X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=5f40713b17c7f935af438197124b84668f1a24a5;hb=4815037f13748676b04b91dc761b73cf6f2d6ecd;hp=8e05b4477fd9ab5cafa693fd0f7f178da6b8bf29;hpb=aa5a15ade3b078f6c2cf78db5aa05e0dcb1ce792;p=jalview.git
diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 8e05b44..5f40713 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -1,329 +1,332 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 2
+ * as published by the Free Software Foundation, either version 3
* 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.
- *
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
-import java.io.File;
+import jalview.api.AlignExportSettingI;
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.PDBEntry.Type;
+import jalview.datamodel.SequenceI;
+import jalview.ext.jmol.JmolParser;
+import jalview.structure.StructureImportSettings;
-import jalview.datamodel.*;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.List;
/**
* 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
{
+ private AlignmentViewPanel viewpanel;
+
/**
- * List of valid format strings used in the isValidFormat method
+ * add jalview-derived non-secondary structure annotation from PDB structure
*/
- public static final String[] READABLE_FORMATS = new String[]
- { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH",
- "PDB", "JnetFile" };
+ boolean annotFromStructure = false;
/**
- * List of valid format strings for use by callers of the formatSequences
- * method
+ * add secondary structure from PDB data with built-in algorithms
*/
- public static final String[] WRITEABLE_FORMATS = new String[]
- { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "AMSA" };
+ boolean localSecondaryStruct = false;
/**
- * List of extensions corresponding to file format types in WRITABLE_FNAMES
- * that are writable by the application.
+ * process PDB data with web services
*/
- public static final String[] WRITABLE_EXTENSIONS = new String[]
- { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar" };
+ boolean serviceSecondaryStruct = false;
+
+ private AlignmentFileI alignFile = null;
+
+ String inFile;
/**
- * List of writable formats by the application. Order must correspond with the
- * WRITABLE_EXTENSIONS list of formats.
+ * character used to write newlines
+ */
+ protected String newline = System.getProperty("line.separator");
+
+ private AlignExportSettingI exportSettings;
+
+ /**
+ * List of valid format strings used in the isValidFormat method
*/
- public static final String[] WRITABLE_FNAMES = new String[]
- { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview" };
+ // public static final String[] READABLE_FORMATS = new String[] { "BLC",
+ // "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH", "PDB",
+ // "JnetFile", "RNAML", "PHYLIP", "JSON",
+ // IdentifyFile.FeaturesFile, "HTML", "mmCIF" };
/**
* List of readable format file extensions by application in order
* 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, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
+ // "sto,stk", "xml,rnaml", "phy", "json", ".gff2,gff3", "jar,jvp",
+ // "html", "cif" };
+
+ //
+ // /**
+ // * 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", "Stockholm", "RNAML",
+ // "PHYLIP", "JSON", IdentifyFile.FeaturesFile,
+ // "Jalview", HtmlFile.FILE_DESC, "mmCIF" };
+
+ /**
+ * 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", "STH",
+ // "PHYLIP", "JSON" };
+
+ /**
+ * 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, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
+ // "sto,stk", "phy", "json", "jvp" };
/**
- * List of readable formats by application in order corresponding to
- * READABLE_EXTENSIONS
+ * List of writable formats by the application. Order must correspond with the
+ * WRITABLE_EXTENSIONS list of formats.
*/
- public static final String[] READABLE_FNAMES = new String[]
- { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Jalview" };
+ // public static final String[] WRITABLE_FNAMES = new String[] { "Fasta",
+ // "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "STH", "PHYLIP",
+ // "JSON", "Jalview" };
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);
+ + prettyPrint(FileFormat.getReadableFormats());
- /**
- *
- * @param els
- * @return grammatically correct(ish) list consisting of els elements.
