X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=552f00edc24cbc8fea60631a5ce93f6369dc71e0;hb=19f8ee5562523508666b4472ad624b9e549a3cea;hp=6679a03a907e3e01224a66c4b7385aa0088761cb;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git
diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 6679a03..552f00e 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -1,91 +1,137 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- *
+ * 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 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
+ * 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 .
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
+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.ext.jmol.JmolParser;
+import jalview.structure.StructureImportSettings;
+import jalview.util.MessageManager;
+
import java.io.File;
+import java.io.IOException;
import java.io.InputStream;
-
-import jalview.datamodel.*;
+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;
+
+ public static String FILE = "File";
+
+ public static String URL = "URL";
+
+ public static String PASTE = "Paste";
+
+ public static String CLASSLOADER = "ClassLoader";
+
/**
- * 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" }; // , "SimpleBLAST" };
+ 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", "STH",
- "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, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar",
- "sto,stk" };
+ boolean serviceSecondaryStruct = false;
+
+ private AlignFile 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",
- "STH" };
+ public static final String[] READABLE_FORMATS = new String[] { "BLC",
+ "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH", "PDB",
+ "JnetFile", "RNAML", PhylipFile.FILE_DESC, JSONFile.FILE_DESC,
+ 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, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa", "jar",
- "sto,stk" }; // ,
-
- // ".blast"
- // };
+ public static final String[] READABLE_EXTENSIONS = new String[] {
+ "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
+ "sto,stk", "xml,rnaml", PhylipFile.FILE_EXT, JSONFile.FILE_EXT,
+ ".gff2,gff3", "jar,jvp", HtmlFile.FILE_EXT, "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", "Jalview",
- "Stockholm" };// ,
+ public static final String[] READABLE_FNAMES = new String[] { "Fasta",
+ "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Stockholm", "RNAML",
+ PhylipFile.FILE_DESC, JSONFile.FILE_DESC, 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",
+ PhylipFile.FILE_DESC, JSONFile.FILE_DESC };
- // "SimpleBLAST"
- // };
+ /**
+ * 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", PhylipFile.FILE_EXT, JSONFile.FILE_EXT, "jvp" };
+
+ /**
+ * 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", "STH",
+ PhylipFile.FILE_DESC, JSONFile.FILE_DESC, "Jalview" };
public static String INVALID_CHARACTERS = "Contains invalid characters";
@@ -93,8 +139,24 @@ public class AppletFormatAdapter
public static String SUPPORTED_FORMATS = "Formats currently supported are\n"
+ prettyPrint(READABLE_FORMATS);
+ public AppletFormatAdapter()
+ {
+ }
+
+ public AppletFormatAdapter(AlignmentViewPanel viewpanel)
+ {
+ this.viewpanel = viewpanel;
+ }
+
+ public AppletFormatAdapter(AlignmentViewPanel alignPanel,
+ AlignExportSettingI settings)
+ {
+ viewpanel = alignPanel;
+ exportSettings = settings;
+ }
+
/**
- *
+ *
* @param els
* @return grammatically correct(ish) list consisting of els elements.
*/
@@ -104,29 +166,12 @@ public class AppletFormatAdapter
for (int i = 0, iSize = els.length - 1; i < iSize; i++)
{
list.append(els[i]);
- list.append(",");
+ 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;
-
- /**
- * character used to write newlines
- */
- protected String newline = System.getProperty("line.separator");
-
public void setNewlineString(String nl)
{
newline = nl;
@@ -139,7 +184,7 @@ public class AppletFormatAdapter
/**
* 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
@@ -151,7 +196,7 @@ public class AppletFormatAdapter
/**
* validate format is valid for IO
- *
+ *
* @param format
* a format string to be compared with either READABLE_FORMATS or
* WRITEABLE_FORMATS
@@ -162,12 +207,16 @@ public class AppletFormatAdapter
public static final boolean isValidFormat(String format,
boolean forwriting)
{
+ if (format == null)
+ {
+ return false;
+ }
boolean valid = false;
String[] format_list = (forwriting) ? WRITEABLE_FORMATS
: READABLE_FORMATS;
- for (int i = 0; i < format_list.length; i++)
+ for (String element : format_list)
{
- if (format_list[i].equalsIgnoreCase(format))
+ if (element.equalsIgnoreCase(format))
{
return true;
}
@@ -178,17 +227,17 @@ public class AppletFormatAdapter
/**
* 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!
