X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=7cc2125266f19d8114d120173b7c770f25e178af;hb=b95ecdde59db976d721fe9aec626105947825b9e;hp=cff3890b5855c01be10e83d0bb5fa28603396c1e;hpb=d1707d4c26db76cfeb640f0dbeb3e3427fd40eb7;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index cff3890..7cc2125 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -73,7 +73,7 @@ public class Alignment implements AlignmentI
     groups = Collections.synchronizedList(new ArrayList<SequenceGroup>());
     hiddenSequences = new HiddenSequences(this);
     hiddenCols = new HiddenColumns();
-    codonFrameList = new ArrayList<AlignedCodonFrame>();
+    codonFrameList = new ArrayList<>();
 
     nucleotide = Comparison.isNucleotide(seqs);
 
@@ -143,9 +143,8 @@ public class Alignment implements AlignmentI
    */
   public static AlignmentI createAlignment(CigarArray compactAlignment)
   {
-    throw new Error(
-            MessageManager
-                    .getString("error.alignment_cigararray_not_implemented"));
+    throw new Error(MessageManager
+            .getString("error.alignment_cigararray_not_implemented"));
     // this(compactAlignment.refCigars);
   }
 
@@ -188,7 +187,6 @@ public class Alignment implements AlignmentI
     return AlignmentUtils.getSequencesByName(this);
   }
 
-
   @Override
   public SequenceI getSequenceAt(int i)
   {
@@ -405,7 +403,7 @@ public class Alignment implements AlignmentI
   @Override
   public SequenceGroup[] findAllGroups(SequenceI s)
   {
-    ArrayList<SequenceGroup> temp = new ArrayList<SequenceGroup>();
+    ArrayList<SequenceGroup> temp = new ArrayList<>();
 
     synchronized (groups)
     {
@@ -456,7 +454,7 @@ public class Alignment implements AlignmentI
             return;
           }
         }
-        sg.setContext(this);
+        sg.setContext(this, true);
         groups.add(sg);
       }
     }
@@ -475,7 +473,9 @@ public class Alignment implements AlignmentI
       return;
     }
     // remove annotation very quickly
-    AlignmentAnnotation[] t, todelete = new AlignmentAnnotation[annotations.length], tokeep = new AlignmentAnnotation[annotations.length];
+    AlignmentAnnotation[] t,
+            todelete = new AlignmentAnnotation[annotations.length],
+            tokeep = new AlignmentAnnotation[annotations.length];
     int i, p, k;
     if (gp == null)
     {
@@ -533,7 +533,7 @@ public class Alignment implements AlignmentI
       }
       for (SequenceGroup sg : groups)
       {
-        sg.setContext(null);
+        sg.setContext(null, false);
       }
       groups.clear();
     }
@@ -549,7 +549,7 @@ public class Alignment implements AlignmentI
       {
         removeAnnotationForGroup(g);
         groups.remove(g);
-        g.setContext(null);
+        g.setContext(null, false);
       }
     }
   }
@@ -608,7 +608,7 @@ public class Alignment implements AlignmentI
       sqname = sq.getName();
       if (sqname.equals(token) // exact match
               || (b && // allow imperfect matches - case varies
-              (sqname.equalsIgnoreCase(token))))
+                      (sqname.equalsIgnoreCase(token))))
       {
         return getSequenceAt(i);
       }
@@ -689,7 +689,6 @@ public class Alignment implements AlignmentI
     return -1;
   }
 
