ART-2a and ART-2a-Euclid classes consolidated

JonasSchaub · Feb 9, 2025 · 28342d9 · 28342d9
1 parent 96ccc01
commit 28342d9
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Showing 11 changed files with 995 additions and 1,653 deletions.
diff --git a/src/main/java/de/unijena/cheminf/clustering/art2a/Art2aData.java b/src/main/java/de/unijena/cheminf/clustering/art2a/Art2aData.java
@@ -75,7 +75,7 @@ public class Art2aData {
      * Min-max components of original data matrix (see method 
      * Art2aUtils.getMinMaxComponents() for data structure)
      */
-    private final Art2aUtils.MinMaxValue[] minMaxComponentsOfDataMatrix;
+    private final Utils.MinMaxValue[] minMaxComponentsOfDataMatrix;
     /**
      * Offset for contrast enhancement
      */
@@ -114,7 +114,7 @@ private Art2aData (
         float[][] aDataMatrix,        
         float[][] aContrastEnhancedUnitMatrix,
         boolean[] aDataVectorZeroLengthFlags,
-        Art2aUtils.MinMaxValue[] aMinMaxComponentsOfDataMatrix,
+        Utils.MinMaxValue[] aMinMaxComponentsOfDataMatrix,
         float anOffsetForContrastEnhancement,
         boolean aHasPreprocessedData
     ) {
@@ -140,7 +140,7 @@ private Art2aData (
      */
     protected Art2aData (
         float[][] aDataMatrix, 
-        Art2aUtils.MinMaxValue[] aMinMaxComponentsOfDataMatrix,
+        Utils.MinMaxValue[] aMinMaxComponentsOfDataMatrix,
         float anOffsetForContrastEnhancement
     ) {
         this (
@@ -151,7 +151,7 @@ protected Art2aData (
             anOffsetForContrastEnhancement,
             false
         );
-        if (!Art2aUtils.isMatrixValid(aDataMatrix)) {
+        if (!Utils.isMatrixValid(aDataMatrix)) {
             Art2aData.LOGGER.log(
                 Level.SEVERE, 
                 "Art2aData.Constructor: aDataMatrix is invalid."
@@ -193,7 +193,7 @@ protected Art2aData (
     protected Art2aData (
         float[][] aContrastEnhancedUnitMatrix,
         boolean[] aDataVectorZeroLengthFlags,
-        Art2aUtils.MinMaxValue[] aMinMaxComponentsOfDataMatrix,
+        Utils.MinMaxValue[] aMinMaxComponentsOfDataMatrix,
         float anOffsetForContrastEnhancement
     ) {
         this (
@@ -204,7 +204,7 @@ protected Art2aData (
             anOffsetForContrastEnhancement,
             true
         );
-        if (!Art2aUtils.isMatrixValid(aContrastEnhancedUnitMatrix)) {
+        if (!Utils.isMatrixValid(aContrastEnhancedUnitMatrix)) {
             Art2aData.LOGGER.log(
                 Level.SEVERE, 
                 "Art2aData.Constructor: aContrastEnhancedUnitMatrix is invalid."
@@ -269,12 +269,11 @@ protected boolean[] getDataVectorZeroLengthFlags() {
     }
 
     /**
-     * Min-max components of original data matrix (see method 
-     * Art2aUtils.getMinMaxComponents() for data structure)
+     * Min-max components of original data matrix (see method Utils.getMinMaxComponents() for data structure)
      * 
      * @return Min-max components of original data matrix
      */
-    protected Art2aUtils.MinMaxValue[] getMinMaxComponentsOfDataMatrix() {
+    protected Utils.MinMaxValue[] getMinMaxComponentsOfDataMatrix() {
         return this.minMaxComponentsOfDataMatrix;
     }
 

diff --git a/src/main/java/de/unijena/cheminf/clustering/art2a/Art2aEuclidData.java b/src/main/java/de/unijena/cheminf/clustering/art2a/Art2aEuclidData.java
@@ -74,9 +74,9 @@ public class Art2aEuclidData {
     private final boolean[] dataVectorZeroLengthFlags;
     /**
      * Min-max components of original data matrix (see method 
-     * Art2aEuclidUtils.getMinMaxComponents() for data structure)
+     * Utils.getMinMaxComponents() for data structure)
      */
-    private final Art2aEuclidUtils.MinMaxValue[] minMaxComponentsOfDataMatrix;
+    private final Utils.MinMaxValue[] minMaxComponentsOfDataMatrix;
     /**
      * Offset for contrast enhancement
      */
@@ -115,7 +115,7 @@ private Art2aEuclidData (
         float[][] aDataMatrix,        
         float[][] aContrastEnhancedMatrix,
         boolean[] aDataVectorZeroLengthFlags,
-        Art2aEuclidUtils.MinMaxValue[] aMinMaxComponentsOfDataMatrix,
+        Utils.MinMaxValue[] aMinMaxComponentsOfDataMatrix,
         float anOffsetForContrastEnhancement,
         boolean aHasPreprocessedData
     ) {
@@ -141,7 +141,7 @@ private Art2aEuclidData (
      */
     protected Art2aEuclidData (
         float[][] aDataMatrix, 
-        Art2aEuclidUtils.MinMaxValue[] aMinMaxComponentsOfDataMatrix,
+        Utils.MinMaxValue[] aMinMaxComponentsOfDataMatrix,
         float anOffsetForContrastEnhancement
     ) {
         this (
@@ -152,7 +152,7 @@ protected Art2aEuclidData (
             anOffsetForContrastEnhancement,
             false
         );
-        if (!Art2aEuclidUtils.isMatrixValid(aDataMatrix)) {
+        if (!Utils.isMatrixValid(aDataMatrix)) {
             Art2aEuclidData.LOGGER.log(
                 Level.SEVERE, 
                 "Art2aEuclidData.Constructor: aDataMatrix is invalid."
@@ -194,7 +194,7 @@ protected Art2aEuclidData (
     protected Art2aEuclidData (
         float[][] aContrastEnhancedMatrix,
         boolean[] aDataVectorZeroLengthFlags,
-        Art2aEuclidUtils.MinMaxValue[] aMinMaxComponentsOfDataMatrix,
+        Utils.MinMaxValue[] aMinMaxComponentsOfDataMatrix,
         float anOffsetForContrastEnhancement
     ) {
         this (
@@ -205,7 +205,7 @@ protected Art2aEuclidData (
             anOffsetForContrastEnhancement,
             true
         );
-        if (!Art2aEuclidUtils.isMatrixValid(aContrastEnhancedMatrix)) {
+        if (!Utils.isMatrixValid(aContrastEnhancedMatrix)) {
             Art2aEuclidData.LOGGER.log(
                 Level.SEVERE, 
                 "Art2aEuclidData.Constructor: aContrastEnhancedMatrix is invalid."
@@ -270,12 +270,11 @@ protected boolean[] getDataVectorZeroLengthFlags() {
     }
 
     /**
-     * Min-max components of original data matrix (see method 
- Art2aEuclidUtils.getMinMaxComponents() for data structure)
+     * Min-max components of original data matrix (see method Utils.getMinMaxComponents() for data structure)
      * 
      * @return Min-max components of original data matrix
      */
-    protected Art2aEuclidUtils.MinMaxValue[] getMinMaxComponentsOfDataMatrix() {
+    protected Utils.MinMaxValue[] getMinMaxComponentsOfDataMatrix() {
         return this.minMaxComponentsOfDataMatrix;
     }