X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=0709a2f93eb77de0171f0d0fb15a7826718662a5;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=d9b0b55c4b02ff501631281869ef5c074101e140;hpb=74a515589df94a3378da48f275bd08f7595bca19;p=jalview.git
diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index d9b0b55..0709a2f 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -1,122 +1,165 @@
/*
- * 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 2.7)
+ * 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 .
*/
package jalview.io;
import java.io.File;
+import java.io.InputStream;
import jalview.datamodel.*;
/**
- * A low level class for alignment and feature IO
- * with alignment formatting methods used by both applet
- * and application for generating flat alignment files.
- * It also holds the lists of magic format names
- * that the applet and application will allow the user to read or write files with.
- *
+ * A low level class for alignment and feature IO with alignment formatting
+ * methods used by both applet and application for generating flat alignment
+ * files. It also holds the lists of magic format names that the applet and
+ * application will allow the user to read or write files with.
+ *
* @author $author$
* @version $Revision$
*/
public class AppletFormatAdapter
{
- /**
- * List of valid format strings used in the isValidFormat method
+ /**
+ * List of valid format strings used in the isValidFormat method
*/
public static final String[] READABLE_FORMATS = new String[]
- {
- "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH", "PDB", "JnetFile"
- };
+ { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH",
+ "PDB", "JnetFile" }; // , "SimpleBLAST" };
+
/**
- * List of valid format strings for use by callers of the formatSequences method
+ * List of valid format strings for use by callers of the formatSequences
+ * method
*/
public static final String[] WRITEABLE_FORMATS = new String[]
- {
- "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM" , "AMSA"
- };
+ { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "AMSA" };
+
/**
- * List of extensions corresponding to file format types
- * in WRITABLE_FNAMES that are writable by the
- * application.
+ * List of extensions corresponding to file format types in WRITABLE_FNAMES
+ * that are writable by the application.
*/
public static final String[] WRITABLE_EXTENSIONS = new String[]
- { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc","amsa","jar" };
+ { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar" };
+
/**
- * List of writable formats by the application. Order must
- * correspond with the WRITABLE_EXTENSIONS list of formats.
+ * List of writable formats by the application. Order must correspond with the
+ * WRITABLE_EXTENSIONS list of formats.
*/
public static final String[] WRITABLE_FNAMES = new String[]
- { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview" };
+ { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview" };
/**
* List of readable format file extensions by application in order
- * corresponding to READABLE_FNAMES
+ * corresponding to READABLE_FNAMES
*/
- public static final String[] READABLE_EXTENSIONS = new String[]
- {
- "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
- "amsa","jar"
- };
+ public static final String[] READABLE_EXTENSIONS = new String[]
+ { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar",
+ "sto,stk" }; // ,
+
+ // ".blast"
+ // };
+
/**
- * List of readable formats by application in order
- * corresponding to READABLE_EXTENSIONS
+ * List of readable formats by application in order corresponding to
+ * READABLE_EXTENSIONS
*/
- public static final String[] READABLE_FNAMES = new String[]
- {
- "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA","Jalview"
- };
-
+ public static final String[] READABLE_FNAMES = new String[]
+ { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview",
+ "Stockholm" };// ,
+
+ // "SimpleBLAST"
+ // };
+
public static String INVALID_CHARACTERS = "Contains invalid characters";
+
// TODO: make these messages dynamic
- public static String SUPPORTED_FORMATS = "Formats currently supported are\n" +
- prettyPrint(READABLE_FORMATS);
+ public static String SUPPORTED_FORMATS = "Formats currently supported are\n"
+ + prettyPrint(READABLE_FORMATS);
+
/**
*
* @param els
* @return grammatically correct(ish) list consisting of els elements.
