mapping bug fixes

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

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 83d2499..c474142 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -40,6 +40,8 @@ public class Alignment
 
   HiddenSequences hiddenSequences = new HiddenSequences(this);
 
+  public Hashtable alignmentProperties;
+
   private void initAlignment(SequenceI[] seqs)
   {
     int i = 0;
@@ -106,6 +108,8 @@ public class Alignment
 
   public SequenceI[] getSequencesArray()
   {
+    if (sequences==null)
+      return null;
     SequenceI[] reply = new SequenceI[sequences.size()];
     for (int i = 0; i < sequences.size(); i++)
     {
@@ -458,17 +462,11 @@ public class Alignment
 
     return true;
   }
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param aa DOCUMENT ME!
+  /* (non-Javadoc)
+   * @see jalview.datamodel.AlignmentI#deleteAnnotation(jalview.datamodel.AlignmentAnnotation)
    */
-  public void deleteAnnotation(AlignmentAnnotation aa)
+  public boolean deleteAnnotation(AlignmentAnnotation aa)
   {
-    if(aa.sequenceRef!=null)
-      aa.sequenceRef.removeAlignmentAnnotation(aa);
-
     int aSize = 1;
 
     if (annotations != null)
@@ -478,25 +476,32 @@ public class Alignment
 
     if (aSize < 1)
     {
-      return;
+      return false;
     }
 
     AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize - 1];
 
+    boolean swap=false;
     int tIndex = 0;
 
     for (int i = 0; i < aSize; i++)
     {
       if (annotations[i] == aa)
       {
+        swap=true;
         continue;
       }
-
-      temp[tIndex] = annotations[i];
-      tIndex++;
+      if (tIndex<temp.length)
+        temp[tIndex++] = annotations[i];
     }
 
-    annotations = temp;
+    if (swap)
+    {
+      annotations = temp;
+      if(aa.sequenceRef!=null)
+        aa.sequenceRef.removeAlignmentAnnotation(aa);
+    }
+    return swap;
   }
 
   /**
@@ -702,4 +707,106 @@ public class Alignment
     return cal;
   }
 
+  public void setProperty(Object key, Object value)
+  {
+    if(alignmentProperties==null)
+      alignmentProperties = new Hashtable();
+
+    alignmentProperties.put(key,value);
+  }
+
+  public Object getProperty(Object key)
+  {
+    if(alignmentProperties!=null)
+      return alignmentProperties.get(key);
+    else
+      return null;
+  }
+
+  public Hashtable getProperties()
+  {
+    return alignmentProperties;
+  }
+  AlignedCodonFrame[] codonFrameList=null;
+  /* (non-Javadoc)
+   * @see jalview.datamodel.AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame)
+   */
+  public void addCodonFrame(AlignedCodonFrame codons)
+  {
+    if (codons==null)
+      return;
+    if (codonFrameList==null)
+    {
+      codonFrameList = new AlignedCodonFrame[] { codons };
+      return;
+    }
+    AlignedCodonFrame[] t = new AlignedCodonFrame[codonFrameList.length+1];
+    System.arraycopy(codonFrameList, 0, t, 0, codonFrameList.length);
+    t[codonFrameList.length] = codons;
+    codonFrameList = t;
+  }
+
+  /* (non-Javadoc)
+   * @see jalview.datamodel.AlignmentI#getCodonFrame(int)
+   */
+  public AlignedCodonFrame getCodonFrame(int index)
+  {
+    return codonFrameList[index];
+  }
+
+  /* (non-Javadoc)
+   * @see jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
+   */
+  public AlignedCodonFrame[] getCodonFrame(SequenceI seq)
+  {
+    if (seq==null || codonFrameList==null)
+      return null;
+    Vector cframes=new Vector();
+    for (int f=0;f<codonFrameList.length; f++)
+    {
+      if (codonFrameList[f].involvesSequence(seq))
+        cframes.addElement(codonFrameList[f]);
+    }
+    if (cframes.size()==0)
+      return null;
+    AlignedCodonFrame[] cfr = new AlignedCodonFrame[cframes.size()];
+    cframes.copyInto(cfr);
+    return cfr;
+  }
+
+  /* (non-Javadoc)
+   * @see jalview.datamodel.AlignmentI#getCodonFrames()
+   */
+  public AlignedCodonFrame[] getCodonFrames()
+  {
+    return codonFrameList;
+  }
+
+  /* (non-Javadoc)
+   * @see jalview.datamodel.AlignmentI#removeCodonFrame(jalview.datamodel.AlignedCodonFrame)
+   */
+  public boolean removeCodonFrame(AlignedCodonFrame codons)
+  {
+    if (codons==null || codonFrameList==null)
+      return false;
+    boolean removed=false;
+    int i=0,iSize=codonFrameList.length;
+    while (i<iSize)
+    {
+      if (codonFrameList[i]==codons)
+      {
+        removed=true;
+        if (i+1<iSize)
+        {
+          System.arraycopy(codonFrameList,i+1,codonFrameList, i, iSize-i-1);
+        }
+        iSize--;
+      }
+      else
+      {
+        i++;
+      }
+    }
+    return removed;
+  }
 }