- */
- public static String prettyPrint(String[] els)
+ public AppletFormatAdapter()
{
- StringBuffer list = new StringBuffer();
- for (int i = 0, iSize = els.length - 1; i < iSize; i++)
- {
- list.append(els[i]);
- list.append(",");
- }
- list.append(" and " + els[els.length - 1] + ".");
- return list.toString();
}
- public static String FILE = "File";
-
- public static String URL = "URL";
-
- public static String PASTE = "Paste";
-
- public static String CLASSLOADER = "ClassLoader";
-
- AlignFile afile = null;
-
- String inFile;
+ public AppletFormatAdapter(AlignmentViewPanel viewpanel)
+ {
+ this.viewpanel = viewpanel;
+ }
- /**
- * check that this format is valid for reading
- *
- * @param format
- * a format string to be compared with READABLE_FORMATS
- * @return true if format is readable
- */
- public static final boolean isValidFormat(String format)
+ public AppletFormatAdapter(AlignmentViewPanel alignPanel,
+ AlignExportSettingI settings)
{
- return isValidFormat(format, false);
+ viewpanel = alignPanel;
+ exportSettings = settings;
}
/**
- * validate format is valid for IO
+ * Formats a grammatically correct(ish) list consisting of the given objects
*
- * @param format
- * a format string to be compared with either READABLE_FORMATS
- * or WRITEABLE_FORMATS
- * @param forwriting
- * when true, format is checked for containment in
- * WRITEABLE_FORMATS
- * @return true if format is valid
+ * @param things
+ * @return
*/
- public static final boolean isValidFormat(String format,
- boolean forwriting)
+ public static String prettyPrint(List things)
{
- boolean valid = false;
- String[] format_list = (forwriting) ? WRITEABLE_FORMATS
- : READABLE_FORMATS;
- for (int i = 0; i < format_list.length; i++)
+ StringBuffer list = new StringBuffer();
+ for (int i = 0, iSize = things.size() - 1; i < iSize; i++)
{
- if (format_list[i].equalsIgnoreCase(format))
- {
- return true;
- }
+ list.append(things.get(i).toString());
+ list.append(", ");
}
+ // could i18n 'and' here
+ list.append(" and " + things.get(things.size() - 1).toString() + ".");
+ return list.toString();
+ }
+
+ public void setNewlineString(String nl)
+ {
+ newline = nl;
+ }
- return valid;
+ public String getNewlineString()
+ {
+ return newline;
}
/**
* Constructs the correct filetype parser for a characterised datasource
- *
+ *
* @param inFile
- * data/data location
- * @param type
- * type of datasource
- * @param format
- * File format of data provided by datasource
- *
- * @return DOCUMENT ME!
+ * data/data location
+ * @param sourceType
+ * type of datasource
+ * @param fileFormat
+ *
+ * @return
*/
- public Alignment readFile(String inFile, String type, String format)
- throws java.io.IOException
+ public AlignmentI readFile(String file, DataSourceType sourceType,
+ FileFormatI fileFormat) throws IOException
{
- // TODO: generalise mapping between format string and io. class instances
- // using Constructor.invoke reflection
- this.inFile = inFile;
+ this.inFile = file;
try
{
- if (format.equals("FASTA"))
- {
- afile = new FastaFile(inFile, type);
- }
- else if (format.equals("MSF"))
- {
- afile = new MSFfile(inFile, type);
- }
- else if (format.equals("PileUp"))
- {
- afile = new PileUpfile(inFile, type);
- }
- else if (format.equals("CLUSTAL"))
- {
- afile = new ClustalFile(inFile, type);
- }
- else if (format.equals("BLC"))
- {
- afile = new BLCFile(inFile, type);
- }
- else if (format.equals("PIR"))
- {
- afile = new PIRFile(inFile, type);
- }
- else if (format.equals("PFAM"))
- {
- afile = new PfamFile(inFile, type);
- }
- else if (format.equals("JnetFile"))
- {
- afile = new JPredFile(inFile, type);
- ((JPredFile) afile).removeNonSequences();
- }
- else if (format.equals("PDB"))
- {
- afile = new MCview.PDBfile(inFile, type);
+ if (fileFormat == FileFormat.PDB || fileFormat == FileFormat.MMCif)
+ {
+ // TODO obtain config value from preference settings.
