*/
package jalview.io;
-import jalview.api.AlignExportSettingI;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.List;
+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 java.io.File;
-import java.io.IOException;
-import java.io.InputStream;
-import java.util.List;
+import jalview.util.Platform;
/**
* A low level class for alignment and feature IO with alignment formatting
*/
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;
+
+ private File selectedFile;
public static String INVALID_CHARACTERS = "Contains invalid characters";
public static String getSupportedFormats()
{
return "Formats currently supported are\n"
- + prettyPrint(FileFormats.getInstance().getReadableFormats());
+ + 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
{
- this.inFile = file;
+ return readFile(null, file, sourceType, fileFormat);
+ }
+
+ public AlignmentI readFile(File selectedFile, String file,
+ DataSourceType sourceType, FileFormatI fileFormat)
+ throws IOException
+ {
+ return readFile(selectedFile, file, sourceType, fileFormat, null);
+ }
+
+ public AlignmentI readFile(File selectedFile, String file,
+ DataSourceType sourceType, FileFormatI fileFormat,
+ StructureImportSettings.TFType tempfacType) throws IOException
+ {
+
+ this.selectedFile = selectedFile;
+ this.inFile = selectedFile != null ? selectedFile.getPath() : file;
try
{
if (fileFormat.isStructureFile())
String structureParser = StructureImportSettings
.getDefaultPDBFileParser();
boolean isParseWithJMOL = structureParser.equalsIgnoreCase(
- StructureImportSettings.StructureParser.JMOL_PARSER
- .toString());
+ StructureImportSettings.StructureParser.JMOL_PARSER
+ .toString());
StructureImportSettings.addSettings(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct);
+ if (tempfacType != null)
+ {
+ StructureImportSettings.setTemperatureFactorType(tempfacType);
+ }
if (isParseWithJMOL)
{
- alignFile = new JmolParser(inFile, sourceType);
+ // needs a File option
+ alignFile = new JmolParser(
+ selectedFile == null ? inFile : selectedFile, sourceType,
+ StructureImportSettings.getTemperatureFactorType());
}
else
{
- // todo is MCview parsing obsolete yet? JAL-2120
+ // 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.PDB
- .equals(fileFormat) ? 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.getReader(new FileParse(inFile,
- sourceType));
+ alignFile = fileFormat.getReader(new FileParse(inFile, sourceType));
}
return buildAlignmentFromFile();
} catch (Exception e)
{
e.printStackTrace();
- System.err.println("Failed to read alignment using the '"
- + fileFormat + "' reader.\n" + e);
+ jalview.bin.Console.errPrintln("Failed to read alignment using the '" + fileFormat
+ + "' reader.\n" + e);
if (e.getMessage() != null
&& e.getMessage().startsWith(INVALID_CHARACTERS))
else
{
StructureImportSettings.setShowSeqFeatures(true);
- alignFile = new MCview.PDBfile(annotFromStructure,
+ alignFile = new mc_view.PDBfile(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct, source);
}
((StructureFile) alignFile).setDbRefType(Type.PDB);
} catch (Exception e)
{
e.printStackTrace();
- System.err.println("Failed to read alignment using the '" + format
+ jalview.bin.Console.errPrintln("Failed to read alignment using the '" + format
+ "' reader.\n" + e);
if (e.getMessage() != null
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.getWriter(alignment);
+ AlignmentFileWriterI afile = format.getWriter(alignment);
afile.setNewlineString(newline);
afile.setExportSettings(exportSettings);
String afileresp = afile.print(seqs, jvsuffix);
if (afile.hasWarningMessage())
{
- System.err.println("Warning raised when writing as " + format
+ jalview.bin.Console.errPrintln("Warning raised when writing as " + format
+ " : " + afile.getWarningMessage());
}
return afileresp;
} catch (Exception e)
{
- System.err.println("Failed to write alignment as a '"
- + format.getName()
- + "' file\n");
