Fixing some previous errors with parsing and implemented Gene Ranges for mutation searching algorithms

Author: adam-stogsdill

README.md

@@ -15,3 +15,7 @@ This program will implement the Cytogenic Location organization technique which
 ### CTFR (cystic fibrosis transmembrane conductance regulator)
 
 FIRST GENE USABLE IN PROGRAM. Located at 7q31.2. https://ghr.nlm.nih.gov/gene/CFTR#location
+
+### AAAS(aladin WD repeat nucleoporin)
+
+Located at 12q13.13. https://ghr.nlm.nih.gov/gene/AAAS#

resources/GeneDatabaseInformation/AAAS.fasta

@@ -3,6 +3,8 @@ q,
 1,
 3,
 13,
+122073544,
+122144269,
 TGAGTGGAAAACAAAAGGAAAACTTATTTATTCTTAGAGGTGGGAATGTGGGGAGTGGGGCAGAACAGGT
 GGTGGCCCTGGGAGAGGGTCCCAAGGGGCAGAGGTTGGGGATGTCTCAGTAAAGAGGGGCAGGTCATGAA
 TAGAGCCTCCACCCCCAGCAGGGGGTTCCTGGGCCCGCCCAAGCACTGGGCTAAAACGTGGAAACTGGGC

resources/GeneDatabaseInformation/ABAT.fasta

@@ -3,6 +3,8 @@ q,
 3,
 1,
 2,
+117479963,
+117668665,
 AATTGGAAGCAAATGACATCACAGCAGGTCAGAGAAAAAGGGTTGAGCGGCAGGCACCCAGAGTAGTAGG
 TCTTTGGCATTAGGAGCTTGAGCCCAGACGGCCCTAGCAGGGACCCCAGCGCCCGAGAGACCATGCAGAG
 GTCGCCTCTGGAAAAGGCCAGCGTTGTCTCCAAACTTTTTTTCAGGTGAGAAGGTGGCCAACCGAGCTTC

resources/GeneDatabaseInformation/CTFR.fasta

@@ -37,21 +37,22 @@ public Gene(String sequence, GeneCytogenicLocation loc) {
     public Gene(String sequence) {
         String[] parsed_sequence = sequence.split(",");
         try {
-            GeneCreation.check_if_Possible(parsed_sequence[5].toCharArray());
+            GeneCreation.check_if_Possible(parsed_sequence[7].toCharArray());
         } catch (GeneCreationError e) {
             e.printStackTrace();
             return;
         }
         try {
             this.loc = new GeneCytogenicLocation(Integer.valueOf(parsed_sequence[0]), parsed_sequence[1].charAt(0),
-                    Integer.valueOf(parsed_sequence[2]), Integer.valueOf(parsed_sequence[3]), Integer.valueOf(parsed_sequence[4]));
+                    Integer.valueOf(parsed_sequence[2]), Integer.valueOf(parsed_sequence[3]), Integer.valueOf(parsed_sequence[4]),
+                    Integer.valueOf(parsed_sequence[5]), Integer.valueOf(parsed_sequence[6]));
             //System.out.println(this.loc);
         }catch(GeneCreationError e){
             e.printStackTrace();
         }catch (GenomeDatabaseError e){
             e.printStackTrace();
         }
-        this.gene_information = parsed_sequence[5].toCharArray();
+        this.gene_information = parsed_sequence[7].toCharArray();
     }
 
 

src/bin/main/Gene_Main/Gene.java

@@ -16,38 +16,44 @@ public class GeneCytogenicLocation {
     private int region;
     private int band;
     private int sub_band;
+    private int start;
+    private int stop;
 
-    public GeneCytogenicLocation(int chromosome, char arm, int region, int band) throws GeneCreationError, GenomeDatabaseError {
+    public GeneCytogenicLocation(int chromosome, char arm, int region, int band, int start, int stop) throws GeneCreationError, GenomeDatabaseError {
         if (chromosome < 1 || chromosome > 23)
             throw new GeneCreationError(GENEERROR.INVALID_CHROMOSOME);
         if (arm != 'p' && arm != 'q')
             throw new GeneCreationError(GENEERROR.INVALID_ARM);
         if (!GenomeRanges.singleDigit(region) || !GenomeRanges.singleDigit(band))
             throw new GenomeDatabaseError(GenomeError.INVALID_NUMBER_LENGTH);
-        Location(chromosome, arm, region, band, 0);
+        Location(chromosome, arm, region, band, 0, start, stop);
     }
 
-    public GeneCytogenicLocation(int chromosome, char arm, int region, int band, int sub_band) throws GeneCreationError, GenomeDatabaseError {
+    public GeneCytogenicLocation(int chromosome, char arm, int region, int band, int sub_band, int start, int stop) throws GeneCreationError, GenomeDatabaseError {
         if (chromosome < 1 || chromosome > 23)
             throw new GeneCreationError(GENEERROR.INVALID_CHROMOSOME);
         if (arm != 'p' && arm != 'q')
             throw new GeneCreationError(GENEERROR.INVALID_ARM);
         if (!GenomeRanges.singleDigit(region) || !GenomeRanges.singleDigit(band) || !GenomeRanges.singleDigit(sub_band))
             throw new GenomeDatabaseError(GenomeError.INVALID_NUMBER_LENGTH);
 
-        Location(chromosome, arm, region, band, sub_band);
+        Location(chromosome, arm, region, band, sub_band, start, stop);
     }
 
-    private void Location(int chromosome, char arm, int region, int band, int sub_band){
+    private void Location(int chromosome, char arm, int region, int band, int sub_band, int start, int stop){
         this.chromosome = chromosome;
         this.arm = arm;
         this.region = region;
         this.band = band;
         this.sub_band = sub_band;
+        this.start = start;
+        this.stop = stop;
     }
 
     @Override
     public String toString(){
         return "" + chromosome + arm + region + band + "." + sub_band;
     }
+
+    public String getRange() {return "("+ this.start + "-" + this.stop+")";}
 }

src/bin/main/Gene_Main/GeneCytogenicLocation.java

@@ -29,7 +29,8 @@ public static void LoadDatabase() throws IOException, GeneCreationError {
 
     public static String printDatabase(){
         for(String s: geneDatabase.keySet()){
-            System.out.printf("Gene_Name:%s\t%s\n\t%s\n", s,geneDatabase.get(s).getCytogenicLocation().toString(), geneDatabase.get(s));
+            System.out.printf("Gene_Name:%s\t%s\tRange:%s\n\t%s\n", s,geneDatabase.get(s).getCytogenicLocation().toString(), geneDatabase.get(s).getCytogenicLocation().getRange()
+                    , geneDatabase.get(s));
         }
         return "";
     }

src/bin/main/Gene_Main/GeneDatabase.java

@@ -19,6 +19,7 @@ public class GenomeDatabaseMain {
     National Center for Biotechnology Information
      */
     public static void LoadDatabase() {
+        //TODO FIX LOADING
         try {
             BufferedReader bf = new BufferedReader(new FileReader("resources/GenomeRanges"));
             String string;

src/bin/main/GenomeDatabaseInformation/GenomeDatabaseMain.java

@@ -30,7 +30,7 @@ public static void main(String[] args) {
 
         j.setVisible(true);*/
 
-        GenomeDatabaseMain.LoadDatabase();
+        //GenomeDatabaseMain.LoadDatabase();
 
         //Gene g = new Gene("RACTA");