--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/KinaMine-Galaxy-7-7/src/kinamine/Reporter.java	Tue Feb 20 14:31:15 2018 -0500
@@ -0,0 +1,236 @@
+/**
+ *****************************************************************************
+ * <p>
+ * Copyright (c) Regents of the University of Minnesota. All Rights Reserved.
+ * <p>
+ * Author: Kevin Murray University of Minnesota - (murra668@umn.edu)
+ * <p>
+ *****************************************************************************
+ */
+package kinamine;
+
+import java.io.*;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Map.Entry;
+import java.util.Set;
+import javafx.util.Pair;
+
+/**
+ * Reporter class to write reports. Currently writes out in .csv format.
+ *
+ * @version 1.0
+ * @author murra668
+ * new author: blank121@umn.edu as of August 2017
+ */
+public class Reporter {
+
+    /**
+     * Write reports for run.
+     *
+     * @param run
+     * @param outPath
+     * @param outGroup
+     */
+    static void writeReports(Run run, String outPath, String outGroup) {
+
+        /** Write substrates report. */
+        String outputFileSub = outPath + outGroup + "_Substrates.csv";
+        Reporter.substrates(run, outputFileSub);
+
+        /** Write substrate background frequency report. */
+        String outputFileFreq = outPath + outGroup + "_SubBackFreq.csv";
+        Reporter.frequencies(run, outputFileFreq);
+
+    }
+
+    /**
+     * Writes substrates report from the ids and motifs of each peptide.
+     *
+     * @param run
+     * @param outputFileName
+     */
+    private static void substrates(Run run, String outputFileName) {
+
+        /** Format header */
+//        String header = "Substrates," + "Species," + "Reference," + "-7," + "-6,"
+//                + "-5," + "-4," + "-3," + "-2," + "-1," + "0," + "1,"
+//                + "2," + "3," + "4," + "5," + "6," + "7," + "Phosphite"
+//                + "\n";
+        String header = "Substrates," + "Species," + "Reference," + "-7," + "-6,"
+                + "-5," + "-4," + "-3," + "-2," + "-1," + "0," + "1,"
+                + "2," + "3," + "4," + "5," + "6," + "7," 
+                +" ," +" ,"+ " ,"+ "Phosphite"
+                + "\n";
+
+        /** Initialize details */
+        String detail = null;
+
+        try (FileWriter writer = new FileWriter(outputFileName)) {
+
+            /* Write the column headers */
+            writer.append(header);
+
+           Collection<Motif> motifs = run.motifs.values();
+
+            /** Loop through each motif */
+            for (Motif motif : motifs) {
+
+                /** Format ID and blanks */
+                detail = "," + "," + motif.ref + ",";
+
+                String seq = motif.seq;
+                int index = motif.index;
+//changing the numbers for index only changed where in the excel doc these motifs
+//showed up
+//I should fuck with this and try to reallign it
+//I should do that now
+                if (index < 8) {
+                    for (int i = index; i < 8; i++) {
+                        detail += ",";
+                    }
+                    for (int j = 0; j < seq.length(); j++) {
+                        detail += seq.charAt(j) + ",";
+                    }
+                    if (seq.length() - index < 7) {
+                        for (int i = seq.length() - index; i < 7; i++) {
+                            detail += ",";
+                        }
+                    }
+                } else if (seq.length() < 15) {
+                    for (int j = 0; j < seq.length(); j++) {
+                        detail += seq.charAt(j) + ",";
+                    }
+                    for (int i = seq.length(); i < 15; i++) {
+                        detail += ",";
+                    }
+
+                } else {
+                    for (int j = 0; j < seq.length(); j++) {
+                        detail += seq.charAt(j) + ",";
+                    }
+                }
+
+//
+//                if (index < 5) {
+//                    for (int i = index; i < 5; i++) {
+//                        detail += ",";
+//                    }
+//                    for (int j = 0; j < seq.length(); j++) {
+//                        detail += seq.charAt(j) + ",";
+//                    }
+//                    if (seq.length() - index < 4) {
+//                        for (int i = seq.length() - index; i < 4; i++) {
+//                            detail += ",";
+//                        }
+//                    }
+//                } else if (seq.length() < 9) {
+//                    for (int j = 0; j < seq.length(); j++) {
+//                        detail += seq.charAt(j) + ",";
+//                    }
+//                    for (int i = seq.length(); i < 9; i++) {
+//                        detail += ",";
+//                    }
+//
+//                } else {
+//                    for (int j = 0; j < seq.length(); j++) {
+//                        detail += seq.charAt(j) + ",";
+//                    }
+//                }
+////////////////////////////////////////////////////////////////////////////////
+                /** Format trailing blanks */
+                detail += "," + "," + "," + seq + ",";
+                
+                for (String id : motif.regenSeqs){
+                    detail += id + ",";
+                }
+                detail += "\n";
+
+                /** Append each line of the report. */
+                writer.append(detail);
+            }
+
+            writer.flush();
+            writer.close();
+
+        } catch (IOException e) {
+            e.printStackTrace();
+        }
+    }
+
+    /**
+     * Write substrates background frequency report from each protein in the
+     * database.
+     *
+     * @param run
+     * @param outputFileName
+     */
+    private static void frequencies(Run run, String outputFileName) {
+
+        /** Initialize the header */
+        StringBuffer header = new StringBuffer();
+        header.append("Amino Acids,");
+
+        /** Write each protein accession. */
+        Object[] prots = run.database.keySet().toArray();
+        for (Object ref : prots) {
+            header.append(ref).append(",");
+        }
+        header.append("\n");
+
+        try (FileWriter writer = new FileWriter(outputFileName)) {
+
+            /* Write the column headers. */
+            writer.append(header);
+
+            Collection<Protein> proteins = run.database.values();
+
+            /** Write frequency of each amino acid. */
+            for (char acid : AminoAcid.ACIDS) {
+                StringBuffer detail = new StringBuffer();
+                detail.append(acid).append(",");
+                for (Protein protein : proteins) {
+                    detail.append(protein.comp.get(acid)).append(",");
+                }
+                detail.append("\n");
+                writer.append(detail);
+            }
+
+            writer.append("Properties\n");
+
+            /** Write the property frequency of each amino acid. */
+            for (String prop : AminoAcid.PROPS) {
+                StringBuffer props = new StringBuffer();
+                props.append(prop).append(",");
+                for (Protein protein : proteins) {
+                    props.append(protein.props.get(prop)).append(",");
+                }
+                props.append("\n");
+                writer.append(props);
+            }
+
+            writer.append("\n");
+
+            StringBuffer tyr = new StringBuffer("Number of Y,");
+            StringBuffer phosphTyr = new StringBuffer("Number of pY,");
+            StringBuffer aa = new StringBuffer("Total AAs,");
+
+            /** Write the number of tyrosine, phospho-tyrosine, and length. */
+            for (Protein protein : proteins) {
+                tyr.append(protein.numTyr).append(",");
+                phosphTyr.append(protein.phosphoTyr).append(",");
+                aa.append(protein.seq.length()).append(",");
+            }
+
+            writer.append(tyr + "\n");
+            writer.append(phosphTyr + "\n");
+            writer.append(aa + "\n");
+
+            writer.flush();
+            writer.close();
+
+        } catch (IOException e) {
+            e.printStackTrace();
+        }
+    }
+}