JAL-4090 release weds 25th Oct 23 - JAL-4308 release notes

[jalview.git] / src / jalview / ws / jws1 / Annotate3D.java

diff --git a/src/jalview/ws/jws1/Annotate3D.java b/src/jalview/ws/jws1/Annotate3D.java
index cf228d6..4165eae 100644 (file)
--- a/src/jalview/ws/jws1/Annotate3D.java
+++ b/src/jalview/ws/jws1/Annotate3D.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -21,6 +21,7 @@
 package jalview.ws.jws1;
 
 import jalview.datamodel.AlignmentI;
+import jalview.io.FileFormat;
 import jalview.io.FileParse;
 import jalview.io.FormatAdapter;
 import jalview.io.InputStreamParser;
@@ -43,7 +44,7 @@ public class Annotate3D
 
   public Annotate3D()
   {
-    System.out.println("Annotate3D");
+    jalview.bin.Console.outPrintln("Annotate3D");
     // try {
     // Create a URL for the desired page
     // String id = "1HR2";
@@ -54,7 +55,7 @@ public class Annotate3D
     // OutputStream out1 = null;
     // out = new BufferedWriter(new OutputStreamWriter(out1, "temp.rnaml"));
     // while ((str = in.readLine()) != null) {
-    // System.out.println(str);
+    // jalview.bin.Console.outPrintln(str);
     // out.write(str);
     // }
     // in.close();
@@ -85,8 +86,10 @@ public class Annotate3D
       AlignmentI al = null;
       while (r.hasNext())
       {
-        FileParse fp = new InputStreamParser(r.next(), source.getDataName());
-        AlignmentI nal = new FormatAdapter().readFromFile(fp, "RNAML");
+        FileParse fp = new InputStreamParser(r.next(),
+                source.getDataName());
+        AlignmentI nal = new FormatAdapter().readFromFile(fp,
+                FileFormat.Rnaml);
         if (al == null)
         {
           al = nal;
@@ -105,9 +108,8 @@ public class Annotate3D
       }
       else
       {
-        throw new IOException(
-                MessageManager
-                        .getString("exception.unexpected_handling_rnaml_translation_for_pdb"),
+        throw new IOException(MessageManager.getString(
+                "exception.unexpected_handling_rnaml_translation_for_pdb"),
                 x);
       }
     }
@@ -115,19 +117,19 @@ public class Annotate3D
 
   public Annotate3D(String path) throws InterruptedException
   {
-    System.out.println("Annotate3D");
+    jalview.bin.Console.outPrintln("Annotate3D");
     try
     {
       // //URL url = new
       // URL("http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="+inFile);
-      // System.out.println("Step1");
+      // jalview.bin.Console.outPrintln("Step1");
       // FileReader r = new FileReader(inFile);
       // BufferedReader in = new BufferedReader(r);
       // StringBuffer content = new StringBuffer();
-      // System.out.println("Step2");
+      // jalview.bin.Console.outPrintln("Step2");
       // while(in.readLine()!=null){
       // content.append(in.readLine());
-      // //System.out.println("Step3"+in.readLine());
+      // //jalview.bin.Console.outPrintln("Step3"+in.readLine());
       // }
       //
       // String data = URLEncoder.encode("data", "UTF-8") + "=" +
@@ -143,21 +145,21 @@ public class Annotate3D
       // FileReader r = new FileReader(path);
       // BufferedReader in = new BufferedReader(r);
       // StringBuffer content = new StringBuffer();
-      // System.out.println("Step1");
+      // jalview.bin.Console.outPrintln("Step1");
       // while(in.readLine()!=null){
       // content.append(in.readLine());
       //
       // }
-      // System.out.println("Step2");
+      // jalview.bin.Console.outPrintln("Step2");
       // String data = URLEncoder.encode("data", "UTF-8") + "=" +
       // URLEncoder.encode(content.toString(), "UTF-8");
-      // System.out.println("Step2");
+      // jalview.bin.Console.outPrintln("Step2");
       // URL url = new
       // URL("http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="+data);
       // DataInputStream is = new DataInputStream(url.openStream());
       // String str;
       // while ((str = is.readLine()) != null) {
-      // System.out.println(str);
+      // jalview.bin.Console.outPrintln(str);
       // //out.write(str);
       // }
       FileReader r = new FileReader(path);
@@ -167,23 +169,23 @@ public class Annotate3D
 
       while ((str = in.readLine()) != null)
       {
-        // System.out.println(str);
+        // jalview.bin.Console.outPrintln(str);
 
         content = content + str;
       }
-      System.out.println("pdbfile=" + content.toString());
-      System.out.println("capacité=" + content.length());
+      jalview.bin.Console.outPrintln("pdbfile=" + content.toString());
+      jalview.bin.Console.outPrintln("capacité=" + content.length());
       String paramfile = URLEncoder.encode(content.toString(), "UTF-8");
-      System.out.println("param=" + paramfile);
+      jalview.bin.Console.outPrintln("param=" + paramfile);
       URL url = new URL(
               "http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="
                       + content);
-      BufferedReader is = new BufferedReader(new InputStreamReader(
-              url.openStream()));
+      BufferedReader is = new BufferedReader(
+              new InputStreamReader(url.openStream()));
       String str4;
       while ((str4 = is.readLine()) != null)
       {
-        System.out.println(str4);
+        jalview.bin.Console.outPrintln(str4);
         // out.write(str);
       }
       in.close();
@@ -205,7 +207,7 @@ public class Annotate3D
       // BufferedReader in1 = new BufferedReader(is);
 
       // OutputStream out1 = null;
-      // System.out.println("Step3");
+      // jalview.bin.Console.outPrintln("Step3");
       // BufferedWriter out = new BufferedWriter(new OutputStreamWriter(out1,
       // "temp.rnaml"));
       //
@@ -214,11 +216,11 @@ public class Annotate3D
 
       // return;
 
-      // System.out.println(data.length());
-      // System.out.println("step2");
+      // jalview.bin.Console.outPrintln(data.length());
+      // jalview.bin.Console.outPrintln("step2");
       // URL url = new
       // URL("http://paradise-ibmc.u-strasbg.fr/webservices/annotate3d?data="+data);
-      // System.out.println("step3");
+      // jalview.bin.Console.outPrintln("step3");
       // URLConnection conn = url.openConnection();
       // conn.setDoOutput(true);
       // OutputStreamWriter writer = new
@@ -235,7 +237,7 @@ public class Annotate3D
       // //String line;
       // while ((line = reader.readLine()) != null) {
       // answer.append(line);
-      // System.out.println(line);
+      // jalview.bin.Console.outPrintln(line);
       // }
       // writer.close();
       // reader.close();
@@ -259,9 +261,9 @@ public class Annotate3D
   // out = new BufferedWriter(new FileWriter("temp.rnaml"));
 
   // while ((str = in.readLine()) != null) {
-  // System.out.println(str);
+  // jalview.bin.Console.outPrintln(str);
   // out.write(str);
-  // System.out.println(str);
+  // jalview.bin.Console.outPrintln(str);
   // in.close();
 
   // out.close();
@@ -273,7 +275,7 @@ public class Annotate3D
 
   // public BufferedWriter getReader()
   // {
-  // System.out.println("The buffer");
+  // jalview.bin.Console.outPrintln("The buffer");
 
   // return out;