JAL-838 added 'SeqSpace' PID mode, added parameters to findDistances and

findSimilarities (not yet acted on!)

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 2c6b61d..fdadb13 100644 (file)
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -21,6 +21,7 @@
 package jalview.analysis;
 
 import jalview.analysis.scoremodels.ScoreModels;
+import jalview.analysis.scoremodels.SimilarityParams;
 import jalview.api.analysis.DistanceScoreModelI;
 import jalview.api.analysis.ScoreModelI;
 import jalview.api.analysis.SimilarityScoreModelI;
@@ -231,6 +232,10 @@ public class NJTree
   {
     this.sequence = sqs;
     this.node = new Vector<SequenceNode>();
+    if (!(treeType.equals(NEIGHBOUR_JOINING)))
+    {
+      treeType = AVERAGE_DISTANCE;
+    }
     this.type = treeType;
     this.pwtype = modelType;
     if (seqView != null)
@@ -248,11 +253,6 @@ public class NJTree
       sdata.addOperation(CigarArray.M, end - start + 1);
       this.seqData = new AlignmentView(sdata, start);
     }
-    // System.err.println("Made seqData");// dbg
-    if (!(treeType.equals(NEIGHBOUR_JOINING)))
-    {
-      treeType = AVERAGE_DISTANCE;
-    }
 
     if (sm == null && !(modelType.equals("PID")))
     {
@@ -274,17 +274,19 @@ public class NJTree
 
     noseqs = i++;
 
+    // TODO pass choice of params from GUI in constructo
     if (sm instanceof DistanceScoreModelI)
     {
-      distance = ((DistanceScoreModelI) sm).findDistances(seqData);
+      distance = ((DistanceScoreModelI) sm).findDistances(seqData,
+              SimilarityParams.Jalview);
     }
     else if (sm instanceof SimilarityScoreModelI)
     {
       /*
        * compute similarity and invert it to give a distance measure
        */
-      MatrixI result = ((SimilarityScoreModelI) sm)
-              .findSimilarities(seqData);
+      MatrixI result = ((SimilarityScoreModelI) sm).findSimilarities(
+              seqData, SimilarityParams.Jalview);
       result.reverseRange(true);
       distance = result;
     }

diff --git a/src/jalview/analysis/PCA.java b/src/jalview/analysis/PCA.java
index 1797296..1f923b1 100755 (executable)
--- a/src/jalview/analysis/PCA.java
+++ b/src/jalview/analysis/PCA.java
@@ -20,6 +20,7 @@
  */
 package jalview.analysis;
 
+import jalview.analysis.scoremodels.SimilarityParams;
 import jalview.api.analysis.DistanceScoreModelI;
 import jalview.api.analysis.ScoreModelI;
 import jalview.api.analysis.SimilarityScoreModelI;
@@ -228,13 +229,16 @@ public class PCA implements Runnable
   MatrixI computeSimilarity(AlignmentView av)
   {
     MatrixI result = null;
+    // TODO pass choice of params from GUI in constructo
     if (scoreModel instanceof SimilarityScoreModelI)
     {
-      result = ((SimilarityScoreModelI) scoreModel).findSimilarities(av);
+      result = ((SimilarityScoreModelI) scoreModel).findSimilarities(av,
+              SimilarityParams.SeqSpace);
     }
     else if (scoreModel instanceof DistanceScoreModelI)
     {
-      result = ((DistanceScoreModelI) scoreModel).findDistances(av);
+      result = ((DistanceScoreModelI) scoreModel).findDistances(av,
+              SimilarityParams.SeqSpace);
       result.reverseRange(false);
     }
     else

diff --git a/src/jalview/analysis/scoremodels/FeatureDistanceModel.java b/src/jalview/analysis/scoremodels/FeatureDistanceModel.java
index 9245898..636c19b 100644 (file)
--- a/src/jalview/analysis/scoremodels/FeatureDistanceModel.java
+++ b/src/jalview/analysis/scoremodels/FeatureDistanceModel.java
@@ -23,6 +23,7 @@ package jalview.analysis.scoremodels;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
 import jalview.api.analysis.DistanceScoreModelI;
+import jalview.api.analysis.SimilarityParamsI;
 import jalview.api.analysis.ViewBasedAnalysisI;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.SeqCigar;
@@ -58,7 +59,8 @@ public class FeatureDistanceModel implements DistanceScoreModelI,
    * of columns processed.
    */
   @Override
-  public MatrixI findDistances(AlignmentView seqData)
+  public MatrixI findDistances(AlignmentView seqData,
+          SimilarityParamsI options)
   {
     List<String> dft = fr.getDisplayedFeatureTypes();
     SeqCigar[] seqs = seqData.getSequences();

