JAL-2674 testing

diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java
index a6fe541..d534c8f 100644 (file)
--- a/src/jalview/analysis/Dna.java
+++ b/src/jalview/analysis/Dna.java
@@ -71,6 +71,10 @@ public class Dna
 
   private final AlignmentI dataset;
 
+  private ShiftList vismapping;
+
+  private int[] startcontigs;
+
   /*
    * Working variables for the translation.
    * 
@@ -101,6 +105,45 @@ public class Dna
     this.annotations = viewport.getAlignment().getAlignmentAnnotation();
     this.dnaWidth = viewport.getAlignment().getWidth();
     this.dataset = viewport.getAlignment().getDataset();
+    initContigs();
+  }
+
+  /**
+   * Initialise contigs used as starting point for translateCodingRegion
+   */
+  private void initContigs()
+  {
+    vismapping = new ShiftList(); // map from viscontigs to seqstring
+    // intervals
+
+    int npos = 0;
+    int[] lastregion = null;
+    ArrayList<Integer> tempcontigs = new ArrayList<>();
+    while (contigs.hasNext())
+    {
+      int[] region = contigs.next();
+      if (lastregion == null)
+      {
+        vismapping.addShift(npos, region[0]);
+      }
+      else
+      {
+        // hidden region
+        vismapping.addShift(npos, region[0] - lastregion[1] + 1);
+      }
+      lastregion = region;
+      tempcontigs.add(region[0]);
+      tempcontigs.add(region[1]);
+    }
+
+    startcontigs = new int[tempcontigs.size()];
+    int i = 0;
+    for (Integer val : tempcontigs)
+    {
+      startcontigs[i] = val;
+      i++;
+    }
+    tempcontigs = null;
   }
 
   /**
@@ -393,38 +436,12 @@ public class Dna
           List<SequenceI> proteinSeqs)
   {
     List<int[]> skip = new ArrayList<>();
-    int skipint[] = null;
-    ShiftList vismapping = new ShiftList(); // map from viscontigs to seqstring
-    // intervals
-    int vc = 0;
-
+    int[] skipint = null;
     int npos = 0;
-    int[] lastregion = null;
-    while (contigs.hasNext())
-    {
-      int[] region = contigs.next();
-      if (lastregion == null)
-      {
-        vismapping.addShift(npos, region[0]);
-      }
-      else
-      {
-        // hidden region
-        vismapping.addShift(npos, region[0] - lastregion[1] + 1);
-      }
-      lastregion = region;
-      vc++;
-    }
+    int vc = 0;
 
-    int[] scontigs = new int[vc];
-    vc = 0;
-    while (contigs.hasNext())
-    {
-      int[] region = contigs.next();
-      scontigs[vc] = region[0];
-      scontigs[vc + 1] = region[1];
-      vc++;
-    }
+    int[] scontigs = new int[startcontigs.length];
+    System.arraycopy(startcontigs, 0, scontigs, 0, startcontigs.length);
 
     // allocate a roughly sized buffer for the protein sequence
     StringBuilder protein = new StringBuilder(seqstring.length() / 2);

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 2a66fd8..b499a74 100755 (executable)
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -561,8 +561,8 @@ public class SeqCanvas extends Panel implements ViewportListenerI
     else
     {
       int screenY = 0;
-      int blockStart = startRes;
-      int blockEnd = endRes;
+      int blockStart;
+      int blockEnd;
 
       HiddenColumns hidden = av.getAlignment().getHiddenColumns();
       VisibleBlocksVisBoundsIterator regions = (VisibleBlocksVisBoundsIterator) hidden

diff --git a/src/jalview/datamodel/HiddenColumns.java b/src/jalview/datamodel/HiddenColumns.java
index f8a7f0c..839cee2 100644 (file)
--- a/src/jalview/datamodel/HiddenColumns.java
+++ b/src/jalview/datamodel/HiddenColumns.java
@@ -1641,14 +1641,14 @@ public class HiddenColumns
 
     private List<int[]> localHidden = new ArrayList<>();
 
-    private int lasthiddenregion;
+    private int nexthiddenregion;
 
     VisibleColsIterator(int firstcol, int lastcol, boolean useCopy)
     {
       last = lastcol;
       current = firstcol;
       next = firstcol;
-      lasthiddenregion = -1;
+      nexthiddenregion = 0;
 
       try
       {
@@ -1663,7 +1663,7 @@ public class HiddenColumns
         {
           int i = 0;
           for (i = 0; i < hiddenColumns.size()
-                  && (current < hiddenColumns.get(i)[0]); ++i)
+                  && (current <= hiddenColumns.get(i)[0]); ++i)
           {
             if (current >= hiddenColumns.get(i)[0]
                     && current <= hiddenColumns.get(i)[1])
@@ -1671,13 +1671,12 @@ public class HiddenColumns
               // current is hidden, move to right
               current = hiddenColumns.get(i)[1] + 1;
               next = current;
+              nexthiddenregion = i + 1;
             }
           }
 
