X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fio%2FFileFormat.java;h=e94e1cefcaa2642a9bf3c2a21eb5385afbe85220;hb=e185cfd4324bf9e2277e25cfc280cc8a23e75360;hp=a7113f637bd2ca03625026c2c8328e30050c8a86;hpb=8b27085fa7fc5f2877e078421284c2636b85b8c6;p=jalview.git
diff --git a/src/jalview/io/FileFormat.java b/src/jalview/io/FileFormat.java
index a7113f6..e94e1ce 100644
--- a/src/jalview/io/FileFormat.java
+++ b/src/jalview/io/FileFormat.java
@@ -1,33 +1,45 @@
+/*
+ * 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
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.io;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
import jalview.ext.jmol.JmolParser;
import jalview.structure.StructureImportSettings;
import java.io.IOException;
-import java.util.HashMap;
-import java.util.Map;
public enum FileFormat implements FileFormatI
{
- Fasta("FASTA", "fa, fasta, mfa, fastq", true, true)
+ Fasta("Fasta", "fa, fasta, mfa, fastq", true, true)
{
@Override
- public AlignmentFileI getAlignmentFile(String inFile,
- DataSourceType sourceType) throws IOException
- {
- return new FastaFile(inFile, sourceType);
- }
-
- @Override
- public AlignmentFileI getAlignmentFile(FileParse source)
+ public AlignmentFileReaderI getReader(FileParse source)
throws IOException
{
return new FastaFile(source);
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileWriterI getWriter(AlignmentI al)
{
return new FastaFile();
}
@@ -35,44 +47,31 @@ public enum FileFormat implements FileFormatI
Pfam("PFAM", "pfam", true, true)
{
@Override
- public AlignmentFileI getAlignmentFile(String inFile,
- DataSourceType sourceType) throws IOException
- {
- return new PfamFile(inFile, sourceType);
- }
-
- @Override
- public AlignmentFileI getAlignmentFile(FileParse source)
+ public AlignmentFileReaderI getReader(FileParse source)
throws IOException
{
return new PfamFile(source);
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileWriterI getWriter(AlignmentI al)
{
return new PfamFile();
}
},
- Stockholm("STH", "sto,stk", true, true)
+ Stockholm("Stockholm", "sto,stk", true, true)
{
@Override
- public AlignmentFileI getAlignmentFile(String inFile,
- DataSourceType sourceType) throws IOException
- {
- return new StockholmFile(inFile, sourceType);
- }
- @Override
- public AlignmentFileI getAlignmentFile(FileParse source)
+ public AlignmentFileReaderI getReader(FileParse source)
throws IOException
{
return new StockholmFile(source);
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileWriterI getWriter(AlignmentI al)
{
- return new StockholmFile();
+ return new StockholmFile(al);
}
},
@@ -80,20 +79,14 @@ public enum FileFormat implements FileFormatI
PIR("PIR", "pir", true, true)
{
@Override
- public AlignmentFileI getAlignmentFile(String inFile,
- DataSourceType sourceType) throws IOException
- {
- return new PIRFile(inFile, sourceType);
- }
- @Override
- public AlignmentFileI getAlignmentFile(FileParse source)
+ public AlignmentFileReaderI getReader(FileParse source)
throws IOException
{
return new PIRFile(source);
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileWriterI getWriter(AlignmentI al)
{
return new PIRFile();
}
@@ -101,39 +94,44 @@ public enum FileFormat implements FileFormatI
BLC("BLC", "BLC", true, true)
{
@Override
- public AlignmentFileI getAlignmentFile(String inFile,
- DataSourceType sourceType) throws IOException
- {
- return new BLCFile(inFile, sourceType);
- } @Override
- public AlignmentFileI getAlignmentFile(FileParse source)
+ public AlignmentFileReaderI getReader(FileParse source)
throws IOException
{
return new BLCFile(source);
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileWriterI getWriter(AlignmentI al)
{
return new BLCFile();
}
},
- Html("HTML", "html", true, false)
