X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=25d770d7264402395888d163a15ccd1a22bad918;hb=09cce494f72431183bd3c37e77913170a08c3ac3;hp=41488ea9001f6df106e9f9771b9c8a71c1203dad;hpb=bc096ecbcd3cf4bbf17a24f9e9df88806789d688;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 41488ea..25d770d 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -30,6 +30,7 @@ import jalview.util.MessageManager;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.Enumeration;
+import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Hashtable;
 import java.util.List;
@@ -62,6 +63,8 @@ public class Alignment implements AlignmentI
 
   HiddenSequences hiddenSequences;
 
+  HiddenColumns hiddenCols;
+
   public Hashtable alignmentProperties;
 
   private List<AlignedCodonFrame> codonFrameList;
@@ -70,7 +73,8 @@ public class Alignment implements AlignmentI
   {
     groups = Collections.synchronizedList(new ArrayList<SequenceGroup>());
     hiddenSequences = new HiddenSequences(this);
-    codonFrameList = new ArrayList<AlignedCodonFrame>();
+    hiddenCols = new HiddenColumns();
+    codonFrameList = new ArrayList<>();
 
     nucleotide = Comparison.isNucleotide(seqs);
 
@@ -125,7 +129,7 @@ public class Alignment implements AlignmentI
   public Alignment(SeqCigar[] alseqs)
   {
     SequenceI[] seqs = SeqCigar.createAlignmentSequences(alseqs,
-            gapCharacter, new ColumnSelection(), null);
+            gapCharacter, new HiddenColumns(), null);
     initAlignment(seqs);
   }
 
@@ -402,7 +406,7 @@ public class Alignment implements AlignmentI
   @Override
   public SequenceGroup[] findAllGroups(SequenceI s)
   {
-    ArrayList<SequenceGroup> temp = new ArrayList<SequenceGroup>();
+    ArrayList<SequenceGroup> temp = new ArrayList<>();
 
     synchronized (groups)
     {
@@ -453,7 +457,7 @@ public class Alignment implements AlignmentI
             return;
           }
         }
-        sg.setContext(this);
+        sg.setContext(this, true);
         groups.add(sg);
       }
     }
@@ -530,7 +534,7 @@ public class Alignment implements AlignmentI
       }
       for (SequenceGroup sg : groups)
       {
-        sg.setContext(null);
+        sg.setContext(null, false);
       }
       groups.clear();
     }
@@ -546,7 +550,7 @@ public class Alignment implements AlignmentI
       {
         removeAnnotationForGroup(g);
         groups.remove(g);
-        g.setContext(null);
+        g.setContext(null, false);
       }
     }
   }
@@ -1011,6 +1015,10 @@ public class Alignment implements AlignmentI
     }
     else if (dataset == null && data != null)
     {
+      if (data == this)
+      {
+        throw new IllegalArgumentException("Circular dataset reference");
+      }
       if (!(data instanceof Alignment))
       {
         throw new Error(
@@ -1060,21 +1068,18 @@ 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)
@@ -1117,7 +1122,7 @@ 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++)
     {
@@ -1323,6 +1328,12 @@ public class Alignment implements AlignmentI
   }
 
   @Override
+  public HiddenColumns getHiddenColumns()
+  {
+    return hiddenCols;
+  }
+
+  @Override
   public CigarArray getCompactAlignment()
   {
     synchronized (sequences)
@@ -1396,7 +1407,7 @@ 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))
@@ -1473,7 +1484,7 @@ public class Alignment implements AlignmentI
     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)
@@ -1614,7 +1625,7 @@ 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)
     {
@@ -1631,20 +1642,18 @@ 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);
       }
@@ -1842,7 +1851,7 @@ 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());
@@ -1942,4 +1951,43 @@ public class Alignment implements AlignmentI
     }
     return new int[] { startPos, endPos };
   }
+  @Override
+  public void setHiddenColumns(HiddenColumns cols)
+  {
+    hiddenCols = cols;
+  }
+
+  Map<Object, ContactMatrixI> contactmaps = new HashMap<Object, ContactMatrixI>();
+  @Override
+  public
+  ContactListI getContactListFor(AlignmentAnnotation _aa, int column)
+  {
+    ContactMatrixI cm = contactmaps.get(_aa.annotationId);
+    if (cm == null)
+    {
+      return null;
+    }
+    return cm.getContactList(column);
+  }
+
+  @Override
+  public AlignmentAnnotation addContactList(ContactMatrixI cm)
+  {
+    Annotation _aa[] = new Annotation[getWidth()];
+    Annotation dummy = new Annotation(0.0f);
+    for (int i = 0; i < _aa.length; _aa[i++] = dummy)
+    {
+      ;
+    }
+    AlignmentAnnotation aa = new AlignmentAnnotation("Contact Matrix",
+            "Contact Matrix", _aa);
+    aa.graph = AlignmentAnnotation.CUSTOMRENDERER;
+    aa.graphMin = cm.getMin();
+    aa.graphMax = cm.getMax();
+    aa.editable = false;
+    // aa.autoCalculated = true;
+    contactmaps.put(aa.annotationId, cm);
+    addAnnotation(aa);
+    return aa;
+  }
 }