*/
package jalview.io;
-import jalview.api.AlignExportSettingI;
+import java.util.Locale;
+
+import jalview.api.AlignExportSettingsI;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.SequenceI;
import jalview.ext.jmol.JmolParser;
import jalview.structure.StructureImportSettings;
+import jalview.util.Platform;
import java.io.File;
import java.io.IOException;
*/
boolean serviceSecondaryStruct = false;
- private AlignmentFileI alignFile = null;
+ private AlignmentFileReaderI alignFile = null;
String inFile;
*/
protected String newline = System.getProperty("line.separator");
- private AlignExportSettingI exportSettings;
+ private AlignExportSettingsI exportSettings;
- /**
- * 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", "RNAML", "PHYLIP", "JSON",
- // IdentifyFile.FeaturesFile, "HTML", "mmCIF" };
+ private File selectedFile;
- /**
- * 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",
- // "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" };
+ public static String INVALID_CHARACTERS = "Contains invalid characters";
/**
- * List of writable formats by the application. Order must correspond with the
- * WRITABLE_EXTENSIONS list of formats.
+ * Returns an error message with a list of supported readable file formats
+ *
+ * @return
*/
- // 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(FileFormat.getReadableFormats());
+ public static String getSupportedFormats()
+ {
+ return "Formats currently supported are\n"
+ + prettyPrint(FileFormats.getInstance().getReadableFormats());
+ }
public AppletFormatAdapter()
{
}
public AppletFormatAdapter(AlignmentViewPanel alignPanel,
- AlignExportSettingI settings)
+ AlignExportSettingsI settings)
{
viewpanel = alignPanel;
exportSettings = settings;
public AlignmentI readFile(String file, DataSourceType sourceType,
FileFormatI fileFormat) throws IOException
{
+ return readFile(null, file, sourceType, fileFormat);
+ }
+
+ public AlignmentI readFile(File selectedFile, String file,
+ DataSourceType sourceType, FileFormatI fileFormat)
+ throws IOException
+ {
+
+ this.selectedFile = selectedFile;
+ if (selectedFile != null)
+ {
+ this.inFile = selectedFile.getPath();
+ }
this.inFile = file;
try
{
- if (fileFormat == FileFormat.PDB || fileFormat == FileFormat.MMCif)
+ if (fileFormat.isStructureFile())
{
- // 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());
+ String structureParser = StructureImportSettings
+ .getDefaultPDBFileParser();
+ boolean isParseWithJMOL = structureParser.equalsIgnoreCase(
+ StructureImportSettings.StructureParser.JMOL_PARSER
+ .toString());
+ StructureImportSettings.addSettings(annotFromStructure,
+ localSecondaryStruct, serviceSecondaryStruct);
if (isParseWithJMOL)
{
- StructureImportSettings.addSettings(annotFromStructure,
- localSecondaryStruct, serviceSecondaryStruct);
- alignFile = new JmolParser(annotFromStructure,
- localSecondaryStruct, serviceSecondaryStruct, inFile,
- sourceType);
+ // needs a File option
+ alignFile = new JmolParser(
+ selectedFile == null ? inFile : selectedFile, sourceType);
}
else
{
- StructureImportSettings.addSettings(annotFromStructure,
- localSecondaryStruct, serviceSecondaryStruct);
+ // todo is mc_view parsing obsolete yet? JAL-2120
StructureImportSettings.setShowSeqFeatures(true);
- alignFile = new MCview.PDBfile(annotFromStructure,
+ alignFile = new mc_view.PDBfile(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct, inFile,
sourceType);
}
- ((StructureFile) alignFile)
- .setDbRefType(fileFormat == FileFormat.PDB ? Type.PDB
- : Type.MMCIF);
+ ((StructureFile) alignFile).setDbRefType(
+ FileFormat.PDB.equals(fileFormat) ? Type.PDB : Type.MMCIF);
+ }
+ else if (selectedFile != null)
+ {
+ alignFile = fileFormat
+ .getReader(new FileParse(selectedFile, sourceType));
}
else
{
- alignFile = fileFormat.getAlignmentFile(inFile, sourceType);
+ // alignFile = fileFormat.getAlignmentFile(inFile, sourceType);
+ alignFile = fileFormat.getReader(new FileParse(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 '"
- + fileFormat + "' 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))
ex.printStackTrace();
}
}
- if (fileFormat == FileFormat.Html)
+ if (FileFormat.Html.equals(fileFormat))
{
throw new IOException(e.getMessage());
}
}
- throw new FileFormatException(SUPPORTED_FORMATS);
