X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileParse.java;h=69e801c7f3747dd776a4c0508e415771e1f94cc2;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=f4f765c63f3ab1866da1d00981827e078b8cae54;hpb=1233e68299e9a3c8b2a075f18e5179d8480e2aee;p=jalview.git

diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index f4f765c..69e801c 100755
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -1,224 +1,465 @@
 /*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview 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 3 of the License, or (at your option) any later version.
+ *  
+ * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 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.
+import java.util.zip.GZIPInputStream;
+
+/**
+ * implements a random access wrapper around a particular datasource, for
+ * passing to identifyFile and AlignFile objects.
  */
 public class FileParse
 {
-  public File inFile=null;
+  /**
+   * text specifying source of data. usually filename or url.
+   */
+  private String dataName = "unknown source";
+
+  public File inFile = null;
+
+  public int index = 1; // sequence counter for FileParse object created from
+
+  // same data source
+
   protected char suffixSeparator = '#';
+
   /**
-   * '#' separated string tagged on to end of filename 
-   * or url that was clipped off to resolve to valid filename
+   * character used to write newlines
    */
-  protected String suffix=null; 
-  protected String type=null;
-  protected BufferedReader dataIn=null;
-  protected String errormessage="UNITIALISED SOURCE";
-  protected boolean error=true;
-  protected String warningMessage=null;
+  protected String newline = System.getProperty("line.separator");
+
+  public void setNewlineString(String nl)
+  {
+    newline = nl;
+  }
+
+  public String getNewlineString()
+  {
+    return newline;
+  }
+
+  /**
+   * '#' 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;
+
+  protected String warningMessage = null;
+
   /**
    * size of readahead buffer used for when initial stream position is marked.
    */
-  final int READAHEAD_LIMIT=2048;
+  final int READAHEAD_LIMIT = 2048;
+
   public FileParse()
   {
   }
+
   /**
-   * Attempt to open a file as a datasource.
-   * Sets error and errormessage if fileStr was invalid.
+   * Create a new FileParse instance reading from the same datasource starting
+   * at the current position. WARNING! Subsequent reads from either object will
+   * affect the read position of the other, but not the error state.
+   * 
+   * @param from
+   */
+  public FileParse(FileParse from) throws IOException
+  {
+    if (from == null)
+    {
+      throw new Error(
+              "Implementation error. Null FileParse in copy constructor");
+    }
+    if (from == this)
+      return;
+    index = ++from.index;
+    inFile = from.inFile;
+    suffixSeparator = from.suffixSeparator;
+    suffix = from.suffix;
+    errormessage = from.errormessage; // inherit potential error messages
+    error = false; // reset any error condition.
+    type = from.type;
+    dataIn = from.dataIn;
+    if (dataIn != null)
+    {
+      mark();
+    }
+    dataName = from.dataName;
+  }
+
+  /**
+   * 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 {
-    error=false;
+  private boolean checkFileSource(String fileStr) throws IOException
+  {
+    error = false;
     this.inFile = new File(fileStr);
     // check to see if it's a Jar file in disguise.
-    if (!inFile.exists()) {
+    if (!inFile.exists())
+    {
       errormessage = "FILE NOT FOUND";
-      error=true;
+      error = true;
     }
-    if (!inFile.canRead()) {
+    if (!inFile.canRead())
+    {
       errormessage = "FILE CANNOT BE OPENED FOR READING";
-      error=true;
+      error = true;
     }
-    if (inFile.isDirectory()) {
-      // this is really a 'complex' filetype - but we don't handle directory reads yet.
+    if (inFile.isDirectory())
+    {
+      // this is really a 'complex' filetype - but we don't handle directory
+      // reads yet.