*/
- public Alignment readFile(String inFile, String type, String format)
+ public AlignmentI readFile(String inFile, String type, String format)
throws java.io.IOException
{
// TODO: generalise mapping between format string and io. class instances
@@ -198,55 +247,73 @@ public class AppletFormatAdapter
{
if (format.equals("FASTA"))
{
- afile = new FastaFile(inFile, type);
+ alignFile = new FastaFile(inFile, type);
}
else if (format.equals("MSF"))
{
- afile = new MSFfile(inFile, type);
+ alignFile = new MSFfile(inFile, type);
}
else if (format.equals("PileUp"))
{
- afile = new PileUpfile(inFile, type);
+ alignFile = new PileUpfile(inFile, type);
}
else if (format.equals("CLUSTAL"))
{
- afile = new ClustalFile(inFile, type);
+ alignFile = new ClustalFile(inFile, type);
}
else if (format.equals("BLC"))
{
- afile = new BLCFile(inFile, type);
+ alignFile = new BLCFile(inFile, type);
}
else if (format.equals("PIR"))
{
- afile = new PIRFile(inFile, type);
+ alignFile = new PIRFile(inFile, type);
}
else if (format.equals("PFAM"))
{
- afile = new PfamFile(inFile, type);
+ alignFile = new PfamFile(inFile, type);
}
else if (format.equals("JnetFile"))
{
- afile = new JPredFile(inFile, type);
- ((JPredFile) afile).removeNonSequences();
+ alignFile = new JPredFile(inFile, type);
+ ((JPredFile) alignFile).removeNonSequences();
}
- else if (format.equals("PDB"))
+ else if (format.equals("PDB") || format.equalsIgnoreCase("mmCIF"))
{
- afile = new MCview.PDBfile(inFile, type);
+ StructureImportSettings.addSettings(annotFromStructure,
+ localSecondaryStruct, serviceSecondaryStruct);
+ alignFile = new JmolParser(inFile, type);
+ ((StructureFile) alignFile).setDbRefType(format);
}
else if (format.equals("STH"))
{
- afile = new StockholmFile(inFile, type);
+ alignFile = new StockholmFile(inFile, type);
}
else if (format.equals("SimpleBLAST"))
{
- afile = new SimpleBlastFile(inFile, type);
+ alignFile = new SimpleBlastFile(inFile, type);
}
-
- Alignment al = new Alignment(afile.getSeqsAsArray());
-
- afile.addAnnotations(al);
-
- return al;
+ else if (format.equals(PhylipFile.FILE_DESC))
+ {
+ alignFile = new PhylipFile(inFile, type);
+ }
+ else if (format.equals(JSONFile.FILE_DESC))
+ {
+ alignFile = new JSONFile(inFile, type);
+ }
+ else if (format.equals(HtmlFile.FILE_DESC))
+ {
+ alignFile = new HtmlFile(inFile, type);
+ }
+ else if (format.equals("RNAML"))
+ {
+ alignFile = new RnamlFile(inFile, type);
+ }
+ else if (format.equals(IdentifyFile.FeaturesFile))
+ {
+ alignFile = new FeaturesFile(true, inFile, type);
+ }
+ return buildAlignmentFrom(alignFile);
} catch (Exception e)
{
e.printStackTrace();
@@ -265,10 +332,8 @@ public class AppletFormatAdapter
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, "Paste");
+ return buildAlignmentFrom(alignFile);
} catch (Exception ex)
{
@@ -280,7 +345,10 @@ public class AppletFormatAdapter
ex.printStackTrace();
}
}
-
+ if (format.equalsIgnoreCase("HTML"))
+ {
+ throw new IOException(e.getMessage());
+ }
// If we get to this stage, the format was not supported
throw new java.io.IOException(SUPPORTED_FORMATS);
}
@@ -288,15 +356,15 @@ public class AppletFormatAdapter
/**
* Constructs the correct filetype parser for an already open datasource
- *
+ *
* @param source
* an existing datasource
* @param format
* File format of data that will be provided by datasource
- *
+ *
* @return DOCUMENT ME!
