JAL-2089 patch broken merge to master for Release 2.10.0b1

[jalview.git] / src / jalview / util / MappingUtils.java

diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java
index 0780b2a..1fe452d 100644 (file)
--- a/src/jalview/util/MappingUtils.java
+++ b/src/jalview/util/MappingUtils.java
@@ -374,7 +374,8 @@ public final class MappingUtils
               /*
                * Found a sequence mapping. Locate the start/end mapped residues.
                */
-              List<AlignedCodonFrame> mapping = Arrays.asList(new AlignedCodonFrame[] { acf });
+              List<AlignedCodonFrame> mapping = Arrays
+                      .asList(new AlignedCodonFrame[] { acf });
               SearchResults sr = buildSearchResults(selected,
                       startResiduePos, mapping);
               for (Match m : sr.getResults())
@@ -555,9 +556,9 @@ public final class MappingUtils
    * @param fromGapChar
    */
   protected static void mapHiddenColumns(int[] hidden,
-          List<AlignedCodonFrame> mappings,
-          ColumnSelection mappedColumns, List<SequenceI> fromSequences,
-          List<SequenceI> toSequences, char fromGapChar)
+          List<AlignedCodonFrame> mappings, ColumnSelection mappedColumns,
+          List<SequenceI> fromSequences, List<SequenceI> toSequences,
+          char fromGapChar)
   {
     for (int col = hidden[0]; col <= hidden[1]; col++)
     {
@@ -589,9 +590,9 @@ public final class MappingUtils
    * @param fromGapChar
    */
   protected static void mapColumn(int col,
-          List<AlignedCodonFrame> mappings,
-          ColumnSelection mappedColumns, List<SequenceI> fromSequences,
-          List<SequenceI> toSequences, char fromGapChar)
+          List<AlignedCodonFrame> mappings, ColumnSelection mappedColumns,
+          List<SequenceI> fromSequences, List<SequenceI> toSequences,
+          char fromGapChar)
   {
     int[] mappedTo = findMappedColumns(col, mappings, fromSequences,
             toSequences, fromGapChar);
@@ -646,8 +647,7 @@ public final class MappingUtils
        * Get the residue position and find the mapped position.
        */
       int residuePos = fromSeq.findPosition(col);
-      SearchResults sr = buildSearchResults(fromSeq, residuePos,
-              mappings);
+      SearchResults sr = buildSearchResults(fromSeq, residuePos, mappings);
       for (Match m : sr.getResults())
       {
         int mappedStartResidue = m.getStart();
@@ -754,6 +754,23 @@ public final class MappingUtils
   public static List<AlignedCodonFrame> findMappingsForSequence(
           SequenceI sequence, List<AlignedCodonFrame> mappings)
   {
+    return findMappingsForSequenceAndOthers(sequence, mappings, null);
+  }
+
+  /**
+   * Returns a list of any mappings that are from or to the given (aligned or
+   * dataset) sequence, optionally limited to mappings involving one of a given
+   * list of sequences.
+   * 
+   * @param sequence
+   * @param mappings
+   * @param filterList
+   * @return
+   */
+  public static List<AlignedCodonFrame> findMappingsForSequenceAndOthers(
+          SequenceI sequence, List<AlignedCodonFrame> mappings,
+          List<SequenceI> filterList)
+  {
     List<AlignedCodonFrame> result = new ArrayList<AlignedCodonFrame>();
     if (sequence == null || mappings == null)
     {
@@ -763,14 +780,39 @@ public final class MappingUtils
     {
       if (mapping.involvesSequence(sequence))
       {
-        result.add(mapping);
+        if (filterList != null)
+        {
+          for (SequenceI otherseq : filterList)
+          {
+            SequenceI otherDataset = otherseq.getDatasetSequence();
+            if (otherseq == sequence
+                    || otherseq == sequence.getDatasetSequence()
+                    || (otherDataset != null && (otherDataset == sequence || otherDataset == sequence
+                            .getDatasetSequence())))
+            {
+              // skip sequences in subset which directly relate to sequence
+              continue;
+            }
+            if (mapping.involvesSequence(otherseq))
+            {
+              // selected a mapping contained in subselect alignment
+              result.add(mapping);
+              break;
+            }
+          }
+        }
+        else
+        {
+          result.add(mapping);
+        }
       }
     }
     return result;
   }
 
   /**
-   * Returns the total length of the supplied ranges
+   * Returns the total length of the supplied ranges, which may be as single
+   * [start, end] or multiple [start, end, start, end ...]
    * 
    * @param ranges
    * @return
@@ -784,7 +826,16 @@ public final class MappingUtils
     int length = 0;
     for (int[] range : ranges)
     {
-      length += Math.abs(range[1] - range[0]) + 1;
+      if (range.length % 2 != 0)
+      {
+        System.err.println("Error unbalance start/end ranges: "
+                + ranges.toString());
+        return 0;
+      }
+      for (int i = 0; i < range.length - 1; i += 2)
+      {
+        length += Math.abs(range[i + 1] - range[i]) + 1;
+      }
     }
     return length;
   }
@@ -821,4 +872,65 @@ public final class MappingUtils
     }
     return false;
   }
+
+  /**
+   * Removes a specified number of positions from the start of a ranges list.
+   * For example, could be used to adjust cds ranges to allow for an incomplete
+   * start codon. Subranges are removed completely, or their start positions
+   * adjusted, until the required number of positions has been removed from the
+   * range. Reverse strand ranges are supported. The input array is not
+   * modified.
+   * 
+   * @param removeCount
+   * @param ranges
+   *          an array of [start, end, start, end...] positions
+   * @return a new array with the first removeCount positions removed
+   */
+  public static int[] removeStartPositions(int removeCount,
+          final int[] ranges)
+  {
+    if (removeCount <= 0)
+    {
+      return ranges;
+    }
+
+    int[] copy = Arrays.copyOf(ranges, ranges.length);
+    int sxpos = -1;
+    int cdspos = 0;
+    for (int x = 0; x < copy.length && sxpos == -1; x += 2)
+    {
+      cdspos += Math.abs(copy[x + 1] - copy[x]) + 1;
+      if (removeCount < cdspos)
+      {
+        /*
+         * we have removed enough, time to finish
+         */
+        sxpos = x;
+
+        /*
+         * increment start of first exon, or decrement if reverse strand
+         */
+        if (copy[x] <= copy[x + 1])
+        {
+          copy[x] = copy[x + 1] - cdspos + removeCount + 1;
+        }
+        else
+        {
+          copy[x] = copy[x + 1] + cdspos - removeCount - 1;
+        }
+        break;
+      }
+    }
+
+    if (sxpos > 0)
+    {
+      /*
+       * we dropped at least one entire sub-range - compact the array
+       */
+      int[] nxon = new int[copy.length - sxpos];
+      System.arraycopy(copy, sxpos, nxon, 0, copy.length - sxpos);
+      return nxon;
+    }
+    return copy;
+  }
 }