*/
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.AlignmentI;
import jalview.datamodel.AlignmentView;
+import jalview.datamodel.SeqDistanceContactMatrix;
import jalview.datamodel.PDBEntry.Type;
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;
*/
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
{
+ 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
{
String structureParser = StructureImportSettings
.getDefaultPDBFileParser();
boolean isParseWithJMOL = structureParser.equalsIgnoreCase(
- StructureImportSettings.StructureParser.JMOL_PARSER
- .toString());
+ StructureImportSettings.StructureParser.JMOL_PARSER
+ .toString());
StructureImportSettings.addSettings(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct);
if (isParseWithJMOL)
{
- alignFile = new JmolParser(inFile, sourceType);
+ // needs a File option
+ alignFile = new JmolParser(
+ selectedFile == null ? inFile : selectedFile, sourceType);
}
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);
+ System.err.println("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);
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)
} catch (Exception e)
{
System.err.println("Failed to write alignment as a '"
- + format.getName()
- + "' file\n");
+ + format.getName() + "' file\n");
e.printStackTrace();
}
/**
* 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 data
+ * @param dataObject
+ * File or String
* @return the protocol for the input data
*/
- public static DataSourceType checkProtocol(String data)
+ public static DataSourceType checkProtocol(Object dataObject)
{
+ if (dataObject instanceof File)
+ {
+ return DataSourceType.FILE;
+ }
+
+ String data = dataObject.toString();
DataSourceType protocol = DataSourceType.PASTE;
- String ft = data.toLowerCase().trim();
+ 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())
git://source.jalview.org / jalview.git / blobdiff