*/
- public Alignment readFromFile(FileParse source, String format)
+ public AlignmentI readFromFile(FileParse source, String format)
throws java.io.IOException
{
// TODO: generalise mapping between format string and io. class instances
@@ -309,55 +377,93 @@ public class AppletFormatAdapter
{
if (format.equals("FASTA"))
{
- afile = new FastaFile(source);
+ alignFile = new FastaFile(source);
}
else if (format.equals("MSF"))
{
- afile = new MSFfile(source);
+ alignFile = new MSFfile(source);
}
else if (format.equals("PileUp"))
{
- afile = new PileUpfile(source);
+ alignFile = new PileUpfile(source);
}
else if (format.equals("CLUSTAL"))
{
- afile = new ClustalFile(source);
+ alignFile = new ClustalFile(source);
}
else if (format.equals("BLC"))
{
- afile = new BLCFile(source);
+ alignFile = new BLCFile(source);
}
else if (format.equals("PIR"))
{
- afile = new PIRFile(source);
+ alignFile = new PIRFile(source);
}
else if (format.equals("PFAM"))
{
- afile = new PfamFile(source);
+ alignFile = new PfamFile(source);
}
else if (format.equals("JnetFile"))
{
- afile = new JPredFile(source);
- ((JPredFile) afile).removeNonSequences();
+ alignFile = new JPredFile(source);
+ ((JPredFile) alignFile).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(source);
+ }
+ else
+ {
+ StructureImportSettings.setShowSeqFeatures(true);
+ alignFile = new MCview.PDBfile(annotFromStructure,
+ localSecondaryStruct, serviceSecondaryStruct, source);
+ }
+ ((StructureFile) alignFile).setDbRefType(Type.PDB);
+ }
+ else if (format.equalsIgnoreCase("mmCIF"))
+ {
+ StructureImportSettings.addSettings(annotFromStructure,
+ localSecondaryStruct, serviceSecondaryStruct);
+ alignFile = new JmolParser(source);
+ ((StructureFile) alignFile).setDbRefType(Type.MMCIF);
}
else if (format.equals("STH"))
{
- afile = new StockholmFile(source);
+ alignFile = new StockholmFile(source);
+ }
+ else if (format.equals("RNAML"))
+ {
+ alignFile = new RnamlFile(source);
}
else if (format.equals("SimpleBLAST"))
{
- afile = new SimpleBlastFile(source);
+ alignFile = new SimpleBlastFile(source);
+ }
+ else if (format.equals(PhylipFile.FILE_DESC))
+ {
+ alignFile = new PhylipFile(source);
+ }
+ else if (format.equals(IdentifyFile.FeaturesFile))
+ {
+ alignFile = new FeaturesFile(inFile, type);
+ }
+ else if (format.equals(JSONFile.FILE_DESC))
+ {
+ alignFile = new JSONFile(source);
+ }
+ else if (format.equals(HtmlFile.FILE_DESC))
+ {
+ alignFile = new HtmlFile(source);
}
- Alignment al = new Alignment(afile.getSeqsAsArray());
-
- afile.addAnnotations(al);
+ return buildAlignmentFrom(alignFile);
- return al;
} catch (Exception e)
{
e.printStackTrace();
@@ -376,10 +482,8 @@ public class AppletFormatAdapter
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, "Paste");
+ return buildAlignmentFrom(alignFile);
} catch (Exception ex)
{
@@ -398,10 +502,61 @@ public class AppletFormatAdapter
}
/**
+ * boilerplate method to handle data from an AlignFile and construct a new
+ * alignment or import to an existing alignment
+ *
+ * @param alignFile2
+ * @return AlignmentI instance ready to pass to a UI constructor
+ */
+ private AlignmentI buildAlignmentFrom(AlignFile alignFile2)
+ {
+ // 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(String 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
- *
+ *
* @param format
* string name of alignment format
* @param alignment
@@ -409,7 +564,7 @@ public class AppletFormatAdapter
* @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,
@@ -418,7 +573,6 @@ public class AppletFormatAdapter
try
{
AlignFile afile = null;
-
