From: James Procter <j.procter@dundee.ac.uk>
Date: Sat, 13 May 2023 15:50:47 +0000 (+0100)
Subject: JAL-2349 JAL-3855 PAE tests covers ContactListI.getMappedPositons
X-Git-Tag: Release_2_11_3_0~14^2~3^2^2~33
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=108f2d4b40f172ad6a34647133dbb18dfab150f7;p=jalview.git

JAL-2349 JAL-3855 PAE tests covers ContactListI.getMappedPositons
---

diff --git a/src/jalview/datamodel/ContactListImpl.java b/src/jalview/datamodel/ContactListImpl.java
index 6a37864..b71c4b7 100644
--- a/src/jalview/datamodel/ContactListImpl.java
+++ b/src/jalview/datamodel/ContactListImpl.java
@@ -96,4 +96,9 @@ public class ContactListImpl implements ContactListI
     }
     return cr;
   }
+  @Override
+  public int[] getMappedPositionsFor(int cStart, int cEnd)
+  {
+    return     clist.getMappedPositionsFor(cStart, cEnd);
+  }
 }
diff --git a/src/jalview/datamodel/ContactListProviderI.java b/src/jalview/datamodel/ContactListProviderI.java
index a4e0b79..75de1a4 100644
--- a/src/jalview/datamodel/ContactListProviderI.java
+++ b/src/jalview/datamodel/ContactListProviderI.java
@@ -30,7 +30,7 @@ public interface ContactListProviderI
 
 
   /**
-   * Return positions in local reference corresponding to cStart and cEnd in matrix data
+   * Return positions in local reference corresponding to cStart and cEnd in matrix data. Positions are base 1 column indices for sequence associated matrices.
    * @param cStart
    * @param cEnd
    * @return int[] { start, end (inclusive) for each contiguous segment}
diff --git a/test/jalview/datamodel/PAEContactMatrixTest.java b/test/jalview/datamodel/PAEContactMatrixTest.java
index 7426cba..71e824e 100644
--- a/test/jalview/datamodel/PAEContactMatrixTest.java
+++ b/test/jalview/datamodel/PAEContactMatrixTest.java
@@ -6,6 +6,8 @@ import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
+import jalview.analysis.AlignmentUtils;
+import jalview.analysis.SeqsetUtils;
 import jalview.gui.JvOptionPane;
 import jalview.util.MapList;
 import jalview.ws.datamodel.MappableContactMatrixI;
@@ -81,6 +83,22 @@ public class PAEContactMatrixTest
     // last column
     assertNotNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(10)));
 
+    // verify MappedPositions includes discontinuity
+    int[] mappedCl = newseq.getContactListFor(newaa, 5).getMappedPositionsFor(0, 4);
+    assertEquals(4,mappedCl.length,"getMappedPositionsFor doesn't support discontinuous mappings to contactList");
+    
+    // make it harder. 
+    
+    SequenceI alseq = newseq.getSubSequence(6, 10);
+    alseq.insertCharAt(2, 2, '-');
+    AlignmentI alForSeq=new Alignment(new SequenceI[] { alseq });
+    newaa = AlignmentUtils.addReferenceAnnotationTo(alForSeq, alseq, newaa, null);
+    ContactListI alcl = alForSeq.getContactListFor(newaa, 1);
+    assertNotNull(alcl);
+    mappedCl = alcl.getMappedPositionsFor(0, 4);
+    assertNotNull(mappedCl);
+    assertEquals(4,mappedCl.length,"getMappedPositionsFor doesn't support discontinuous mappings to contactList");
+    
     // remap2 - test with original matrix map from 1-5 remapped to 5-9
     
     seq = new Sequence("Seq/1-5","ASDQE");
@@ -114,7 +132,6 @@ public class PAEContactMatrixTest
     
     newaa = newseq.addContactList(remapped);
     verify_mapping(newseq, newaa);
-    
   }
   /**
    * checks that the PAE matrix is located at positions 1-9 in newseq, and columns are not truncated.
@@ -134,16 +151,19 @@ public class PAEContactMatrixTest
     assertNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(10)));
     
     verifyPAEmatrix(newseq, newaa, 4, 4, 8);
-    
-
   }
 
   private void verifyPAEmatrix(SequenceI seq, AlignmentAnnotation aa, int topl, int rowl, int rowr)
   {
+    int[] mappedCl;
     for (int f=rowl;f<=rowr;f++) {
       ContactListI clist = seq.getContactListFor(aa, f);
       assertNotNull(clist,"No ContactListI for position "+(f));
       assertEquals(clist.getContactAt(0), (double) f-topl+1,"for column "+f+" relative to "+topl);
+      mappedCl = clist.getMappedPositionsFor(0, 0);
+      assertNotNull(mappedCl);
+      assertEquals(mappedCl[0],mappedCl[1]);
+      assertEquals(mappedCl[0],seq.findIndex(seq.getStart()+topl));
       assertEquals(clist.getContactAt(f-topl),1d, "for column and row "+f+" relative to "+topl);
     }    
   }