+ // Set value to 'true' to test PDB processing with Jmol: JAL-1213
+ boolean isParseWithJMOL = StructureImportSettings
+ .getDefaultPDBFileParser().equalsIgnoreCase(
+ StructureImportSettings.StructureParser.JMOL_PARSER
+ .toString());
+ if (isParseWithJMOL)
+ {
+ StructureImportSettings.addSettings(annotFromStructure,
+ localSecondaryStruct, serviceSecondaryStruct);
+ alignFile = new JmolParser(annotFromStructure,
+ localSecondaryStruct, serviceSecondaryStruct, inFile,
+ sourceType);
+ }
+ else
+ {
+ StructureImportSettings.addSettings(annotFromStructure,
+ localSecondaryStruct, serviceSecondaryStruct);
+ StructureImportSettings.setShowSeqFeatures(true);
+ alignFile = new MCview.PDBfile(annotFromStructure,
+ localSecondaryStruct, serviceSecondaryStruct, inFile,
+ sourceType);
+ }
+ ((StructureFile) alignFile)
+ .setDbRefType(fileFormat == FileFormat.PDB ? Type.PDB
+ : Type.MMCIF);
}
- else if (format.equals("STH"))
+ else
{
- afile = new StockholmFile(inFile, type);
- }
-
- Alignment al = new Alignment(afile.getSeqsAsArray());
-
- afile.addAnnotations(al);
-
- return al;
+ alignFile = fileFormat.getAlignmentFile(inFile, sourceType);
+ }
+ // new FastaFile(inFile, sourceType);
+ // new MSFfile(inFile, sourceType);
+ // new PileUpfile(inFile, sourceType);
+ // new ClustalFile(inFile, sourceType);
+ // new BLCFile(inFile, sourceType);
+ // new PIRFile(inFile, sourceType);
+ // new PfamFile(inFile, sourceType);
+ // alignFile = new JPredFile(inFile, sourceType);
+ // ((JPredFile) alignFile).removeNonSequences();
+ // new StockholmFile(inFile, sourceType);
+ // new SimpleBlastFile(inFile, sourceType);
+ // new PhylipFile(inFile, sourceType);
+ // new JSONFile(inFile, sourceType);
+ // new HtmlFile(inFile, sourceType);
+ // new RnamlFile(inFile, sourceType);
+ // alignFile = new FeaturesFile(true, inFile, sourceType);
+ return buildAlignmentFromFile();
} catch (Exception e)
{
e.printStackTrace();
- System.err.println("Failed to read alignment using the '" + format
- + "' reader.\n" + e);
+ System.err.println("Failed to read alignment using the '"
+ + fileFormat + "' reader.\n" + e);
if (e.getMessage() != null
&& e.getMessage().startsWith(INVALID_CHARACTERS))
{
- throw new java.io.IOException(e.getMessage());
+ throw new IOException(e.getMessage());
}
// Finally test if the user has pasted just the sequence, no id
- if (type.equalsIgnoreCase("Paste"))
+ if (sourceType == DataSourceType.PASTE)
{
try
{
// Possible sequence is just residues with no label
- afile = new FastaFile(">UNKNOWN\n" + inFile, "Paste");
- Alignment al = new Alignment(afile.getSeqsAsArray());
- afile.addAnnotations(al);
- return al;
+ alignFile = new FastaFile(">UNKNOWN\n" + inFile,
+ DataSourceType.PASTE);
+ return buildAlignmentFromFile();
} catch (Exception ex)
{
if (ex.toString().startsWith(INVALID_CHARACTERS))
{
- throw new java.io.IOException(e.getMessage());
+ throw new IOException(e.getMessage());
}
ex.printStackTrace();
}
}
-
- // If we get to this stage, the format was not supported
- throw new java.io.IOException(SUPPORTED_FORMATS);
+ if (fileFormat == FileFormat.Html)
+ {
+ throw new IOException(e.getMessage());
+ }
}
+ throw new FileFormatException(SUPPORTED_FORMATS);
}
/**
* Constructs the correct filetype parser for an already open datasource
- *
+ *
* @param source
- * an existing datasource
+ * an existing datasource
* @param format
- * File format of data that will be provided by datasource
- *
- * @return DOCUMENT ME!
