X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignedCodonFrame.java;h=0e9444fb89111438e625afa3c45e61b566d7e2bb;hb=c16c1633e1a5acc9f44e4de40b9abbb8a59b99b4;hp=f4e2d97ee4826e6135b06ea3e275d056c45c97aa;hpb=d7563d2df09ba5146008951448b941a69bf74744;p=jalview.git

diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java
index f4e2d97..0e9444f 100644
--- a/src/jalview/datamodel/AlignedCodonFrame.java
+++ b/src/jalview/datamodel/AlignedCodonFrame.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.datamodel;
 
 import java.util.Enumeration;
@@ -13,25 +31,29 @@ import jalview.util.MapList;
 public class AlignedCodonFrame
 {
   /**
-   * array of nucleotide positions for aligned codons at column of aligned proteins.
+   * array of nucleotide positions for aligned codons at column of aligned
+   * proteins.
    */
   public int[][] codons = null;
+
   /**
-   * width of protein sequence alignement
-   * implicit assertion that codons.length >= aaWidth
+   * width of protein sequence alignement implicit assertion that codons.length >=
+   * aaWidth
    */
-  public int aaWidth=0;
+  public int aaWidth = 0;
+
   /**
    * initialise codon frame with a nominal alignment width
+   * 
    * @param aWidth
    */
   public AlignedCodonFrame(int aWidth)
   {
-    if (aWidth<=0)
-   {
-      codons=null;
+    if (aWidth <= 0)
+    {
+      codons = null;
       return;
-   }
+    }
     codons = new int[aWidth][];
     for (int res = 0; res < aWidth; res++)
       codons[res] = null;
@@ -39,6 +61,7 @@ public class AlignedCodonFrame
 
   /**
    * ensure that codons array is at least as wide as aslen residues
+   * 
    * @param aslen
    * @return (possibly newly expanded) codon array
    */
@@ -57,29 +80,37 @@ public class AlignedCodonFrame
     }
     return codons;
   }
+
   /**
-   * @return width of aligned translated amino acid residues 
+   * @return width of aligned translated amino acid residues
    */
   public int getaaWidth()
   {
     return aaWidth;
   }
+
   /**
-   * TODO: not an ideal solution - we reference the aligned amino acid sequences in order to make insertions on them
-   * Better would be dnaAlignment and aaAlignment reference....
+   * TODO: not an ideal solution - we reference the aligned amino acid sequences
+   * in order to make insertions on them Better would be dnaAlignment and
+   * aaAlignment reference....
    */
-  Vector a_aaSeqs=new Vector();
+  Vector a_aaSeqs = new Vector();
+
   /**
-   * increase aaWidth by one and insert a new aligned codon position space at aspos.
+   * increase aaWidth by one and insert a new aligned codon position space at
+   * aspos.
+   * 
    * @param aspos
    */
   public void insertAAGap(int aspos, char gapCharacter)
-  {            
-    // this aa appears before the aligned codons at aspos - so shift them in each pair of mapped sequences
+  {
+    // this aa appears before the aligned codons at aspos - so shift them in
+    // each pair of mapped sequences
     aaWidth++;
-    if (a_aaSeqs!=null)
+    if (a_aaSeqs != null)
     {
-      // we actually have to modify the aligned sequences here, so use the a_aaSeqs vector
+      // we actually have to modify the aligned sequences here, so use the
+      // a_aaSeqs vector
       Enumeration sq = a_aaSeqs.elements();
       while (sq.hasMoreElements())
       {
@@ -87,11 +118,11 @@ public class AlignedCodonFrame
       }
     }
     checkCodonFrameWidth(aspos);
-    if (aspos<aaWidth)
+    if (aspos < aaWidth)
     {
       aaWidth++;
-      System.arraycopy(codons, aspos, codons, aspos+1, aaWidth-aspos);
-      codons[aspos]=null; // clear so new codon position can be marked.
+      System.arraycopy(codons, aspos, codons, aspos + 1, aaWidth - aspos);
+      codons[aspos] = null; // clear so new codon position can be marked.
     }
   }
 
