JAL-1619 Javadoc

[jalview.git] / src / jalview / analysis / AlignmentUtils.java

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 929a855..681589c 100644 (file)
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -20,11 +20,17 @@
  */
 package jalview.analysis;
 
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
+import jalview.schemes.ResidueProperties;
+import jalview.util.MapList;
 
 import java.util.ArrayList;
+import java.util.LinkedHashMap;
 import java.util.List;
+import java.util.Map;
 
 /**
  * grab bag of useful alignment manipulation operations Expect these to be
@@ -121,6 +127,16 @@ public class AlignmentUtils
     }
     AlignmentI newAl = new jalview.datamodel.Alignment(
             sq.toArray(new SequenceI[0]));
+    for (SequenceI s : sq)
+    {
+      if (s.getAnnotation() != null)
+      {
+        for (AlignmentAnnotation aa : s.getAnnotation())
+        {
+          newAl.addAnnotation(aa);
+        }
+      }
+    }
     newAl.setDataset(core.getDataset());
     return newAl;
   }
@@ -148,4 +164,148 @@ public class AlignmentUtils
     }
     return result;
   }
+
+  /**
+   * Returns a map of lists of sequences in the alignment, keyed by sequence
+   * name. For use in mapping between different alignment views of the same
+   * sequences.
+   * 
+   * @see jalview.datamodel.AlignmentI#getSequencesByName()
+   */
+  public static Map<String, List<SequenceI>> getSequencesByName(
+          AlignmentI al)
+  {
+    Map<String, List<SequenceI>> theMap = new LinkedHashMap<String, List<SequenceI>>();
+    for (SequenceI seq : al.getSequences())
+    {
+      String name = seq.getName();
+      if (name != null)
+      {
+        List<SequenceI> seqs = theMap.get(name);
+        if (seqs == null)
+        {
+          seqs = new ArrayList<SequenceI>();
+          theMap.put(name, seqs);
+        }
+        seqs.add(seq);
+      }
+    }
+    return theMap;
+  }
+
+  /**
+   * Build mapping of protein to cDNA alignment. Mappings are made between
+   * sequences which have the same name and compatible lengths. Returns true if
+   * at least one sequence mapping was made, else false.
+   * 
+   * @param proteinAlignment
+   * @param cdnaAlignment
+   * @return
+   */
+  public static boolean mapProteinToCdna(final AlignmentI proteinAlignment,
+          final AlignmentI cdnaAlignment)
+  {
+    boolean mapped = false;
+    List<SequenceI> thisSeqs = proteinAlignment.getSequences();
+  
+    /*
+     * Build a look-up of cDNA sequences by name, for matching purposes.
+     */
+    Map<String, List<SequenceI>> cdnaSeqs = cdnaAlignment
+            .getSequencesByName();
+  
+    for (SequenceI aaSeq : thisSeqs)
+    {
+      AlignedCodonFrame acf = new AlignedCodonFrame(
+              proteinAlignment.getWidth());
+      List<SequenceI> candidates = cdnaSeqs.get(aaSeq.getName());
+      if (candidates == null)
+      {
+        /*
+         * No cDNA sequence with matching name, so no mapping for this protein
+         * sequence
+         */
+        continue;
+      }
+      for (SequenceI cdnaSeq : candidates)
+      {
+        MapList map = mapProteinToCdna(aaSeq, cdnaSeq);
+        if (map != null)
+        {
+          acf.addMap(cdnaSeq, aaSeq, map);
+          mapped = true;
+        }
+      }
+      proteinAlignment.addCodonFrame(acf);
+    }
+    return mapped;
+  }
+
+  /**
+   * Build a mapping (if possible) of a protein to a cDNA sequence. The cDNA
+   * must be three times the length of the protein, possibly after ignoring
+   * start and/or stop codons. Returns null if no mapping is determined.
+   * 
+   * @param proteinSeqs
+   * @param cdnaSeq
+   * @return
+   */
+  public static MapList mapProteinToCdna(SequenceI proteinSeq,
+          SequenceI cdnaSeq)
+  {
+    String aaSeqString = proteinSeq.getDatasetSequence()
+            .getSequenceAsString();
+    String cdnaSeqString = cdnaSeq.getDatasetSequence()
+            .getSequenceAsString();
+    if (aaSeqString == null || cdnaSeqString == null)
+    {
+      return null;
+    }
+
+    final int mappedLength = 3 * aaSeqString.length();
+    int cdnaLength = cdnaSeqString.length();
+    int cdnaStart = 1;
+    int cdnaEnd = cdnaLength;
+    final int proteinStart = 1;
+    final int proteinEnd = aaSeqString.length();
+
+    /*
+     * If lengths don't match, try ignoring stop codon.
+     */
+    if (cdnaLength != mappedLength)
+    {
+      for (Object stop : ResidueProperties.STOP)
+      {
+        if (cdnaSeqString.toUpperCase().endsWith((String) stop))
+        {
+          cdnaEnd -= 3;
+          cdnaLength -= 3;
+          break;
+        }
+      }
+    }
+
+    /*
+     * If lengths still don't match, try ignoring start codon.
+     */
+    if (cdnaLength != mappedLength
+            && cdnaSeqString.toUpperCase().startsWith(
+                    ResidueProperties.START))
+    {
+      cdnaStart += 3;
+      cdnaLength -= 3;
+    }
+
+    if (cdnaLength == mappedLength)
+    {
+      MapList map = new MapList(new int[]
+      { cdnaStart, cdnaEnd }, new int[]
+      { proteinStart, proteinEnd }, 3, 1);
+      return map;
+    }
+    else
+    {
+      return null;
+    }
+  }
 }