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

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

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index ea330d8..34fe221 100644 (file)
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -73,7 +73,9 @@ 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 +448,8 @@ 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 +511,7 @@ 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 +937,7 @@ public class AlignmentUtils
               .println("alignCdsSequenceAsProtein needs aligned sequence!");
       return false;
     }
-    
+
     List<AlignedCodonFrame> dnaMappings = MappingUtils
             .findMappingsForSequence(cdsSeq, mappings);
     for (AlignedCodonFrame mapping : dnaMappings)
@@ -958,7 +959,8 @@ 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 +1099,7 @@ 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 +1712,9 @@ 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);
@@ -1731,8 +1734,7 @@ public class AlignmentUtils
            */
           AlignedCodonFrame dnaToCdsMapping = new AlignedCodonFrame();
           MapList dnaToCdsMap = new MapList(mapList.getFromRanges(),
-                  cdsRange, 1,
-                  1);
+                  cdsRange, 1, 1);
           dnaToCdsMapping.addMap(dnaSeq.getDatasetSequence(), cdsSeqDss,
                   dnaToCdsMap);
           if (!mappings.contains(dnaToCdsMapping))
@@ -1747,16 +1749,16 @@ 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
@@ -1786,7 +1788,7 @@ public class AlignmentUtils
           /*
            * transfer any features on dna that overlap the CDS
            */
-          transferFeatures(dnaSeq, cdsSeq, cdsToProteinMap, null,
+          transferFeatures(dnaSeq, cdsSeq, dnaToCdsMap, null,
                   SequenceOntologyI.CDS);
         }
       }
@@ -1833,7 +1835,8 @@ 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;
     }
@@ -1849,7 +1852,8 @@ 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())
         {
@@ -1917,7 +1921,7 @@ public class AlignmentUtils
         }
       }
     }
-    
+
     /*
      * assign 'from id' held in the mapping if set (e.g. EMBL protein_id),
      * else generate a sequence name
@@ -2483,7 +2487,9 @@ 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());
@@ -2492,8 +2498,7 @@ 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);
@@ -2742,7 +2747,7 @@ public class AlignmentUtils
           }
           newCol++;
         }
-        
+
         /*
          * trim trailing gaps
          */