       errormessage = "FILE IS A DIRECTORY";
-      error=true;
+      error = true;
     }
-    if (!error) {
+    if (!error)
+    {
+      if (fileStr.toLowerCase().endsWith(".gz"))
+      {
+        try
+        {
+          dataIn = tryAsGzipSource(new FileInputStream(fileStr));
+          dataName = fileStr;
+          return error;
+        } catch (Exception x)
+        {
+          warningMessage = "Failed  to resolve as a GZ stream ("
+                  + x.getMessage() + ")";
+          x.printStackTrace();
+        }
+        ;
+      }
+      
       dataIn = new BufferedReader(new FileReader(fileStr));
+      dataName = fileStr;
     }
     return error;
   }
-  private boolean checkURLSource(String fileStr) throws IOException, MalformedURLException
+  private BufferedReader tryAsGzipSource(InputStream inputStream) throws Exception
+  {
+    BufferedReader inData = new BufferedReader(new InputStreamReader(new GZIPInputStream(inputStream)));
+    inData.mark(2048);
+    inData.read();
+    inData.reset();
+    return inData;
+  }
+  private boolean checkURLSource(String fileStr) throws IOException,
+          MalformedURLException
   {
     errormessage = "URL NOT FOUND";
     URL url = new URL(fileStr);
-    dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
+    //
+    // GZIPInputStream code borrowed from Aquaria (soon to be open sourced) via Kenny Sabir
+    Exception e=null;
+    if (fileStr.toLowerCase().endsWith(".gz")) {
+      try {
+          InputStream inputStream = url.openStream();
+          dataIn = tryAsGzipSource(inputStream);
+          dataName = fileStr;
+          return false;
+      } catch (Exception ex) {
+        e=ex;
+      }
+    }
+
+    try {
+      dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
+    } catch (IOException q) {
+      if (e!=null)
+      {
+        throw new IOException("Failed to resolve GZIP stream", e);
+      }
+      throw q;
+    }
+    // record URL as name of datasource.
+    dataName = fileStr;
     return false;
   }
+
   /**
-   * sets the suffix string (if any) and returns remainder (if suffix was detected) 
+   * 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) {
+  private String extractSuffix(String fileStr)
+  {
     // first check that there wasn't a suffix string tagged on.
     int sfpos = fileStr.lastIndexOf(suffixSeparator);
-    if (sfpos>-1 && sfpos<fileStr.length()-1) {
-      suffix = fileStr.substring(sfpos+1);
+    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 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 
+   * 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
+          throws MalformedURLException, IOException
   {
     this.type = type;
-    error=false;
+    error = false;
 
     if (type.equals(AppletFormatAdapter.FILE))
     {
-      if (checkFileSource(fileStr)) {  
+      if (checkFileSource(fileStr))
+      {
         String suffixLess = extractSuffix(fileStr);
-        if (suffixLess!=null)
+        if (suffixLess != null)
         {
           if (checkFileSource(suffixLess))
           {
-            throw new IOException("Problem opening "+inFile+" (also tried "+suffixLess+") : "+errormessage);
+            throw new IOException("Problem opening " + inFile
+                    + " (also tried " + suffixLess + ") : " + errormessage);
           }
-        } else
+        }
+        else
         {
-          throw new IOException("Problem opening "+inFile+" : "+errormessage);
+          throw new IOException("Problem opening " + inFile + " : "
+                  + errormessage);
         }
       }
     }
     else if (type.equals(AppletFormatAdapter.URL))
     {
-      try {
-        checkURLSource(fileStr);
-        if (suffixSeparator=='#')
-          extractSuffix(fileStr); // URL lref is stored for later reference.
-      } catch (IOException e) {
-        String suffixLess = extractSuffix(fileStr);
-        if (suffixLess==null)
+      try
+      {
+        try
         {
-          throw(e);
-        } else {
-          try {
-            checkURLSource(suffixLess);
+          checkURLSource(fileStr);
+          if (suffixSeparator == '#')
+            extractSuffix(fileStr); // URL lref is stored for later reference.
+        } catch (IOException e)
+        {
+          String suffixLess = extractSuffix(fileStr);
+          if (suffixLess == null)
+          {
+            throw (e);
           }
-          catch (IOException e2) {
-            errormessage = "BAD URL WITH OR WITHOUT SUFFIX";
-            throw(e); // just pass back original - everything was wrong.
+          else
+          {
+            try
+            {
+              checkURLSource(suffixLess);
+            } catch (IOException e2)
+            {
+              errormessage = "BAD URL WITH OR WITHOUT SUFFIX";
+              throw (e); // just pass back original - everything was wrong.
