X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileParse.java;h=4c69ce0fcdee5134761e15ae69893617c3cb4de3;hb=f49e86c9f8e7c0301f2b8824d0c033a3df291e6a;hp=0c46a17217a165451a1b52803c7157031dd407db;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index 0c46a17..4c69ce0 100755
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -1,63 +1,290 @@
-/*
-* 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
+ * 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;
+  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
+   */
+  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();
+    }
+  }
+  /**
+   * 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));
+    }
+    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(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));
+    }
+    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;
+      }
+    }
+    if (dataIn==null)
+    {
+      // 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+")";
+    }
+  }
+}