diff --git a/src/jalview/analysis/scoremodels/PIDDistanceModel.java b/src/jalview/analysis/scoremodels/PIDDistanceModel.java
index 154ff02..9688037 100644 (file)
--- a/src/jalview/analysis/scoremodels/PIDDistanceModel.java
+++ b/src/jalview/analysis/scoremodels/PIDDistanceModel.java
@@ -21,6 +21,7 @@
 package jalview.analysis.scoremodels;
 
 import jalview.api.analysis.DistanceScoreModelI;
+import jalview.api.analysis.SimilarityParamsI;
 import jalview.datamodel.AlignmentView;
 import jalview.math.Matrix;
 import jalview.math.MatrixI;
@@ -30,7 +31,8 @@ public class PIDDistanceModel implements DistanceScoreModelI
 {
 
   @Override
-  public MatrixI findDistances(AlignmentView seqData)
+  public MatrixI findDistances(AlignmentView seqData,
+          SimilarityParamsI options)
   {
     String[] sequenceString = seqData
             .getSequenceStrings(Comparison.GAP_SPACE);

diff --git a/src/jalview/analysis/scoremodels/PIDModel.java b/src/jalview/analysis/scoremodels/PIDModel.java
index 58667c0..aff1210 100644 (file)
--- a/src/jalview/analysis/scoremodels/PIDModel.java
+++ b/src/jalview/analysis/scoremodels/PIDModel.java
@@ -62,11 +62,11 @@ public class PIDModel implements SimilarityScoreModelI,
   }
 
   @Override
-  public MatrixI findSimilarities(AlignmentView seqData)
+  public MatrixI findSimilarities(AlignmentView seqData,
+          SimilarityParamsI options)
   {
-    // TODO reuse code in ScoreMatrix instead somehow
     String[] seqs = seqData.getSequenceStrings(' ');
-    return findSimilarities(seqs, SimilarityParams.Jalview);
+    return findSimilarities(seqs, options);
   }
 
   /**
@@ -80,6 +80,7 @@ public class PIDModel implements SimilarityScoreModelI,
   protected MatrixI findSimilarities(String[] seqs,
           SimilarityParamsI options)
   {
+    // TODO reuse code in ScoreMatrix instead somehow
     double[][] values = new double[seqs.length][];
     for (int row = 0; row < seqs.length; row++)
     {

diff --git a/src/jalview/analysis/scoremodels/SWDistanceModel.java b/src/jalview/analysis/scoremodels/SWDistanceModel.java
index 5e711db..b27cf26 100644 (file)
--- a/src/jalview/analysis/scoremodels/SWDistanceModel.java
+++ b/src/jalview/analysis/scoremodels/SWDistanceModel.java
@@ -22,6 +22,7 @@ package jalview.analysis.scoremodels;
 
 import jalview.analysis.AlignSeq;
 import jalview.api.analysis.DistanceScoreModelI;
+import jalview.api.analysis.SimilarityParamsI;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.SequenceI;
 import jalview.math.Matrix;
@@ -32,7 +33,8 @@ public class SWDistanceModel implements DistanceScoreModelI
 {
 
   @Override
-  public MatrixI findDistances(AlignmentView seqData)
+  public MatrixI findDistances(AlignmentView seqData,
+          SimilarityParamsI options)
   {
     SequenceI[] sequenceString = seqData.getVisibleAlignment(
             Comparison.GAP_SPACE).getSequencesArray();

diff --git a/src/jalview/analysis/scoremodels/ScoreMatrix.java b/src/jalview/analysis/scoremodels/ScoreMatrix.java
index 7f71d0f..84835a4 100644 (file)
--- a/src/jalview/analysis/scoremodels/ScoreMatrix.java
+++ b/src/jalview/analysis/scoremodels/ScoreMatrix.java
@@ -21,6 +21,7 @@
 package jalview.analysis.scoremodels;
 
