Applying adjustablenw_params.patch (JAL-4159)

diff --git a/.gitignore b/.gitignore
index 59c4a99..4a81616 100644 (file)
--- a/.gitignore
+++ b/.gitignore
@@ -17,6 +17,7 @@ TESTNG
 /jalviewApplet.jar
 /benchmarking/lib
 *.class
+*.patch
 /site
 /site-resources
 /libjs

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index fa90f74..d394024 100755 (executable)
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -20,8 +20,6 @@
  */
 package jalview.analysis;
 
-import java.util.Locale;
-
 import jalview.analysis.scoremodels.PIDModel;
 import jalview.analysis.scoremodels.ScoreMatrix;
 import jalview.analysis.scoremodels.ScoreModels;
@@ -46,10 +44,9 @@ import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
 import java.util.StringTokenizer;
+import java.util.Locale;
 
 /**
- * 
- * 
  * @author $author$
  * @version $Revision$
  */
@@ -57,12 +54,13 @@ public class AlignSeq
 {
   private static final int MAX_NAME_LENGTH = 30;
 
-  //&!
-  //private static final int GAP_OPEN_COST = 120;
-  private static final int GAP_OPEN_COST = 100;
+  private static final int DEFAULT_OPENCOST = 120;
+
+  private static final int DEFAULT_EXTENDCOST = 20;
+  
+  private int GAP_OPEN_COST=DEFAULT_OPENCOST;
 
-  //private static final int GAP_EXTEND_COST = 20;
-  private static final int GAP_EXTEND_COST = 5;
+  private int GAP_EXTEND_COST=DEFAULT_EXTENDCOST;
 
   private static final int GAP_INDEX = -1;
 
@@ -156,12 +154,12 @@ public class AlignSeq
   /**
    * Creates a new AlignSeq object.
    * 
-   * @param s1
-   *          DOCUMENT ME!
-   * @param s2
-   *          DOCUMENT ME!
+   * @param s1,string1
+   *          s1 reference sequence for string1
+   * @param s2,string2
+   *          s2 reference sequence for string2
    * @param type
-   *          DOCUMENT ME!
+   *          molecule type, either AlignSeq.PEP or AlignSeq.DNA
    */
   public AlignSeq(SequenceI s1, String string1, SequenceI s2,
           String string2, String type)
@@ -170,6 +168,23 @@ public class AlignSeq
             string2.toUpperCase(Locale.ROOT), type);
   }
 
+  public AlignSeq(SequenceI s1, SequenceI s2, String type, int opencost,
+          int extcost)
+  {
+    this(s1,s2,type);
+    GAP_OPEN_COST=opencost;
+    GAP_EXTEND_COST=extcost;
+  }
+
+  public AlignSeq(SequenceI s12, String string1, SequenceI s22,
+          String string2, String type2, int defaultOpencost,
+          int defaultExtendcost)
+  {
+    this(s12,string1,s22,string2,type2);
+    GAP_OPEN_COST=defaultOpencost;
+    GAP_EXTEND_COST=defaultExtendcost;
+  }
+
   /**
    * DOCUMENT ME!
    * 
@@ -325,6 +340,13 @@ public class AlignSeq
   public void seqInit(SequenceI s1, String string1, SequenceI s2,
           String string2, String type)
   {
+    seqInit(s1,string1,s2,string2,type,GAP_OPEN_COST,GAP_EXTEND_COST);
+  }
+  public void seqInit(SequenceI s1, String string1, SequenceI s2,
+          String string2, String type, int opening,int extension)
+  {
+    GAP_OPEN_COST=opening;
+    GAP_EXTEND_COST=extension;
     this.s1 = s1;
     this.s2 = s2;
     setDefaultParams(type);
@@ -791,25 +813,26 @@ public class AlignSeq
   {
     int n = seq1.length;
     int m = seq2.length;
-
+    final int GAP_EX_COST=GAP_EXTEND_COST;
+    final int GAP_OP_COST = GAP_OPEN_COST;
     // top left hand element
     score[0][0] = scoreMatrix.getPairwiseScore(s1str.charAt(0),
             s2str.charAt(0)) * 10;
-    E[0][0] = -GAP_EXTEND_COST;
+    E[0][0] = -GAP_EX_COST;
     F[0][0] = 0;
 
