Merge branch 'features/JAL-2295setChimeraAttributes' into

[jalview.git] / src / jalview / analysis / AlignmentUtils.java

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index c521d9b..232cb5d 100644 (file)
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -42,6 +42,7 @@ import jalview.util.Comparison;
 import jalview.util.DBRefUtils;
 import jalview.util.MapList;
 import jalview.util.MappingUtils;
+import jalview.util.RangeComparator;
 import jalview.util.StringUtils;
 
 import java.io.UnsupportedEncodingException;
@@ -60,6 +61,7 @@ import java.util.Map;
 import java.util.Map.Entry;
 import java.util.NoSuchElementException;
 import java.util.Set;
+import java.util.SortedMap;
 import java.util.TreeMap;
 
 /**
@@ -73,7 +75,9 @@ public class AlignmentUtils
 {
 
   private static final int CODON_LENGTH = 3;
+
   private static final String SEQUENCE_VARIANT = "sequence_variant:";
+
   private static final String ID = "ID";
 
   /**
@@ -446,8 +450,8 @@ public class AlignmentUtils
      */
     if (cdnaLength != mappedLength && cdnaLength > 2)
     {
-      String lastCodon = String.valueOf(cdnaSeqChars, cdnaLength - CODON_LENGTH, CODON_LENGTH)
-              .toUpperCase();
+      String lastCodon = String.valueOf(cdnaSeqChars,
+              cdnaLength - CODON_LENGTH, CODON_LENGTH).toUpperCase();
       for (String stop : ResidueProperties.STOP)
       {
         if (lastCodon.equals(stop))
@@ -509,8 +513,7 @@ public class AlignmentUtils
 
     int aaPos = 0;
     int dnaPos = cdnaStart;
-    for (; dnaPos < cdnaSeqChars.length - 2
-            && aaPos < aaSeqChars.length; dnaPos += CODON_LENGTH, aaPos++)
+    for (; dnaPos < cdnaSeqChars.length - 2 && aaPos < aaSeqChars.length; dnaPos += CODON_LENGTH, aaPos++)
     {
       String codon = String.valueOf(cdnaSeqChars, dnaPos, CODON_LENGTH);
       final String translated = ResidueProperties.codonTranslate(codon);
@@ -936,7 +939,7 @@ public class AlignmentUtils
               .println("alignCdsSequenceAsProtein needs aligned sequence!");
       return false;
     }
-    
+
     List<AlignedCodonFrame> dnaMappings = MappingUtils
             .findMappingsForSequence(cdsSeq, mappings);
     for (AlignedCodonFrame mapping : dnaMappings)
@@ -958,7 +961,8 @@ public class AlignmentUtils
                   .getFromRanges());
           int mappedToLength = MappingUtils
                   .getLength(mapList.getToRanges());
-          boolean addStopCodon = (cdsLength == mappedFromLength * CODON_LENGTH + CODON_LENGTH)
+          boolean addStopCodon = (cdsLength == mappedFromLength
+                  * CODON_LENGTH + CODON_LENGTH)
                   || (peptide.getDatasetSequence().getLength() == mappedFromLength - 1);
           if (cdsLength != mappedToLength && !addStopCodon)
           {
@@ -1097,7 +1101,7 @@ public class AlignmentUtils
     // TODO resolve JAL-2022 so this fudge can be removed
     int mappedSequenceCount = protein.getHeight() - unmappedProtein.size();
     addUnmappedPeptideStarts(alignedCodons, mappedSequenceCount);
-    
+
     return alignedCodons;
   }
 