@@ -99,77 +130,90 @@ public class AlignedCodonFrame
   {
     aaWidth = aapos;
   }
+
   /**
    * tied array of na Sequence objects.
    */
-  SequenceI[] dnaSeqs=null;
+  SequenceI[] dnaSeqs = null;
+
   /**
-   * tied array of Mappings to protein sequence Objects and 
-     SequenceI[] aaSeqs=null;
-   * MapLists where eac maps from the corresponding dnaSeqs element to corresponding aaSeqs element  
+   * tied array of Mappings to protein sequence Objects and SequenceI[]
+   * aaSeqs=null; MapLists where eac maps from the corresponding dnaSeqs element
+   * to corresponding aaSeqs element
    */
-  Mapping[] dnaToProt=null;
+  Mapping[] dnaToProt = null;
+
   /**
-   * add a mapping between the dataset sequences for the associated dna and protein sequence objects
+   * add a mapping between the dataset sequences for the associated dna and
+   * protein sequence objects
+   * 
    * @param dnaseq
    * @param aaseq
    * @param map
    */
   public void addMap(SequenceI dnaseq, SequenceI aaseq, MapList map)
-  { 
-    int nlen=1;
-    if (dnaSeqs!=null)
+  {
+    int nlen = 1;
+    if (dnaSeqs != null)
     {
-      nlen = dnaSeqs.length+1;
+      nlen = dnaSeqs.length + 1;
     }
     SequenceI[] ndna = new SequenceI[nlen];
     Mapping[] ndtp = new Mapping[nlen];
-    if (dnaSeqs!=null)
+    if (dnaSeqs != null)
     {
-      System.arraycopy(dnaSeqs,0,ndna, 0, dnaSeqs.length);
-      System.arraycopy(dnaToProt,0,ndtp, 0, dnaSeqs.length);
+      System.arraycopy(dnaSeqs, 0, ndna, 0, dnaSeqs.length);
+      System.arraycopy(dnaToProt, 0, ndtp, 0, dnaSeqs.length);
     }
     dnaSeqs = ndna;
     dnaToProt = ndtp;
     nlen--;
-    dnaSeqs[nlen] = (dnaseq.getDatasetSequence()==null) ? dnaseq : dnaseq.getDatasetSequence();
+    dnaSeqs[nlen] = (dnaseq.getDatasetSequence() == null) ? dnaseq : dnaseq
+            .getDatasetSequence();
     Mapping mp = new Mapping(map);
-    mp.to = (aaseq.getDatasetSequence()==null) ? aaseq : aaseq.getDatasetSequence();
+    // JBPNote DEBUG! THIS !
+    // dnaseq.transferAnnotation(aaseq, mp);
+    // aaseq.transferAnnotation(dnaseq, new Mapping(map.getInverse()));
+    mp.to = (aaseq.getDatasetSequence() == null) ? aaseq : aaseq
+            .getDatasetSequence();
     a_aaSeqs.addElement(aaseq);
     dnaToProt[nlen] = mp;
   }
 
