JAL-3423 use System.lineSeparator() in code and tests

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

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 4f8897a..2946ba2 100644 (file)
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -74,12 +74,15 @@ import java.util.TreeMap;
  */
 public class AlignmentUtils
 {
-
   private static final int CODON_LENGTH = 3;
 
   private static final String SEQUENCE_VARIANT = "sequence_variant:";
 
-  private static final String ID = "ID";
+  /*
+   * the 'id' attribute is provided for variant features fetched from
+   * Ensembl using its REST service with JSON format 
+   */
+  public static final String VARIANT_ID = "id";
 
   /**
    * A data model to hold the 'normal' base value at a position, and an optional
@@ -1599,11 +1602,12 @@ public class AlignmentUtils
       return false;
     }
     String name = seq2.getName();
-    final DBRefEntry[] xrefs = seq1.getDBRefs();
+    final List<DBRefEntry> xrefs = seq1.getDBRefs();
     if (xrefs != null)
     {
-      for (DBRefEntry xref : xrefs)
+      for (int ix = 0, nx = xrefs.size(); ix < nx; ix++)
       {
+         DBRefEntry xref = xrefs.get(ix);
         String xrefName = xref.getSource() + "|" + xref.getAccessionId();
         // case-insensitive test, consistent with DBRefEntry.equalRef()
         if (xrefName.equalsIgnoreCase(name))
@@ -1799,8 +1803,10 @@ public class AlignmentUtils
           // need to
           // synthesize an xref.
 
-          for (DBRefEntry primRef : dnaDss.getPrimaryDBRefs())
+          List<DBRefEntry> primrefs = dnaDss.getPrimaryDBRefs();
+          for (int ip = 0, np = primrefs.size(); ip < np; ip++)
           {
+                 DBRefEntry primRef = primrefs.get(ip);
             /*
              * create a cross-reference from CDS to the source sequence's
              * primary reference and vice versa
@@ -1814,7 +1820,6 @@ public class AlignmentUtils
 
             dnaSeq.addDBRef(new DBRefEntry(source, version, cdsSeq
                     .getName(), new Mapping(cdsSeqDss, dnaToCdsMap)));
-
             // problem here is that the cross-reference is synthesized -
             // cdsSeq.getName() may be like 'CDS|dnaaccession' or
             // 'CDS|emblcdsacc'
@@ -1827,7 +1832,6 @@ public class AlignmentUtils
                     .getInverse()));
             proteinProduct.addDBRef(proteinToCdsRef);
           }
-
           /*
            * transfer any features on dna that overlap the CDS
            */
@@ -2071,13 +2075,15 @@ public class AlignmentUtils
     List<DBRefEntry> direct = new ArrayList<>();
     HashSet<String> directSources = new HashSet<>();
 
-    if (contig.getDBRefs() != null)
+    List<DBRefEntry> refs = contig.getDBRefs();
+    if (refs != null)
     {
-      for (DBRefEntry dbr : contig.getDBRefs())
+      for (int ib = 0, nb = refs.size(); ib < nb; ib++)
       {
-        if (dbr.hasMap() && dbr.getMap().getMap().isTripletMap())
+         DBRefEntry dbr = refs.get(ib);
+         MapList map;
+        if (dbr.hasMap() && (map = dbr.getMap().getMap()).isTripletMap())
         {
-          MapList map = dbr.getMap().getMap();
           // check if map is the CDS mapping
           if (mapping.getMap().equals(map))
           {
@@ -2087,21 +2093,22 @@ public class AlignmentUtils
         }
       }
     }
-    DBRefEntry[] onSource = DBRefUtils.selectRefs(
+    List<DBRefEntry> onSource = DBRefUtils.selectRefs(
             proteinProduct.getDBRefs(),
             directSources.toArray(new String[0]));
     List<DBRefEntry> propagated = new ArrayList<>();
 
     // and generate appropriate mappings
-    for (DBRefEntry cdsref : direct)
+    for (int ic = 0, nc = direct.size(); ic < nc; ic++)
     {
+       DBRefEntry cdsref = direct.get(ic);
+       Mapping m = cdsref.getMap();
       // clone maplist and mapping
       MapList cdsposmap = new MapList(
               Arrays.asList(new int[][]
               { new int[] { cdsSeq.getStart(), cdsSeq.getEnd() } }),
-              cdsref.getMap().getMap().getToRanges(), 3, 1);
-      Mapping cdsmap = new Mapping(cdsref.getMap().getTo(),
-              cdsref.getMap().getMap());
+              m.getMap().getToRanges(), 3, 1);
+      Mapping cdsmap = new Mapping(m.getTo(),m.getMap());
 
       // create dbref
       DBRefEntry newref = new DBRefEntry(cdsref.getSource(),
@@ -2579,15 +2586,15 @@ public class AlignmentUtils
             peptidePos, var.getSource());
 
     StringBuilder attributes = new StringBuilder(32);
-    String id = (String) var.variant.getValue(ID);
+    String id = (String) var.variant.getValue(VARIANT_ID);
     if (id != null)
     {
       if (id.startsWith(SEQUENCE_VARIANT))
       {
         id = id.substring(SEQUENCE_VARIANT.length());
       }
-      sf.setValue(ID, id);
-      attributes.append(ID).append("=").append(id);
+      sf.setValue(VARIANT_ID, id);
+      attributes.append(VARIANT_ID).append("=").append(id);
       // TODO handle other species variants JAL-2064
       StringBuilder link = new StringBuilder(32);
       try
@@ -2767,19 +2774,25 @@ public class AlignmentUtils
     SequenceIdMatcher matcher = new SequenceIdMatcher(seqs);
     if (xrefs != null)
     {
-      for (SequenceI xref : xrefs)
+       // BH 2019.01.25 streamlined this triply nested loop to remove all iterators
+       
+      for (int ix = 0, nx = xrefs.length; ix < nx; ix++)
       {
-        DBRefEntry[] dbrefs = xref.getDBRefs();
+       SequenceI xref = xrefs[ix];
+        List<DBRefEntry> dbrefs = xref.getDBRefs();
         if (dbrefs != null)
         {
-          for (DBRefEntry dbref : dbrefs)
+          for (int ir = 0, nir = dbrefs.size(); ir < nir; ir++)
           {
-            if (dbref.getMap() == null || dbref.getMap().getTo() == null
-                    || dbref.getMap().getTo().isProtein() != isProtein)
+                 DBRefEntry dbref = dbrefs.get(ir);
+                 Mapping map = dbref.getMap();
+                 SequenceI mto;
+            if (map == null || (mto = map.getTo()) == null
+                    || mto.isProtein() != isProtein)
             {
               continue;
             }
-            SequenceI mappedTo = dbref.getMap().getTo();
+            SequenceI mappedTo = mto;
             SequenceI match = matcher.findIdMatch(mappedTo);
             if (match == null)
             {