+            }
           }
         }
+      } catch (Exception e)
+      {
+        errormessage = "CANNOT ACCESS DATA AT URL '" + fileStr + "' ("
+                + e.getMessage() + ")";
+        error = true;
       }
     }
     else if (type.equals(AppletFormatAdapter.PASTE))
     {
       errormessage = "PASTE INACCESSIBLE!";
       dataIn = new BufferedReader(new StringReader(fileStr));
+      dataName = "Paste";
     }
     else if (type.equals(AppletFormatAdapter.CLASSLOADER))
     {
       errormessage = "RESOURCE CANNOT BE LOCATED";
-      java.io.InputStream is = getClass().getResourceAsStream("/" + fileStr);
-      if (is==null) {
+      java.io.InputStream is = getClass()
+              .getResourceAsStream("/" + fileStr);
+      if (is == null)
+      {
         String suffixLess = extractSuffix(fileStr);
-        if (suffixLess!=null)
+        if (suffixLess != null)
           is = getClass().getResourceAsStream("/" + suffixLess);
       }
       if (is != null)
       {
         dataIn = new BufferedReader(new java.io.InputStreamReader(is));
-      } else {
+        dataName = fileStr;
+      }
+      else
+      {
         error = true;
       }
     }
-    error=false;
+    else
+    {
+      errormessage = "PROBABLE IMPLEMENTATION ERROR : Datasource Type given as '"
+              + (type != null ? type : "null") + "'";
+      error = true;
+    }
+    if (dataIn == null || error)
+    {
+      // pass up the reason why we have no source to read from
+      throw new IOException("Failed to read data from source:\n"
+              + errormessage);
+    }
+    error = false;
     dataIn.mark(READAHEAD_LIMIT);
   }
-  public String nextLine()
-      throws IOException
+
+  /**
+   * mark the current position in the source as start for the purposes of it
+   * being analysed by IdentifyFile().identify
+   * 
+   * @throws IOException
+   */
+  public void mark() throws IOException
+  {
+    if (dataIn != null)
+    {
+      dataIn.mark(READAHEAD_LIMIT);
+    }
+    else
+    {
+      throw new IOException("Unitialised Source Stream");
+    }
+  }
+
+  public String nextLine() throws IOException
   {
     if (!error)
       return dataIn.readLine();
-    throw new IOException("Invalid Source Stream:"+errormessage);
+    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
+   * 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;
+    errormessage = "EXCEPTION ON CLOSE";
+    error = true;
     dataIn.close();
-    dataIn=null;
-    errormessage="SOURCE IS CLOSED";
+    dataIn = null;
+    errormessage = "SOURCE IS CLOSED";
   }
+
   /**
    * rewinds the datasource the beginning.
-   *
+   * 
    */
   public void reset() throws IOException
   {
-    if (dataIn!=null && !error) {
+    if (dataIn != null && !error)
+    {
       dataIn.reset();
-    } else {
-      throw new IOException("Implementation Error: Reset called for invalid source.");
+    }
+    else
+    {
+      throw new IOException(
+              "Implementation Error: Reset called for invalid source.");
     }
   }
+
   /**
    * 
    * @return true if there is a warning for the user
    */
-  public boolean hasWarningMessage() {
-    return (warningMessage!=null && warningMessage.length()>0);
+  public boolean hasWarningMessage()
+  {
+    return (warningMessage != null && warningMessage.length() > 0);
   }
+
   /**
    * 
    * @return empty string or warning message about file that was just parsed.
    */
-  public String getWarningMessage() {
+  public String getWarningMessage()
+  {
     return warningMessage;
   }
+
+  public String getInFile()
+  {
+    if (inFile != null)
+    {
+      return inFile.getAbsolutePath() + " (" + index + ")";
+    }
+    else
+    {
+      return "From Paste + (" + index + ")";
+    }
+  }
+
+  /**
+   * @return the dataName
+   */
+  public String getDataName()
+  {
+    return dataName;
+  }
+
+  /**
+   * set the (human readable) name or URI for this datasource
+   * 
+   * @param dataname
+   */
+  protected void setDataName(String dataname)
+  {
+    dataName = dataname;
+  }
+
+  /**
+   * get the underlying bufferedReader for this data source.
+   * 
+   * @return null if no reader available
+   * @throws IOException
+   */
+  public Reader getReader()
+  {
+    if (dataIn != null) // Probably don't need to test for readiness &&
+                        // dataIn.ready())
+    {
+      return dataIn;
+    }
+    return null;
+  }
 }