-
   public SequenceI[] getdnaSeqs()
   {
     return dnaSeqs;
   }
+
   public SequenceI[] getAaSeqs()
   {
-    if (dnaToProt==null)
+    if (dnaToProt == null)
       return null;
     SequenceI[] sqs = new SequenceI[dnaToProt.length];
-    for (int sz=0; sz<dnaToProt.length; sz++)
+    for (int sz = 0; sz < dnaToProt.length; sz++)
     {
-      sqs[sz]  = dnaToProt[sz].to;
+      sqs[sz] = dnaToProt[sz].to;
     }
     return sqs;
   }
+
   public MapList[] getdnaToProt()
   {
-    if (dnaToProt==null)
+    if (dnaToProt == null)
       return null;
     MapList[] sqs = new MapList[dnaToProt.length];
-    for (int sz=0; sz<dnaToProt.length; sz++)
+    for (int sz = 0; sz < dnaToProt.length; sz++)
     {
-      sqs[sz]  = dnaToProt[sz].map;
+      sqs[sz] = dnaToProt[sz].map;
     }
     return sqs;
   }
+
   public Mapping[] getProtMappings()
   {
     return dnaToProt;
   }
+
   /**
    * 
    * @param sequenceRef
@@ -177,18 +221,19 @@ public class AlignedCodonFrame
    */
   public SequenceI getAaForDnaSeq(SequenceI dnaSeqRef)
   {
-    if (dnaSeqs==null)
+    if (dnaSeqs == null)
     {
       return null;
     }
     SequenceI dnads = dnaSeqRef.getDatasetSequence();
-    for (int ds=0;ds<dnaSeqs.length; ds++)
+    for (int ds = 0; ds < dnaSeqs.length; ds++)
     {
-      if (dnaSeqs[ds]==dnaSeqRef || dnaSeqs[ds]==dnads)
+      if (dnaSeqs[ds] == dnaSeqRef || dnaSeqs[ds] == dnads)
         return dnaToProt[ds].to;
     }
     return null;
   }
+
   /**
    * 
    * @param sequenceRef
@@ -196,65 +241,79 @@ public class AlignedCodonFrame
    */
   public SequenceI getDnaForAaSeq(SequenceI aaSeqRef)
   {
-    if (dnaToProt==null)
+    if (dnaToProt == null)
     {
       return null;
     }
     SequenceI aads = aaSeqRef.getDatasetSequence();
-    for (int as=0;as<dnaToProt.length; as++)
+    for (int as = 0; as < dnaToProt.length; as++)
     {
-      if (dnaToProt[as].to==aaSeqRef || dnaToProt[as].to==aads)
+      if (dnaToProt[as].to == aaSeqRef || dnaToProt[as].to == aads)
         return dnaSeqs[as];
     }
     return null;
   }
+
   /**
    * test to see if codon frame involves seq in any way
-   * @param seq a nucleotide or protein sequence
-   * @return true if a mapping exists to or from this sequence to any translated sequence
+   * 
+   * @param seq
+   *                a nucleotide or protein sequence
+   * @return true if a mapping exists to or from this sequence to any translated
+   *         sequence
    */
   public boolean involvesSequence(SequenceI seq)
   {
-    return getAaForDnaSeq(seq)!=null || getDnaForAaSeq(seq)!=null;
+    return getAaForDnaSeq(seq) != null || getDnaForAaSeq(seq) != null;
   }
+
   /**
-   * Add search results for regions in other sequences that translate or are translated from a particular position in seq 
+   * Add search results for regions in other sequences that translate or are
+   * translated from a particular position in seq
+   * 
    * @param seq
-   * @param index position in seq
-   * @param results where highlighted regions go
+   * @param index
+   *                position in seq
+   * @param results
+   *                where highlighted regions go
    */
-  public void markMappedRegion(SequenceI seq, int index, SearchResults results)
+  public void markMappedRegion(SequenceI seq, int index,
+          SearchResults results)
   {
+    if (dnaToProt == null)
+    {
+      return;
+    }
     int[] codon;
     SequenceI ds = seq.getDatasetSequence();
-    for (int mi = 0; mi<dnaToProt.length; mi++)
+    for (int mi = 0; mi < dnaToProt.length; mi++)
     {
-      if (dnaSeqs[mi]==seq || dnaSeqs[mi]==ds)
+      if (dnaSeqs[mi] == seq || dnaSeqs[mi] == ds)
       {
         // DEBUG System.err.println("dna pos "+index);
-        codon = dnaToProt[mi].map.locateInTo(index,index);
-        if (codon!=null)
+        codon = dnaToProt[mi].map.locateInTo(index, index);
+        if (codon != null)
         {
-          for (int i=0; i<codon.length; i+=2)
-            {
-              results.addResult(dnaToProt[mi].to, codon[i], codon[i+1]);
-            }
+          for (int i = 0; i < codon.length; i += 2)
+          {
+            results.addResult(dnaToProt[mi].to, codon[i], codon[i + 1]);
+          }
         }
-      } else
-        if (dnaToProt[mi].to==seq || dnaToProt[mi].to==ds)
+      }
+      else if (dnaToProt[mi].to == seq || dnaToProt[mi].to == ds)
+      {
+        // DEBUG System.err.println("aa pos "+index);
         {
-          // DEBUG System.err.println("aa pos "+index);
+          codon = dnaToProt[mi].map.locateInFrom(index, index);
+          if (codon != null)
           {
-            codon = dnaToProt[mi].map.locateInFrom(index, index);
-            if (codon!=null)
+            for (int i = 0; i < codon.length; i += 2)
             {
-            for (int i=0; i<codon.length; i+=2)
-              {
-                results.addResult(dnaSeqs[mi], codon[i], codon[i+1]);
-              }
+              results.addResult(dnaSeqs[mi], codon[i], codon[i + 1]);
+            }
           }
         }
-        }
+      }
     }
   }
 }