*/
package jalview.io;
+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.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;
-import java.io.InputStream;
-import java.util.List;
-
/**
* A low level class for alignment and feature IO with alignment formatting
* methods used by both applet and application for generating flat alignment
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);
+ selectedFile == null ? inFile : selectedFile, sourceType,
+ StructureImportSettings.getTemperatureFactorType());
}
else
{
} catch (Exception e)
{
e.printStackTrace();
- System.err.println("Failed to read alignment using the '" + fileFormat
+ jalview.bin.Console.errPrintln("Failed to read alignment using the '" + fileFormat
+ "' reader.\n" + e);
if (e.getMessage() != null
} 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
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 '"
+ jalview.bin.Console.errPrintln("Failed to write alignment as a '"
+ format.getName() + "' file\n");
e.printStackTrace();
}
{
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()
+ 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
+ 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(
+ 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();
}
}