-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-\r
-package jalview.io;\r
-\r
-import java.io.*;\r
-import java.net.*;\r
-\r
-public class FileParse {\r
-\r
- public File inFile;\r
- public int fileSize;\r
- public int noLines;\r
-\r
- protected String type;\r
- protected BufferedReader dataIn;\r
-\r
- public FileParse() {}\r
-\r
- public FileParse(String fileStr, String type) throws MalformedURLException, IOException\r
- {\r
-\r
- this.type = type;\r
-\r
- if (type.equals("File")) {\r
- this.inFile = new File(fileStr);\r
- this.fileSize = (int)inFile.length();\r
-\r
- dataIn = new BufferedReader(new FileReader( fileStr ));\r
-\r
- } else if (type.equals("URL")) {\r
- URL url = new URL(fileStr);\r
- this.fileSize = 0;\r
- dataIn = new BufferedReader(new InputStreamReader( url.openStream() ));\r
- } else if(type.equals("Paste"))\r
- {\r
- dataIn = new BufferedReader(new StringReader(fileStr));\r
- }\r
- }\r
-\r
- public String nextLine() throws IOException {\r
- String next = dataIn.readLine();\r
- if (next != null) {\r
- noLines++;\r
- }\r
- return next;\r
- }\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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;
+ }
+ }
+ 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+")";
+ }
+ }
+
+ public Reader getReader() throws IOException
+ {
+ if (dataIn!=null && dataIn.ready())
+ {
+ return dataIn;
+ }
+ return null;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff