X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileParse.java;h=05a7212b5fba1692407ded180b6e2be9f6e29be9;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=af3bbeca10db20c4b1f5fa044a8d78089d517ab0;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index af3bbec..05a7212 100755
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -1,72 +1,410 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 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;
-  public int fileSize;
-  public int noLines;
-  protected String type;
-  protected BufferedReader dataIn;
-
-  public FileParse()
-  {
-  }
-
-  public FileParse(String fileStr, String type)
-      throws MalformedURLException, IOException
-  {
-    this.type = type;
-
-    if (type.equals("File"))
-    {
-      this.inFile = new File(fileStr);
-      this.fileSize = (int) inFile.length();
-
-      dataIn = new BufferedReader(new FileReader(fileStr));
-    }
-    else if (type.equals("URL"))
-    {
-      URL url = new URL(fileStr);
-      this.fileSize = 0;
-      dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
-    }
-    else if (type.equals("Paste"))
-    {
-      dataIn = new BufferedReader(new StringReader(fileStr));
-    }
-  }
-
-  public String nextLine()
-      throws IOException
-  {
-    String next = dataIn.readLine();
-
-    if (next != null)
-    {
-      noLines++;
-    }
-
-    return next;
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * 
+ * 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/>.
+ */
+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
+{
+  /**
+   * 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 = '#';
+  /**
+   * character used to write newlines 
+   */
+  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;
+
+  public FileParse()
+  {
+  }
+
+  /**
+   * 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;
+    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));
+      dataName = 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()));
+    // record URL as name of datasource.
+    dataName = fileStr;
+    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(suffixSeparator);
+    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)
+        {
+          if (checkFileSource(suffixLess))
+          {
+            throw new IOException("Problem opening " + inFile
+                    + " (also tried " + suffixLess + ") : " + errormessage);
+          }
+        }
+        else
+        {
+          throw new IOException("Problem opening " + inFile + " : "
+                  + errormessage);
+        }
+      }
+    }
+    else if (type.equals(AppletFormatAdapter.URL))
+    {
+      try
+      {
+        try
+        {
+          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);
+          }
+          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)
+      {
+        String suffixLess = extractSuffix(fileStr);
+        if (suffixLess != null)
+          is = getClass().getResourceAsStream("/" + suffixLess);
+      }
+      if (is != null)
+      {
+        dataIn = new BufferedReader(new java.io.InputStreamReader(is));
+        dataName = fileStr;
+      }
+      else
+      {
+        error = true;
+      }
+    }
+    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);
+  }
+
+  /**
+   * 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);
+  }
+
+  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.");
+    }
+  }
+
+  /**
+   * 
+   * @return true if there is a warning for the user
+   */
+  public boolean hasWarningMessage()
+  {
+    return (warningMessage != null && warningMessage.length() > 0);
+  }
+
+  /**
+   * 
+   * @return empty string or warning message about file that was just parsed.
+   */
+  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;
+  }
+}