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 java.io.File;
/**
* 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" };
+ // 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, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
- "sto,stk", "xml,rnaml", "phy", "json",
- ".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", "Stockholm", "RNAML",
- "PHYLIP", "JSON", IdentifyFile.FeaturesFile,
- "Jalview", HtmlFile.FILE_DESC, "mmCIF" };
+ // 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" };
+ // 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 final String[] WRITABLE_EXTENSIONS = new String[] {
+ // "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
+ // "sto,stk", "phy", "json", "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",
- "PHYLIP", "JSON", "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());
public AppletFormatAdapter()
{
}
/**
- *
- * @param els
- * @return grammatically correct(ish) list consisting of els elements.
+ * Formats a grammatically correct(ish) list consisting of the given objects
+ *
+ * @param things
+ * @return
*/
- public static String prettyPrint(String[] els)
+ public static String prettyPrint(List<? extends Object> things)
{
StringBuffer list = new StringBuffer();
- for (int i = 0, iSize = els.length - 1; i < iSize; i++)
+ for (int i = 0, iSize = things.size() - 1; i < iSize; i++)
{
- list.append(els[i]);
+ list.append(things.get(i).toString());
list.append(", ");
}
- list.append(" and " + els[els.length - 1] + ".");
+ // could i18n 'and' here
+ list.append(" and " + things.get(things.size() - 1).toString() + ".");
return list.toString();
}
}
/**
- * 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)
- {
- return isValidFormat(format, false);
- }
-
- /**
- * validate format is valid for IO
- *
- * @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
- */
- 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 (String element : format_list)
- {
- if (element.equalsIgnoreCase(format))
- {
- return true;
- }
- }
-
- return valid;
- }
-
- /**
* Constructs the correct filetype parser for a characterised datasource
*
* @param inFile
{
if (fileFormat == FileFormat.PDB || fileFormat == FileFormat.MMCif)
{
- StructureImportSettings.addSettings(annotFromStructure,
- localSecondaryStruct, serviceSecondaryStruct);
- alignFile = fileFormat.getAlignmentFile(inFile, sourceType);
+ // 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
{
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);
+ // 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);
+ + fileFormat + "' reader.\n" + e);
if (e.getMessage() != null
&& e.getMessage().startsWith(INVALID_CHARACTERS))
{
if (format == FileFormat.PDB || format == FileFormat.MMCif)
{
- StructureImportSettings.addSettings(annotFromStructure,
- localSecondaryStruct, serviceSecondaryStruct);
- alignFile = format.getAlignmentFile(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
{
AlignmentFileI afile = format.getAlignmentFile();
afile.setNewlineString(newline);
- afile.addJVSuffix(jvsuffix);
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.setSeqs(alignment.getSequencesArray());
+ seqs = alignment.getSequencesArray();
}
else
{
- afile.setSeqs(viewpanel.getAlignment().getSequencesArray());
+ seqs = viewpanel.getAlignment().getSequencesArray();
}
- String afileresp = afile.print();
+ String afileresp = afile.print(seqs, jvsuffix);
if (afile.hasWarningMessage())
{
System.err.println("Warning raised when writing as " + format
{
try
{
- FileFormatI idformat = new IdentifyFile().identify(file,
- protocol);
+ FileFormatI idformat = new IdentifyFile().identify(file, protocol);
if (idformat == null)
{
if (debug)
git://source.jalview.org / jalview.git / blobdiff