move setState to TaxaCharacterMatrix<T> #512

LinguaPhylo · Jul 31, 2024 · 17da944 · 17da944
1 parent 76fed0a
commit 17da944
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Showing 5 changed files with 17 additions and 3 deletions.
diff --git a/lphy-base/src/main/java/lphy/base/evolution/alignment/Alignment.java b/lphy-base/src/main/java/lphy/base/evolution/alignment/Alignment.java
@@ -62,7 +62,7 @@ default SequenceType dataType() {
      * @param position   the site position in the 2nd dimension.
      * @param state      the state in integer
      */
-    void setState(int taxon, int position, int state);
+    void setState(int taxon, int position, Integer state);
 
     /**
      * @param taxon      the name of the taxon.

diff --git a/lphy-base/src/main/java/lphy/base/evolution/alignment/ContinuousCharacterData.java b/lphy-base/src/main/java/lphy/base/evolution/alignment/ContinuousCharacterData.java
@@ -20,10 +20,16 @@ public ContinuousCharacterData(Taxa taxa, Double[][] continuousCharacterData) {
         this.continuousCharacterData = continuousCharacterData;
     }
 
+    @Override
     public Double getState(String taxonName, int column) {
         return continuousCharacterData[taxa.indexOfTaxon(taxonName)][column];
     }
 
+    @Override
+    public void setState(int taxon, int position, Double state) {
+        continuousCharacterData[taxon][position] = state;
+    }
+
     public Double getState(int taxonIndex, int column) {
         return continuousCharacterData[taxonIndex][column];
     }

diff --git a/lphy-base/src/main/java/lphy/base/evolution/alignment/FastaAlignment.java b/lphy-base/src/main/java/lphy/base/evolution/alignment/FastaAlignment.java
@@ -46,7 +46,7 @@ public String getFileType() {
 
 
     @Override
-    public void setState(int taxon, int position, int state) {
+    public void setState(int taxon, int position, Integer state) {
         throw new UnsupportedOperationException("Unsupported for FastaAlignment !");
     }
 

diff --git a/lphy-base/src/main/java/lphy/base/evolution/alignment/SimpleAlignment.java b/lphy-base/src/main/java/lphy/base/evolution/alignment/SimpleAlignment.java
@@ -47,7 +47,7 @@ public SimpleAlignment(int nchar, Alignment source) {
      * @param position   the site position in the 2nd dimension of {@link #alignment}.
      * @param state      the state in integer
      */
-    public void setState(int taxon, int position, int state) {
+    public void setState(int taxon, int position, Integer state) {
         if (sequenceType == null)
             throw new IllegalArgumentException("Please define SequenceType, not numStates !");
         // TODO how to distinguish imported alignment and simulated

diff --git a/lphy-base/src/main/java/lphy/base/evolution/alignment/TaxaCharacterMatrix.java b/lphy-base/src/main/java/lphy/base/evolution/alignment/TaxaCharacterMatrix.java
@@ -15,6 +15,14 @@ public interface TaxaCharacterMatrix<T> extends NChar, HasTaxa, MultiDimensional
      */
     T getState(String taxon, int characterColumn);
 
+    /**
+     * Set int states.
+     * @param taxon      the index of taxon in the 1st dimension.
+     * @param position   the site position in the 2nd dimension.
+     * @param state      the state in integer
+     */
+    void setState(int taxon, int position, T state);
+
     /**
      * @return the class of this character (e.g. Double for continuous characters, Integer for discrete characters)
      */