From e8b5b1e551794bf54de00c610363ffd140c62e55 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Tue, 17 Apr 2007 15:57:41 +0000
Subject: [PATCH] refactored to allow seeks on a FileParse datasource so
 IdentifyFile can be applied to an inputstream.

---
 src/jalview/io/FileParse.java    |  271 +++++++++++++++++++++--------
 src/jalview/io/IdentifyFile.java |  352 ++++++++++++++++++++------------------
 2 files changed, 385 insertions(+), 238 deletions(-)

diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index 982a9ee..e234c98 100755
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -1,68 +1,203 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.io;
-
-import java.io.*;
-import java.net.*;
-
-public class FileParse
-{
-  public File inFile;
-  protected String type;
-  protected BufferedReader dataIn;
-
-  public FileParse()
-  {
-  }
-
-  public FileParse(String fileStr, String type)
-      throws MalformedURLException, IOException
-  {
-    this.type = type;
-
-    if (type.equals(AppletFormatAdapter.FILE))
-    {
-      this.inFile = new File(fileStr);
-      dataIn = new BufferedReader(new FileReader(fileStr));
-    }
-    else if (type.equals(AppletFormatAdapter.URL))
-    {
-      URL url = new URL(fileStr);
-      dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
-    }
-    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
-  {
-    return dataIn.readLine();
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.io;
+
+import java.io.*;
+import java.net.*;
+/** 
+ * implements a random access wrapper around a particular datasource, for passing to
+ * identifyFile and AlignFile objects.
+ */
+public class FileParse
+{
+  public File inFile=null;
+  /**
+   * '#' separated string tagged on to end of filename 
+   * or url that was clipped off to resolve to valid filename
+   */
+  protected String suffix=null; 
+  protected String type=null;
+  protected BufferedReader dataIn=null;
+  protected String errormessage="UNITIALISED SOURCE";
+  protected boolean error=true;
+  /**
+   * size of readahead buffer used for when initial stream position is marked.
+   */
+  final int READAHEAD_LIMIT=2048;
+  public FileParse()
+  {
+  }
+  /**
+   * Attempt to open a file as a datasource.
+   * Sets error and errormessage if fileStr was invalid.
+   * @param fileStr
+   * @return this.error (true if the source was invalid)
+   */
+  private boolean checkFileSource(String fileStr) throws IOException {
+    this.inFile = new File(fileStr);
+    // check to see if it's a Jar file in disguise.
+    if (!inFile.exists()) {
+      errormessage = "FILE NOT FOUND";
+      error=true;
+    }
+    if (!inFile.canRead()) {
+      errormessage = "FILE CANNOT BE OPENED FOR READING";
+      error=true;
+    }
+    if (inFile.isDirectory()) {
+      // this is really a 'complex' filetype - but we don't handle directory reads yet.
+      errormessage = "FILE IS A DIRECTORY";
+      error=true;
+    }
+    if (!error) {
+      dataIn = new BufferedReader(new FileReader(fileStr));
+    }
+    return error;
+  }
+  private boolean checkURLSource(String fileStr) throws IOException, MalformedURLException
+  {
+    errormessage = "URL NOT FOUND";
+    URL url = new URL(fileStr);
+    dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
+    return false;
+  }
+  /**
+   * sets the suffix string (if any) and returns remainder (if suffix was detected) 
+   * @param fileStr
+   * @return truncated fileStr or null
+   */
+  private String extractSuffix(String fileStr) {
+    // first check that there wasn't a suffix string tagged on.
+    int sfpos = fileStr.lastIndexOf('#');
+    if (sfpos>-1 && sfpos<fileStr.length()-1) {
+      suffix = fileStr.substring(sfpos+1);
+      // System.err.println("DEBUG: Found Suffix:"+suffix);
+      return fileStr.substring(0,sfpos);
+    }
+    return null;
+  }
+  /**
+   * Create a datasource for input to Jalview.
+   * See AppletFormatAdapter for the types of sources that are handled.
+   * @param fileStr - datasource locator/content
+   * @param type - protocol of source 
+   * @throws MalformedURLException
+   * @throws IOException
+   */
+  public FileParse(String fileStr, String type)
+      throws MalformedURLException, IOException
+  {
+    this.type = type;
+    error=false;
+
+    if (type.equals(AppletFormatAdapter.FILE))
+    {
+      if (checkFileSource(fileStr)) {  
+        String suffixLess = extractSuffix(fileStr);
+        if (suffixLess!=null && checkFileSource(suffixLess))
+        {
+          throw new IOException("Problem opening "+inFile+" (also tried "+fileStr+") : "+errormessage);
+        }
+          // returns normally.
+      } else {
+          throw new IOException("Problem opening "+inFile+" : "+errormessage);
+      }
+    }
+    else if (type.equals(AppletFormatAdapter.URL))
+    {
+      try {
+        checkURLSource(fileStr);
+        String suffixLess = extractSuffix(fileStr); // URL lref is stored for later reference.
