JAL-2647 more iterators

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

diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java
index 0128624..c3408bd 100644 (file)
--- a/src/jalview/analysis/Dna.java
+++ b/src/jalview/analysis/Dna.java
@@ -45,7 +45,6 @@ import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Comparator;
 import java.util.List;
-import java.util.Map;
 
 public class Dna
 {
@@ -57,19 +56,19 @@ public class Dna
    * 'final' variables describe the inputs to the translation, which should not
    * be modified.
    */
-  final private List<SequenceI> selection;
+  private final List<SequenceI> selection;
 
-  final private String[] seqstring;
+  private final String[] seqstring;
 
-  final private int[] contigs;
+  private final List<int[]> contigs;
 
-  final private char gapChar;
+  private final char gapChar;
 
-  final private AlignmentAnnotation[] annotations;
+  private final AlignmentAnnotation[] annotations;
 
-  final private int dnaWidth;
+  private final int dnaWidth;
 
-  final private AlignmentI dataset;
+  private final AlignmentI dataset;
 
   /*
    * Working variables for the translation.
@@ -92,7 +91,7 @@ public class Dna
    * @param viewport
    * @param visibleContigs
    */
-  public Dna(AlignViewportI viewport, int[] visibleContigs)
+  public Dna(AlignViewportI viewport, List<int[]> visibleContigs)
   {
     this.selection = Arrays.asList(viewport.getSequenceSelection());
     this.seqstring = viewport.getViewAsString(true);
@@ -120,8 +119,7 @@ public class Dna
    * @param ac2
    * @return
    */
-  public static final int compareCodonPos(AlignedCodon ac1,
-          AlignedCodon ac2)
+  public static final int compareCodonPos(AlignedCodon ac1, AlignedCodon ac2)
   {
     return comparator.compare(ac1, ac2);
     // return jalview_2_8_2compare(ac1, ac2);
@@ -163,7 +161,7 @@ public class Dna
 
     int s;
     int sSize = selection.size();
-    List<SequenceI> pepseqs = new ArrayList<SequenceI>();
+    List<SequenceI> pepseqs = new ArrayList<>();
     for (s = 0; s < sSize; s++)
     {
       SequenceI newseq = translateCodingRegion(selection.get(s),
@@ -215,7 +213,7 @@ public class Dna
       if (dnarefs != null)
       {
         // intersect with pep
-        List<DBRefEntry> mappedrefs = new ArrayList<DBRefEntry>();
+        List<DBRefEntry> mappedrefs = new ArrayList<>();
         DBRefEntry[] refs = dna.getDBRefs();
         for (int d = 0; d < refs.length; d++)
         {
@@ -393,26 +391,30 @@ public class Dna
           String seqstring, AlignedCodonFrame acf,
           List<SequenceI> proteinSeqs)
   {
-    List<int[]> skip = new ArrayList<int[]>();
+    List<int[]> skip = new ArrayList<>();
     int skipint[] = null;
     ShiftList vismapping = new ShiftList(); // map from viscontigs to seqstring
     // intervals
-    int vc;
-    int[] scontigs = new int[contigs.length];
+    int vc = 0;
+    int[] scontigs = new int[contigs.size() * 2];
     int npos = 0;
-    for (vc = 0; vc < contigs.length; vc += 2)
+    int[] lastregion = null;
+    for (int[] region : contigs)
     {
-      if (vc == 0)
+      if (lastregion == null)
       {
-        vismapping.addShift(npos, contigs[vc]);
+        vismapping.addShift(npos, region[0]);
       }
       else
       {
         // hidden region
-        vismapping.addShift(npos, contigs[vc] - contigs[vc - 1] + 1);
+        vismapping.addShift(npos, region[0] - lastregion[1] + 1);
       }
-      scontigs[vc] = contigs[vc];
-      scontigs[vc + 1] = contigs[vc + 1];
+      lastregion = region;
+
+      scontigs[vc] = region[0];
+      scontigs[vc + 1] = region[1];
+      vc++;
     }
 
     // allocate a roughly sized buffer for the protein sequence
@@ -689,7 +691,7 @@ public class Dna
          */
         MapList map = new MapList(scontigs, new int[] { 1, resSize }, 3, 1);
 
-        transferCodedFeatures(selection, newseq, map, null, null);
+        transferCodedFeatures(selection, newseq, map);
 
         /*
          * Construct a dataset sequence for our new peptide.
@@ -758,25 +760,15 @@ public class Dna
 
   /**
    * Given a peptide newly translated from a dna sequence, copy over and set any
-   * features on the peptide from the DNA. If featureTypes is null, all features
-   * on the dna sequence are searched (rather than just the displayed ones), and
-   * similarly for featureGroups.
+   * features on the peptide from the DNA.
    * 
    * @param dna
    * @param pep
    * @param map
-   * @param featureTypes
-   *          hash whose keys are the displayed feature type strings
-   * @param featureGroups
-   *          hash where keys are feature groups and values are Boolean objects
-   *          indicating if they are displayed.
    */
   private static void transferCodedFeatures(SequenceI dna, SequenceI pep,
-          MapList map, Map<String, Object> featureTypes,
-          Map<String, Boolean> featureGroups)
+          MapList map)
   {
-    SequenceFeature[] sfs = dna.getSequenceFeatures();
-    Boolean fgstate;
     DBRefEntry[] dnarefs = DBRefUtils.selectRefs(dna.getDBRefs(),
             DBRefSource.DNACODINGDBS);
     if (dnarefs != null)
@@ -790,24 +782,15 @@ public class Dna
         }
       }
     }
-    if (sfs != null)
+    for (SequenceFeature sf : dna.getFeatures().getAllFeatures())
     {
-      for (SequenceFeature sf : sfs)
-      {
-        fgstate = (featureGroups == null) ? null
-                : featureGroups.get(sf.featureGroup);
-        if ((featureTypes == null || featureTypes.containsKey(sf.getType()))
-                && (fgstate == null || fgstate.booleanValue()))
+        if (FeatureProperties.isCodingFeature(null, sf.getType()))
         {
-          if (FeatureProperties.isCodingFeature(null, sf.getType()))
+          // if (map.intersectsFrom(sf[f].begin, sf[f].end))
           {
-            // if (map.intersectsFrom(sf[f].begin, sf[f].end))
-            {
 
-            }
           }
         }
-      }
     }
   }
 
@@ -821,7 +804,7 @@ public class Dna
   public AlignmentI reverseCdna(boolean complement)
   {
     int sSize = selection.size();
-    List<SequenceI> reversed = new ArrayList<SequenceI>();
+    List<SequenceI> reversed = new ArrayList<>();
     for (int s = 0; s < sSize; s++)
     {
       SequenceI newseq = reverseSequence(selection.get(s).getName(),