+ * File format of data that will be provided by datasource
+ *
+ * @return
*/
- public Alignment readFromFile(FileParse source, String format)
- throws java.io.IOException
+ public AlignmentI readFromFile(FileParse source, FileFormatI format)
+ throws IOException
{
- // TODO: generalise mapping between format string and io. class instances
- // using Constructor.invoke reflection
- // This is exactly the same as the readFile method except we substitute
- // 'inFile, type' with 'source'
this.inFile = source.getInFile();
- String type = source.type;
+ DataSourceType type = source.dataSourceType;
try
{
- if (format.equals("FASTA"))
- {
- afile = new FastaFile(source);
- }
- else if (format.equals("MSF"))
- {
- afile = new MSFfile(source);
- }
- else if (format.equals("PileUp"))
- {
- afile = new PileUpfile(source);
- }
- else if (format.equals("CLUSTAL"))
- {
- afile = new ClustalFile(source);
- }
- else if (format.equals("BLC"))
- {
- afile = new BLCFile(source);
- }
- else if (format.equals("PIR"))
- {
- afile = new PIRFile(source);
- }
- else if (format.equals("PFAM"))
+ if (format == FileFormat.PDB || format == FileFormat.MMCif)
{
- afile = new PfamFile(source);
- }
- else if (format.equals("JnetFile"))
- {
- afile = new JPredFile(source);
- ((JPredFile) afile).removeNonSequences();
- }
- else if (format.equals("PDB"))
- {
- afile = new MCview.PDBfile(source);
+ // TODO obtain config value from preference settings
+ boolean isParseWithJMOL = false;
+ if (isParseWithJMOL)
+ {
+ StructureImportSettings.addSettings(annotFromStructure,
+ localSecondaryStruct, serviceSecondaryStruct);
+ alignFile = new JmolParser(annotFromStructure,
+ localSecondaryStruct, serviceSecondaryStruct, source);
+ }
+ else
+ {
+ StructureImportSettings.setShowSeqFeatures(true);
+ alignFile = new MCview.PDBfile(annotFromStructure,
+ localSecondaryStruct, serviceSecondaryStruct, source);
+ }
+ ((StructureFile) alignFile).setDbRefType(Type.PDB);
}
- else if (format.equals("STH"))
+ else
{
- afile = new StockholmFile(source);
+ alignFile = format.getAlignmentFile(source);
}
- Alignment al = new Alignment(afile.getSeqsAsArray());
-
- afile.addAnnotations(al);
+ return buildAlignmentFromFile();
- return al;
} catch (Exception e)
{
e.printStackTrace();
@@ -333,25 +336,24 @@ public class AppletFormatAdapter
if (e.getMessage() != null
&& e.getMessage().startsWith(INVALID_CHARACTERS))
{
- throw new java.io.IOException(e.getMessage());
+ throw new FileFormatException(e.getMessage());
}
// Finally test if the user has pasted just the sequence, no id
- if (type.equalsIgnoreCase("Paste"))
+ if (type == DataSourceType.PASTE)
{
try
{
// Possible sequence is just residues with no label
- afile = new FastaFile(">UNKNOWN\n" + inFile, "Paste");
- Alignment al = new Alignment(afile.getSeqsAsArray());
- afile.addAnnotations(al);
- return al;
+ alignFile = new FastaFile(">UNKNOWN\n" + inFile,
+ DataSourceType.PASTE);
+ return buildAlignmentFromFile();
} catch (Exception ex)
{
if (ex.toString().startsWith(INVALID_CHARACTERS))
{
- throw new java.io.IOException(e.getMessage());
+ throw new IOException(e.getMessage());
}
ex.printStackTrace();
@@ -359,81 +361,104 @@ public class AppletFormatAdapter
}
// If we get to this stage, the format was not supported
- throw new java.io.IOException(SUPPORTED_FORMATS);