*/
- public static String prettyPrint(String[] els) {
+ public static String prettyPrint(String[] els)
+ {
StringBuffer list = new StringBuffer();
- for (int i=0,iSize=els.length-1; iUNKNOWN\n" + inFile, "Paste");
+ Alignment al = new Alignment(afile.getSeqsAsArray());
+ afile.addAnnotations(al);
+ return al;
+
+ } catch (Exception ex)
{
if (ex.toString().startsWith(INVALID_CHARACTERS))
{
@@ -229,17 +390,22 @@ public class AppletFormatAdapter
}
/**
- * Construct an output class for an alignment in a particular filetype
- *
- * @param format string name of alignment format
- * @param alignment the alignment to be written out
- * @param jvsuffix passed to AlnFile class controls whether /START-END is added to sequence names
- *
+ * Construct an output class for an alignment in a particular filetype TODO:
+ * allow caller to detect errors and warnings encountered when generating
+ * output
+ *
+ * @param format
+ * string name of alignment format
+ * @param alignment
+ * the alignment to be written out
+ * @param jvsuffix
+ * passed to AlnFile class controls whether /START-END is added to
+ * sequence names
+ *
* @return alignment flat file contents
*/
- public String formatSequences(String format,
- AlignmentI alignment,
- boolean jvsuffix)
+ public String formatSequences(String format, AlignmentI alignment,
+ boolean jvsuffix)
{
try
{
@@ -280,55 +446,273 @@ public class AppletFormatAdapter
else if (format.equalsIgnoreCase("AMSA"))
{
afile = new AMSAFile(alignment);
- } else {
- throw new Exception("Implementation error: Unknown file format string");
}
-
+ else
+ {
+ throw new Exception(
+ "Implementation error: Unknown file format string");
+ }
+ afile.setNewlineString(newline);
afile.addJVSuffix(jvsuffix);
afile.setSeqs(alignment.getSequencesArray());
- return afile.print();
- }
- catch (Exception e)
+ String afileresp = afile.print();
+ if (afile.hasWarningMessage())
+ {
+ System.err.println("Warning raised when writing as " + format
+ + " : " + afile.getWarningMessage());
+ }
+ return afileresp;
+ } catch (Exception e)
{
- System.err.println("Failed to write alignment as a '" + format +
- "' file\n");
+ System.err.println("Failed to write alignment as a '" + format
+ + "' file\n");
e.printStackTrace();
}
return null;
}
+
+ public static String checkProtocol(String file)
+ {
+ String protocol = FILE;
+ String ft = file.toLowerCase().trim();
+ if (ft.indexOf("http:") ==0 || ft.indexOf("https:") ==0 || ft.indexOf("file:") == 0)
+ {
+ protocol = URL;
+ }
+ return protocol;
+ }
+
public static void main(String[] args)
{
- int i=0;
- while (i>file\n"
+ + file + ">>endfile");
+ }
+
+ // This might throw a security exception in certain browsers
+ // Netscape Communicator for instance.
+ try
+ {
+ boolean rtn = false;
+ InputStream is = System.getSecurityManager().getClass()
+ .getResourceAsStream("/" + file);
+ if (is != null)
+ {
+ rtn = true;
+ is.close();
+ }
+ if (debug)
+ {
+ System.err.println("Resource '" + file + "' was "
+ + (rtn ? "" : "not") + " located by classloader.");
+ }
+ ;
+ if (rtn)
+ {
+ protocol = AppletFormatAdapter.CLASSLOADER;
+ }
+
+ } catch (Exception ex)
+ {
+ System.err
+ .println("Exception checking resources: " + file + " " + ex);
+ }
+
+ if (file.indexOf("://") > -1)
+ {
+ protocol = AppletFormatAdapter.URL;
+ }
+ else
+ {
+ // skipping codebase prepend check.
+ protocol = AppletFormatAdapter.FILE;
+ }
+ FileParse fp = null;
+ try
+ {
+ if (debug)
+ {
+ System.out.println("Trying to get contents of resource as "
+ + protocol + ":");
+ }
+ fp = new FileParse(file, protocol);
+ if (!fp.isValid())
+ {
+ fp = null;
+ }
+ else
+ {
+ if (debug)
+ {
+ System.out.println("Successful.");
+ }
+ }
+ } catch (Exception e)
+ {
+ if (debug)
+ {
+ System.err.println("Exception when accessing content: " + e);
+ }
+ fp = null;
+ }
+ if (fp == null)
+ {
+ if (debug)
+ {
+ System.out.println("Accessing as paste.");
+ }
+ protocol = AppletFormatAdapter.PASTE;
+ fp = null;
+ try
+ {
+ fp = new FileParse(file, protocol);
+ if (!fp.isValid())
+ {
+ fp = null;
+ }
+ } catch (Exception e)
+ {
+ System.err.println("Failed to access content as paste!");
+ e.printStackTrace();
+ fp = null;
+ }
+ }
+ if (fp == null)
+ {
+ return null;
+ }
+ if (format == null || format.length() == 0)
+ {
+ return protocol;
+ }
+ else
+ {
+ try
+ {
+ String idformat = new jalview.io.IdentifyFile().Identify(file,
+ protocol);
+ if (idformat == null)
+ {
+ if (debug)
+ {
+ System.out.println("Format not identified. Inaccessible file.");
+ }
+ return null;
+ }
+ if (debug)
+ {
+ System.out.println("Format identified as " + idformat
+ + "and expected as " + format);
+ }
+ if (idformat.equals(format))
+ {
+ if (debug)
+ {
+ System.out.println("Protocol identified as " + protocol);
+ }
+ return protocol;
+ }
+ else
+ {
+ if (debug)
+ {
+ System.out
+ .println("File deemed not accessible via " + protocol);
+ }
+ fp.close();
+ return null;
+ }
+ } catch (Exception e)
+ {
+ if (debug)
+ {
+ System.err.println("File deemed not accessible via " + protocol);
+ e.printStackTrace();
+ }
+ ;
+
+ }
+ }
+ return null;
}
}