@@ -1710,8 +1714,9 @@ public class AlignmentUtils
            */
           List<int[]> cdsRange = Collections.singletonList(new int[] { 1,
               cdsSeq.getLength() });
-          MapList cdsToProteinMap = new MapList(cdsRange, mapList.getToRanges(),
-                  mapList.getFromRatio(), mapList.getToRatio());
+          MapList cdsToProteinMap = new MapList(cdsRange,
+                  mapList.getToRanges(), mapList.getFromRatio(),
+                  mapList.getToRatio());
           AlignedCodonFrame cdsToProteinMapping = new AlignedCodonFrame();
           cdsToProteinMapping.addMap(cdsSeqDss, proteinProduct,
                   cdsToProteinMap);
@@ -1746,16 +1751,16 @@ public class AlignmentUtils
            * same source and accession, so need a different accession for
            * the CDS from the dna sequence
            */
-          
+
           // specific use case:
           // Genomic contig ENSCHR:1, contains coding regions for ENSG01,
           // ENSG02, ENSG03, with transcripts and products similarly named.
           // cannot add distinct dbrefs mapping location on ENSCHR:1 to ENSG01
-          
+
           // JBPNote: ?? can't actually create an example that demonstrates we
           // need to
           // synthesize an xref.
-          
+
           for (DBRefEntry primRef : dnaDss.getPrimaryDBRefs())
           {
             // creates a complementary cross-reference to the source sequence's
@@ -1832,7 +1837,8 @@ public class AlignmentUtils
     int mappedFromLength = MappingUtils.getLength(aMapping.getMap()
             .getFromRanges());
     int dnaLength = seqDss.getLength();
-    if (mappedFromLength == dnaLength || mappedFromLength == dnaLength - CODON_LENGTH)
+    if (mappedFromLength == dnaLength
+            || mappedFromLength == dnaLength - CODON_LENGTH)
     {
       return seqDss;
     }
@@ -1848,7 +1854,8 @@ public class AlignmentUtils
       for (SequenceToSequenceMapping map : acf.getMappings())
       {
         Mapping mapping = map.getMapping();
-        if (mapping != aMapping && mapping.getMap().getFromRatio() == CODON_LENGTH
+        if (mapping != aMapping
+                && mapping.getMap().getFromRatio() == CODON_LENGTH
                 && proteinProduct == mapping.getTo()
                 && seqDss != map.getFromSeq())
         {
@@ -1916,7 +1923,7 @@ public class AlignmentUtils
         }
       }
     }
-    
+
     /*
      * assign 'from id' held in the mapping if set (e.g. EMBL protein_id),
      * else generate a sequence name
@@ -2259,14 +2266,7 @@ public class AlignmentUtils
      * ranges are assembled in order. Other cases should not use this method,
      * but instead construct an explicit mapping for CDS (e.g. EMBL parsing).
      */
-    Collections.sort(result, new Comparator<int[]>()
-    {
-      @Override
-      public int compare(int[] o1, int[] o2)
-      {
-        return Integer.compare(o1[0], o2[0]);
-      }
-    });
+    Collections.sort(result, new RangeComparator(true));
     return result;
   }
 
@@ -2482,7 +2482,9 @@ public class AlignmentUtils
         StringBuilder link = new StringBuilder(32);
         try
         {
-          link.append(desc).append(" ").append(id)
+          link.append(desc)
+                  .append(" ")
+                  .append(id)
                   .append("|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=")
                   .append(URLEncoder.encode(id, "UTF-8"));
           sf.addLink(link.toString());
@@ -2491,8 +2493,7 @@ public class AlignmentUtils
           // as if
         }
       }
-      String clinSig = (String) var.variant
-              .getValue(CLINICAL_SIGNIFICANCE);
+      String clinSig = (String) var.variant.getValue(CLINICAL_SIGNIFICANCE);
       if (clinSig != null)
       {
         sf.setValue(CLINICAL_SIGNIFICANCE, clinSig);
@@ -2741,7 +2742,7 @@ public class AlignmentUtils
           }
           newCol++;
         }
-        
+
         /*
          * trim trailing gaps
          */
@@ -2834,7 +2835,7 @@ public class AlignmentUtils
    * @param unmapped
    * @return
    */
-  static Map<Integer, Map<SequenceI, Character>> buildMappedColumnsMap(
+  static SortedMap<Integer, Map<SequenceI, Character>> buildMappedColumnsMap(
           AlignmentI unaligned, AlignmentI aligned, List<SequenceI> unmapped)
   {
     /*
@@ -2842,7 +2843,7 @@ public class AlignmentUtils
      * {unalignedSequence, characterPerSequence} at that position.
      * TreeMap keeps the entries in ascending column order. 
      */
-    Map<Integer, Map<SequenceI, Character>> map = new TreeMap<Integer, Map<SequenceI, Character>>();
+    SortedMap<Integer, Map<SequenceI, Character>> map = new TreeMap<Integer, Map<SequenceI, Character>>();
 
     /*
      * record any sequences that have no mapping so can't be realigned