+ throw new FileFormatException(SUPPORTED_FORMATS);
+ }
+ }
+
+ /**
+ * boilerplate method to handle data from an AlignFile and construct a new
+ * alignment or import to an existing alignment
+ *
+ * @return AlignmentI instance ready to pass to a UI constructor
+ */
+ private AlignmentI buildAlignmentFromFile()
+ {
+ // Standard boilerplate for creating alignment from parser
+ // alignFile.configureForView(viewpanel);
+
+ AlignmentI al = new Alignment(alignFile.getSeqsAsArray());
+
+ alignFile.addAnnotations(al);
+
+ alignFile.addGroups(al);
+
+ return al;
+ }
+
+ /**
+ * create an alignment flatfile from a Jalview alignment view
+ *
+ * @param format
+ * @param jvsuffix
+ * @param av
+ * @param selectedOnly
+ * @return flatfile in a string
+ */
+ public String formatSequences(FileFormatI format, boolean jvsuffix,
+ AlignmentViewPanel ap, boolean selectedOnly)
+ {
+
+ AlignmentView selvew = ap.getAlignViewport().getAlignmentView(
+ selectedOnly, false);
+ AlignmentI aselview = selvew.getVisibleAlignment(ap.getAlignViewport()
+ .getGapCharacter());
+ List ala = (ap.getAlignViewport()
+ .getVisibleAlignmentAnnotation(selectedOnly));
+ if (ala != null)
+ {
+ for (AlignmentAnnotation aa : ala)
+ {
+ aselview.addAnnotation(aa);
+ }
}
+ viewpanel = ap;
+ return formatSequences(format, aselview, jvsuffix);
}
/**
- * Construct an output class for an alignment in a particular filetype
- * TODO: allow caller to detect errors and warnings encountered when generating output
+ * 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
+ * string name of alignment format
* @param alignment
- * the alignment to be written out
+ * the alignment to be written out
* @param jvsuffix
- * passed to AlnFile class controls whether /START-END is added
- * to sequence names
- *
+ * 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,
+ public String formatSequences(FileFormatI format, AlignmentI alignment,
boolean jvsuffix)
{
try
{
- AlignFile afile = null;
+ AlignmentFileI afile = format.getAlignmentFile(alignment);
- if (format.equalsIgnoreCase("FASTA"))
- {
- afile = new FastaFile();
- }
- else if (format.equalsIgnoreCase("MSF"))
- {
- afile = new MSFfile();
- }
- else if (format.equalsIgnoreCase("PileUp"))
- {
- afile = new PileUpfile();
- }
- else if (format.equalsIgnoreCase("CLUSTAL"))
- {
- afile = new ClustalFile();
- }
- else if (format.equalsIgnoreCase("BLC"))
- {
- afile = new BLCFile();
- }
- else if (format.equalsIgnoreCase("PIR"))
- {
- afile = new PIRFile();
- }
- else if (format.equalsIgnoreCase("PFAM"))
- {
- afile = new PfamFile();
- }
- else if (format.equalsIgnoreCase("STH"))
- {
- afile = new StockholmFile();
- }
- else if (format.equalsIgnoreCase("AMSA"))
+ afile.setNewlineString(newline);
+ afile.setExportSettings(exportSettings);
+ afile.configureForView(viewpanel);
+
+ // check whether we were given a specific alignment to export, rather than
+ // the one in the viewpanel
+ SequenceI[] seqs = null;
+ if (viewpanel == null || viewpanel.getAlignment() == null
+ || viewpanel.getAlignment() != alignment)
{
- afile = new AMSAFile(alignment);
+ seqs = alignment.getSequencesArray();
}
else
{
- throw new Exception(
- "Implementation error: Unknown file format string");
+ seqs = viewpanel.getAlignment().getSequencesArray();
}
- afile.addJVSuffix(jvsuffix);
-
- afile.setSeqs(alignment.getSequencesArray());