 import jalview.api.analysis.PairwiseScoreModelI;
+import jalview.api.analysis.SimilarityParamsI;
 import jalview.api.analysis.SimilarityScoreModelI;
 import jalview.datamodel.AlignmentView;
 import jalview.math.Matrix;
@@ -345,19 +346,22 @@ public class ScoreMatrix implements SimilarityScoreModelI,
    * </ul>
    */
   @Override
-  public MatrixI findSimilarities(AlignmentView seqstrings)
+  public MatrixI findSimilarities(AlignmentView seqstrings,
+          SimilarityParamsI options)
   {
     char gapChar = scoreGapAsAny ? (seqstrings.isNa() ? 'N' : 'X') : ' ';
     String[] seqs = seqstrings.getSequenceStrings(gapChar);
-    return findSimilarities(seqs);
+    return findSimilarities(seqs, options);
   }
 
   /**
    * @param seqs
    * @return
    */
-  protected MatrixI findSimilarities(String[] seqs)
+  protected MatrixI findSimilarities(String[] seqs,
+          SimilarityParamsI options)
   {
+    // todo use options in calculation
     double[][] values = new double[seqs.length][];
     for (int row = 0; row < seqs.length; row++)
     {

diff --git a/src/jalview/analysis/scoremodels/SimilarityParams.java b/src/jalview/analysis/scoremodels/SimilarityParams.java
index 8b6b7d0..4cc5b1f 100644 (file)
--- a/src/jalview/analysis/scoremodels/SimilarityParams.java
+++ b/src/jalview/analysis/scoremodels/SimilarityParams.java
@@ -4,18 +4,45 @@ import jalview.api.analysis.SimilarityParamsI;
 
 public class SimilarityParams implements SimilarityParamsI
 {
+  /**
+   * Based on Jalview's Comparison.PID method, which includes gaps and counts
+   * them as matching; it counts over the length of the shorter sequence
+   */
   public static final SimilarityParamsI Jalview = new SimilarityParams(
           true, true, true, true);
 
+  /**
+   * 'SeqSpace' mode PCA calculation includes gaps but does not count them as
+   * matching; it uses the longest sequence length
+   */
+  public static final SimilarityParamsI SeqSpace = new SimilarityParams(
+          true, false, true, true);
+
+  /**
+   * as described in the Raghava-Barton paper; considers pairwise similarity
+   * only (excludes gap-gap) and does not match gaps
+   */
   public static final SimilarityParamsI PID1 = new SimilarityParams(false,
           false, true, false);
 
+  /**
+   * as described in the Raghava-Barton paper; considers pairwise similarity
+   * only (excludes gap-gap) and does not match gaps
+   */
   public static final SimilarityParamsI PID2 = new SimilarityParams(false,
           false, false, false);
 
+  /**
+   * as described in the Raghava-Barton paper; considers pairwise similarity
+   * only (excludes gap-gap) and does not match gaps
+   */
   public static final SimilarityParamsI PID3 = new SimilarityParams(false,
           false, false, true);
 
+  /**
+   * as described in the Raghava-Barton paper; considers pairwise similarity
+   * only (excludes gap-gap) and does not match gaps
+   */
   public static final SimilarityParamsI PID4 = new SimilarityParams(false,
           false, true, true);
 

diff --git a/src/jalview/api/analysis/DistanceScoreModelI.java b/src/jalview/api/analysis/DistanceScoreModelI.java
index 27003e8..0a39c0b 100644 (file)
--- a/src/jalview/api/analysis/DistanceScoreModelI.java
+++ b/src/jalview/api/analysis/DistanceScoreModelI.java
@@ -5,7 +5,8 @@ import jalview.math.MatrixI;
 
