X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FMappingUtils.java;h=09d4b1306136770e74ca31d089c1c8b9c485bdb5;hb=ad09c54f294b945fd4d037a93f5fa8eced6c1797;hp=f75286a377a807916eb73a5cb76c8a1537e39e35;hpb=5e8ec77d921ff2d604811e5e4ba7e9211b0f48de;p=jalview.git

diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java
index f75286a..09d4b13 100644
--- a/src/jalview/util/MappingUtils.java
+++ b/src/jalview/util/MappingUtils.java
@@ -219,8 +219,9 @@ public final class MappingUtils
              * Shift Delete start position left, as it acts on positions to its
              * right.
              */
-            int mappedEditPos = action == Action.DELETE_GAP ? match[0]
-                    - mappedCount : match[0];
+            int mappedEditPos = action == Action.DELETE_GAP
+                    ? match[0] - mappedCount
+                    : match[0];
             Edit e = result.new Edit(action, new SequenceI[] { targetSeq },
                     mappedEditPos, mappedCount, gapChar);
             result.addEdit(e);
@@ -230,15 +231,15 @@ public final class MappingUtils
              */
             if (action == Action.INSERT_GAP)
             {
-              copyTarget.setSequence(new String(StringUtils.insertCharAt(
-                      copyTarget.getSequence(), mappedEditPos, mappedCount,
-                      gapChar)));
+              copyTarget.setSequence(new String(
+                      StringUtils.insertCharAt(copyTarget.getSequence(),
+                              mappedEditPos, mappedCount, gapChar)));
             }
             else if (action == Action.DELETE_GAP)
             {
-              copyTarget.setSequence(new String(StringUtils.deleteChars(
-                      copyTarget.getSequence(), mappedEditPos,
-                      mappedEditPos + mappedCount)));
+              copyTarget.setSequence(new String(
+                      StringUtils.deleteChars(copyTarget.getSequence(),
+                              mappedEditPos, mappedEditPos + mappedCount)));
             }
           }
         }
@@ -363,8 +364,9 @@ public final class MappingUtils
 
       for (AlignedCodonFrame acf : codonFrames)
       {
-        SequenceI mappedSequence = targetIsNucleotide ? acf
-                .getDnaForAaSeq(selected) : acf.getAaForDnaSeq(selected);
+        SequenceI mappedSequence = targetIsNucleotide
+                ? acf.getDnaForAaSeq(selected)
+                : acf.getAaForDnaSeq(selected);
         if (mappedSequence != null)
         {
           for (SequenceI seq : mapTo.getAlignment().getSequences())
@@ -377,7 +379,8 @@ public final class MappingUtils
                * Found a sequence mapping. Locate the start/end mapped residues.
                */
               List<AlignedCodonFrame> mapping = Arrays
-                      .asList(new AlignedCodonFrame[] { acf });
+                      .asList(new AlignedCodonFrame[]
+                      { acf });
               SearchResultsI sr = buildSearchResults(selected,
                       startResiduePos, mapping);
               for (SearchResultMatchI m : sr.getResults())
@@ -398,11 +401,11 @@ public final class MappingUtils
                * returns a base 1 position, SequenceGroup uses base 0
                */
               int mappedStartCol = seq.findIndex(mappedStartResidue) - 1;
-              minStartCol = minStartCol == -1 ? mappedStartCol : Math.min(
-                      minStartCol, mappedStartCol);
+              minStartCol = minStartCol == -1 ? mappedStartCol
+                      : Math.min(minStartCol, mappedStartCol);
               int mappedEndCol = seq.findIndex(mappedEndResidue) - 1;
-              maxEndCol = maxEndCol == -1 ? mappedEndCol : Math.max(
-                      maxEndCol, mappedEndCol);
+              maxEndCol = maxEndCol == -1 ? mappedEndCol
+                      : Math.max(maxEndCol, mappedEndCol);
               mappedGroup.addSequence(seq, false);
               break;
             }
@@ -429,8 +432,8 @@ public final class MappingUtils
    *          the mappings available
    * @return
    */
-  public static CommandI mapOrderCommand(OrderCommand command,
-          boolean undo, AlignmentI mapTo, List<AlignedCodonFrame> mappings)
+  public static CommandI mapOrderCommand(OrderCommand command, boolean undo,
+          AlignmentI mapTo, List<AlignedCodonFrame> mappings)
   {
     SequenceI[] sortOrder = command.getSequenceOrder(undo);
     List<SequenceI> mappedOrder = new ArrayList<>();
@@ -518,7 +521,6 @@ public final class MappingUtils
     AlignViewportI protein = targetIsNucleotide ? mapFrom : mapTo;
     List<AlignedCodonFrame> codonFrames = protein.getAlignment()
             .getCodonFrames();
-    // ColumnSelection mappedColumns = new ColumnSelection();
 
     if (colsel == null)
     {
@@ -540,9 +542,11 @@ public final class MappingUtils
               toSequences, fromGapChar);
     }
 
-    for (int[] hidden : hiddencols)
+    Iterator<int[]> regions = hiddencols.iterator();
+    while (regions.hasNext())
     {
-      mapHiddenColumns(hidden, codonFrames, newHidden, fromSequences,
+      mapHiddenColumns(regions.next(), codonFrames, newHidden,
+              fromSequences,
               toSequences, fromGapChar);
     }
     return; // mappedColumns;
@@ -593,10 +597,9 @@ public final class MappingUtils
    * @param toSequences
    * @param fromGapChar
    */
-  protected static void mapColumn(int col,
-          List<AlignedCodonFrame> mappings, ColumnSelection mappedColumns,
-          List<SequenceI> fromSequences, List<SequenceI> toSequences,
-          char fromGapChar)
+  protected static void mapColumn(int col, List<AlignedCodonFrame> mappings,
+          ColumnSelection mappedColumns, List<SequenceI> fromSequences,
+          List<SequenceI> toSequences, char fromGapChar)
   {
     int[] mappedTo = findMappedColumns(col, mappings, fromSequences,
             toSequences, fromGapChar);
@@ -702,8 +705,8 @@ public final class MappingUtils
     {
       if (mapping.involvesSequence(seq))
       {
-        List<char[]> codons = mapping.getMappedCodons(
-                seq.getDatasetSequence(), dsPos);
+        List<char[]> codons = mapping
+                .getMappedCodons(seq.getDatasetSequence(), dsPos);
         if (codons != null)
         {
           result.addAll(codons);
@@ -791,8 +794,9 @@ public final class MappingUtils
             SequenceI otherDataset = otherseq.getDatasetSequence();
             if (otherseq == sequence
                     || otherseq == sequence.getDatasetSequence()
-                    || (otherDataset != null && (otherDataset == sequence || otherDataset == sequence
-                            .getDatasetSequence())))
+                    || (otherDataset != null && (otherDataset == sequence
+                            || otherDataset == sequence
+                                    .getDatasetSequence())))
             {
               // skip sequences in subset which directly relate to sequence
               continue;
@@ -832,8 +836,8 @@ public final class MappingUtils
     {
       if (range.length % 2 != 0)
       {
-        System.err.println("Error unbalance start/end ranges: "
-                + ranges.toString());
+        System.err.println(
+                "Error unbalance start/end ranges: " + ranges.toString());
         return 0;
       }
       for (int i = 0; i < range.length - 1; i += 2)