-
- String afileresp = afile.print();
+ String afileresp = afile.print(seqs, jvsuffix);
if (afile.hasWarningMessage())
{
- System.err.println("Warning raised when writing as "+format+" : "+afile.getWarningMessage());
+ System.err.println("Warning raised when writing as " + format
+ + " : " + afile.getWarningMessage());
}
return afileresp;
} catch (Exception e)
@@ -446,6 +471,18 @@ public class AppletFormatAdapter
return null;
}
+ public static DataSourceType checkProtocol(String file)
+ {
+ DataSourceType protocol = DataSourceType.FILE;
+ String ft = file.toLowerCase().trim();
+ if (ft.indexOf("http:") == 0 || ft.indexOf("https:") == 0
+ || ft.indexOf("file:") == 0)
+ {
+ protocol = DataSourceType.URL;
+ }
+ return protocol;
+ }
+
public static void main(String[] args)
{
int i = 0;
@@ -462,8 +499,10 @@ public class AppletFormatAdapter
System.gc();
long memf = -r.totalMemory() + r.freeMemory();
long t1 = -System.currentTimeMillis();
- Alignment al = afa.readFile(args[i], FILE, new IdentifyFile()
- .Identify(args[i], FILE));
+ AlignmentI al = afa
+ .readFile(args[i], DataSourceType.FILE,
+ new IdentifyFile().identify(args[i],
+ DataSourceType.FILE));
t1 += System.currentTimeMillis();
System.gc();
memf += r.totalMemory() - r.freeMemory();
@@ -471,6 +510,16 @@ public class AppletFormatAdapter
{
System.out.println("Alignment contains " + al.getHeight()
+ " sequences and " + al.getWidth() + " columns.");
+ try
+ {
+ System.out.println(new AppletFormatAdapter().formatSequences(
+ FileFormat.Fasta, al, true));
+ } catch (Exception e)
+ {
+ System.err
+ .println("Couln't format the alignment for output as a FASTA file.");
+ e.printStackTrace(System.err);
+ }
}
else
{
@@ -480,7 +529,6 @@ public class AppletFormatAdapter
System.out
.println("Difference between free memory now and before is "
+ (memf / (1024.0 * 1024.0) * 1.0) + " MB");
-
} catch (Exception e)
{
System.err.println("Exception when dealing with " + i
@@ -494,6 +542,178 @@ public class AppletFormatAdapter
}
i++;
}
+ }
+
+ /**
+ * try to discover how to access the given file as a valid datasource that
+ * will be identified as the given type.
+ *
+ * @param file
+ * @param format
+ * @return protocol that yields the data parsable as the given type
+ */
+ public static DataSourceType resolveProtocol(String file,
+ FileFormatI format)
+ {
+ return resolveProtocol(file, format, false);
+ }
+
+ public static DataSourceType resolveProtocol(String file,
+ FileFormatI format, boolean debug)
+ {
+ // TODO: test thoroughly!
+ DataSourceType protocol = null;
+ if (debug)
+ {
+ System.out.println("resolving datasource started with:\n>>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 = DataSourceType.CLASSLOADER;
+ }
+
+ } catch (Exception ex)
+ {
+ System.err
+ .println("Exception checking resources: " + file + " " + ex);
+ }
+
+ if (file.indexOf("://") > -1)
+ {
+ protocol = DataSourceType.URL;
+ }
+ else
+ {
+ // skipping codebase prepend check.
+ protocol = DataSourceType.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 = DataSourceType.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)
+ {
+ return protocol;
+ }
+ else
+ {
+ try
+ {
+ FileFormatI idformat = new 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;
+ }
+
+ public AlignmentFileI getAlignFile()
+ {
+ return alignFile;
}
}