+      } catch (IOException e) {
+        String suffixLess = extractSuffix(fileStr);
+        if (suffixLess==null)
+        {
+          throw(e);
+        } else {
+          try {
+            checkURLSource(suffixLess);
+          }
+          catch (IOException e2) {
+            errormessage = "BAD URL WITH OR WITHOUT SUFFIX";
+            throw(e); // just pass back original - everything was wrong.
+          }
+        }
+      }
+    }
+    else if (type.equals(AppletFormatAdapter.PASTE))
+    {
+      errormessage = "PASTE INACCESSIBLE!";
+      dataIn = new BufferedReader(new StringReader(fileStr));
+    }
+    else if (type.equals(AppletFormatAdapter.CLASSLOADER))
+    {
+      errormessage = "RESOURCE CANNOT BE LOCATED";
+      java.io.InputStream is = getClass().getResourceAsStream("/" + fileStr);
+      if (is==null) {
+        String suffixLess = extractSuffix(fileStr);
+        if (suffixLess!=null)
+          is = getClass().getResourceAsStream("/" + suffixLess);
+      }
+      if (is != null)
+      {
+        dataIn = new BufferedReader(new java.io.InputStreamReader(is));
+      } else {
+        error = true;
+      }
+    }
+    error=false;
+    dataIn.mark(READAHEAD_LIMIT);
+  }
+  public String nextLine()
+      throws IOException
+  {
+    if (!error)
+      return dataIn.readLine();
+    throw new IOException("Invalid Source Stream:"+errormessage);
+  }
+
+  public boolean isValid()
+  {
+    return !error;
+  }
+  /**
+   * closes the datasource and tidies up.
+   * source will be left in an error state
+   */
+  public void close() throws IOException
+  {
+    errormessage="EXCEPTION ON CLOSE";
+    error=true;
+    dataIn.close();
+    dataIn=null;
+    errormessage="SOURCE IS CLOSED";
+  }
+  /**
+   * rewinds the datasource the beginning.
+   *
+   */
+  public void reset() throws IOException
+  {
+    if (dataIn!=null && !error) {
+      dataIn.reset();
+    } else {
+      throw new IOException("Implementation Error: Reset called for invalid source.");
+    }
+  }
+}
diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index f1dfffe..7f3db40 100755
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -1,170 +1,182 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.io;
-
-import java.io.*;
-import java.net.*;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class IdentifyFile
-{
-  /**
-   * DOCUMENT ME!
-   *
-   * @param file DOCUMENT ME!
-   * @param protocol DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public String Identify(String file, String protocol)
-  {
-    String reply = "PFAM";
-    String error = "FILE NOT FOUND";
-    try
-    {
-      BufferedReader reader = null;
-
-      if (protocol.equals(AppletFormatAdapter.FILE))
-      {
-        reader = new BufferedReader(new FileReader(file));
-      }
-      else if (protocol.equals(AppletFormatAdapter.URL))
-      {
-        error = "URL NOT FOUND";
-        URL url = new URL(file);
-        reader = new BufferedReader(new InputStreamReader(
-            url.openStream()));
-
-      }
-      else if (protocol.equals(AppletFormatAdapter.PASTE))
-      {
-        reader = new BufferedReader(new StringReader(file));
-      }
-      else if (protocol.equals(AppletFormatAdapter.CLASSLOADER))
-      {
-        java.io.InputStream is = getClass().getResourceAsStream("/" +
-            file);
-        reader = new BufferedReader(new java.io.InputStreamReader(is));
-      }
-
-      String data;
-
-      while ( (data = reader.readLine()) != null)
-      {
-        data = data.toUpperCase();
-
-        if ( (data.indexOf("# STOCKHOLM") > -1))
-        {
-          reply = "STH";
-
-          break;
-        }
-
-        if ( (data.indexOf("#") == 0) || (data.length() < 1))
-        {
-          continue;
-        }
-
-        if (data.indexOf("PILEUP") > -1)
-        {
-          reply = "PileUp";
-
-          break;
-        }
-
-        if ( (data.indexOf("//") == 0) ||
-            ( (data.indexOf("!!") > -1) &&
-             (data.indexOf("!!") < data.indexOf(
-                 "_MULTIPLE_ALIGNMENT "))))
-        {
-          reply = "MSF";
-
-          break;
-        }
-        else if (data.indexOf("CLUSTAL") > -1)
-        {
-          reply = "CLUSTAL";
-
-          break;
-        }
-        else if ( (data.indexOf(">P1;") > -1) ||
-                 (data.indexOf(">DL;") > -1))
-        {
-          reply = "PIR";
-
-          break;
-        }
-        else if (data.indexOf(">") > -1)
-        {
-          // could be BLC file, read next line to confirm
-          data = reader.readLine();
-
-          if (data.indexOf(">") > -1)
-          {
-            reply = "BLC";
-          }
-          else
-          {
-            //Is this a single line BLC file?
