Smiles importer test for improvements

src/main/java/de/unijena/cheminf/mortar/model/io/DynamicSMILESFileFormat.java

@@ -0,0 +1,163 @@
+/*
+ * MORTAR - MOlecule fRagmenTAtion fRamework
+ * Copyright (C) 2024  Felix Baensch, Jonas Schaub (felix.baensch@w-hs.de, jonas.schaub@uni-jena.de)
+ *
+ * Source code is available at <https://github.com/FelixBaensch/MORTAR>
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in all
+ * copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ */
+
+package de.unijena.cheminf.mortar.model.io;
+
+/**
+ * Data wrapper for defining the outline of a SMILES file or CSV file containing SMILES codes.
+ *
+ * @author Jonas Schaub
+ * @version 1.0.0.0
+ */
+public class DynamicSMILESFileFormat {
+    //<editor-fold desc="public static final class constants">
+    /**
+     * Placeholder separator char for files that have only one column.
+     */
+    public static final Character PLACEHOLDER_SEPARATOR_CHAR = '0';
+    //
+    /**
+     * Placeholder ID column position for files without an ID column.
+     */
+    public static final int PLACEHOLDER_ID_COLUMN_POSITION = -1;
+    //
+    /**
+     * Default SMILES column position for files with only one column.
+     */
+    public static final int DEFAULT_SMILES_COLUMN_POSITION = 0;
+    //</editor-fold>
+    //
+    //<editor-fold desc="private final class constants">
+    /**
+     * Whether the file has a headline that needs to be skipped while parsing or not.
+     */
+    private final boolean hasHeaderLine;
+    //
+    /**
+     * Character separating the columns of the file.
+     */
+    private final Character separatorChar;
+    //
+    /**
+     * Position of the column whose elements should be parsed as SMILES strings.
+     */
+    private final int smilesCodeColumnPosition;
+    //
+    /**
+     * Whether the file has an ID column or not.
+     */
+    private final boolean hasIDColumn;
+    //
+    /**
+     * Position of the column whose elements should be parsed as IDs of the structures.
+     */
+    private final int idColumnPosition;
+    //</editor-fold>
+    //
+    //<editor-fold desc="Constructors">
+    /**
+     * Defines the format as a file that has only one column of SMILES codes and nothing else, so no ID column and no
+     * separator character.
+     * All other fields will be set to their placeholder values.
+     *
+     * @param aHasHeaderLine whether the first line in the file is a header or contains a valid SMILES code as well
+     */
+    public DynamicSMILESFileFormat(boolean aHasHeaderLine) {
+        this(aHasHeaderLine, DynamicSMILESFileFormat.PLACEHOLDER_SEPARATOR_CHAR,
+                DynamicSMILESFileFormat.DEFAULT_SMILES_COLUMN_POSITION,
+                DynamicSMILESFileFormat.PLACEHOLDER_ID_COLUMN_POSITION);
+    }
+    //
+    /**
+     * Defines the format as a file that has at least two columns, defines the character that separates the columns, the
+     * position of the SMILES code column and the ID/name column, and whether the first line in the file is a header or
+     * contains a valid SMILES code as well.
+     * <br>No parameter checks to keep this data container flexible and be able to use the placeholder values here as well, so be careful!
+     *
+     * @param aHasHeaderLine whether the first line in the file is a header or contains a valid SMILES code as well
+     * @param aSeparatorChar character that separates the columns
+     * @param aSMILESCodeColumnPosition position of the SMILES code column
+     * @param anIDColumnPosition position of the ID/name column
+     */
+    public DynamicSMILESFileFormat(boolean aHasHeaderLine, Character aSeparatorChar, int aSMILESCodeColumnPosition, int anIDColumnPosition) {
+        this.hasHeaderLine = aHasHeaderLine;
+        this.separatorChar = aSeparatorChar;
+        this.smilesCodeColumnPosition = aSMILESCodeColumnPosition;
+        this.hasIDColumn = anIDColumnPosition != DynamicSMILESFileFormat.PLACEHOLDER_ID_COLUMN_POSITION;
+        this.idColumnPosition = anIDColumnPosition;
+    }
+    //</editor-fold>
+    //
+    //<editor-fold desc="properties get">
+    /**
+     * Whether the first line in the file is a header or contains a valid SMILES code as well.
+     *
+     * @return whether the first line of the file should be parsed as well or skipped
+     */
+    public boolean hasHeaderLine() {
+        return this.hasHeaderLine;
+    }
+    //
+    /**
+     * Character that separates the columns. If the file has only one column, this field will be set to its placeholder
+     * value (check whether the file has an ID/name column).
+     *
+     * @return character separating the columns
+     */
+    public Character getSeparatorChar() {
+        return this.separatorChar;
+    }
+    //
+    /**
+     * Position of the SMILES column in the file.
+     *
+     * @return position of SMILES column
+     */
+    public int getSMILESCodeColumnPosition() {
+        return this.smilesCodeColumnPosition;
+    }
+    //
+    /**
+     * Whether the file has an additional column containing names/IDs of the structures. If false, it can be assumed that
+     * the files has only one column, the SMILES column. The separator character and the ID column position will be set
+     * to their placeholder values.
+     *
+     * @return whether the file has an additional column containing names/IDs of the structures
+     */
+    public boolean hasIDColumn() {
+        return this.hasIDColumn;
+    }
+    //
+    /**
+     * Position of the ID/name column in the file. If the file has only one column, this field will be set to its placeholder
+     * value (check whether the file has an ID/name column).
+     *
+     * @return position of ID/name column
+     */
+    public int getIDColumnPosition() {
+        return this.idColumnPosition;
+    }
+    //</editor-fold>
+}