1);
+    result = cig.getCigarstring();
+    assertEquals(result, "2D9M5D");
+
+    // group ends just after end of hidden region
+    sg1.setEndRes(21);
+    cig = new CigarArray(al, hc, sg1);
+    result = cig.getCigarstring();
+    assertEquals(result, "2D9M5D1M");
+
+    // group ends 2 after end of hidden region
+    sg1.setEndRes(22);
+    cig = new CigarArray(al, hc, sg1);
+    result = cig.getCigarstring();
+    assertEquals(result, "2D9M5D2M");
+  }
+}