Squashed initial commit

2024-09-10 13:47:29 -04:00
commit 8ebb6ad265
6221 changed files with 2512206 additions and 0 deletions
--- a/qhtcp-workflow/apps/java/weka-clustering/src/Matrix.java
+++ b/qhtcp-workflow/apps/java/weka-clustering/src/Matrix.java
@@ -0,0 +1,130 @@
+/*
+ * To change this template, choose Tools | Templates
+ * and open the template in the editor.
+ */
+
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.Iterator;
+
+/**
+ *
+ * @author DTian
+ */
+public class Matrix {
+
+    private HashMap matrix; // store data
+    private int rowSize; // row size of matrix
+    private int colSize; // column size of value array
+    private final int lookupTableSize = 9000; //size of look up table
+
+    public int getColSize() {
+        return colSize;
+    }
+
+    public void setColSize(int colSize) {
+        this.colSize = colSize;
+    }
+
+    public HashMap getMatrix() {
+        return matrix;
+    }
+
+    public void setMatrix(HashMap matrix) {
+        this.matrix = matrix;
+    }
+
+    public int getRowSize() {
+        return rowSize;
+    }
+
+    public void setRowSize(int rowSize) {
+        this.rowSize = rowSize;
+    }
+
+    public Matrix() {
+        rowSize = 0;
+        colSize = 0;
+        matrix = new HashMap();
+    }
+
+    /**
+     * constructor with 1 String parameter
+     *
+     * @param filename : the name of the input file
+     *
+     * @result: create a matrix from a input file
+     *
+     */
+    public Matrix(String filename) {
+
+        // Initialize variables
+        this.setRowSize(0);
+        this.setColSize(0);
+        matrix = new HashMap(lookupTableSize);
+
+        try {
+
+            FileReader fr = new FileReader(filename);
+            BufferedReader br = new BufferedReader(fr);
+
+            // strRow is used to read line from file(skip first row)
+            String strRow = br.readLine();
+
+            // The while loop read the data from data file to vvf
+            while ((strRow = br.readLine()) != null) {
+
+                // strArray was used to store the float value from data file in
+                // string format
+                String delimiter = "";
+                if (strRow.indexOf(",") >= 0) { //for CSV file
+                    delimiter = "\\,";
+                } else { // for whitespace delimited file
+                    delimiter = "\\s";
+                }
+
+                String[] strArray = strRow.trim().split(delimiter);
+                String[] strArrValue = Arrays.copyOfRange(strArray, 1, strArray.length);
+                // strArray[0] is the orf name, others are value
+                matrix.put(strArray[0].trim().toLowerCase(), strArrValue);
+                rowSize++;
+                colSize = strArrValue.length;
+            }
+
+            br.close();
+            fr.close();
+        } catch (IOException e) {
+            // catch possible io errors from readLine()
+            System.out.println("IOException error in  'class Matrix, constructor'");
+        }
+    }
+
+    /**
+     *
+     * @param index, the specifed key
+     * @return:  the string array of the value
+     */
+    public String[] getSpecifiedValue(Object key) {
+        return (String[]) matrix.get(key);
+    }
+
+    /**
+     * @return the list of orf names
+     */
+    public ArrayList getOrfNames() {
+        ArrayList result = new ArrayList(this.getRowSize());
+        Iterator it = matrix.keySet().iterator();
+        while (it.hasNext()) {
+            result.add(it.next());
+        }
+        return result;
+    }
+
+    public void addValue(Object key, Object value) {
+        matrix.put(key, value);
+    }
+}