+ jalview.bin.Console.errPrintln("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;
{
try
{
- System.out.println("Reading file: " + f);
+ jalview.bin.Console.outPrintln("Reading file: " + f);
AppletFormatAdapter afa = new AppletFormatAdapter();
Runtime r = Runtime.getRuntime();
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();
if (al != null)
{
- System.out.println("Alignment contains " + al.getHeight()
+ jalview.bin.Console.outPrintln("Alignment contains " + al.getHeight()
+ " sequences and " + al.getWidth() + " columns.");
try
{
- System.out.println(new AppletFormatAdapter().formatSequences(
- FileFormat.Fasta, al, true));
+ jalview.bin.Console.outPrintln(new AppletFormatAdapter()
+ .formatSequences(FileFormat.Fasta, al, true));
} catch (Exception e)
{
- System.err
- .println("Couln't format the alignment for output as a FASTA file.");
+ jalview.bin.Console.errPrintln(
+ "Couln't format the alignment for output as a FASTA file.");
e.printStackTrace(System.err);
}
}
else
{
- System.out.println("Couldn't read alignment");
+ jalview.bin.Console.outPrintln("Couldn't read alignment");
}
- System.out.println("Read took " + (t1 / 1000.0) + " seconds.");
- System.out
- .println("Difference between free memory now and before is "
+ jalview.bin.Console.outPrintln("Read took " + (t1 / 1000.0) + " seconds.");
+ jalview.bin.Console.outPrintln(
+ "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
+ jalview.bin.Console.errPrintln("Exception when dealing with " + i
+ "'th argument: " + args[i] + "\n" + e);
}
}
else
{
- System.err.println("Ignoring argument '" + args[i] + "' (" + i
+ jalview.bin.Console.errPrintln("Ignoring argument '" + args[i] + "' (" + i
+ "'th)- not a readable file.");
}
i++;
DataSourceType protocol = null;
if (debug)
{
- System.out.println("resolving datasource started with:\n>>file\n"
+ jalview.bin.Console.outPrintln("resolving datasource started with:\n>>file\n"
+ file + ">>endfile");
}
}
if (debug)
{
- System.err.println("Resource '" + file + "' was "
+ jalview.bin.Console.errPrintln("Resource '" + file + "' was "
+ (rtn ? "" : "not") + " located by classloader.");
}
if (rtn)
{
if (debug)
{
- System.out.println("Trying to get contents of resource as "
- + protocol + ":");
+ jalview.bin.Console.outPrintln(
+ "Trying to get contents of resource as " + protocol + ":");
}
fp = new FileParse(file, protocol);
if (!fp.isValid())
{
if (debug)
{
- System.out.println("Successful.");
+ jalview.bin.Console.outPrintln("Successful.");
}
}
} catch (Exception e)
{
if (debug)
{
- System.err.println("Exception when accessing content: " + e);
+ jalview.bin.Console.errPrintln("Exception when accessing content: " + e);
}
fp = null;
}
{
if (debug)
{
- System.out.println("Accessing as paste.");
+ jalview.bin.Console.outPrintln("Accessing as paste.");
}
protocol = DataSourceType.PASTE;
fp = null;
}
} catch (Exception e)
{
- System.err.println("Failed to access content as paste!");
+ jalview.bin.Console.errPrintln("Failed to access content as paste!");
e.printStackTrace();
fp = null;
}
{
if (debug)
{
- System.out.println("Format not identified. Inaccessible file.");
+ jalview.bin.Console.outPrintln("Format not identified. Inaccessible file.");
}
return null;
}
if (debug)
{
- System.out.println("Format identified as " + idformat
+ jalview.bin.Console.outPrintln("Format identified as " + idformat
+ "and expected as " + format);
}
if (idformat.equals(format))
{
if (debug)
{
- System.out.println("Protocol identified as " + protocol);
+ jalview.bin.Console.outPrintln("Protocol identified as " + protocol);
}
return protocol;
}
{
if (debug)
{
- System.err.println("File deemed not accessible via " + protocol);
+ jalview.bin.Console.errPrintln("File deemed not accessible via " + protocol);
e.printStackTrace();
}
}
return null;
}
- public AlignmentFileI getAlignFile()
+ public AlignmentFileReaderI getAlignFile()
{
return alignFile;
}
git://source.jalview.org / jalview.git / blobdiff