-
   @Override
   public int getHeight()
   {
@@ -1067,21 +1066,18 @@ public class Alignment implements AlignmentI
         currentSeq = currentSeq.createDatasetSequence();
       }
     }
-    if (seqs.contains(currentSeq))
-    {
-      return;
-    }
-    List<SequenceI> toProcess = new ArrayList<SequenceI>();
+
+    List<SequenceI> toProcess = new ArrayList<>();
     toProcess.add(currentSeq);
     while (toProcess.size() > 0)
     {
       // use a queue ?
       SequenceI curDs = toProcess.remove(0);
-      if (seqs.contains(curDs))
+
+      if (!seqs.add(curDs))
       {
         continue;
       }
-      seqs.add(curDs);
       // iterate over database references, making sure we add forward referenced
       // sequences
       if (curDs.getDBRefs() != null)
@@ -1099,10 +1095,9 @@ public class Alignment implements AlignmentI
             }
             if (dbr.getMap().getTo().getDatasetSequence() != null)
             {
-              throw new Error(
-                      "Implementation error: Map.getTo() for dbref " + dbr
-                              + " from " + curDs.getName()
-                              + " is not a dataset sequence.");
+              throw new Error("Implementation error: Map.getTo() for dbref "
+                      + dbr + " from " + curDs.getName()
+                      + " is not a dataset sequence.");
             }
             // we recurse to add all forward references to dataset sequences via
             // DBRefs/etc
@@ -1124,7 +1119,7 @@ public class Alignment implements AlignmentI
       return;
     }
     // try to avoid using SequenceI.equals at this stage, it will be expensive
-    Set<SequenceI> seqs = new LinkedIdentityHashSet<SequenceI>();
+    Set<SequenceI> seqs = new LinkedIdentityHashSet<>();
 
     for (int i = 0; i < getHeight(); i++)
     {
@@ -1239,8 +1234,8 @@ public class Alignment implements AlignmentI
       current = getSequenceAt(i);
       // This should really be a sequence method
       ends[i * 2] = current.findIndex(current.getStart());
-      ends[i * 2 + 1] = current.findIndex(current.getStart()
-              + current.getLength());
+      ends[i * 2 + 1] = current
+              .findIndex(current.getStart() + current.getLength());
       boolean hitres = false;
       for (int j = 0, rs = 0, ssiz = current.getLength(); j < ssiz; j++)
       {
@@ -1409,7 +1404,7 @@ public class Alignment implements AlignmentI
     {
       return null;
     }
-    List<AlignedCodonFrame> cframes = new ArrayList<AlignedCodonFrame>();
+    List<AlignedCodonFrame> cframes = new ArrayList<>();
     for (AlignedCodonFrame acf : getCodonFrames())
     {
       if (acf.involvesSequence(seq))
@@ -1476,31 +1471,26 @@ public class Alignment implements AlignmentI
   {
     // TODO JAL-1270 needs test coverage
     // currently tested for use in jalview.gui.SequenceFetcher
-    boolean samegap = toappend.getGapCharacter() == getGapCharacter();
     char oldc = toappend.getGapCharacter();
+    boolean samegap = oldc == getGapCharacter();
     boolean hashidden = toappend.getHiddenSequences() != null
             && toappend.getHiddenSequences().hiddenSequences != null;
     // get all sequences including any hidden ones
-    List<SequenceI> sqs = (hashidden) ? toappend.getHiddenSequences()
-            .getFullAlignment().getSequences() : toappend.getSequences();
+    List<SequenceI> sqs = (hashidden)
+            ? toappend.getHiddenSequences().getFullAlignment()
+                    .getSequences()
+            : toappend.getSequences();
     if (sqs != null)
     {
       // avoid self append deadlock by
-      List<SequenceI> toappendsq = new ArrayList<SequenceI>();
+      List<SequenceI> toappendsq = new ArrayList<>();
       synchronized (sqs)
       {
         for (SequenceI addedsq : sqs)
         {
           if (!samegap)
           {
-            char[] oldseq = addedsq.getSequence();
-            for (int c = 0; c < oldseq.length; c++)
-            {
-              if (oldseq[c] == oldc)
-              {
-                oldseq[c] = gapCharacter;
-              }
-            }
+            addedsq.replace(oldc, gapCharacter);
           }
           toappendsq.add(addedsq);
         }
@@ -1564,8 +1554,8 @@ public class Alignment implements AlignmentI
             if (ourval instanceof String)
             {
               // append strings
-              this.setProperty(k, ((String) ourval) + "; "
-                      + ((String) toapprop));
+              this.setProperty(k,
+                      ((String) ourval) + "; " + ((String) toapprop));
             }
             else
             {
@@ -1627,15 +1617,14 @@ public class Alignment implements AlignmentI
   @Override
   public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
   {
-    List<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+    List<AlignmentAnnotation> aa = new ArrayList<>();
     AlignmentAnnotation[] alignmentAnnotation = getAlignmentAnnotation();
     if (alignmentAnnotation != null)
     {
       for (AlignmentAnnotation a : alignmentAnnotation)
       {
-        if (a.getCalcId() == calcId
-                || (a.getCalcId() != null && calcId != null && a
-                        .getCalcId().equals(calcId)))
+        if (a.getCalcId() == calcId || (a.getCalcId() != null
+                && calcId != null && a.getCalcId().equals(calcId)))
         {
           aa.add(a);
         }
@@ -1644,20 +1633,19 @@ public class Alignment implements AlignmentI
     return aa;
   }
 