+ AMSA("AMSA", "amsa", true, true)
{
@Override
- public AlignmentFileI getAlignmentFile(String inFile,
- DataSourceType sourceType) throws IOException
+ public AlignmentFileReaderI getReader(FileParse source)
+ throws IOException
+ {
+ return new AMSAFile(source);
+ }
+
+ @Override
+ public AlignmentFileWriterI getWriter(AlignmentI al)
{
- return new HtmlFile(inFile, sourceType);
- } @Override
- public AlignmentFileI getAlignmentFile(FileParse source)
+ return new AMSAFile(al);
+ }
+ },
+ Html("HTML", "html", true, false)
+ {
+ @Override
+ public AlignmentFileReaderI getReader(FileParse source)
throws IOException
{
return new HtmlFile(source);
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileWriterI getWriter(AlignmentI al)
{
return new HtmlFile();
}
@@ -148,40 +146,30 @@ public enum FileFormat implements FileFormatI
Rnaml("RNAML", "xml,rnaml", true, false)
{
@Override
- public AlignmentFileI getAlignmentFile(String inFile,
- DataSourceType sourceType) throws IOException
- {
- return new RnamlFile(inFile, sourceType);
- } @Override
- public AlignmentFileI getAlignmentFile(FileParse source)
+ public AlignmentFileReaderI getReader(FileParse source)
throws IOException
{
return new RnamlFile(source);
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileWriterI getWriter(AlignmentI al)
{
return new RnamlFile();
}
},
- Json("JSON","json", true, true)
+ Json("JSON", "json", true, true)
{
@Override
- public AlignmentFileI getAlignmentFile(String inFile,
- DataSourceType sourceType) throws IOException
- {
- return new JSONFile(inFile, sourceType);
- } @Override
- public AlignmentFileI getAlignmentFile(FileParse source)
+ public AlignmentFileReaderI getReader(FileParse source)
throws IOException
{
return new JSONFile(source);
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileWriterI getWriter(AlignmentI al)
{
return new JSONFile();
}
@@ -193,22 +181,17 @@ public enum FileFormat implements FileFormatI
}
},
- Pileup("PileUp", "?", false, false)
+ Pileup("PileUp", "pileup", true, true)
{
@Override
- public AlignmentFileI getAlignmentFile(String inFile,
- DataSourceType sourceType) throws IOException
- {
- return new PileUpfile(inFile, sourceType);
- } @Override
- public AlignmentFileI getAlignmentFile(FileParse source)
+ public AlignmentFileReaderI getReader(FileParse source)
throws IOException
{
return new PileUpfile(source);
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileWriterI getWriter(AlignmentI al)
{
return new PileUpfile();
}
@@ -217,40 +200,30 @@ public enum FileFormat implements FileFormatI
MSF("MSF", "msf", true, true)
{
@Override
- public AlignmentFileI getAlignmentFile(String inFile,
- DataSourceType sourceType) throws IOException
- {
- return new MSFfile(inFile, sourceType);
- } @Override
- public AlignmentFileI getAlignmentFile(FileParse source)
+ public AlignmentFileReaderI getReader(FileParse source)
throws IOException
{
return new MSFfile(source);
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileWriterI getWriter(AlignmentI al)
{
return new MSFfile();
}
},
- Clustal("CLUSTAL", "aln", true, true)
+ Clustal("Clustal", "aln", true, true)
{
@Override
- public AlignmentFileI getAlignmentFile(String inFile,
- DataSourceType sourceType) throws IOException
- {
- return new ClustalFile(inFile, sourceType);
- } @Override
- public AlignmentFileI getAlignmentFile(FileParse source)
+ public AlignmentFileReaderI getReader(FileParse source)
throws IOException
{
return new ClustalFile(source);
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileWriterI getWriter(AlignmentI al)
{
return new ClustalFile();
}
@@ -258,21 +231,14 @@ public enum FileFormat implements FileFormatI
Phylip("PHYLIP", "phy", true, true)
{
@Override