-          lasthiddenregion = i - 1;
-
           for (i = hiddenColumns.size() - 1; i >= 0
-                  && (last > hiddenColumns.get(i)[1]); --i)
+                  && (last >= hiddenColumns.get(i)[1]); --i)
           {
             if (last >= hiddenColumns.get(i)[0]
                     && last <= hiddenColumns.get(i)[1])
@@ -1688,7 +1687,7 @@ public class HiddenColumns
           }
 
           // make a local copy of the bit we need
-          i = lasthiddenregion + 1;
+          i = nexthiddenregion;
           while (i < hiddenColumns.size()
                   && hiddenColumns.get(i)[0] <= last)
           {
@@ -1697,7 +1696,6 @@ public class HiddenColumns
             localHidden.add(region);
             i++;
           }
-          lasthiddenregion = -1;
         }
       } finally
       {
@@ -1723,20 +1721,20 @@ public class HiddenColumns
       }
       current = next;
       if ((localHidden != null)
-              && (lasthiddenregion + 1 < localHidden.size()))
+              && (nexthiddenregion < localHidden.size()))
       {
         // still some more hidden regions
-        if (next + 1 < localHidden.get(lasthiddenregion + 1)[0])
+        if (next + 1 < localHidden.get(nexthiddenregion)[0])
         {
           // next+1 is still before the next hidden region
           next++;
         }
-        else if ((next + 1 >= localHidden.get(lasthiddenregion + 1)[0])
-                && (next + 1 <= localHidden.get(lasthiddenregion + 1)[1]))
+        else if ((next + 1 >= localHidden.get(nexthiddenregion)[0])
+                && (next + 1 <= localHidden.get(nexthiddenregion)[1]))
         {
           // next + 1 is in the next hidden region
-          next = localHidden.get(lasthiddenregion + 1)[1] + 1;
-          lasthiddenregion++;
+          next = localHidden.get(nexthiddenregion)[1] + 1;
+          nexthiddenregion++;
         }
       }
       else
@@ -1949,7 +1947,6 @@ public class HiddenColumns
           int blockEnd = end;
           int hiddenSoFar = 0;
           int visSoFar = 0;
-          int maxVisible = end - start;
           endsAtHidden = false;
 
           // iterate until a region begins within (start,end]
@@ -1985,9 +1982,9 @@ public class HiddenColumns
 
             i++;
           }
-          if (visSoFar < maxVisible)
+          if (visSoFar < end - start)
           {
-            blockEnd = blockStart + maxVisible - visSoFar;
+            blockEnd = blockStart + end - start - visSoFar;
             int[] contig = new int[] { blockStart, blockEnd };
             vcontigs.add(contig);
 

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 82e4481..f72acae 100755 (executable)
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -852,8 +852,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     else
     {
       int screenY = 0;
-      int blockStart = startRes;
-      int blockEnd = endRes;
+      int blockStart;
+      int blockEnd;
 
       HiddenColumns hidden = av.getAlignment().getHiddenColumns();
       VisibleBlocksVisBoundsIterator regions = (VisibleBlocksVisBoundsIterator) hidden
@@ -1100,8 +1100,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     {
       // package into blocks of visible columns
       int screenY = 0;
-      int blockStart = startRes;
-      int blockEnd = endRes;
+      int blockStart;
+      int blockEnd;
 
       HiddenColumns hidden = av.getAlignment().getHiddenColumns();
       VisibleBlocksVisBoundsIterator regions = (VisibleBlocksVisBoundsIterator) hidden

diff --git a/test/jalview/datamodel/VisibleColsIteratorTest.java b/test/jalview/datamodel/VisibleColsIteratorTest.java
index 92d39be..f9b01bd 100644 (file)
--- a/test/jalview/datamodel/VisibleColsIteratorTest.java
+++ b/test/jalview/datamodel/VisibleColsIteratorTest.java
@@ -55,7 +55,8 @@ public class VisibleColsIteratorTest
     int count = 0;
     while (it.hasNext())
     {
-      it.next();
+      int result = it.next();
+      System.out.println(result);
       count++;
     }
     assertTrue(count == 4, "hasNext() is false after 4 iterations");