     // Calculate the top row first
     for (int j = 1; j < m; j++)
     {
       // What should these values be? 0 maybe
-      E[0][j] = max(score[0][j - 1] - GAP_OPEN_COST,
-              E[0][j - 1] - GAP_EXTEND_COST);
-      F[0][j] = -GAP_EXTEND_COST;
+      E[0][j] = max(score[0][j - 1] - GAP_OP_COST,
+              E[0][j - 1] - GAP_EX_COST);
+      F[0][j] = -GAP_EX_COST;
 
       float pairwiseScore = scoreMatrix.getPairwiseScore(s1str.charAt(0),
               s2str.charAt(j));
-      score[0][j] = max(pairwiseScore * 10, -GAP_OPEN_COST,
-              -GAP_EXTEND_COST);
+      score[0][j] = max(pairwiseScore * 10, -GAP_OP_COST,
+              -GAP_EX_COST);
 
       traceback[0][j] = 1;
     }
@@ -817,9 +840,9 @@ public class AlignSeq
     // Now do the left hand column
     for (int i = 1; i < n; i++)
     {
-      E[i][0] = -GAP_OPEN_COST;
-      F[i][0] = max(score[i - 1][0] - GAP_OPEN_COST,
-              F[i - 1][0] - GAP_EXTEND_COST);
+      E[i][0] = -GAP_OP_COST;
+      F[i][0] = max(score[i - 1][0] - GAP_OP_COST,
+              F[i - 1][0] - GAP_EX_COST);
 
       float pairwiseScore = scoreMatrix.getPairwiseScore(s1str.charAt(i),
               s2str.charAt(0));
@@ -832,10 +855,10 @@ public class AlignSeq
     {
       for (int j = 1; j < m; j++)
       {
-        E[i][j] = max(score[i][j - 1] - GAP_OPEN_COST,
-                E[i][j - 1] - GAP_EXTEND_COST);
-        F[i][j] = max(score[i - 1][j] - GAP_OPEN_COST,
-                F[i - 1][j] - GAP_EXTEND_COST);
+        E[i][j] = max(score[i][j - 1] - GAP_OP_COST,
+                E[i][j - 1] - GAP_EX_COST);
+        F[i][j] = max(score[i - 1][j] - GAP_OP_COST,
+                F[i - 1][j] - GAP_EX_COST);
 
         float pairwiseScore = scoreMatrix.getPairwiseScore(s1str.charAt(i),
                 s2str.charAt(j));
@@ -1013,7 +1036,13 @@ public class AlignSeq
   public static AlignSeq doGlobalNWAlignment(SequenceI s1, SequenceI s2,
           String type)
   {
-    AlignSeq as = new AlignSeq(s1, s2, type);
+    return doGlobalNWAlignment(s1, s2, type, DEFAULT_OPENCOST,DEFAULT_EXTENDCOST);
+  }
+  public static AlignSeq doGlobalNWAlignment(SequenceI s1, SequenceI s2,
+          String type, int opencost,int extcost)
+  {
+  
+    AlignSeq as = new AlignSeq(s1, s2, type,opencost,extcost);
 
     as.calcScoreMatrix();
     as.traceAlignment();

diff --git a/src/jalview/analysis/PaSiMap.java b/src/jalview/analysis/PaSiMap.java
index 4a670bf..ca49dc8 100755 (executable)
--- a/src/jalview/analysis/PaSiMap.java
+++ b/src/jalview/analysis/PaSiMap.java
@@ -202,7 +202,7 @@ public class PaSiMap implements Runnable
   {
     try
     {
-      PairwiseAlignPanel alignment = new PairwiseAlignPanel(seqs, true);
+      PairwiseAlignPanel alignment = new PairwiseAlignPanel(seqs, true, 100, 5);
       float[][] scores = alignment.getAlignmentScores();       //bigger index first -- eg scores[14][13]
 
       Hashtable<SequenceI, Integer> connectivity = seqs.calculateConnectivity(scores, dim);