- public AlignmentFileI getAlignmentFile(String inFile,
- DataSourceType sourceType) throws IOException
- {
- return new PhylipFile(inFile, sourceType);
- }
-
- @Override
- public AlignmentFileI getAlignmentFile(FileParse source)
+ public AlignmentFileReaderI getReader(FileParse source)
throws IOException
{
return new PhylipFile(source);
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileWriterI getWriter(AlignmentI al)
{
return new PhylipFile();
}
@@ -280,16 +246,7 @@ public enum FileFormat implements FileFormatI
Jnet("JnetFile", "", false, false)
{
@Override
- public AlignmentFileI getAlignmentFile(String inFile,
- DataSourceType sourceType) throws IOException
- {
- JPredFile af = new JPredFile(inFile, sourceType);
- af.removeNonSequences();
- return af;
- }
-
- @Override
- public AlignmentFileI getAlignmentFile(FileParse source)
+ public AlignmentFileReaderI getReader(FileParse source)
throws IOException
{
JPredFile af = new JPredFile(source);
@@ -298,79 +255,53 @@ public enum FileFormat implements FileFormatI
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileWriterI getWriter(AlignmentI al)
{
return null; // todo is this called?
}
},
- Features("GFF or Jalview features", "gff2,gff3", false, false)
+ Features("GFF or Jalview features", "gff2,gff3", true, false)
{
@Override
- public AlignmentFileI getAlignmentFile(String inFile,
- DataSourceType sourceType) throws IOException
- {
- return new FeaturesFile(true, inFile, sourceType);
- }
-
- @Override
- public AlignmentFileI getAlignmentFile(FileParse source)
+ public AlignmentFileReaderI getReader(FileParse source)
throws IOException
{
return new FeaturesFile(source);
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileWriterI getWriter(AlignmentI al)
{
return new FeaturesFile();
}
},
- PDB("PDB", "", false, false)
+ ScoreMatrix("Substitution matrix", "", false, false)
{
-
@Override
- public AlignmentFileI getAlignmentFile(String inFile,
- DataSourceType sourceType) throws IOException
+ public AlignmentFileReaderI getReader(FileParse source)
+ throws IOException
{
- // TODO obtain config value from preference settings.
- // Set value to 'true' to test PDB processing with Jmol: JAL-1213
- boolean isParseWithJMOL = StructureImportSettings
- .getDefaultStructureFileFormat() != PDBEntry.Type.PDB;
- if (isParseWithJMOL)
- {
- return new JmolParser(
- StructureImportSettings.isVisibleChainAnnotation(),
- StructureImportSettings.isProcessSecondaryStructure(),
- StructureImportSettings.isExternalSecondaryStructure(),
- inFile,
- sourceType);
- }
- else
- {
- StructureImportSettings.setShowSeqFeatures(true);
- return new MCview.PDBfile(
- StructureImportSettings.isVisibleChainAnnotation(),
- StructureImportSettings.isProcessSecondaryStructure(),
- StructureImportSettings.isExternalSecondaryStructure(),
- inFile,
- sourceType);
- }
+ return new ScoreMatrixFile(source);
}
@Override
- public AlignmentFileI getAlignmentFile(FileParse source)
+ public AlignmentFileWriterI getWriter(AlignmentI al)
+ {
+ return null;
+ }
+ },
+ PDB("PDB", "pdb,ent", true, false)
+ {
+ @Override
+ public AlignmentFileReaderI getReader(FileParse source)
throws IOException
{
boolean isParseWithJMOL = StructureImportSettings
.getDefaultStructureFileFormat() != PDBEntry.Type.PDB;
if (isParseWithJMOL)
{
- return new JmolParser(
- StructureImportSettings.isVisibleChainAnnotation(),
- StructureImportSettings.isProcessSecondaryStructure(),
- StructureImportSettings.isExternalSecondaryStructure(),
- source);
+ return new JmolParser(source);
}
else
{
@@ -384,78 +315,65 @@ public enum FileFormat implements FileFormatI
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileWriterI getWriter(AlignmentI al)
{
return new JmolParser(); // todo or null?
