From 1c472d54a12783c4be933b83d47217b7d56b167f Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 8 Mar 2006 16:51:44 +0000
Subject: [PATCH] Able to read resources from Zip file

---
 src/jalview/io/AnnotationReader.java    |   21 ++++++++++++++-------
 src/jalview/io/AppletFormatAdapter.java |    7 +++++++
 src/jalview/io/FileParse.java           |   28 ++++++++++++----------------
 src/jalview/io/IdentifyFile.java        |   27 ++++++++++++++++-----------
 4 files changed, 49 insertions(+), 34 deletions(-)

diff --git a/src/jalview/io/AnnotationReader.java b/src/jalview/io/AnnotationReader.java
index 958aa65..4325dae 100755
--- a/src/jalview/io/AnnotationReader.java
+++ b/src/jalview/io/AnnotationReader.java
@@ -13,18 +13,25 @@ public class AnnotationReader
 
     try
     {
-
       BufferedReader in = null;
-      try{
-        URL url = new URL(file);
-        in = new BufferedReader(new InputStreamReader(url.openStream()));
+      java.io.InputStream is = getClass().getResourceAsStream("/" + file);
+      if (is != null)
+      {
+        in = new BufferedReader(new java.io.InputStreamReader(is));
       }
-      catch(java.net.MalformedURLException ex)
+      else
       {
-        in = new BufferedReader(new FileReader(file));
+        try
+        {
+          URL url = new URL(file);
+          in = new BufferedReader(new InputStreamReader(url.openStream()));
+        }
+        catch (java.net.MalformedURLException ex)
+        {
+          in = new BufferedReader(new FileReader(file));
+        }
       }
 
-
       String line, label, description, token;
       int graphStyle, index;
       SequenceI refSeq = null;
diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index dca2d0c..5f73898 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -50,6 +50,12 @@
             formats.addElement("PFAM");
         }
 
+
+        public static String FILE = "File";
+        public static String URL = "URL";
+        public static String PASTE = "Paste";
+        public static String CLASSLOADER = "ClassLoader";
+
         AlignFile afile = null;
 
         /**
@@ -95,6 +101,7 @@
                     afile = new PfamFile(inFile, type);
                 }
 
+
                 return afile.getSeqsAsArray();
             }
             catch (Exception e)
diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index af3bbec..adc57cd 100755
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -24,8 +24,6 @@ import java.net.*;
 public class FileParse
 {
   public File inFile;
-  public int fileSize;
-  public int noLines;
   protected String type;
   protected BufferedReader dataIn;
 
@@ -38,35 +36,33 @@ public class FileParse
   {
     this.type = type;
 
-    if (type.equals("File"))
+    if (type.equals(AppletFormatAdapter.FILE))
     {
       this.inFile = new File(fileStr);
-      this.fileSize = (int) inFile.length();
-
       dataIn = new BufferedReader(new FileReader(fileStr));
     }
-    else if (type.equals("URL"))
+    else if (type.equals(AppletFormatAdapter.URL))
     {
       URL url = new URL(fileStr);
-      this.fileSize = 0;
       dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
     }
-    else if (type.equals("Paste"))
+   else if (type.equals(AppletFormatAdapter.PASTE))
     {
       dataIn = new BufferedReader(new StringReader(fileStr));
     }
+    else if (type.equals(AppletFormatAdapter.CLASSLOADER))
+    {
+      java.io.InputStream is = getClass().getResourceAsStream("/" + fileStr);
+      if (is != null)
+      {
+        dataIn = new BufferedReader(new java.io.InputStreamReader(is));
+      }
+    }
   }
 
   public String nextLine()
       throws IOException
   {
-    String next = dataIn.readLine();
-
-    if (next != null)
-    {
-      noLines++;
-    }
-
-    return next;
+    return dataIn.readLine();
   }
 }
diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index f4beccb..2040769 100755
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -39,30 +39,35 @@ public class IdentifyFile
      *
      * @return DOCUMENT ME!
      */
-    public static String Identify(String file, String protocol)
+    public String Identify(String file, String protocol)
     {
         String reply = "PFAM";
         String error =  "FILE NOT FOUND";
-
         try
         {
             BufferedReader reader = null;
 
-            if (protocol.equalsIgnoreCase("File"))
+            if (protocol.equals(AppletFormatAdapter.FILE))
             {
-                reader = new BufferedReader(new FileReader(file));
+              reader = new BufferedReader(new FileReader(file));
             }
-            else if (protocol.equalsIgnoreCase("URL"))
+            else if (protocol.equals(AppletFormatAdapter.URL))
             {
-                error = "URL NOT FOUND";
-                URL url = new URL(file);
-                reader = new BufferedReader(new InputStreamReader(
-                            url.openStream()));
+              error = "URL NOT FOUND";
+              URL url = new URL(file);
+              reader = new BufferedReader(new InputStreamReader(
+                  url.openStream()));
 
             }
-            else if (protocol.equalsIgnoreCase("Paste"))
+            else if (protocol.equals(AppletFormatAdapter.PASTE))
+            {
+              reader = new BufferedReader(new StringReader(file));
+            }
+            else if (protocol.equals(AppletFormatAdapter.CLASSLOADER))
             {
-                reader = new BufferedReader(new StringReader(file));
+              java.io.InputStream is = getClass().getResourceAsStream("/" +
+                  file);
+              reader = new BufferedReader(new java.io.InputStreamReader(is));
             }
 
             String data;
-- 
1.7.10.2