 /**
  * A sequence distance score models, that provides a method to compute distances
- * between pairs of sequences
+ * between pairs of sequences. The options parameter provides configuration
+ * choices for how the similarity score is calculated.
  * 
  * @author gmcarstairs
  *
@@ -18,7 +19,8 @@ public interface DistanceScoreModelI extends ScoreModelI
    * measure
    * 
    * @param seqData
+   * @param options
    * @return
    */
-  MatrixI findDistances(AlignmentView seqData);
+  MatrixI findDistances(AlignmentView seqData, SimilarityParamsI options);
 }

diff --git a/src/jalview/api/analysis/SimilarityScoreModelI.java b/src/jalview/api/analysis/SimilarityScoreModelI.java
index 96208a3..0c2624f 100644 (file)
--- a/src/jalview/api/analysis/SimilarityScoreModelI.java
+++ b/src/jalview/api/analysis/SimilarityScoreModelI.java
@@ -15,10 +15,12 @@ public interface SimilarityScoreModelI extends ScoreModelI
   /**
    * Returns a similarity score for the given sequence regions, that is, a
    * matrix whose value [i][j] is the similarity of sequence i to sequence j by
-   * some measure
+   * some measure. The options parameter provides configuration choices for how
+   * the similarity score is calculated.
    * 
    * @param seqData
+   * @param options
    * @return
    */
-  MatrixI findSimilarities(AlignmentView seqData);
+  MatrixI findSimilarities(AlignmentView seqData, SimilarityParamsI options);
 }

diff --git a/test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java b/test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java
index cd6d7f5..1ebef8e 100644 (file)
--- a/test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java
+++ b/test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java
@@ -113,9 +113,9 @@ public class FeatureDistanceModelTest
             .getAlignPanel()));
     alf.selectAllSequenceMenuItem_actionPerformed(null);
 
-    MatrixI dm = fsm
-            .findDistances(alf.getViewport().getAlignmentView(
-            true));
+    MatrixI dm = fsm.findDistances(
+            alf.getViewport().getAlignmentView(true),
+            SimilarityParams.Jalview);
     assertEquals(dm.getValue(0, 2), 0d,
             "FER1_MESCR (0) should be identical with RAPSA (2)");
     assertTrue(dm.getValue(0, 1) > dm.getValue(0, 2),
@@ -132,9 +132,9 @@ public class FeatureDistanceModelTest
     assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
             .getAlignPanel()));
     alf.selectAllSequenceMenuItem_actionPerformed(null);
-    MatrixI dm = fsm
-            .findDistances(alf.getViewport().getAlignmentView(
-            true));
+    MatrixI dm = fsm.findDistances(
+            alf.getViewport().getAlignmentView(true),
+            SimilarityParams.Jalview);
     assertEquals(dm.getValue(0, 2), 0d,
             "FER1_MESCR (0) should be identical with RAPSA (2)");
     assertTrue(dm.getValue(0, 1) > dm.getValue(0, 2),
@@ -152,9 +152,9 @@ public class FeatureDistanceModelTest
     assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
             .getAlignPanel()));
     alf.selectAllSequenceMenuItem_actionPerformed(null);
-    MatrixI dm = fsm
-            .findDistances(alf.getViewport().getAlignmentView(
-            true));
+    MatrixI dm = fsm.findDistances(
+            alf.getViewport().getAlignmentView(true),
+            SimilarityParams.Jalview);
     assertEquals(
             dm.getValue(0, 2),
             0d,
@@ -253,7 +253,7 @@ public class FeatureDistanceModelTest
     alf.selectAllSequenceMenuItem_actionPerformed(null);
 
     MatrixI distances = fsm.findDistances(alf.getViewport()
-            .getAlignmentView(true));
+            .getAlignmentView(true), SimilarityParams.Jalview);
     assertEquals(distances.width(), 2);
     assertEquals(distances.height(), 2);
     assertEquals(distances.getValue(0, 0), 0d);

diff --git a/test/jalview/analysis/scoremodels/ScoreMatrixTest.java b/test/jalview/analysis/scoremodels/ScoreMatrixTest.java
index 01de741..1076d43 100644 (file)
--- a/test/jalview/analysis/scoremodels/ScoreMatrixTest.java
+++ b/test/jalview/analysis/scoremodels/ScoreMatrixTest.java
@@ -171,7 +171,7 @@ public class ScoreMatrixTest
     String[] seqs = new String[] { "FKL", "R D", "QIA", "GWC" };
     ScoreMatrix sm = ScoreModels.getInstance().getBlosum62();
 
-    MatrixI pairwise = sm.findSimilarities(seqs);
+    MatrixI pairwise = sm.findSimilarities(seqs, SimilarityParams.Jalview);
 
     /*
      * should be NxN where N = number of sequences