-  /**
-   * Returns an iterable collection of any annotations that match on given
-   * sequence ref, calcId and label (ignoring null values).
-   */
   @Override
   public Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq,
           String calcId, String label)
   {
-    ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+    ArrayList<AlignmentAnnotation> aa = new ArrayList<>();
     for (AlignmentAnnotation ann : getAlignmentAnnotation())
     {
-      if (ann.getCalcId() != null && ann.getCalcId().equals(calcId)
-              && ann.sequenceRef != null && ann.sequenceRef == seq
-              && ann.label != null && ann.label.equals(label))
+      if ((calcId == null || (ann.getCalcId() != null
+              && ann.getCalcId().equals(calcId)))
+              && (seq == null || (ann.sequenceRef != null
+                      && ann.sequenceRef == seq))
+              && (label == null
+                      || (ann.label != null && ann.label.equals(label))))
       {
         aa.add(ann);
       }
@@ -1855,7 +1843,7 @@ public class Alignment implements AlignmentI
   @Override
   public Set<String> getSequenceNames()
   {
-    Set<String> names = new HashSet<String>();
+    Set<String> names = new HashSet<>();
     for (SequenceI seq : getSequences())
     {
       names.add(seq.getName());
@@ -1921,44 +1909,18 @@ public class Alignment implements AlignmentI
   }
 
   @Override
-  public int[] getVisibleStartAndEndIndex(List<int[]> hiddenCols)
+  public void setHiddenColumns(HiddenColumns cols)
   {
-    int[] alignmentStartEnd = new int[] { 0, getWidth() - 1 };
-    int startPos = alignmentStartEnd[0];
-    int endPos = alignmentStartEnd[1];
-
-    int[] lowestRange = new int[] { -1, -1 };
-    int[] higestRange = new int[] { -1, -1 };
-
-    for (int[] hiddenCol : hiddenCols)
-    {
-      lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
-      higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
-    }
-
-    if (lowestRange[0] == -1 && lowestRange[1] == -1)
-    {
-      startPos = alignmentStartEnd[0];
-    }
-    else
-    {
-      startPos = lowestRange[1] + 1;
-    }
-
-    if (higestRange[0] == -1 && higestRange[1] == -1)
-    {
-      endPos = alignmentStartEnd[1];
-    }
-    else
-    {
-      endPos = higestRange[0] - 1;
-    }
-    return new int[] { startPos, endPos };
+    hiddenCols = cols;
   }
 
   @Override
-  public void setHiddenColumns(HiddenColumns cols)
+  public void setupJPredAlignment()
   {
-    hiddenCols = cols;
+    SequenceI repseq = getSequenceAt(0);
+    setSeqrep(repseq);
+    HiddenColumns cs = new HiddenColumns();
+    cs.hideList(repseq.getInsertions());
+    setHiddenColumns(cs);
   }
 }