}
- },
- MMCif("mmCIF", "cif", false, false)
- {
@Override
- public AlignmentFileI getAlignmentFile(String inFile,
- DataSourceType sourceType) throws IOException
+ public boolean isStructureFile()
{
- return new JmolParser(
- StructureImportSettings.isVisibleChainAnnotation(),
- StructureImportSettings.isProcessSecondaryStructure(),
- StructureImportSettings.isExternalSecondaryStructure(),
- inFile, sourceType);
+ return true;
}
-
+ },
+ MMCif("mmCIF", "cif", true, false)
+ {
@Override
- public AlignmentFileI getAlignmentFile(FileParse source)
+ public AlignmentFileReaderI getReader(FileParse source)
throws IOException
{
- return new JmolParser(
- StructureImportSettings.isVisibleChainAnnotation(),
- StructureImportSettings.isProcessSecondaryStructure(),
- StructureImportSettings.isExternalSecondaryStructure(),
- source);
+ return new JmolParser(source);
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileWriterI getWriter(AlignmentI al)
{
return new JmolParser(); // todo or null?
}
+
+ @Override
+ public boolean isStructureFile()
+ {
+ return true;
+ }
},
- Jalview("Jalview", "jar,jvp", true, false)
+ Jalview("Jalview", "jvp, jar", true, true)
{
-
@Override
- public AlignmentFileI getAlignmentFile(String inFile,
- DataSourceType sourceType) throws IOException
+ public AlignmentFileReaderI getReader(FileParse source)
+ throws IOException
{
return null;
}
@Override
- public AlignmentFileI getAlignmentFile(FileParse source)
- throws IOException
+ public AlignmentFileWriterI getWriter(AlignmentI al)
{
return null;
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public boolean isTextFormat()
{
- return null;
+ return false;
}
- };
- /**
- * A lookup map of enums by upper-cased name
- */
- private static Map names;
- static
- {
- names = new HashMap();
- for (FileFormat format : FileFormat.values())
+ @Override
+ public boolean isIdentifiable()
{
- names.put(format.toString().toUpperCase(), format);
+ return false;
}
- }
+ };
private boolean writable;
@@ -472,27 +390,6 @@ public enum FileFormat implements FileFormatI
}
@Override
- public String getShortDescription()
- {
- return toString();
- }
-
- /**
- * Returns the file format with the given name, or null if format is null or
- * invalid. Unlike valueOf(), this is not case-sensitive, to be kind to
- * writers of javascript.
- *
- * @param format
- * @return
- */
- public static FileFormatI forName(String format)
- {
- // or could store format.getShortDescription().toUpperCase()
- // in order to decouple 'given name' from enum name
- return format == null ? null : names.get(format.toUpperCase());
- }
-
- @Override
public boolean isReadable()
{
return readable;
@@ -527,4 +424,36 @@ public enum FileFormat implements FileFormatI
{
return extensions;
}
+
+ /**
+ * Answers the display name of the file format (as for example shown in menu
+ * options). This name should not be locale (language) dependent.
+ */
+ @Override
+ public String getName()
+ {
+ return name;
+ }
+
+ @Override
+ public boolean isTextFormat()
+ {
+ return true;
+ }
+
+ @Override
+ public boolean isStructureFile()
+ {
+ return false;
+ }
+
+ /**
+ * By default, answers true, indicating the format is one that can be
+ * identified by IdentifyFile. Formats that cannot be identified should
+ * override this method to return false.
+ */
+ public boolean isIdentifiable()
+ {
+ return true;
+ }
}