-            reader.readLine();
-            String data2 = reader.readLine();
-            if (data2 != null
-                && data.indexOf("*") > -1
-                && data.indexOf("*") == data2.indexOf("*"))
-            {
-              reply = "BLC";
-            }
-            else
-            {
-              reply = "FASTA";
-            }
-          }
-
-          break;
-        }
-        else if (data.indexOf("HEADER") == 0 ||
-                 data.indexOf("ATOM") == 0)
-        {
-          reply = "PDB";
-          break;
-        }
-        else if (data.indexOf(":") < data.indexOf(",")) //  && data.indexOf(",")<data.indexOf(",", data.indexOf(",")))
-        {
-          // file looks like a concise JNet file
-          reply = "JnetFile";
-          break;
-        }
-      }
-
-      reader.close();
-    }
-    catch (Exception ex)
-    {
-      System.err.println("File Identification failed!\n" + ex);
-      return error;
-    }
-
-    return reply;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.io;
+
+import java.io.*;
+import java.net.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class IdentifyFile
+{
+  /**
+   * Identify a datasource's file content. 
+   * @note Do not use this method
+   * for stream sources - create a FileParse object instead. 
+   *
+   * @param file DOCUMENT ME!
+   * @param protocol DOCUMENT ME! 
+   * @return ID String
+   */
+  public String Identify(String file, String protocol)
+  {
+    FileParse parser = null;
+    try {
+      parser = new FileParse(file, protocol);
+      if (parser.isValid()) {
+        return Identify(parser);
+      }
+    } catch (Exception e) {
+      System.err.println("Error whilst identifying");
+      e.printStackTrace(System.err);
+    }
+    if (parser!=null)
+      return parser.errormessage;
+    return "UNIDENTIFIED FILE PARSING ERROR";
+  }
+  public String Identify(FileParse source) {
+    return Identify(source, true); // preserves original behaviour prior to version 2.3
+  }
+  /**
+   * Identify contents of source, closing it or resetting source to start afterwards.
+   * @param source
+   * @param closeSource
+   * @return filetype string
+   */
+  public String Identify(FileParse source, boolean closeSource) {
+    String reply = "PFAM";
+    String data;
+    try {
+      while ( (data = source.nextLine()) != null)
+      {
+        data = data.toUpperCase();
+
+        if ( (data.indexOf("# STOCKHOLM") > -1))
+        {
+          reply = "STH";
+
+          break;
+        }
+
+        if ( (data.indexOf("#") == 0) || (data.length() < 1))
+        {
+          continue;
+        }
+
+        if (data.indexOf("PILEUP") > -1)
+        {
+          reply = "PileUp";
+
+          break;
+        }
+
+        if ( (data.indexOf("//") == 0) ||
+            ( (data.indexOf("!!") > -1) &&
+             (data.indexOf("!!") < data.indexOf(
+                 "_MULTIPLE_ALIGNMENT "))))
+        {
+          reply = "MSF";
+
+          break;
+        }
+        else if (data.indexOf("CLUSTAL") > -1)
+        {
+          reply = "CLUSTAL";
+
+          break;
+        }
+        else if ( (data.indexOf(">P1;") > -1) ||
+                 (data.indexOf(">DL;") > -1))
+        {
+          reply = "PIR";
+
+          break;
+        }
+        else if (data.indexOf(">") > -1)
+        {
+          // could be BLC file, read next line to confirm
+          data = source.nextLine();
+
+          if (data.indexOf(">") > -1)
+          {
+            reply = "BLC";
+          }
+          else
+          {
+            //Is this a single line BLC file?
+            source.nextLine();
+            String data2 = source.nextLine();
+            if (data2 != null
+                && data.indexOf("*") > -1
+                && data.indexOf("*") == data2.indexOf("*"))
+            {
+              reply = "BLC";
+            }
+            else
+            {
+              reply = "FASTA";
+            }
+          }
+
+          break;
+        }
+        else if (data.indexOf("HEADER") == 0 ||
+                 data.indexOf("ATOM") == 0)
+        {
+          reply = "PDB";
+          break;
+        }
+        else if (data.indexOf(":") < data.indexOf(",")) //  && data.indexOf(",")<data.indexOf(",", data.indexOf(",")))
+        {
+          // file looks like a concise JNet file
+          reply = "JnetFile";
+          break;
+        }
+        else  if (source.inFile!=null) 
+        {
+            String fileStr=source.inFile.getName();
+            // possibly a Jalview archive. 
+            if (fileStr.lastIndexOf(".jar")>-1 || fileStr.lastIndexOf(".zip")>-1) 
+            {
+              reply = "Jalview";
+            }
+        } else if (data.startsWith("PK")) {
+          reply="Jalview"; // archive.
+          break;
+        }
+      }
+      if (closeSource) {
+        source.close();
+      } else {
+        source.reset(); // so the file can be parsed from the beginning again.
+      }
+    }
+    catch (Exception ex)
+    {
+      System.err.println("File Identification failed!\n" + ex);
+      return source.errormessage;
+    }
+
+    return reply;
+  }
+}
-- 
1.7.10.2