modified family_circle_plotter.java

martin-g · May 20, 2011 · 5972eb0 · 5972eb0
1 parent 1c25a42
commit 5972eb0
Showing 1 changed file with 11 additions and 11 deletions.
diff --git a/downstream_analyses/family_circle_plotter.java b/downstream_analyses/family_circle_plotter.java
@@ -7,10 +7,10 @@
 import java.awt.image.BufferedImage;
 
 public class family_circle_plotter{
-Hashtable gene_feat;
-Hashtable chr_len;
-Hashtable syn_pair;
-Hashtable syn_gene;
+Hashtable<String, String> gene_feat; 
+Hashtable<String, String> chr_len;   
+Hashtable<String, Integer> syn_pair;
+Hashtable<String, Integer> syn_gene;
 Vector <String>  member;
 Vector <String> family_pair;
 Vector <Integer> index;
@@ -27,8 +27,8 @@ public void read_gff(String fpath)
   FileInputStream fstream = new FileInputStream(fpath);
   DataInputStream in = new DataInputStream(fstream);
   BufferedReader br = new BufferedReader(new InputStreamReader(in));
-  gene_feat=new Hashtable();
-  chr_len=new Hashtable();
+  gene_feat=new Hashtable<String, String>();
+  chr_len=new Hashtable<String, String>();  
   String strLine;
   while ((strLine = br.readLine()) != null)   
     {
@@ -62,8 +62,8 @@ public void read_synteny(String fpath)
   gene1=new Vector <String>();
   gene2=new Vector <String>();
   Ks= new Vector <Float>();
-  syn_gene=new Hashtable();
-  syn_pair=new Hashtable();
+  syn_gene=new Hashtable<String, Integer>();
+  syn_pair=new Hashtable<String, Integer>();
   String strLine;
   int i=0;
   while ((strLine = br.readLine()) != null)
@@ -198,9 +198,9 @@ public void paint (Graphics g) {
     }
     double unit;
     unit=(360-(double)(space*lcells))/(double)lnt;
-    Hashtable lstart=new Hashtable();
+    Hashtable<String, Double> lstart=new Hashtable<String, Double>();
     double temp1,temp2,temp3,temp4;
-    lstart.put(xchr.get(0),0);
+    lstart.put(xchr.get(0),(double)0);
     g.drawArc(hmargin-thick,hmargin-thick,xdim-hmargin-hmargin+2*thick,ydim-vmargin-vmargin+2*thick,0,(int)(unit*Double.parseDouble(chr_len.get(xchr.get(0)).toString())));    
     g.drawArc(hmargin,hmargin,xdim-hmargin-hmargin,ydim-vmargin-vmargin,0,(int)(unit*Double.parseDouble(chr_len.get(xchr.get(0)).toString())));
     temp1=center_x+Math.cos(0*3.14159/180)*(radius+(double)thick);
@@ -312,7 +312,7 @@ public static void main(String args[])
 System.out.println("Usage: java family_circle_plotter -g gff_file -s synteny_file -c control_file -f gene_family_file -o output_PNG_file");
 System.exit(1);
 }
-HashMap option = new HashMap();
+HashMap<String, String> option = new HashMap<String, String>();
 int i;
 for(i=0;i<args.length/2;i++)
 {