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 3deb8e0..49bd4e9 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -3787,7 +3787,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     else
     {
       JInternalFrame frame = new JInternalFrame();
-      frame.setContentPane(new PairwiseAlignPanel(viewport, false));
+      frame.setContentPane(new PairwiseAlignPanel(viewport));
       Desktop.addInternalFrame(frame,
               MessageManager.getString("action.pairwise_alignment"), 600,
               500);

diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index fafee94..a499365 100755 (executable)
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -47,6 +47,10 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
 
   private float[][] alignmentScores;   // scores used by PaSiMap
 
+  private int GAP_OPEN_COST;
+
+  private int GAP_EXTEND_COST;
+
   AlignmentViewport av;
 
   Vector<SequenceI> sequences;
@@ -60,9 +64,9 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
    */
   public PairwiseAlignPanel(AlignmentViewport viewport)
   {
-    this(viewport, false);
+    this(viewport, false, 120, 20);    // default penalties used in AlignSeq
   }
-  public PairwiseAlignPanel(AlignmentViewport viewport, boolean endGaps)
+  public PairwiseAlignPanel(AlignmentViewport viewport, boolean endGaps, int gapOpenCost, int gapExtendCost)
   {
     super();
     this.av = viewport;
@@ -104,7 +108,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
       for (int j = 0; j < i; j++)
       {
         AlignSeq as = new AlignSeq(seqs[i], seqStrings[i], seqs[j],
-                seqStrings[j], type);
+                seqStrings[j], type, gapOpenCost, gapExtendCost);
 
         if (as.s1str.length() == 0 || as.s2str.length() == 0)
         {

diff --git a/test/jalview/analysis/AlignSeqTest.java b/test/jalview/analysis/AlignSeqTest.java
index a9a9730..03bdd0b 100644 (file)
--- a/test/jalview/analysis/AlignSeqTest.java
+++ b/test/jalview/analysis/AlignSeqTest.java
@@ -76,4 +76,16 @@ public class AlignSeqTest
     String s = "aArRnNzZxX *.-?";
     assertArrayEquals(expected, as.indexEncode(s));
   }
+  @Test(groups= {"Functional"})
+  public void testGlobalAlignment()
+  {
+    String seq1="CAGCTAGCG",seq2="CCATACGA";
+    Sequence sq1=new Sequence("s1",seq1),sq2=new Sequence("s2",seq2);
+    // AlignSeq doesn't report the unaligned regions at either end of sequences
+    //String alseq1="-CAGCTAGCG-",alseq2="CCA--TA-CGA";
+    // so we check we have the aligned segment correct only
+    String alseq1="CAGCTAGCG",alseq2="CA--TA-CG";
+    AlignSeq as = AlignSeq.doGlobalNWAlignment(sq1,sq2,AlignSeq.DNA);
+    assertEquals(as.getAStr1()+"\n"+as.getAStr2(),alseq1+"\n"+alseq2);
+  }
 }

diff --git a/test/jalview/gui/PairwiseAlignmentPanelTest.java b/test/jalview/gui/PairwiseAlignmentPanelTest.java
index 34e5877..750698a 100644 (file)
--- a/test/jalview/gui/PairwiseAlignmentPanelTest.java
+++ b/test/jalview/gui/PairwiseAlignmentPanelTest.java
@@ -55,7 +55,7 @@ public class PairwiseAlignmentPanelTest
     sg.setEndRes(35);
     viewport.setSelectionGroup(sg);
 
-    PairwiseAlignPanel testee = new PairwiseAlignPanel(viewport, false);
+    PairwiseAlignPanel testee = new PairwiseAlignPanel(viewport);
 
     String text = ((JTextArea) PA.getValue(testee, "textarea")).getText();
     String expected = "Score = 80.0\n" + "Length of alignment = 4\n"
@@ -80,7 +80,7 @@ public class PairwiseAlignmentPanelTest
             DataSourceType.PASTE);
     AlignViewport viewport = af.getViewport();
 
-    PairwiseAlignPanel testee = new PairwiseAlignPanel(viewport, false);
+    PairwiseAlignPanel testee = new PairwiseAlignPanel(viewport);
 
     String text = ((JTextArea) PA.getValue(testee, "textarea")).getText();
     String expected = "Score = 80.0\n" + "Length of alignment = 4\n"