JAL-1114 - refactor methods handling Vectors and Hashtables to Lists and Maps, and...

[jalview.git] / src / jalview / datamodel / Alignment.java

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 6a4dcbf..23fe057 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -43,6 +43,8 @@ public class Alignment implements AlignmentI
   public static final int PROTEIN = 0;
 
   public static final int NUCLEOTIDE = 1;
+  
+  public boolean hasRNAStructure = false;
 
   /** DOCUMENT ME!! */
   public AlignmentAnnotation[] annotations;
@@ -120,6 +122,13 @@ public class Alignment implements AlignmentI
   {
     return sequences;
   }
+  @Override
+  public List<SequenceI> getSequences(
+          Map<SequenceI, SequenceCollectionI> hiddenReps)
+  {
+    // TODO: in jalview 2.8 we don't do anything with hiddenreps - fix design to work on this.
+    return sequences;
+  }
 
   public SequenceI[] getSequencesArray()
   {
@@ -143,7 +152,7 @@ public class Alignment implements AlignmentI
    */
   public SequenceI getSequenceAt(int i)
   {
-    if (i < sequences.size())
+    if (i>-1 && i < sequences.size())
     {
       return (SequenceI) sequences.elementAt(i);
     }
@@ -593,8 +602,8 @@ public class Alignment implements AlignmentI
     for (int i = 0; i < sequences.size(); i++)
     {
       Sequence seq = (Sequence) sequences.elementAt(i);
-      seq.setSequence(seq.getSequenceAsString().replace('.', gc).replace(
-              '-', gc).replace(' ', gc));
+      seq.setSequence(seq.getSequenceAsString().replace('.', gc)
+              .replace('-', gc).replace(' ', gc));
     }
   }
 
@@ -652,6 +661,11 @@ public class Alignment implements AlignmentI
    */
   public boolean deleteAnnotation(AlignmentAnnotation aa)
   {
+    return deleteAnnotation(aa, true);
+  }
+  
+  public boolean deleteAnnotation(AlignmentAnnotation aa, boolean unhook)
+  {
     int aSize = 1;
 
     if (annotations != null)
@@ -683,7 +697,9 @@ public class Alignment implements AlignmentI
     if (swap)
     {
       annotations = temp;
-      unhookAnnotation(aa);
+      if (unhook) {
+        unhookAnnotation(aa);
+      }
     }
     return swap;
   }
@@ -725,6 +741,10 @@ public class Alignment implements AlignmentI
    */
   public void addAnnotation(AlignmentAnnotation aa, int pos)
   {
+    if(aa.getRNAStruc()!= null){
+      hasRNAStructure=true;
+    }
+    
     int aSize = 1;
     if (annotations != null)
     {
@@ -792,10 +812,9 @@ public class Alignment implements AlignmentI
     annotations = temp;
   }
 
+  @Override
   /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
+   * returns all annotation on the alignment
    */
   public AlignmentAnnotation[] getAlignmentAnnotation()
   {
@@ -825,6 +844,11 @@ public class Alignment implements AlignmentI
       return false;
     }
   }
+  
+  public boolean hasRNAStructure(){
+    //TODO can it happen that structure is removed from alignment?
+    return hasRNAStructure;
+  }
 
   public void setDataset(Alignment data)
   {
@@ -1202,13 +1226,12 @@ public class Alignment implements AlignmentI
     {
       this.addCodonFrame(acod[a]);
     }
-    Vector sg = toappend.getGroups();
+    List<SequenceGroup> sg = toappend.getGroups();
     if (sg != null)
     {
-      Enumeration el = sg.elements();
-      while (el.hasMoreElements())
+      for (SequenceGroup _sg:sg)
       {
-        addGroup((SequenceGroup) el.nextElement());
+        addGroup(_sg);
       }
     }
     if (toappend.getHiddenSequences() != null)
@@ -1275,4 +1298,47 @@ public class Alignment implements AlignmentI
     }
   }
 
+  @Override
+  public AlignmentAnnotation findOrCreateAnnotation(String name, boolean autoCalc,
+          SequenceI seqRef, SequenceGroup groupRef)
+  {
+    for (AlignmentAnnotation annot : 
+            getAlignmentAnnotation())
+    {
+      if (annot.autoCalculated == autoCalc
+              && annot.getCalcId().equals(name)
+              && annot.sequenceRef == seqRef && annot.groupRef == groupRef)
+      {
+        return annot;
+      }
+    }
+    AlignmentAnnotation annot = new AlignmentAnnotation(name, name,
+            new Annotation[1], 0f, 0f, AlignmentAnnotation.BAR_GRAPH);
+    annot.hasText = false;
+    annot.setCalcId(new String(name));
+    annot.autoCalculated = autoCalc;
+    if (seqRef != null)
+    {
+      annot.setSequenceRef(seqRef);
+    }
+    annot.groupRef = groupRef;
+    addAnnotation(annot);
+
+    return annot;
+  }
+
+  @Override
+  public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
+  {
+    ArrayList<AlignmentAnnotation> aa=new ArrayList<AlignmentAnnotation>();
+    for (AlignmentAnnotation a:getAlignmentAnnotation())
+    {
+      if (a.getCalcId()==calcId || (a.getCalcId()!=null && calcId!=null && a.getCalcId().equals(calcId)))
+      {
+        aa.add(a);
+      }
+    }
+    return aa;
+  }
+
 }