Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop

diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index b36a0a5..e089a11 100644 (file)
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -465,6 +465,7 @@ public class AlignmentView
    * alignment.
    * 
    * @param c
+   *          gap character to use to recreate the alignment
    * @return
    */
   private SequenceI[] getVisibleSeqs(char c)
@@ -472,13 +473,9 @@ public class AlignmentView
     SequenceI[] aln = new SequenceI[sequences.length];
     for (int i = 0, j = sequences.length; i < j; i++)
     {
-      aln[i] = sequences[i].getSeq('-');
-    }
-    // Remove hidden regions from sequence objects.
-    String seqs[] = getSequenceStrings('-');
-    for (int i = 0, j = aln.length; i < j; i++)
-    {
-      aln[i].setSequence(seqs[i]);
+      aln[i] = sequences[i].getSeq(c);
+      // Remove hidden regions from sequence
+      aln[i].setSequence(getASequenceString(c, i));
     }
     return aln;
   }
@@ -514,8 +511,38 @@ public class AlignmentView
   }
 
   /**
+   * build a string excluding hidden regions from a particular sequence in the
+   * view
+   * 
+   * @param c
+   * @param n
+   * @return
+   */
+  private String getASequenceString(char c, int n)
+  {
+    String sqn;
+    String fullseq = sequences[n].getSequenceString(c);
+    if (contigs != null)
+    {
+      sqn = "";
+      int p = 0;
+      for (int h = 0; h < contigs.length; h += 3)
+      {
+        sqn += fullseq.substring(p, contigs[h + 1]);
+        p = contigs[h + 1] + contigs[h + 2];
+      }
+      sqn += fullseq.substring(p);
+    }
+    else
+    {
+      sqn = fullseq;
+    }
+    return sqn;
+  }
+
+  /**
    * get an array of visible sequence strings for a view on an alignment using
-   * the given gap character
+   * the given gap character uses getASequenceString
    * 
    * @param c
    *          char
@@ -526,22 +553,7 @@ public class AlignmentView
     String[] seqs = new String[sequences.length];
     for (int n = 0; n < sequences.length; n++)
     {
-      String fullseq = sequences[n].getSequenceString(c);
-      if (contigs != null)
-      {
-        seqs[n] = "";
-        int p = 0;
-        for (int h = 0; h < contigs.length; h += 3)
-        {
-          seqs[n] += fullseq.substring(p, contigs[h + 1]);
-          p = contigs[h + 1] + contigs[h + 2];
-        }
-        seqs[n] += fullseq.substring(p);
-      }
-      else
-      {
-        seqs[n] = fullseq;
-      }
+      seqs[n] = getASequenceString(c, n);
     }
     return seqs;
   }

diff --git a/test/jalview/datamodel/AlignmentViewTest.java b/test/jalview/datamodel/AlignmentViewTest.java
new file mode 100644 (file)
index 0000000..706e5a6
--- /dev/null
+++ b/test/jalview/datamodel/AlignmentViewTest.java
@@ -0,0 +1,21 @@
+package jalview.datamodel;
+import static org.testng.Assert.assertEquals;
+
+import org.testng.annotations.Test;
+
+public class AlignmentViewTest
+{
+  @Test(groups = { "Functional" })
+  public void testGetVisibleAlignmentGapChar()
+  {
+    SeqCigar ss = new SeqCigar(new Sequence("One", "A..CDE"));
+    CigarArray ca = new CigarArray(new CigarSimple[] { ss });
+    AlignmentView av = new AlignmentView(ca);
+    String dots = av.getSequenceStrings('.')[0];
+    assertEquals(dots, "A..CDE");
+    String dollars = av.getSequenceStrings('$')[0];
+    assertEquals(dollars, "A$$CDE");
+    assertEquals(av.getVisibleAlignment('$').getSequenceAt(0)
+            .getSequenceAsString(), "A$$CDE");
+  }
+}

diff --git a/test/jalview/io/JalviewExportPropertiesTests.java b/test/jalview/io/JalviewExportPropertiesTests.java
new file mode 100644 (file)
index 0000000..faf4ef9
--- /dev/null
+++ b/test/jalview/io/JalviewExportPropertiesTests.java
@@ -0,0 +1,84 @@
+/*
+ * 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.io;
+
+import static org.testng.AssertJUnit.assertTrue;
+
+import jalview.datamodel.SequenceGroup;
+import jalview.gui.AlignFrame;
+
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+/**
+ * tests which verify that properties and preferences are correctly interpreted
+ * when exporting/importing data
+ * 
+ * @author jprocter
+ *
+ */
+public class JalviewExportPropertiesTests
+{
+
+  /**
+   * @throws java.lang.Exception
+   */
+  @BeforeClass(alwaysRun = true)
+  public static void setUpBeforeClass() throws Exception
+  {
+    jalview.bin.Jalview.main(new String[]
+    { "-props", "test/jalview/io/testProps.jvprops" });
+  }
+
+  /**
+   * @throws java.lang.Exception
+   */
+  @AfterClass
+  public static void tearDownAfterClass() throws Exception
+  {
+    jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
+
+  }
+  @Test(groups ={ "Functional" })
+  public void testImportExportPeriodGaps() throws Exception
+  {
+    jalview.bin.Cache.setProperty("GAP_SYMBOL", ".");
+    assertTrue("Couldn't set gap character to '.'",
+            ".".equals("" + jalview.bin.Cache.getProperty("GAP_SYMBOL")));
+    AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
+            "examples/uniref50.fa", FormatAdapter.FILE);
+    assertTrue("Didn't read in the example file correctly.", af != null);
+    assertTrue("Didn't set the gap character correctly", af.getViewport()
+            .getAlignment().getSequenceAt(0).getCharAt(5) == '.');
+
+    SequenceGroup sg = new SequenceGroup();
+    sg.addSequence(af.getViewport().getAlignment().getSequenceAt(0),false);
+    sg.addSequence(af.getViewport().getAlignment().getSequenceAt(1),false);
+    sg.setStartRes(1);
+    sg.setEndRes(7);
+    af.getViewport().setSelectionGroup(sg);
+    String fseqs = new FormatAdapter(af.alignPanel).formatSequences(
+            "FASTA", af.alignPanel, true);
+    assertTrue("Couldn't find '.' in the exported region\n" + fseqs,
+            fseqs.indexOf(".") > -1);
+  }
+}