if (format.equalsIgnoreCase("FASTA"))
{
afile = new FastaFile();
@@ -455,15 +609,42 @@ public class AppletFormatAdapter
{
afile = new AMSAFile(alignment);
}
+ else if (format.equalsIgnoreCase(PhylipFile.FILE_DESC))
+ {
+ afile = new PhylipFile();
+ }
+ else if (format.equalsIgnoreCase(JSONFile.FILE_DESC))
+ {
+ afile = new JSONFile();
+ }
+ else if (format.equalsIgnoreCase("RNAML"))
+ {
+ afile = new RnamlFile();
+ }
+
else
{
throw new Exception(
- "Implementation error: Unknown file format string");
+ MessageManager
+ .getString("error.implementation_error_unknown_file_format_string"));
}
+
afile.setNewlineString(newline);
afile.addJVSuffix(jvsuffix);
+ afile.setExportSettings(exportSettings);
+ afile.configureForView(viewpanel);
- afile.setSeqs(alignment.getSequencesArray());
+ // check whether we were given a specific alignment to export, rather than
+ // the one in the viewpanel
+ if (viewpanel == null || viewpanel.getAlignment() == null
+ || viewpanel.getAlignment() != alignment)
+ {
+ afile.setSeqs(alignment.getSequencesArray());
+ }
+ else
+ {
+ afile.setSeqs(viewpanel.getAlignment().getSequencesArray());
+ }
String afileresp = afile.print();
if (afile.hasWarningMessage())
@@ -506,47 +687,43 @@ public class AppletFormatAdapter
{
System.out.println("Reading file: " + f);
AppletFormatAdapter afa = new AppletFormatAdapter();
- String fName = f.getName();
+ Runtime r = Runtime.getRuntime();
+ System.gc();
+ long memf = -r.totalMemory() + r.freeMemory();
+ long t1 = -System.currentTimeMillis();
+ AlignmentI al = afa.readFile(args[i], FILE,
+ new IdentifyFile().identify(args[i], FILE));
+ t1 += System.currentTimeMillis();
+ System.gc();
+ memf += r.totalMemory() - r.freeMemory();
+ if (al != null)
{
- Runtime r = Runtime.getRuntime();
- 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));
- t1 += System.currentTimeMillis();
- System.gc();
- memf += r.totalMemory() - r.freeMemory();
- if (al != null)
+ System.out.println("Alignment contains " + al.getHeight()
+ + " sequences and " + al.getWidth() + " columns.");
+ try
{
- System.out.println("Alignment contains " + al.getHeight()
- + " sequences and " + al.getWidth() + " columns.");
- try
- {
- System.out.println(new AppletFormatAdapter()
- .formatSequences("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
+ System.out.println(new AppletFormatAdapter().formatSequences(
+ "FASTA", al, true));
+ } catch (Exception e)
{
- System.out.println("Couldn't read alignment");
+ System.err
+ .println("Couln't format the alignment for output as a FASTA file.");
+ e.printStackTrace(System.err);
}
- System.out.println("Read took " + (t1 / 1000.0) + " seconds.");
- System.out
- .println("Difference between free memory now and before is "
- + (memf / (1024.0 * 1024.0) * 1.0) + " MB");
}
+ else
+ {
+ System.out.println("Couldn't read alignment");
+ }
+ System.out.println("Read took " + (t1 / 1000.0) + " seconds.");
+ 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
+ "'th argument: " + args[i] + "\n" + e);
}
-
}
else
{
@@ -560,7 +737,7 @@ public class AppletFormatAdapter
/**
* 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
@@ -681,7 +858,7 @@ public class AppletFormatAdapter
{
try
{
- String idformat = new jalview.io.IdentifyFile().Identify(file,
+ String idformat = new jalview.io.IdentifyFile().identify(file,
protocol);
if (idformat == null)
{
@@ -728,4 +905,13 @@ public class AppletFormatAdapter
return null;
}
+ public AlignFile getAlignFile()
+ {
+ return alignFile;
+ }
+
+ public void setAlignFile(AlignFile alignFile)
+ {
+ this.alignFile = alignFile;
+ }
}