+ throw new FileFormatException(getSupportedFormats());
}
/**
DataSourceType type = source.dataSourceType;
try
{
- if (format == FileFormat.PDB || format == FileFormat.MMCif)
+ if (FileFormat.PDB.equals(format) || FileFormat.MMCif.equals(format))
{
// TODO obtain config value from preference settings
boolean isParseWithJMOL = false;
{
StructureImportSettings.addSettings(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct);
- alignFile = new JmolParser(annotFromStructure,
- localSecondaryStruct, serviceSecondaryStruct, source);
+ alignFile = new JmolParser(source);
}
else
{
StructureImportSettings.setShowSeqFeatures(true);
- alignFile = new MCview.PDBfile(annotFromStructure,
+ alignFile = new mc_view.PDBfile(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct, source);
}
((StructureFile) alignFile).setDbRefType(Type.PDB);
}
else
{
- alignFile = format.getAlignmentFile(source);
+ alignFile = format.getReader(source);
}
return buildAlignmentFromFile();
}
// If we get to this stage, the format was not supported
- throw new FileFormatException(SUPPORTED_FORMATS);
+ throw new FileFormatException(getSupportedFormats());
}
}
AlignmentViewPanel ap, boolean selectedOnly)
{
- AlignmentView selvew = ap.getAlignViewport().getAlignmentView(
- selectedOnly, false);
- AlignmentI aselview = selvew.getVisibleAlignment(ap.getAlignViewport()
- .getGapCharacter());
+ AlignmentView selvew = ap.getAlignViewport()
+ .getAlignmentView(selectedOnly, false);
+ AlignmentI aselview = selvew
+ .getVisibleAlignment(ap.getAlignViewport().getGapCharacter());
List<AlignmentAnnotation> ala = (ap.getAlignViewport()
.getVisibleAlignmentAnnotation(selectedOnly));
if (ala != null)
{
try
{
- AlignmentFileI afile = format.getAlignmentFile();
+ AlignmentFileWriterI afile = format.getWriter(alignment);
afile.setNewlineString(newline);
afile.setExportSettings(exportSettings);
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.getName() + "' file\n");
e.printStackTrace();
}
return null;
}
- public static DataSourceType checkProtocol(String file)
+ /**
+ * Determines the protocol (i.e DataSourceType.{FILE|PASTE|URL}) for the input
+ * data
+ *
+ * BH 2018 allows File or String, and can return RELATIVE_URL
+ *
+ * @param dataObject
+ * File or String
+ * @return the protocol for the input data
+ */
+ public static DataSourceType checkProtocol(Object dataObject)
{
- DataSourceType protocol = DataSourceType.FILE;
- String ft = file.toLowerCase().trim();
+ if (dataObject instanceof File)
+ {
+ return DataSourceType.FILE;
+ }
+
+ String data = dataObject.toString();
+ DataSourceType protocol = DataSourceType.PASTE;
+ String ft = data.toLowerCase(Locale.ROOT).trim();
if (ft.indexOf("http:") == 0 || ft.indexOf("https:") == 0
|| ft.indexOf("file:") == 0)
{
protocol = DataSourceType.URL;
}
+ else if (Platform.isJS())
+ {
+ protocol = DataSourceType.RELATIVE_URL;
+ }
+ else if (new File(data).exists())
+ {
+ protocol = DataSourceType.FILE;
+ }
return protocol;
}
+ /**
+ * @param args
+ * @j2sIgnore
+ */
public static void main(String[] args)
{
int i = 0;
System.gc();
long memf = -r.totalMemory() + r.freeMemory();
long t1 = -System.currentTimeMillis();
- AlignmentI al = afa
- .readFile(args[i], DataSourceType.FILE,
- new IdentifyFile().identify(args[i],
- DataSourceType.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();
+ " sequences and " + al.getWidth() + " columns.");
try
{
- System.out.println(new AppletFormatAdapter().formatSequences(
- FileFormat.Fasta, al, true));
+ 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.");
+ System.err.println(
+ "Couln't format the alignment for output as a FASTA file.");
e.printStackTrace(System.err);
}
}
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 "
+ System.out.println(
+ "Difference between free memory now and before is "
+ (memf / (1024.0 * 1024.0) * 1.0) + " MB");
} catch (Exception e)
{
{
if (debug)
{
- System.out.println("Trying to get contents of resource as "
- + protocol + ":");
+ System.out.println(
+ "Trying to get contents of resource as " + protocol + ":");
}
fp = new FileParse(file, protocol);
if (!fp.isValid())
return null;
}
- public AlignmentFileI getAlignFile()
+ public AlignmentFileReaderI getAlignFile()
{
return alignFile;
}
git://source.jalview.org / jalview.git / blobdiff