*/
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
*/
protected String newline = System.getProperty("line.separator");
- private AlignExportSettingI exportSettings;
+ private AlignExportSettingsI exportSettings;
private File selectedFile;
}
public AppletFormatAdapter(AlignmentViewPanel alignPanel,
- AlignExportSettingI settings)
+ AlignExportSettingsI settings)
{
viewpanel = alignPanel;
exportSettings = settings;
{
return readFile(null, file, sourceType, fileFormat);
}
-
- public AlignmentI readFile(File selectedFile, String file, DataSourceType sourceType,
- FileFormatI fileFormat) throws IOException
+
+ 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;
- if (selectedFile != null)
- this.inFile = selectedFile.getPath();
- this.inFile = file;
+ this.inFile = selectedFile != null ? selectedFile.getPath() : file;
try
{
if (fileFormat.isStructureFile())
.toString());
StructureImportSettings.addSettings(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct);
+ if (tempfacType != null)
+ {
+ StructureImportSettings.setTemperatureFactorType(tempfacType);
+ }
if (isParseWithJMOL)
{
// needs a File option
- alignFile = new JmolParser(selectedFile == null ? inFile : selectedFile, sourceType);
+ 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);
}
- else if (selectedFile != null) {
- alignFile = fileFormat.getReader(new FileParse(selectedFile, sourceType));
- } else
+ else if (selectedFile != null)
+ {
+ alignFile = fileFormat
+ .getReader(new FileParse(selectedFile, sourceType));
+ }
+ else
{
// alignFile = fileFormat.getAlignmentFile(inFile, sourceType);
alignFile = fileFormat.getReader(new FileParse(inFile, sourceType));
} 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
- + "' reader.\n" + e);
+ jalview.bin.Console.errPrintln("Failed to read alignment using the '"
+ + format + "' reader.\n" + e);
if (e.getMessage() != null
&& e.getMessage().startsWith(INVALID_CHARACTERS))
String afileresp = afile.print(seqs, jvsuffix);
if (afile.hasWarningMessage())
{
- System.err.println("Warning raised when writing as " + format
- + " : " + afile.getWarningMessage());
+ 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 '"
+ jalview.bin.Console.errPrintln("Failed to write alignment as a '"
+ format.getName() + "' file\n");
e.printStackTrace();
}
return null;
}
-
/**
* 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
+ * @param dataObject
+ * File or String
* @return the protocol for the input data
*/
public static DataSourceType checkProtocol(Object dataObject)
{
- if(dataObject instanceof File)
+ 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 (jalview.bin.Jalview.isJS)
+ else if (Platform.isJS())
{
protocol = DataSourceType.RELATIVE_URL;
}
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();
memf += r.totalMemory() - r.freeMemory();
if (al != null)
{
- System.out.println("Alignment contains " + al.getHeight()
- + " sequences and " + al.getWidth() + " columns.");
+ jalview.bin.Console.outPrintln("Alignment contains "
+ + al.getHeight() + " sequences and " + al.getWidth()
+ + " columns.");
try
{
- System.out.println(new AppletFormatAdapter()
+ jalview.bin.Console.outPrintln(new AppletFormatAdapter()
.formatSequences(FileFormat.Fasta, al, true));
} catch (Exception e)
{
- System.err.println(
+ 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(
+ 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
- + "'th)- not a readable file.");
+ 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"
- + file + ">>endfile");
+ jalview.bin.Console
+ .outPrintln("resolving datasource started with:\n>>file\n"
+ + file + ">>endfile");
}
// This might throw a security exception in certain browsers
}
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(
+ jalview.bin.Console.outPrintln(
"Trying to get contents of resource as " + protocol + ":");
}
fp = new FileParse(file, protocol);
{
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();
}
}
git://source.jalview.org / jalview.git / blobdiff